initial
Browse filesThis view is limited to 50 files because it contains too many changes. See raw diff
- .gitignore +0 -0
- Data/BIOMD0000000003/Goldbeter1991.csv +513 -0
- Data/BIOMD0000000003/Goldbeter1991.xml +485 -0
- Data/BIOMD0000000003/Goldbeter1991_conditions.json +29 -0
- Data/BIOMD0000000003/initial_conditions.json +8 -0
- Data/BIOMD0000000004/Goldbeter1991.csv +513 -0
- Data/BIOMD0000000004/Goldbeter1991.xml +466 -0
- Data/BIOMD0000000004/Goldbeter1991_conditions.json +47 -0
- Data/BIOMD0000000004/initial_conditions.json +10 -0
- Data/BIOMD0000000005/Tyson1991.csv +513 -0
- Data/BIOMD0000000005/Tyson1991.xml +615 -0
- Data/BIOMD0000000005/Tyson1991_conditions.json +56 -0
- Data/BIOMD0000000005/initial_conditions.json +11 -0
- Data/BIOMD0000000006/Tyson1991.csv +513 -0
- Data/BIOMD0000000006/Tyson1991.xml +346 -0
- Data/BIOMD0000000006/Tyson1991_conditions.json +20 -0
- Data/BIOMD0000000006/initial_conditions.json +7 -0
- Data/BIOMD0000000008/Gardner1998.csv +513 -0
- Data/BIOMD0000000008/Gardner1998.xml +695 -0
- Data/BIOMD0000000008/Gardner1998_conditions.json +47 -0
- Data/BIOMD0000000008/initial_conditions.json +10 -0
- Data/BIOMD0000000009/Huang1996.csv +0 -0
- Data/BIOMD0000000009/Huang1996.xml +1429 -0
- Data/BIOMD0000000009/Huang1996_conditions.json +236 -0
- Data/BIOMD0000000009/initial_conditions.json +31 -0
- Data/BIOMD0000000010/Kholodenko2000.csv +513 -0
- Data/BIOMD0000000010/Kholodenko2000.xml +733 -0
- Data/BIOMD0000000010/Kholodenko2000_conditions.json +74 -0
- Data/BIOMD0000000010/initial_conditions.json +13 -0
- Data/BIOMD0000000011/Levchenko2000.csv +0 -0
- Data/BIOMD0000000011/Levchenko2000.xml +1780 -0
- Data/BIOMD0000000011/Levchenko2000_conditions.json +200 -0
- Data/BIOMD0000000011/initial_conditions.json +27 -0
- Data/BIOMD0000000012/Elowitz2000.csv +513 -0
- Data/BIOMD0000000012/Elowitz2000.xml +1052 -0
- Data/BIOMD0000000012/Elowitz2000_conditions.json +56 -0
- Data/BIOMD0000000012/initial_conditions.json +11 -0
- Data/BIOMD0000000013/Poolman2004.csv +0 -0
- Data/BIOMD0000000013/Poolman2004.xml +2559 -0
- Data/BIOMD0000000013/Poolman2004_conditions.json +164 -0
- Data/BIOMD0000000013/initial_conditions.json +23 -0
- Data/BIOMD0000000014/Levchenko2000.csv +0 -0
- Data/BIOMD0000000014/Levchenko2000.xml +0 -0
- Data/BIOMD0000000014/Levchenko2000_conditions.json +776 -0
- Data/BIOMD0000000014/initial_conditions.json +91 -0
- Data/BIOMD0000000015/Curto1998.csv +0 -0
- Data/BIOMD0000000015/Curto1998.xml +0 -0
- Data/BIOMD0000000015/Curto1998_conditions.json +146 -0
- Data/BIOMD0000000015/initial_conditions.json +21 -0
- Data/BIOMD0000000016/Goldbeter1995.csv +513 -0
.gitignore
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Data/BIOMD0000000003/Goldbeter1991.csv
ADDED
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| 1 |
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time,C,M,X
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| 2 |
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Data/BIOMD0000000003/Goldbeter1991.xml
ADDED
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_180324" version="4">
|
| 3 |
+
<model id="BIOMD0000000003" metaid="_180340" name="Goldbeter1991 - Min Mit Oscil">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Goldbeter1991 - Min Mit Oscil</div>
|
| 7 |
+
<div class="dc:description">
|
| 8 |
+
<p>Minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase.</p>
|
| 9 |
+
</div>
|
| 10 |
+
<div class="dc:provenance">
|
| 11 |
+
<p>This model has been generated by MathSBML 2.4.6 (14-January-2005) 14-January-2005 18:33:39.806932.</p>
|
| 12 |
+
</div>
|
| 13 |
+
<div class="dc:bibliographicCitation">
|
| 14 |
+
<p>This model is described in the article:</p>
|
| 15 |
+
<div class="bibo:title">
|
| 16 |
+
<a href="http://identifiers.org/pubmed/1833774" title="Access to this publication">A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase.</a>
|
| 17 |
+
</div>
|
| 18 |
+
<div class="bibo:authorList">Goldbeter A.</div>
|
| 19 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. U.S.A. 1991; 88(20):9107-11</div>
|
| 20 |
+
<p>Abstract:</p>
|
| 21 |
+
<div class="bibo:abstract">
|
| 22 |
+
<p>A minimal model for the mitotic oscillator is presented. The model, built on recent experimental advances, is based on the cascade of post-translational modification that modulates the activity of cdc2 kinase during the cell cycle. The model pertains to the situation encountered in early amphibian embryos, where the accumulation of cyclin suffices to trigger the onset of mitosis. In the first cycle of the bicyclic cascade model, cyclin promotes the activation of cdc2 kinase through reversible dephosphorylation, and in the second cycle, cdc2 kinase activates a cyclin protease by reversible phosphorylation. That cyclin activates cdc2 kinase while the kinase triggers the degradation of cyclin has suggested that oscillations may originate from such a negative feedback loop [Félix, M. A., Labbé, J. C., Dorée, M., Hunt, T. & Karsenti, E. (1990) Nature (London) 346, 379-382]. This conjecture is corroborated by the model, which indicates that sustained oscillations of the limit cycle type can arise in the cascade, provided that a threshold exists in the activation of cdc2 kinase by cyclin and in the activation of cyclin proteolysis by cdc2 kinase. The analysis shows how miototic oscillations may readily arise from time lags associated with these thresholds and from the delayed negative feedback provided by cdc2-induced cyclin degradation. A mechanism for the origin of the thresholds is proposed in terms of the phenomenon of zero-order ultrasensitivity previously described for biochemical systems regulated by covalent modification.</p>
|
| 23 |
+
</div>
|
| 24 |
+
</div>
|
| 25 |
+
<div class="dc:publisher">
|
| 26 |
+
<p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 27 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000003">BIOMD0000000003</a>
|
| 28 |
+
. </p>
|
| 29 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 30 |
+
. </p>
|
| 31 |
+
</div>
|
| 32 |
+
<div class="dc:license">
|
| 33 |
+
<p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 34 |
+
for more information. </p>
|
| 35 |
+
</div>
|
| 36 |
+
</body>
|
| 37 |
+
</notes>
|
| 38 |
+
<annotation>
|
| 39 |
+
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|
| 40 |
+
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| 41 |
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|
| 47 |
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| 49 |
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|
| 67 |
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|
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|
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|
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|
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|
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</annotation>
|
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<listOfCompartments>
|
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<compartment id="cell" metaid="_230461" name="cell" sboTerm="SBO:0000290" size="1" units="volume">
|
| 113 |
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<annotation>
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
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|
| 124 |
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|
| 125 |
+
</compartment>
|
| 126 |
+
</listOfCompartments>
|
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<listOfSpecies>
|
| 128 |
+
<species compartment="cell" id="C" initialConcentration="0.01" metaid="_230475" name="Cyclin" sboTerm="SBO:0000252" substanceUnits="substance">
|
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| 132 |
+
<bqbiol:isVersionOf>
|
| 133 |
+
<rdf:Bag>
|
| 134 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q4KLA0"/>
|
| 135 |
+
<rdf:li rdf:resource="http://identifiers.org/interpro/IPR006670"/>
|
| 136 |
+
</rdf:Bag>
|
| 137 |
+
</bqbiol:isVersionOf>
|
| 138 |
+
</rdf:Description>
|
| 139 |
+
|
| 140 |
+
</rdf:RDF>
|
| 141 |
+
</annotation>
|
| 142 |
+
</species>
|
| 143 |
+
<species compartment="cell" id="M" initialConcentration="0.01" metaid="_230495" name="CDC-2 Kinase" sboTerm="SBO:0000252" substanceUnits="substance">
|
| 144 |
+
<annotation>
|
| 145 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 146 |
+
<rdf:Description rdf:about="#_230495">
|
| 147 |
+
<bqbiol:hasVersion>
|
| 148 |
+
<rdf:Bag>
|
| 149 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P24033"/>
|
| 150 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P35567"/>
|
| 151 |
+
</rdf:Bag>
|
| 152 |
+
</bqbiol:hasVersion>
|
| 153 |
+
</rdf:Description>
|
| 154 |
+
|
| 155 |
+
</rdf:RDF>
|
| 156 |
+
</annotation>
|
| 157 |
+
</species>
|
| 158 |
+
<species compartment="cell" id="X" initialConcentration="0.01" metaid="_230515" name="Cyclin Protease" sboTerm="SBO:0000297" substanceUnits="substance">
|
| 159 |
+
<annotation>
|
| 160 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 161 |
+
<rdf:Description rdf:about="#_230515">
|
| 162 |
+
<bqbiol:isVersionOf>
|
| 163 |
+
<rdf:Bag>
|
| 164 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005680"/>
|
| 165 |
+
</rdf:Bag>
|
| 166 |
+
</bqbiol:isVersionOf>
|
| 167 |
+
|
| 168 |
+
<bqbiol:hasVersion>
|
| 169 |
+
<rdf:Bag>
|
| 170 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_7165.1"/>
|
| 171 |
+
</rdf:Bag>
|
| 172 |
+
</bqbiol:hasVersion>
|
| 173 |
+
</rdf:Description>
|
| 174 |
+
|
| 175 |
+
</rdf:RDF>
|
| 176 |
+
</annotation>
|
| 177 |
+
</species>
|
| 178 |
+
</listOfSpecies>
|
| 179 |
+
<listOfParameters>
|
| 180 |
+
<parameter constant="false" id="V1" metaid="_961185" name="V1" sboTerm="SBO:0000186"/>
|
| 181 |
+
<parameter constant="false" id="V3" metaid="_961186" name="V3" sboTerm="SBO:0000186"/>
|
| 182 |
+
<parameter id="VM1" metaid="_961187" name="VM1" sboTerm="SBO:0000025" value="3"/>
|
| 183 |
+
<parameter id="VM3" metaid="_961190" name="VM3" sboTerm="SBO:0000186" value="1"/>
|
| 184 |
+
<parameter id="Kc" metaid="_961192" name="Kc" sboTerm="SBO:0000027" value="0.5"/>
|
| 185 |
+
</listOfParameters>
|
| 186 |
+
<listOfRules>
|
| 187 |
+
<assignmentRule metaid="rule1" variable="V1">
|
| 188 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 189 |
+
<apply>
|
| 190 |
+
<times/>
|
| 191 |
+
<ci> C </ci>
|
| 192 |
+
<ci> VM1 </ci>
|
| 193 |
+
<apply>
|
| 194 |
+
<power/>
|
| 195 |
+
<apply>
|
| 196 |
+
<plus/>
|
| 197 |
+
<ci> C </ci>
|
| 198 |
+
<ci> Kc </ci>
|
| 199 |
+
</apply>
|
| 200 |
+
<cn type="integer"> -1 </cn>
|
| 201 |
+
</apply>
|
| 202 |
+
</apply>
|
| 203 |
+
</math>
|
| 204 |
+
</assignmentRule>
|
| 205 |
+
<assignmentRule metaid="rule2" variable="V3">
|
| 206 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 207 |
+
<apply>
|
| 208 |
+
<times/>
|
| 209 |
+
<ci> M </ci>
|
| 210 |
+
<ci> VM3 </ci>
|
| 211 |
+
</apply>
|
| 212 |
+
</math>
|
| 213 |
+
</assignmentRule>
|
| 214 |
+
</listOfRules>
|
| 215 |
+
<listOfReactions>
|
| 216 |
+
<reaction fast="false" id="reaction1" metaid="_230535" name="creation of cyclin" reversible="false" sboTerm="SBO:0000393">
|
| 217 |
+
<annotation>
|
| 218 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 219 |
+
<rdf:Description rdf:about="#_230535">
|
| 220 |
+
<bqbiol:isVersionOf>
|
| 221 |
+
<rdf:Bag>
|
| 222 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006412"/>
|
| 223 |
+
</rdf:Bag>
|
| 224 |
+
</bqbiol:isVersionOf>
|
| 225 |
+
</rdf:Description>
|
| 226 |
+
|
| 227 |
+
</rdf:RDF>
|
| 228 |
+
</annotation>
|
| 229 |
+
<listOfProducts>
|
| 230 |
+
<speciesReference metaid="_355966" species="C"/>
|
| 231 |
+
</listOfProducts>
|
| 232 |
+
<kineticLaw metaid="_355978">
|
| 233 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 234 |
+
<apply>
|
| 235 |
+
<times/>
|
| 236 |
+
<ci> cell </ci>
|
| 237 |
+
<ci> vi </ci>
|
| 238 |
+
</apply>
|
| 239 |
+
</math>
|
| 240 |
+
<listOfParameters>
|
| 241 |
+
<parameter id="vi" metaid="_961167" sboTerm="SBO:0000048" value="0.025"/>
|
| 242 |
+
</listOfParameters>
|
| 243 |
+
</kineticLaw>
|
| 244 |
+
</reaction>
|
| 245 |
+
<reaction fast="false" id="reaction2" metaid="_230555" name="default degradation of cyclin" reversible="false" sboTerm="SBO:0000179">
|
| 246 |
+
<annotation>
|
| 247 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 248 |
+
<rdf:Description rdf:about="#_230555">
|
| 249 |
+
<bqbiol:isVersionOf>
|
| 250 |
+
<rdf:Bag>
|
| 251 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 252 |
+
</rdf:Bag>
|
| 253 |
+
</bqbiol:isVersionOf>
|
| 254 |
+
</rdf:Description>
|
| 255 |
+
|
| 256 |
+
</rdf:RDF>
|
| 257 |
+
</annotation>
|
| 258 |
+
<listOfReactants>
|
| 259 |
+
<speciesReference metaid="_355990" species="C"/>
|
| 260 |
+
</listOfReactants>
|
| 261 |
+
<kineticLaw metaid="_356002">
|
| 262 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 263 |
+
<apply>
|
| 264 |
+
<times/>
|
| 265 |
+
<ci> C </ci>
|
| 266 |
+
<ci> cell </ci>
|
| 267 |
+
<ci> kd </ci>
|
| 268 |
+
</apply>
|
| 269 |
+
</math>
|
| 270 |
+
<listOfParameters>
|
| 271 |
+
<parameter id="kd" metaid="_961168" sboTerm="SBO:0000022" value="0.01"/>
|
| 272 |
+
</listOfParameters>
|
| 273 |
+
</kineticLaw>
|
| 274 |
+
</reaction>
|
| 275 |
+
<reaction fast="false" id="reaction3" metaid="_230575" name="cdc2 kinase triggered degration of cyclin" reversible="false" sboTerm="SBO:0000179">
|
| 276 |
+
<annotation>
|
| 277 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 278 |
+
<rdf:Description rdf:about="#_230575">
|
| 279 |
+
<bqbiol:isVersionOf>
|
| 280 |
+
<rdf:Bag>
|
| 281 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 282 |
+
</rdf:Bag>
|
| 283 |
+
</bqbiol:isVersionOf>
|
| 284 |
+
</rdf:Description>
|
| 285 |
+
|
| 286 |
+
</rdf:RDF>
|
| 287 |
+
</annotation>
|
| 288 |
+
<listOfReactants>
|
| 289 |
+
<speciesReference metaid="_356014" species="C"/>
|
| 290 |
+
</listOfReactants>
|
| 291 |
+
<listOfModifiers>
|
| 292 |
+
<modifierSpeciesReference metaid="_356026" species="X"/>
|
| 293 |
+
</listOfModifiers>
|
| 294 |
+
<kineticLaw metaid="_356038">
|
| 295 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 296 |
+
<apply>
|
| 297 |
+
<times/>
|
| 298 |
+
<ci> C </ci>
|
| 299 |
+
<ci> cell </ci>
|
| 300 |
+
<ci> vd </ci>
|
| 301 |
+
<ci> X </ci>
|
| 302 |
+
<apply>
|
| 303 |
+
<power/>
|
| 304 |
+
<apply>
|
| 305 |
+
<plus/>
|
| 306 |
+
<ci> C </ci>
|
| 307 |
+
<ci> Kd </ci>
|
| 308 |
+
</apply>
|
| 309 |
+
<cn type="integer"> -1 </cn>
|
| 310 |
+
</apply>
|
| 311 |
+
</apply>
|
| 312 |
+
</math>
|
| 313 |
+
<listOfParameters>
|
| 314 |
+
<parameter id="vd" metaid="_961170" sboTerm="SBO:0000186" value="0.25"/>
|
| 315 |
+
<parameter id="Kd" metaid="_961171" sboTerm="SBO:0000027" value="0.02"/>
|
| 316 |
+
</listOfParameters>
|
| 317 |
+
</kineticLaw>
|
| 318 |
+
</reaction>
|
| 319 |
+
<reaction fast="false" id="reaction4" metaid="_230595" name="activation of cdc2 kinase" reversible="false" sboTerm="SBO:0000330">
|
| 320 |
+
<annotation>
|
| 321 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 322 |
+
<rdf:Description rdf:about="#_230595">
|
| 323 |
+
<bqbiol:isVersionOf>
|
| 324 |
+
<rdf:Bag>
|
| 325 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 326 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0045737"/>
|
| 327 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 328 |
+
</rdf:Bag>
|
| 329 |
+
</bqbiol:isVersionOf>
|
| 330 |
+
</rdf:Description>
|
| 331 |
+
|
| 332 |
+
</rdf:RDF>
|
| 333 |
+
</annotation>
|
| 334 |
+
<listOfProducts>
|
| 335 |
+
<speciesReference metaid="_356050" species="M"/>
|
| 336 |
+
</listOfProducts>
|
| 337 |
+
<kineticLaw metaid="_356062">
|
| 338 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 339 |
+
<apply>
|
| 340 |
+
<times/>
|
| 341 |
+
<ci> cell </ci>
|
| 342 |
+
<apply>
|
| 343 |
+
<plus/>
|
| 344 |
+
<cn type="integer"> 1 </cn>
|
| 345 |
+
<apply>
|
| 346 |
+
<times/>
|
| 347 |
+
<cn type="integer"> -1 </cn>
|
| 348 |
+
<ci> M </ci>
|
| 349 |
+
</apply>
|
| 350 |
+
</apply>
|
| 351 |
+
<ci> V1 </ci>
|
| 352 |
+
<apply>
|
| 353 |
+
<power/>
|
| 354 |
+
<apply>
|
| 355 |
+
<plus/>
|
| 356 |
+
<ci> K1 </ci>
|
| 357 |
+
<apply>
|
| 358 |
+
<times/>
|
| 359 |
+
<cn type="integer"> -1 </cn>
|
| 360 |
+
<ci> M </ci>
|
| 361 |
+
</apply>
|
| 362 |
+
<cn type="integer"> 1 </cn>
|
| 363 |
+
</apply>
|
| 364 |
+
<cn type="integer"> -1 </cn>
|
| 365 |
+
</apply>
|
| 366 |
+
</apply>
|
| 367 |
+
</math>
|
| 368 |
+
<listOfParameters>
|
| 369 |
+
<parameter id="K1" metaid="_961172" sboTerm="SBO:0000027" value="0.005"/>
|
| 370 |
+
</listOfParameters>
|
| 371 |
+
</kineticLaw>
|
| 372 |
+
</reaction>
|
| 373 |
+
<reaction fast="false" id="reaction5" metaid="_230615" name="deactivation of cdc2 kinase" reversible="false" sboTerm="SBO:0000216">
|
| 374 |
+
<annotation>
|
| 375 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 376 |
+
<rdf:Description rdf:about="#_230615">
|
| 377 |
+
<bqbiol:isVersionOf>
|
| 378 |
+
<rdf:Bag>
|
| 379 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.10.2"/>
|
| 380 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0045736"/>
|
| 381 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 382 |
+
</rdf:Bag>
|
| 383 |
+
</bqbiol:isVersionOf>
|
| 384 |
+
</rdf:Description>
|
| 385 |
+
|
| 386 |
+
</rdf:RDF>
|
| 387 |
+
</annotation>
|
| 388 |
+
<listOfReactants>
|
| 389 |
+
<speciesReference metaid="_356074" species="M"/>
|
| 390 |
+
</listOfReactants>
|
| 391 |
+
<kineticLaw metaid="_356086">
|
| 392 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 393 |
+
<apply>
|
| 394 |
+
<times/>
|
| 395 |
+
<ci> cell </ci>
|
| 396 |
+
<ci> M </ci>
|
| 397 |
+
<ci> V2 </ci>
|
| 398 |
+
<apply>
|
| 399 |
+
<power/>
|
| 400 |
+
<apply>
|
| 401 |
+
<plus/>
|
| 402 |
+
<ci> K2 </ci>
|
| 403 |
+
<ci> M </ci>
|
| 404 |
+
</apply>
|
| 405 |
+
<cn type="integer"> -1 </cn>
|
| 406 |
+
</apply>
|
| 407 |
+
</apply>
|
| 408 |
+
</math>
|
| 409 |
+
<listOfParameters>
|
| 410 |
+
<parameter id="V2" metaid="_961173" sboTerm="SBO:0000186" value="1.5"/>
|
| 411 |
+
<parameter id="K2" metaid="_961174" sboTerm="SBO:0000027" value="0.005"/>
|
| 412 |
+
</listOfParameters>
|
| 413 |
+
</kineticLaw>
|
| 414 |
+
</reaction>
|
| 415 |
+
<reaction fast="false" id="reaction6" metaid="_230635" name="activation of cyclin protease" reversible="false" sboTerm="SBO:0000216">
|
| 416 |
+
<listOfProducts>
|
| 417 |
+
<speciesReference metaid="_356098" species="X"/>
|
| 418 |
+
</listOfProducts>
|
| 419 |
+
<kineticLaw metaid="_356110">
|
| 420 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 421 |
+
<apply>
|
| 422 |
+
<times/>
|
| 423 |
+
<ci> cell </ci>
|
| 424 |
+
<ci> V3 </ci>
|
| 425 |
+
<apply>
|
| 426 |
+
<plus/>
|
| 427 |
+
<cn type="integer"> 1 </cn>
|
| 428 |
+
<apply>
|
| 429 |
+
<times/>
|
| 430 |
+
<cn type="integer"> -1 </cn>
|
| 431 |
+
<ci> X </ci>
|
| 432 |
+
</apply>
|
| 433 |
+
</apply>
|
| 434 |
+
<apply>
|
| 435 |
+
<power/>
|
| 436 |
+
<apply>
|
| 437 |
+
<plus/>
|
| 438 |
+
<ci> K3 </ci>
|
| 439 |
+
<apply>
|
| 440 |
+
<times/>
|
| 441 |
+
<cn type="integer"> -1 </cn>
|
| 442 |
+
<ci> X </ci>
|
| 443 |
+
</apply>
|
| 444 |
+
<cn type="integer"> 1 </cn>
|
| 445 |
+
</apply>
|
| 446 |
+
<cn type="integer"> -1 </cn>
|
| 447 |
+
</apply>
|
| 448 |
+
</apply>
|
| 449 |
+
</math>
|
| 450 |
+
<listOfParameters>
|
| 451 |
+
<parameter id="K3" metaid="_961175" sboTerm="SBO:0000027" value="0.005"/>
|
| 452 |
+
</listOfParameters>
|
| 453 |
+
</kineticLaw>
|
| 454 |
+
</reaction>
|
| 455 |
+
<reaction fast="false" id="reaction7" metaid="_230655" name="deactivation of cyclin protease" reversible="false" sboTerm="SBO:0000330">
|
| 456 |
+
<listOfReactants>
|
| 457 |
+
<speciesReference metaid="_356122" species="X"/>
|
| 458 |
+
</listOfReactants>
|
| 459 |
+
<kineticLaw metaid="_356134">
|
| 460 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 461 |
+
<apply>
|
| 462 |
+
<times/>
|
| 463 |
+
<ci> cell </ci>
|
| 464 |
+
<ci> V4 </ci>
|
| 465 |
+
<ci> X </ci>
|
| 466 |
+
<apply>
|
| 467 |
+
<power/>
|
| 468 |
+
<apply>
|
| 469 |
+
<plus/>
|
| 470 |
+
<ci> K4 </ci>
|
| 471 |
+
<ci> X </ci>
|
| 472 |
+
</apply>
|
| 473 |
+
<cn type="integer"> -1 </cn>
|
| 474 |
+
</apply>
|
| 475 |
+
</apply>
|
| 476 |
+
</math>
|
| 477 |
+
<listOfParameters>
|
| 478 |
+
<parameter id="K4" metaid="_961177" sboTerm="SBO:0000027" value="0.005"/>
|
| 479 |
+
<parameter id="V4" metaid="_961180" sboTerm="SBO:0000186" value="0.5"/>
|
| 480 |
+
</listOfParameters>
|
| 481 |
+
</kineticLaw>
|
| 482 |
+
</reaction>
|
| 483 |
+
</listOfReactions>
|
| 484 |
+
</model>
|
| 485 |
+
</sbml>
|
Data/BIOMD0000000003/Goldbeter1991_conditions.json
ADDED
|
@@ -0,0 +1,29 @@
|
|
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|
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|
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|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"C": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.1895088127217516,
|
| 7 |
+
0.5814597911680786
|
| 8 |
+
],
|
| 9 |
+
"period": 214.0
|
| 10 |
+
},
|
| 11 |
+
"M": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.006037189339947,
|
| 16 |
+
0.7093082437081485
|
| 17 |
+
],
|
| 18 |
+
"period": 214.0
|
| 19 |
+
},
|
| 20 |
+
"X": {
|
| 21 |
+
"trajectory_type": 3,
|
| 22 |
+
"trajectory_type_name": "oscillation",
|
| 23 |
+
"bounds": [
|
| 24 |
+
6.346061705374726e-05,
|
| 25 |
+
0.6415575361980881
|
| 26 |
+
],
|
| 27 |
+
"period": 215.0
|
| 28 |
+
}
|
| 29 |
+
}
|
Data/BIOMD0000000003/initial_conditions.json
ADDED
|
@@ -0,0 +1,8 @@
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"C": 0.23901494118204017,
|
| 5 |
+
"M": 0.008987225703866234,
|
| 6 |
+
"X": 9.08824000739145e-05
|
| 7 |
+
}
|
| 8 |
+
}
|
Data/BIOMD0000000004/Goldbeter1991.csv
ADDED
|
@@ -0,0 +1,513 @@
|
|
|
|
|
|
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|
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|
|
|
|
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|
|
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|
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|
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|
|
|
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|
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|
|
|
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|
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|
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|
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|
|
|
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|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
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|
|
|
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|
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|
|
|
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|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
|
|
| 1 |
+
time,C,M,X,MI,XI
|
| 2 |
+
0.0,0.4535009323056436,0.06977168400902338,0.0008026743700016656,0.9302283159909792,0.9991973256299989
|
| 3 |
+
0.136986301369863,0.45627552153107503,0.07251271758367003,0.0008394184168661481,0.9274872824163325,0.9991605815831346
|
| 4 |
+
0.273972602739726,0.45904506822230823,0.07538984851360726,0.0008784850079812807,0.9246101514863952,0.9991215149920195
|
| 5 |
+
0.410958904109589,0.4618094947343441,0.07840985702877698,0.0009200521191690668,0.9215901429712254,0.9990799478808319
|
| 6 |
+
0.547945205479452,0.464568721989471,0.08157962012792681,0.0009643093787281053,0.9184203798720756,0.999035690621273
|
| 7 |
+
0.684931506849315,0.46732266553743596,0.0849061070156509,0.0010114639369088493,0.9150938929843515,0.998988536063092
|
| 8 |
+
0.821917808219178,0.4700712328943432,0.08839642307960004,0.0010617402906200983,0.9116035769204024,0.9989382597093809
|
| 9 |
+
0.958904109589041,0.47281432443814775,0.09205777709044577,0.0011153815297968515,0.9079422229095566,0.998884618470204
|
| 10 |
+
1.095890410958904,0.47555183176602683,0.09589746515547394,0.001172653566831401,0.9041025348445285,0.9988273464331694
|
| 11 |
+
1.2328767123287672,0.4782836382824552,0.09992283040219814,0.0012338441729989394,0.9000771695978044,0.9987661558270018
|
| 12 |
+
1.36986301369863,0.48100961752060095,0.10414124651950094,0.0012992679888846994,0.8958587534805015,0.9987007320111161
|
| 13 |
+
1.506849315068493,0.4837296318138018,0.10856009122669495,0.001369272872236542,0.8914399087733074,0.9986307271277642
|
| 14 |
+
1.643835616438356,0.4864435315439018,0.11318671108867477,0.0014442373620782247,0.8868132889113276,0.9985557626379226
|
| 15 |
+
1.7808219178082192,0.4891511543269148,0.1180283891430058,0.0015245727439622053,0.8819716108569966,0.9984754272560386
|
| 16 |
+
1.917808219178082,0.49185232375808274,0.12309231617538868,0.0016107357878836167,0.8769076838246137,0.9983892642121172
|
| 17 |
+
2.054794520547945,0.4945468477449995,0.12838556202459928,0.0017032371285961646,0.8716144379754032,0.9982967628714046
|
| 18 |
+
2.191780821917808,0.49723451675544006,0.13391504548181818,0.001802636838584016,0.8660849545181841,0.9981973631614167
|
| 19 |
+
2.328767123287671,0.49991510211534984,0.1396875039592998,0.0019095466739500915,0.8603124960407026,0.9980904533260506
|
| 20 |
+
2.4657534246575343,0.5025883538850113,0.14570946296042891,0.002024659163082236,0.8542905370395734,0.9979753408369185
|
| 21 |
+
2.602739726027397,0.5052539982418901,0.15198721422768516,0.002148751106054198,0.8480127857723172,0.9978512488939466
|
| 22 |
+
2.73972602739726,0.5079117345678694,0.15852678425602926,0.002282689659039575,0.8414732157439729,0.9977173103409613
|
| 23 |
+
2.8767123287671232,0.5105612322866447,0.1653339085047609,0.0024274430337229147,0.8346660914952413,0.9975725569662779
|
| 24 |
+
3.013698630136986,0.5132021270199194,0.17241400769660187,0.002584115077981366,0.8275859923034004,0.9974158849220195
|
| 25 |
+
3.150684931506849,0.5158340160915756,0.17977217081757624,0.0027539528181606873,0.820227829182426,0.9972460471818402
|
| 26 |
+
3.287671232876712,0.5184564532015903,0.18741312735136226,0.0029383819792231005,0.81258687264864,0.9970616180207778
|
| 27 |
+
3.4246575342465753,0.5210689423896345,0.19534123123650163,0.003139019832258874,0.8046587687635006,0.9968609801677419
|
| 28 |
+
3.5616438356164384,0.5236709306732429,0.20356043598514284,0.003357740194792449,0.7964395640148594,0.9966422598052084
|
| 29 |
+
3.698630136986301,0.5262617992362142,0.21207428039414045,0.0035967047759268697,0.7879257196058618,0.996403295224074
|
| 30 |
+
3.835616438356164,0.5288408532137896,0.22088586815593406,0.0038584064990867663,0.7791141318440682,0.996141593500914
|
| 31 |
+
3.9726027397260273,0.5314073093561922,0.22999784811394614,0.0041457596529780524,0.7700021518860561,0.9958542403470227
|
| 32 |
+
4.10958904109589,0.5339602810200959,0.2394123941909782,0.004462180321994451,0.7605876058090241,0.9955378196780063
|
| 33 |
+
4.2465753424657535,0.5364987611213063,0.24913118496270867,0.004811687666849765,0.7508688150372935,0.9951883123331509
|
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66.57534246575342,0.2626822479379787,0.010827985347776145,0.00010990753235941277,0.9891720146522265,0.9998900924676423
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| 513 |
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70.0,0.3378848818565796,0.019991022157990132,0.00020671963619907678,0.9800089778420126,0.9997932803638022
|
Data/BIOMD0000000004/Goldbeter1991.xml
ADDED
|
@@ -0,0 +1,466 @@
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_042589" version="4">
|
| 3 |
+
<model id="BIOMD0000000004" metaid="_000001" name="Goldbeter1991 - Min Mit Oscil, Expl Inact">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Goldbeter1991 - Min Mit Oscil, Expl Inact</div>
|
| 7 |
+
<div class="dc:description"> <p>This model represents the inactive forms of CDC-2 Kinase and Cyclin Protease as separate species, unlike the ODEs in the published paper, in which the equations for the inactive forms are substituted into the equations for the active forms using a mass conservation rule M+MI=1,X+XI=1. Mass is still conserved in this model through the explicit reactions M<->MI and X<->XI. The terms in the kinetic laws are identical to the corresponding terms in the kinetic laws in the published paper.</p>
|
| 8 |
+
</div>
|
| 9 |
+
<div class="dc:provenance"> <p>This model has been generated by MathSBML 2.4.6 (14-January-2005) 14-January-2005 18:37:35.503857.</p>
|
| 10 |
+
</div>
|
| 11 |
+
<div class="dc:bibliographicCitation"> <p>This model is described in the article:</p>
|
| 12 |
+
<div class="bibo:title"> <a href="http://identifiers.org/pubmed/1833774" title="Access to this publication">A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase.</a>
|
| 13 |
+
</div>
|
| 14 |
+
<div class="bibo:authorList">Goldbeter A.</div>
|
| 15 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. USA 1991 Oct; 88(20):9107-11</div>
|
| 16 |
+
<p>Abstract:</p>
|
| 17 |
+
<div class="bibo:abstract"> <p>A minimal model for the mitotic oscillator is presented. The model, built on recent experimental advances, is based on the cascade of post-translational modification that modulates the activity of cdc2 kinase during the cell cycle. The model pertains to the situation encountered in early amphibian embryos, where the accumulation of cyclin suffices to trigger the onset of mitosis. In the first cycle ofthe bicyclic cascade model, cyclin promotes the activation of cdc2 kinase through reversible dephosphorylation, and in the second cycle, cdc2 kinase activates a cyclin protease by reversible phosphorylation. That cyclin activates cdc2 kinase while the kinase triggers the degradation of cyclin has suggested that oscillations may originate from such a negative feedback loop [Félix, M. A., Labbé, J. C., Dorée, M., Hunt, T. & Karsenti, E. (1990) Nature (London) 346, 379-382]. Thisconjecture is corroborated by the model, which indicates that sustained oscillations of the limit cycle type can arise in the cascade, provided that a threshold exists in the activation of cdc2 kinase by cyclin and in the activation of cyclinproteolysis by cdc2 kinase. The analysis shows how miototic oscillations may readily arise from time lags associated with these thresholds and from the delayed negative feedback provided by cdc2-induced cyclin degradation. A mechanism for theorigin of the thresholds is proposed in terms of the phenomenon of zero-order ultrasensitivity previously described for biochemical systems regulated by covalent modification.</p>
|
| 18 |
+
</div>
|
| 19 |
+
</div>
|
| 20 |
+
<div class="dc:publisher"> <p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 21 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000004">BIOMD0000000004</a>
|
| 22 |
+
. </p>
|
| 23 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 24 |
+
. </p>
|
| 25 |
+
</div>
|
| 26 |
+
<div class="dc:license"> <p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 27 |
+
for more information. </p>
|
| 28 |
+
</div>
|
| 29 |
+
</body>
|
| 30 |
+
|
| 31 |
+
</notes>
|
| 32 |
+
<annotation>
|
| 33 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 34 |
+
<rdf:Description rdf:about="#_000001">
|
| 35 |
+
<dc:creator>
|
| 36 |
+
<rdf:Bag>
|
| 37 |
+
<rdf:li rdf:parseType="Resource">
|
| 38 |
+
<vCard:N rdf:parseType="Resource">
|
| 39 |
+
<vCard:Family>Shapiro</vCard:Family>
|
| 40 |
+
<vCard:Given>Bruce</vCard:Given>
|
| 41 |
+
</vCard:N>
|
| 42 |
+
<vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
|
| 43 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 44 |
+
<vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
|
| 45 |
+
</vCard:ORG>
|
| 46 |
+
</rdf:li>
|
| 47 |
+
</rdf:Bag>
|
| 48 |
+
</dc:creator>
|
| 49 |
+
<dcterms:created rdf:parseType="Resource">
|
| 50 |
+
<dcterms:W3CDTF>2005-02-08T17:34:02Z</dcterms:W3CDTF>
|
| 51 |
+
</dcterms:created>
|
| 52 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 53 |
+
<dcterms:W3CDTF>2012-12-11T15:30:15Z</dcterms:W3CDTF>
|
| 54 |
+
</dcterms:modified>
|
| 55 |
+
<bqmodel:is>
|
| 56 |
+
<rdf:Bag>
|
| 57 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/MODEL6614389071"/>
|
| 58 |
+
</rdf:Bag>
|
| 59 |
+
</bqmodel:is>
|
| 60 |
+
<bqmodel:is>
|
| 61 |
+
<rdf:Bag>
|
| 62 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000004"/>
|
| 63 |
+
</rdf:Bag>
|
| 64 |
+
</bqmodel:is>
|
| 65 |
+
<bqmodel:isDescribedBy>
|
| 66 |
+
<rdf:Bag>
|
| 67 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/1833774"/>
|
| 68 |
+
</rdf:Bag>
|
| 69 |
+
</bqmodel:isDescribedBy>
|
| 70 |
+
<bqmodel:isDerivedFrom>
|
| 71 |
+
<rdf:Bag>
|
| 72 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000003"/>
|
| 73 |
+
</rdf:Bag>
|
| 74 |
+
</bqmodel:isDerivedFrom>
|
| 75 |
+
<bqbiol:isVersionOf>
|
| 76 |
+
<rdf:Bag>
|
| 77 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.pathway/hsa04110"/>
|
| 78 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000278"/>
|
| 79 |
+
</rdf:Bag>
|
| 80 |
+
</bqbiol:isVersionOf>
|
| 81 |
+
<bqbiol:isHomologTo>
|
| 82 |
+
<rdf:Bag>
|
| 83 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_152"/>
|
| 84 |
+
</rdf:Bag>
|
| 85 |
+
</bqbiol:isHomologTo>
|
| 86 |
+
<bqbiol:hasTaxon>
|
| 87 |
+
<rdf:Bag>
|
| 88 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/8292"/>
|
| 89 |
+
</rdf:Bag>
|
| 90 |
+
</bqbiol:hasTaxon>
|
| 91 |
+
<bqbiol:hasProperty>
|
| 92 |
+
<rdf:Bag>
|
| 93 |
+
<rdf:li rdf:resource="http://identifiers.org/mamo/MAMO_0000046"/>
|
| 94 |
+
</rdf:Bag>
|
| 95 |
+
</bqbiol:hasProperty>
|
| 96 |
+
</rdf:Description>
|
| 97 |
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|
| 98 |
+
|
| 99 |
+
</rdf:RDF>
|
| 100 |
+
</annotation>
|
| 101 |
+
<listOfCompartments>
|
| 102 |
+
<compartment id="cell" metaid="_060591" name="cell" size="1" units="volume">
|
| 103 |
+
<annotation>
|
| 104 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 105 |
+
<rdf:Description rdf:about="#_060591">
|
| 106 |
+
<bqbiol:is>
|
| 107 |
+
<rdf:Bag>
|
| 108 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005623"/>
|
| 109 |
+
</rdf:Bag>
|
| 110 |
+
</bqbiol:is>
|
| 111 |
+
</rdf:Description>
|
| 112 |
+
|
| 113 |
+
|
| 114 |
+
</rdf:RDF>
|
| 115 |
+
</annotation>
|
| 116 |
+
</compartment>
|
| 117 |
+
</listOfCompartments>
|
| 118 |
+
<listOfSpecies>
|
| 119 |
+
<species compartment="cell" id="C" initialConcentration="0.01" metaid="_060603" name="Cyclin" substanceUnits="substance">
|
| 120 |
+
<annotation>
|
| 121 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 122 |
+
<rdf:Description rdf:about="#_060603">
|
| 123 |
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<bqbiol:isVersionOf>
|
| 124 |
+
<rdf:Bag>
|
| 125 |
+
<rdf:li rdf:resource="http://identifiers.org/interpro/IPR006670"/>
|
| 126 |
+
</rdf:Bag>
|
| 127 |
+
</bqbiol:isVersionOf>
|
| 128 |
+
</rdf:Description>
|
| 129 |
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|
| 130 |
+
|
| 131 |
+
</rdf:RDF>
|
| 132 |
+
</annotation>
|
| 133 |
+
</species>
|
| 134 |
+
<species compartment="cell" id="M" initialConcentration="0.01" metaid="_060623" name="Active CDC-2 Kinase" substanceUnits="substance">
|
| 135 |
+
<annotation>
|
| 136 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 137 |
+
<rdf:Description rdf:about="#_060623">
|
| 138 |
+
<bqbiol:hasVersion>
|
| 139 |
+
<rdf:Bag>
|
| 140 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P24033"/>
|
| 141 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P35567"/>
|
| 142 |
+
</rdf:Bag>
|
| 143 |
+
</bqbiol:hasVersion>
|
| 144 |
+
</rdf:Description>
|
| 145 |
+
|
| 146 |
+
|
| 147 |
+
</rdf:RDF>
|
| 148 |
+
</annotation>
|
| 149 |
+
</species>
|
| 150 |
+
<species compartment="cell" id="X" initialConcentration="0.01" metaid="_060643" name="Active Cyclin Protease" substanceUnits="substance"/>
|
| 151 |
+
<species compartment="cell" id="MI" initialConcentration="0.99" metaid="_060663" name="Inactive CDC-2 Kinase" substanceUnits="substance">
|
| 152 |
+
<annotation>
|
| 153 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 154 |
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<rdf:Description rdf:about="#_060663">
|
| 155 |
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<bqbiol:hasVersion>
|
| 156 |
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<rdf:Bag>
|
| 157 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P24033"/>
|
| 158 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P35567"/>
|
| 159 |
+
</rdf:Bag>
|
| 160 |
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</bqbiol:hasVersion>
|
| 161 |
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</rdf:Description>
|
| 162 |
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|
| 163 |
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|
| 164 |
+
</rdf:RDF>
|
| 165 |
+
</annotation>
|
| 166 |
+
</species>
|
| 167 |
+
<species compartment="cell" id="XI" initialConcentration="0.99" metaid="_060683" name="Inactive Cyclin Protease" substanceUnits="substance"/>
|
| 168 |
+
</listOfSpecies>
|
| 169 |
+
<listOfParameters>
|
| 170 |
+
<parameter constant="false" id="V1" metaid="_873773" name="V1"/>
|
| 171 |
+
<parameter constant="false" id="V3" metaid="_873774" name="V3"/>
|
| 172 |
+
<parameter id="VM1" metaid="_873776" name="VM1" value="3"/>
|
| 173 |
+
<parameter id="VM3" metaid="_873777" name="VM3" value="1"/>
|
| 174 |
+
<parameter id="Kc" metaid="_873778" name="Kc" value="0.5"/>
|
| 175 |
+
</listOfParameters>
|
| 176 |
+
<listOfRules>
|
| 177 |
+
<assignmentRule metaid="rule1" variable="V1">
|
| 178 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 179 |
+
<apply>
|
| 180 |
+
<times/>
|
| 181 |
+
<ci> C </ci>
|
| 182 |
+
<ci> VM1 </ci>
|
| 183 |
+
<apply>
|
| 184 |
+
<power/>
|
| 185 |
+
<apply>
|
| 186 |
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<plus/>
|
| 187 |
+
<ci> C </ci>
|
| 188 |
+
<ci> Kc </ci>
|
| 189 |
+
</apply>
|
| 190 |
+
<cn type="integer"> -1 </cn>
|
| 191 |
+
</apply>
|
| 192 |
+
</apply>
|
| 193 |
+
</math>
|
| 194 |
+
</assignmentRule>
|
| 195 |
+
<assignmentRule metaid="rule2" variable="V3">
|
| 196 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 197 |
+
<apply>
|
| 198 |
+
<times/>
|
| 199 |
+
<ci> M </ci>
|
| 200 |
+
<ci> VM3 </ci>
|
| 201 |
+
</apply>
|
| 202 |
+
</math>
|
| 203 |
+
</assignmentRule>
|
| 204 |
+
</listOfRules>
|
| 205 |
+
<listOfReactions>
|
| 206 |
+
<reaction fast="false" id="reaction1" metaid="_060703" name="creation of cyclin" reversible="false">
|
| 207 |
+
<annotation>
|
| 208 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 209 |
+
<rdf:Description rdf:about="#_060703">
|
| 210 |
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<bqbiol:isVersionOf>
|
| 211 |
+
<rdf:Bag>
|
| 212 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006412"/>
|
| 213 |
+
</rdf:Bag>
|
| 214 |
+
</bqbiol:isVersionOf>
|
| 215 |
+
</rdf:Description>
|
| 216 |
+
|
| 217 |
+
|
| 218 |
+
</rdf:RDF>
|
| 219 |
+
</annotation>
|
| 220 |
+
<listOfProducts>
|
| 221 |
+
<speciesReference metaid="_361246" species="C"/>
|
| 222 |
+
</listOfProducts>
|
| 223 |
+
<kineticLaw metaid="_361258">
|
| 224 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 225 |
+
<apply>
|
| 226 |
+
<times/>
|
| 227 |
+
<ci> cell </ci>
|
| 228 |
+
<ci> vi </ci>
|
| 229 |
+
</apply>
|
| 230 |
+
</math>
|
| 231 |
+
<listOfParameters>
|
| 232 |
+
<parameter id="vi" metaid="_873755" value="0.025"/>
|
| 233 |
+
</listOfParameters>
|
| 234 |
+
</kineticLaw>
|
| 235 |
+
</reaction>
|
| 236 |
+
<reaction fast="false" id="reaction2" metaid="_060723" name="default degradation of cyclin" reversible="false">
|
| 237 |
+
<annotation>
|
| 238 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 239 |
+
<rdf:Description rdf:about="#_060723">
|
| 240 |
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<bqbiol:isVersionOf>
|
| 241 |
+
<rdf:Bag>
|
| 242 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 243 |
+
</rdf:Bag>
|
| 244 |
+
</bqbiol:isVersionOf>
|
| 245 |
+
</rdf:Description>
|
| 246 |
+
|
| 247 |
+
|
| 248 |
+
</rdf:RDF>
|
| 249 |
+
</annotation>
|
| 250 |
+
<listOfReactants>
|
| 251 |
+
<speciesReference metaid="_361270" species="C"/>
|
| 252 |
+
</listOfReactants>
|
| 253 |
+
<kineticLaw metaid="_361282">
|
| 254 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 255 |
+
<apply>
|
| 256 |
+
<times/>
|
| 257 |
+
<ci> C </ci>
|
| 258 |
+
<ci> cell </ci>
|
| 259 |
+
<ci> kd </ci>
|
| 260 |
+
</apply>
|
| 261 |
+
</math>
|
| 262 |
+
<listOfParameters>
|
| 263 |
+
<parameter id="kd" metaid="_873757" value="0.01"/>
|
| 264 |
+
</listOfParameters>
|
| 265 |
+
</kineticLaw>
|
| 266 |
+
</reaction>
|
| 267 |
+
<reaction fast="false" id="reaction3" metaid="_060743" name="cdc2 kinase triggered degration of cyclin" reversible="false">
|
| 268 |
+
<annotation>
|
| 269 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 270 |
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<rdf:Description rdf:about="#_060743">
|
| 271 |
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<bqbiol:isVersionOf>
|
| 272 |
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<rdf:Bag>
|
| 273 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 274 |
+
</rdf:Bag>
|
| 275 |
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</bqbiol:isVersionOf>
|
| 276 |
+
</rdf:Description>
|
| 277 |
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|
| 278 |
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|
| 279 |
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</rdf:RDF>
|
| 280 |
+
</annotation>
|
| 281 |
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<listOfReactants>
|
| 282 |
+
<speciesReference metaid="_361294" species="C"/>
|
| 283 |
+
</listOfReactants>
|
| 284 |
+
<listOfModifiers>
|
| 285 |
+
<modifierSpeciesReference metaid="_361307" species="X"/>
|
| 286 |
+
</listOfModifiers>
|
| 287 |
+
<kineticLaw metaid="_361319">
|
| 288 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 289 |
+
<apply>
|
| 290 |
+
<times/>
|
| 291 |
+
<ci> C </ci>
|
| 292 |
+
<ci> cell </ci>
|
| 293 |
+
<ci> vd </ci>
|
| 294 |
+
<ci> X </ci>
|
| 295 |
+
<apply>
|
| 296 |
+
<power/>
|
| 297 |
+
<apply>
|
| 298 |
+
<plus/>
|
| 299 |
+
<ci> C </ci>
|
| 300 |
+
<ci> Kd </ci>
|
| 301 |
+
</apply>
|
| 302 |
+
<cn type="integer"> -1 </cn>
|
| 303 |
+
</apply>
|
| 304 |
+
</apply>
|
| 305 |
+
</math>
|
| 306 |
+
<listOfParameters>
|
| 307 |
+
<parameter id="vd" metaid="_873758" value="0.25"/>
|
| 308 |
+
<parameter id="Kd" metaid="_873759" value="0.02"/>
|
| 309 |
+
</listOfParameters>
|
| 310 |
+
</kineticLaw>
|
| 311 |
+
</reaction>
|
| 312 |
+
<reaction fast="false" id="reaction4" metaid="_060763" name="activation of cdc2 kinase" reversible="false">
|
| 313 |
+
<annotation>
|
| 314 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 315 |
+
<rdf:Description rdf:about="#_060763">
|
| 316 |
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<bqbiol:isVersionOf>
|
| 317 |
+
<rdf:Bag>
|
| 318 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 319 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0045737"/>
|
| 320 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 321 |
+
</rdf:Bag>
|
| 322 |
+
</bqbiol:isVersionOf>
|
| 323 |
+
</rdf:Description>
|
| 324 |
+
|
| 325 |
+
|
| 326 |
+
</rdf:RDF>
|
| 327 |
+
</annotation>
|
| 328 |
+
<listOfReactants>
|
| 329 |
+
<speciesReference metaid="_361332" species="MI"/>
|
| 330 |
+
</listOfReactants>
|
| 331 |
+
<listOfProducts>
|
| 332 |
+
<speciesReference metaid="_361344" species="M"/>
|
| 333 |
+
</listOfProducts>
|
| 334 |
+
<kineticLaw metaid="_361356">
|
| 335 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 336 |
+
<apply>
|
| 337 |
+
<times/>
|
| 338 |
+
<ci> cell </ci>
|
| 339 |
+
<ci> MI </ci>
|
| 340 |
+
<ci> V1 </ci>
|
| 341 |
+
<apply>
|
| 342 |
+
<power/>
|
| 343 |
+
<apply>
|
| 344 |
+
<plus/>
|
| 345 |
+
<ci> K1 </ci>
|
| 346 |
+
<ci> MI </ci>
|
| 347 |
+
</apply>
|
| 348 |
+
<cn type="integer"> -1 </cn>
|
| 349 |
+
</apply>
|
| 350 |
+
</apply>
|
| 351 |
+
</math>
|
| 352 |
+
<listOfParameters>
|
| 353 |
+
<parameter id="K1" metaid="_873760" value="0.005"/>
|
| 354 |
+
</listOfParameters>
|
| 355 |
+
</kineticLaw>
|
| 356 |
+
</reaction>
|
| 357 |
+
<reaction fast="false" id="reaction5" metaid="_060783" name="deactivation of cdc2 kinase" reversible="false">
|
| 358 |
+
<annotation>
|
| 359 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 360 |
+
<rdf:Description rdf:about="#_060783">
|
| 361 |
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<bqbiol:isVersionOf>
|
| 362 |
+
<rdf:Bag>
|
| 363 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.10.2"/>
|
| 364 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0045736"/>
|
| 365 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 366 |
+
</rdf:Bag>
|
| 367 |
+
</bqbiol:isVersionOf>
|
| 368 |
+
</rdf:Description>
|
| 369 |
+
|
| 370 |
+
|
| 371 |
+
</rdf:RDF>
|
| 372 |
+
</annotation>
|
| 373 |
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<listOfReactants>
|
| 374 |
+
<speciesReference metaid="_361368" species="M"/>
|
| 375 |
+
</listOfReactants>
|
| 376 |
+
<listOfProducts>
|
| 377 |
+
<speciesReference metaid="_361380" species="MI"/>
|
| 378 |
+
</listOfProducts>
|
| 379 |
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<kineticLaw metaid="_361392">
|
| 380 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 381 |
+
<apply>
|
| 382 |
+
<times/>
|
| 383 |
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<ci> cell </ci>
|
| 384 |
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<ci> M </ci>
|
| 385 |
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<ci> V2 </ci>
|
| 386 |
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<apply>
|
| 387 |
+
<power/>
|
| 388 |
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<apply>
|
| 389 |
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<plus/>
|
| 390 |
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<ci> K2 </ci>
|
| 391 |
+
<ci> M </ci>
|
| 392 |
+
</apply>
|
| 393 |
+
<cn type="integer"> -1 </cn>
|
| 394 |
+
</apply>
|
| 395 |
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</apply>
|
| 396 |
+
</math>
|
| 397 |
+
<listOfParameters>
|
| 398 |
+
<parameter id="V2" metaid="_873761" value="1.5"/>
|
| 399 |
+
<parameter id="K2" metaid="_873762" value="0.005"/>
|
| 400 |
+
</listOfParameters>
|
| 401 |
+
</kineticLaw>
|
| 402 |
+
</reaction>
|
| 403 |
+
<reaction fast="false" id="reaction6" metaid="_060803" name="activation of cyclin protease" reversible="false">
|
| 404 |
+
<listOfReactants>
|
| 405 |
+
<speciesReference metaid="_361404" species="XI"/>
|
| 406 |
+
</listOfReactants>
|
| 407 |
+
<listOfProducts>
|
| 408 |
+
<speciesReference metaid="_361416" species="X"/>
|
| 409 |
+
</listOfProducts>
|
| 410 |
+
<kineticLaw metaid="_361428">
|
| 411 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 412 |
+
<apply>
|
| 413 |
+
<times/>
|
| 414 |
+
<ci> cell </ci>
|
| 415 |
+
<ci> V3 </ci>
|
| 416 |
+
<ci> XI </ci>
|
| 417 |
+
<apply>
|
| 418 |
+
<power/>
|
| 419 |
+
<apply>
|
| 420 |
+
<plus/>
|
| 421 |
+
<ci> K3 </ci>
|
| 422 |
+
<ci> XI </ci>
|
| 423 |
+
</apply>
|
| 424 |
+
<cn type="integer"> -1 </cn>
|
| 425 |
+
</apply>
|
| 426 |
+
</apply>
|
| 427 |
+
</math>
|
| 428 |
+
<listOfParameters>
|
| 429 |
+
<parameter id="K3" metaid="_873763" value="0.005"/>
|
| 430 |
+
</listOfParameters>
|
| 431 |
+
</kineticLaw>
|
| 432 |
+
</reaction>
|
| 433 |
+
<reaction fast="false" id="reaction7" metaid="_060823" name="deactivation of cyclin protease" reversible="false">
|
| 434 |
+
<listOfReactants>
|
| 435 |
+
<speciesReference metaid="_361440" species="X"/>
|
| 436 |
+
</listOfReactants>
|
| 437 |
+
<listOfProducts>
|
| 438 |
+
<speciesReference metaid="_361452" species="XI"/>
|
| 439 |
+
</listOfProducts>
|
| 440 |
+
<kineticLaw metaid="_361464">
|
| 441 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 442 |
+
<apply>
|
| 443 |
+
<times/>
|
| 444 |
+
<ci> cell </ci>
|
| 445 |
+
<ci> V4 </ci>
|
| 446 |
+
<ci> X </ci>
|
| 447 |
+
<apply>
|
| 448 |
+
<power/>
|
| 449 |
+
<apply>
|
| 450 |
+
<plus/>
|
| 451 |
+
<ci> K4 </ci>
|
| 452 |
+
<ci> X </ci>
|
| 453 |
+
</apply>
|
| 454 |
+
<cn type="integer"> -1 </cn>
|
| 455 |
+
</apply>
|
| 456 |
+
</apply>
|
| 457 |
+
</math>
|
| 458 |
+
<listOfParameters>
|
| 459 |
+
<parameter id="K4" metaid="_873765" value="0.005"/>
|
| 460 |
+
<parameter id="V4" metaid="_873768" value="0.5"/>
|
| 461 |
+
</listOfParameters>
|
| 462 |
+
</kineticLaw>
|
| 463 |
+
</reaction>
|
| 464 |
+
</listOfReactions>
|
| 465 |
+
</model>
|
| 466 |
+
</sbml>
|
Data/BIOMD0000000004/Goldbeter1991_conditions.json
ADDED
|
@@ -0,0 +1,47 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"C": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.1895156543459166,
|
| 7 |
+
0.5814480477429518
|
| 8 |
+
],
|
| 9 |
+
"period": 184.0
|
| 10 |
+
},
|
| 11 |
+
"M": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.0060365066431544,
|
| 16 |
+
0.7092696083900643
|
| 17 |
+
],
|
| 18 |
+
"period": 184.0
|
| 19 |
+
},
|
| 20 |
+
"X": {
|
| 21 |
+
"trajectory_type": 3,
|
| 22 |
+
"trajectory_type_name": "oscillation",
|
| 23 |
+
"bounds": [
|
| 24 |
+
6.389159811199635e-05,
|
| 25 |
+
0.6416356765731371
|
| 26 |
+
],
|
| 27 |
+
"period": 184.0
|
| 28 |
+
},
|
| 29 |
+
"MI": {
|
| 30 |
+
"trajectory_type": 3,
|
| 31 |
+
"trajectory_type_name": "oscillation",
|
| 32 |
+
"bounds": [
|
| 33 |
+
0.2907303916099379,
|
| 34 |
+
0.9939634933568476
|
| 35 |
+
],
|
| 36 |
+
"period": 184.0
|
| 37 |
+
},
|
| 38 |
+
"XI": {
|
| 39 |
+
"trajectory_type": 3,
|
| 40 |
+
"trajectory_type_name": "oscillation",
|
| 41 |
+
"bounds": [
|
| 42 |
+
0.3583643234268648,
|
| 43 |
+
0.9999361084018884
|
| 44 |
+
],
|
| 45 |
+
"period": 184.0
|
| 46 |
+
}
|
| 47 |
+
}
|
Data/BIOMD0000000004/initial_conditions.json
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"C": 0.4535009323056436,
|
| 5 |
+
"M": 0.06977168400902338,
|
| 6 |
+
"X": 0.0008026743700016656,
|
| 7 |
+
"MI": 0.9302283159909792,
|
| 8 |
+
"XI": 0.9991973256299989
|
| 9 |
+
}
|
| 10 |
+
}
|
Data/BIOMD0000000005/Tyson1991.csv
ADDED
|
@@ -0,0 +1,513 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
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|
|
|
| 1 |
+
time,C2,CP,M,pM,Y,YP
|
| 2 |
+
0.0,0.0,0.75,0.0,0.25,0.0,0.0
|
| 3 |
+
0.19569471624266144,0.0007465004556155988,0.7464996366449183,0.0008047953149002627,0.25194906758460867,0.00010045610500010512,7.79735298167036e-05
|
| 4 |
+
0.3913894324853229,0.0007437944012247317,0.743792905276845,0.0014824488556883608,0.2539808514659698,0.00010082219909763223,0.0002834329970816632
|
| 5 |
+
0.5870841487279843,0.0007412106533742729,0.741208579276754,0.002061176170124088,0.2559890338962302,0.00010117417799079191,0.0005815725965400944
|
| 6 |
+
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| 490 |
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| 491 |
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| 492 |
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| 495 |
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| 496 |
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| 498 |
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| 499 |
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|
| 500 |
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|
| 504 |
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|
| 505 |
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|
| 506 |
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|
| 507 |
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| 508 |
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|
| 509 |
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|
| 510 |
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|
| 511 |
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|
| 512 |
+
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|
| 513 |
+
100.0,0.0008125462734866237,0.8125428658354937,0.003396060379950768,0.18324852654077403,9.229472106073073e-05,0.004992154768805971
|
Data/BIOMD0000000005/Tyson1991.xml
ADDED
|
@@ -0,0 +1,615 @@
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_000000" version="4">
|
| 3 |
+
<model id="BIOMD0000000005" metaid="_000001" name="Tyson1991 - Cell Cycle 6 var">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Tyson1991 - Cell Cycle 6 var</div>
|
| 7 |
+
<div class="dc:description">
|
| 8 |
+
<p>Mathematical model of the interactions of cdc2 and cyclin.</p>
|
| 9 |
+
</div>
|
| 10 |
+
<div class="dc:bibliographicCitation">
|
| 11 |
+
<p>This model is described in the article:</p>
|
| 12 |
+
<div class="bibo:title">
|
| 13 |
+
<a href="http://identifiers.org/pubmed/1831270" title="Access to this publication">Modeling the cell division cycle: cdc2 and cyclin interactions.</a>
|
| 14 |
+
</div>
|
| 15 |
+
<div class="bibo:authorList">Tyson JJ.</div>
|
| 16 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. U.S.A. 1991; 88(16); 7328-32</div>
|
| 17 |
+
<p>Abstract:</p>
|
| 18 |
+
<div class="bibo:abstract">
|
| 19 |
+
<p>The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. Simulation and analysis of the model show that the control system can operate in three modes: as a steady state with high maturation promoting factor activity, as a spontaneous oscillator, or as an excitable switch. We associate the steady state with metaphase arrest in unfertilized eggs, the spontaneous oscillations with rapid division cycles in early embryos, and the excitable switch with growth-controlled division cycles typical of nonembryonic cells.</p>
|
| 20 |
+
</div>
|
| 21 |
+
</div>
|
| 22 |
+
<div class="dc:publisher">
|
| 23 |
+
<p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 24 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000005">BIOMD0000000005</a>
|
| 25 |
+
. </p>
|
| 26 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 27 |
+
. </p>
|
| 28 |
+
</div>
|
| 29 |
+
<div class="dc:license">
|
| 30 |
+
<p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 31 |
+
for more information. </p>
|
| 32 |
+
</div>
|
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<kineticLaw metaid="_712442">
|
| 327 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 328 |
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<apply>
|
| 329 |
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<times/>
|
| 330 |
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<ci> cell </ci>
|
| 331 |
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<ci> C2 </ci>
|
| 332 |
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<ci> k8notP </ci>
|
| 333 |
+
</apply>
|
| 334 |
+
</math>
|
| 335 |
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<listOfParameters>
|
| 336 |
+
<parameter id="k8notP" metaid="_840213" value="1000000"/>
|
| 337 |
+
</listOfParameters>
|
| 338 |
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</kineticLaw>
|
| 339 |
+
</reaction>
|
| 340 |
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<reaction id="Reaction3" metaid="_000012" name="cdc2k dephosphorylation" reversible="false">
|
| 341 |
+
<annotation>
|
| 342 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 343 |
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|
| 344 |
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<bqbiol:isVersionOf>
|
| 345 |
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|
| 346 |
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<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 347 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 348 |
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</rdf:Bag>
|
| 349 |
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</bqbiol:isVersionOf>
|
| 350 |
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</rdf:Description>
|
| 351 |
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|
| 352 |
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</rdf:RDF>
|
| 353 |
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|
| 354 |
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<listOfReactants>
|
| 355 |
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<speciesReference metaid="_712454" species="CP"/>
|
| 356 |
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</listOfReactants>
|
| 357 |
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<listOfProducts>
|
| 358 |
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<speciesReference metaid="_712466" species="C2"/>
|
| 359 |
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</listOfProducts>
|
| 360 |
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<kineticLaw metaid="_712478">
|
| 361 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 362 |
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<apply>
|
| 363 |
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<times/>
|
| 364 |
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<ci> cell </ci>
|
| 365 |
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<ci> CP </ci>
|
| 366 |
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<ci> k9 </ci>
|
| 367 |
+
</apply>
|
| 368 |
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</math>
|
| 369 |
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<listOfParameters>
|
| 370 |
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<parameter id="k9" metaid="_840215" value="1000"/>
|
| 371 |
+
</listOfParameters>
|
| 372 |
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</kineticLaw>
|
| 373 |
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</reaction>
|
| 374 |
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<reaction id="Reaction4" metaid="_000013" name="cyclin cdc2k-p association" reversible="false">
|
| 375 |
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<annotation>
|
| 376 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 377 |
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<rdf:Description rdf:about="#_000013">
|
| 378 |
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<bqbiol:hasVersion>
|
| 379 |
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<rdf:Bag>
|
| 380 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6216"/>
|
| 381 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6308"/>
|
| 382 |
+
</rdf:Bag>
|
| 383 |
+
</bqbiol:hasVersion>
|
| 384 |
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</rdf:Description>
|
| 385 |
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|
| 386 |
+
</rdf:RDF>
|
| 387 |
+
</annotation>
|
| 388 |
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<listOfReactants>
|
| 389 |
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<speciesReference metaid="_712490" species="CP"/>
|
| 390 |
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<speciesReference metaid="_712502" species="Y"/>
|
| 391 |
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</listOfReactants>
|
| 392 |
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<listOfProducts>
|
| 393 |
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<speciesReference metaid="_712514" species="pM"/>
|
| 394 |
+
</listOfProducts>
|
| 395 |
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<kineticLaw metaid="_712526">
|
| 396 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 397 |
+
<apply>
|
| 398 |
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<times/>
|
| 399 |
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<ci> cell </ci>
|
| 400 |
+
<ci> CP </ci>
|
| 401 |
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<ci> k3 </ci>
|
| 402 |
+
<ci> Y </ci>
|
| 403 |
+
</apply>
|
| 404 |
+
</math>
|
| 405 |
+
<listOfParameters>
|
| 406 |
+
<parameter id="k3" metaid="_840217" value="200"/>
|
| 407 |
+
</listOfParameters>
|
| 408 |
+
</kineticLaw>
|
| 409 |
+
</reaction>
|
| 410 |
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<reaction id="Reaction5" metaid="_000014" name="deactivation of cdc2 kinase" reversible="false">
|
| 411 |
+
<annotation>
|
| 412 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 413 |
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<rdf:Description rdf:about="#_000014">
|
| 414 |
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<bqbiol:isVersionOf>
|
| 415 |
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<rdf:Bag>
|
| 416 |
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<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.10.2"/>
|
| 417 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 418 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0045736"/>
|
| 419 |
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</rdf:Bag>
|
| 420 |
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</bqbiol:isVersionOf>
|
| 421 |
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|
| 422 |
+
<bqbiol:hasVersion>
|
| 423 |
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<rdf:Bag>
|
| 424 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_3178"/>
|
| 425 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6327"/>
|
| 426 |
+
</rdf:Bag>
|
| 427 |
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</bqbiol:hasVersion>
|
| 428 |
+
</rdf:Description>
|
| 429 |
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|
| 430 |
+
</rdf:RDF>
|
| 431 |
+
</annotation>
|
| 432 |
+
<listOfReactants>
|
| 433 |
+
<speciesReference metaid="_712538" species="M"/>
|
| 434 |
+
</listOfReactants>
|
| 435 |
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<listOfProducts>
|
| 436 |
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<speciesReference metaid="_712550" species="pM"/>
|
| 437 |
+
</listOfProducts>
|
| 438 |
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<kineticLaw metaid="_712562">
|
| 439 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 440 |
+
<apply>
|
| 441 |
+
<times/>
|
| 442 |
+
<ci> cell </ci>
|
| 443 |
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<ci> k5notP </ci>
|
| 444 |
+
<ci> M </ci>
|
| 445 |
+
</apply>
|
| 446 |
+
</math>
|
| 447 |
+
<listOfParameters>
|
| 448 |
+
<parameter id="k5notP" metaid="_840219" value="0"/>
|
| 449 |
+
</listOfParameters>
|
| 450 |
+
</kineticLaw>
|
| 451 |
+
</reaction>
|
| 452 |
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<reaction id="Reaction6" metaid="_000015" name="cyclin biosynthesis" reversible="false">
|
| 453 |
+
<annotation>
|
| 454 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 455 |
+
<rdf:Description rdf:about="#_000015">
|
| 456 |
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<bqbiol:isVersionOf>
|
| 457 |
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<rdf:Bag>
|
| 458 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0006412"/>
|
| 459 |
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</rdf:Bag>
|
| 460 |
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</bqbiol:isVersionOf>
|
| 461 |
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</rdf:Description>
|
| 462 |
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|
| 463 |
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</rdf:RDF>
|
| 464 |
+
</annotation>
|
| 465 |
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<listOfReactants>
|
| 466 |
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<speciesReference metaid="_712574" species="EmptySet"/>
|
| 467 |
+
</listOfReactants>
|
| 468 |
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<listOfProducts>
|
| 469 |
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<speciesReference metaid="_712586" species="Y"/>
|
| 470 |
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</listOfProducts>
|
| 471 |
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<kineticLaw metaid="_712598">
|
| 472 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 473 |
+
<apply>
|
| 474 |
+
<times/>
|
| 475 |
+
<ci> cell </ci>
|
| 476 |
+
<ci> k1aa </ci>
|
| 477 |
+
</apply>
|
| 478 |
+
</math>
|
| 479 |
+
<listOfParameters>
|
| 480 |
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<parameter id="k1aa" metaid="_840221" value="0.015"/>
|
| 481 |
+
</listOfParameters>
|
| 482 |
+
</kineticLaw>
|
| 483 |
+
</reaction>
|
| 484 |
+
<reaction id="Reaction7" metaid="_000016" name="default degradation of cyclin" reversible="false">
|
| 485 |
+
<annotation>
|
| 486 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 487 |
+
<rdf:Description rdf:about="#_000016">
|
| 488 |
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<bqbiol:isVersionOf>
|
| 489 |
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<rdf:Bag>
|
| 490 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 491 |
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</rdf:Bag>
|
| 492 |
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</bqbiol:isVersionOf>
|
| 493 |
+
</rdf:Description>
|
| 494 |
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|
| 495 |
+
</rdf:RDF>
|
| 496 |
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</annotation>
|
| 497 |
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<listOfReactants>
|
| 498 |
+
<speciesReference metaid="_712610" species="Y"/>
|
| 499 |
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</listOfReactants>
|
| 500 |
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<listOfProducts>
|
| 501 |
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<speciesReference metaid="_712622" species="EmptySet"/>
|
| 502 |
+
</listOfProducts>
|
| 503 |
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<kineticLaw metaid="_712634">
|
| 504 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 505 |
+
<apply>
|
| 506 |
+
<times/>
|
| 507 |
+
<ci> cell </ci>
|
| 508 |
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<ci> k2 </ci>
|
| 509 |
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<ci> Y </ci>
|
| 510 |
+
</apply>
|
| 511 |
+
</math>
|
| 512 |
+
<listOfParameters>
|
| 513 |
+
<parameter id="k2" metaid="_840223" value="0"/>
|
| 514 |
+
</listOfParameters>
|
| 515 |
+
</kineticLaw>
|
| 516 |
+
</reaction>
|
| 517 |
+
<reaction id="Reaction8" metaid="_000017" name="cdc2 kinase triggered degration of cyclin" reversible="false">
|
| 518 |
+
<annotation>
|
| 519 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 520 |
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<rdf:Description rdf:about="#_000017">
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| 521 |
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<bqbiol:isVersionOf>
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| 522 |
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<rdf:Bag>
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| 523 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 524 |
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</rdf:Bag>
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| 525 |
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</bqbiol:isVersionOf>
|
| 526 |
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</rdf:Description>
|
| 527 |
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|
| 528 |
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|
| 529 |
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|
| 530 |
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<listOfReactants>
|
| 531 |
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<speciesReference metaid="_712646" species="YP"/>
|
| 532 |
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</listOfReactants>
|
| 533 |
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<listOfProducts>
|
| 534 |
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<speciesReference metaid="_712658" species="EmptySet"/>
|
| 535 |
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</listOfProducts>
|
| 536 |
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<kineticLaw metaid="_712670">
|
| 537 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 538 |
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<apply>
|
| 539 |
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<times/>
|
| 540 |
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<ci> cell </ci>
|
| 541 |
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<ci> k7 </ci>
|
| 542 |
+
<ci> YP </ci>
|
| 543 |
+
</apply>
|
| 544 |
+
</math>
|
| 545 |
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<listOfParameters>
|
| 546 |
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<parameter id="k7" metaid="_840225" value="0.6"/>
|
| 547 |
+
</listOfParameters>
|
| 548 |
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</kineticLaw>
|
| 549 |
+
</reaction>
|
| 550 |
+
<reaction id="Reaction9" metaid="_000018" name="activation of cdc2 kinase" reversible="false">
|
| 551 |
+
<annotation>
|
| 552 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 553 |
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<rdf:Description rdf:about="#_000018">
|
| 554 |
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<bqbiol:hasVersion>
|
| 555 |
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<rdf:Bag>
|
| 556 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6257"/>
|
| 557 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6175"/>
|
| 558 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_6294"/>
|
| 559 |
+
</rdf:Bag>
|
| 560 |
+
</bqbiol:hasVersion>
|
| 561 |
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|
| 562 |
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<bqbiol:isVersionOf>
|
| 563 |
+
<rdf:Bag>
|
| 564 |
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<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 565 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 566 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0045737"/>
|
| 567 |
+
</rdf:Bag>
|
| 568 |
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</bqbiol:isVersionOf>
|
| 569 |
+
</rdf:Description>
|
| 570 |
+
|
| 571 |
+
</rdf:RDF>
|
| 572 |
+
</annotation>
|
| 573 |
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<listOfReactants>
|
| 574 |
+
<speciesReference metaid="_712682" species="pM"/>
|
| 575 |
+
</listOfReactants>
|
| 576 |
+
<listOfProducts>
|
| 577 |
+
<speciesReference metaid="_712694" species="M"/>
|
| 578 |
+
</listOfProducts>
|
| 579 |
+
<listOfModifiers>
|
| 580 |
+
<modifierSpeciesReference metaid="_712706" species="CT"/>
|
| 581 |
+
</listOfModifiers>
|
| 582 |
+
<kineticLaw metaid="_712718">
|
| 583 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 584 |
+
<apply>
|
| 585 |
+
<times/>
|
| 586 |
+
<ci> cell </ci>
|
| 587 |
+
<ci> pM </ci>
|
| 588 |
+
<apply>
|
| 589 |
+
<plus/>
|
| 590 |
+
<ci> k4prime </ci>
|
| 591 |
+
<apply>
|
| 592 |
+
<times/>
|
| 593 |
+
<ci> k4 </ci>
|
| 594 |
+
<apply>
|
| 595 |
+
<power/>
|
| 596 |
+
<apply>
|
| 597 |
+
<divide/>
|
| 598 |
+
<ci> M </ci>
|
| 599 |
+
<ci> CT </ci>
|
| 600 |
+
</apply>
|
| 601 |
+
<cn type="integer"> 2 </cn>
|
| 602 |
+
</apply>
|
| 603 |
+
</apply>
|
| 604 |
+
</apply>
|
| 605 |
+
</apply>
|
| 606 |
+
</math>
|
| 607 |
+
<listOfParameters>
|
| 608 |
+
<parameter id="k4" metaid="_840227" value="180"/>
|
| 609 |
+
<parameter id="k4prime" metaid="_840229" value="0.018"/>
|
| 610 |
+
</listOfParameters>
|
| 611 |
+
</kineticLaw>
|
| 612 |
+
</reaction>
|
| 613 |
+
</listOfReactions>
|
| 614 |
+
</model>
|
| 615 |
+
</sbml>
|
Data/BIOMD0000000005/Tyson1991_conditions.json
ADDED
|
@@ -0,0 +1,56 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"C2": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.0,
|
| 7 |
+
0.0009565799818482
|
| 8 |
+
],
|
| 9 |
+
"period": 182.0
|
| 10 |
+
},
|
| 11 |
+
"CP": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.6719037226163864,
|
| 16 |
+
0.9565640988611628
|
| 17 |
+
],
|
| 18 |
+
"period": 182.0
|
| 19 |
+
},
|
| 20 |
+
"M": {
|
| 21 |
+
"trajectory_type": 3,
|
| 22 |
+
"trajectory_type_name": "oscillation",
|
| 23 |
+
"bounds": [
|
| 24 |
+
0.0,
|
| 25 |
+
0.1978812270735694
|
| 26 |
+
],
|
| 27 |
+
"period": 182.0
|
| 28 |
+
},
|
| 29 |
+
"pM": {
|
| 30 |
+
"trajectory_type": 3,
|
| 31 |
+
"trajectory_type_name": "oscillation",
|
| 32 |
+
"bounds": [
|
| 33 |
+
0.0046754149233749,
|
| 34 |
+
0.3136305111710109
|
| 35 |
+
],
|
| 36 |
+
"period": 182.0
|
| 37 |
+
},
|
| 38 |
+
"Y": {
|
| 39 |
+
"trajectory_type": 3,
|
| 40 |
+
"trajectory_type_name": "oscillation",
|
| 41 |
+
"bounds": [
|
| 42 |
+
0.0,
|
| 43 |
+
0.000111623016223
|
| 44 |
+
],
|
| 45 |
+
"period": 182.0
|
| 46 |
+
},
|
| 47 |
+
"YP": {
|
| 48 |
+
"trajectory_type": 3,
|
| 49 |
+
"trajectory_type_name": "oscillation",
|
| 50 |
+
"bounds": [
|
| 51 |
+
0.0,
|
| 52 |
+
0.1601633755902466
|
| 53 |
+
],
|
| 54 |
+
"period": 182.0
|
| 55 |
+
}
|
| 56 |
+
}
|
Data/BIOMD0000000005/initial_conditions.json
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
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|
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|
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|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"C2": 0.0,
|
| 5 |
+
"CP": 0.75,
|
| 6 |
+
"M": 0.0,
|
| 7 |
+
"pM": 0.25,
|
| 8 |
+
"Y": 0.0,
|
| 9 |
+
"YP": 0.0
|
| 10 |
+
}
|
| 11 |
+
}
|
Data/BIOMD0000000006/Tyson1991.csv
ADDED
|
@@ -0,0 +1,513 @@
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|
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|
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|
|
| 1 |
+
time,var_0,var_1
|
| 2 |
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0.0,0.0,0.0
|
| 3 |
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| 4 |
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| 5 |
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| 6 |
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0.8610567514677103,7.619938227845471e-05,0.012892472149140162
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| 8 |
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| 11 |
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| 14 |
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| 15 |
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| 32 |
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109.78473581213306,0.005375326239552123,0.049264001713491004
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| 513 |
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110.0,0.004531133884668349,0.051429969642087486
|
Data/BIOMD0000000006/Tyson1991.xml
ADDED
|
@@ -0,0 +1,346 @@
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_000000" version="4">
|
| 3 |
+
<model id="BIOMD0000000006" metaid="_000001" name="Tyson1991 - Cell Cycle 2 var">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Tyson1991 - Cell Cycle 2 var</div>
|
| 7 |
+
<div class="dc:description">
|
| 8 |
+
<p>Mathematical model of the interactions of cdc2 and cyclin.</p>
|
| 9 |
+
</div>
|
| 10 |
+
<div class="dc:provenance">
|
| 11 |
+
<p>Description taken from the original Cellerator version of the model ( <a href="http://www.cellerator.org/notebooks/Tyson2.html">Tyson (1991, 2 variables)</a>
|
| 12 |
+
at <a href="http://www.cellerator.org/" title="xCellerator: A Mathematica package for biological modeling">http://www.cellerator.org</a>
|
| 13 |
+
). </p>
|
| 14 |
+
</div>
|
| 15 |
+
<div class="dc:bibliographicCitation">
|
| 16 |
+
<p>This model is described in the article:</p>
|
| 17 |
+
<div class="bibo:title">
|
| 18 |
+
<a href="http://identifiers.org/pubmed/1831270" title="Access to this publication">Modeling the cell division cycle: cdc2 and cyclin interactions.</a>
|
| 19 |
+
</div>
|
| 20 |
+
<div class="bibo:authorList">Tyson JJ.</div>
|
| 21 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. U.S.A. 1991; 88(16); 7328-32</div>
|
| 22 |
+
<p>Abstract:</p>
|
| 23 |
+
<div class="bibo:abstract">
|
| 24 |
+
<p>The proteins cdc2 and cyclin form a heterodimer (maturation promoting factor) that controls the major events of the cell cycle. A mathematical model for the interactions of cdc2 and cyclin is constructed. Simulation and analysis of the model show that the control system can operate in three modes: as a steady state with high maturation promoting factor activity, as a spontaneous oscillator, or as an excitable switch. We associate the steady state with metaphase arrest in unfertilized eggs, the spontaneous oscillations with rapid division cycles in early embryos, and the excitable switch with growth-controlled division cycles typical of nonembryonic cells.</p>
|
| 25 |
+
</div>
|
| 26 |
+
</div>
|
| 27 |
+
<div class="bm:modification">
|
| 28 |
+
<p>This is a two variable reduction of the larger 6-variable model published in the same paper. The equations are:</p>
|
| 29 |
+
<p>u'= k4(v-u)(alpha+u^2)-k6*u <br/>
|
| 30 |
+
v'=kappa-k6*u <br/>
|
| 31 |
+
z= v-u <br/>
|
| 32 |
+
with kappa = k1[aa]/[CT] </p>
|
| 33 |
+
<p>In the present implementation, an additional variable z is introduced with z = v-u is made, so that the different variables be interpreted as follows:</p>
|
| 34 |
+
<p>u=[activeMPF]/[CT] <br/>
|
| 35 |
+
v=([cyclin]+[preMPF]+[activeMPF])/[CT] <br/>
|
| 36 |
+
z=([ cyclin]+[preMPF])/[CT] <br/>
|
| 37 |
+
with [CT]=[CDC2]+{CDC2P]+[preMPF]+[aMPF]. </p>
|
| 38 |
+
<p>The reactions included are only to show the flows between z and u, and do not influence the species, as they all are set to <em>boundaryCondition=True</em>
|
| 39 |
+
, meaning, that they are only determined by the rate rules (explicit differential equations) and assignment rules. </p>
|
| 40 |
+
<p>If you set <em>boundaryCondition=False</em>
|
| 41 |
+
and remove the rate rules for v, u and the the assignment rule for z, you get the more symmetrical, but equivalent, version from the Cellerator repository: </p>
|
| 42 |
+
<p>u'= k4*z*(alpha+u^2)-k6*u <br/>
|
| 43 |
+
z'=kappa-z*(alpha+u^2) </p>
|
| 44 |
+
</div>
|
| 45 |
+
<div class="dc:publisher">
|
| 46 |
+
<p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 47 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000006">BIOMD0000000006</a>
|
| 48 |
+
. </p>
|
| 49 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 50 |
+
. </p>
|
| 51 |
+
</div>
|
| 52 |
+
<div class="dc:license">
|
| 53 |
+
<p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 54 |
+
for more information. </p>
|
| 55 |
+
</div>
|
| 56 |
+
</body>
|
| 57 |
+
</notes>
|
| 58 |
+
<annotation>
|
| 59 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 60 |
+
<rdf:Description rdf:about="#_000001">
|
| 61 |
+
<dc:creator>
|
| 62 |
+
<rdf:Bag>
|
| 63 |
+
<rdf:li rdf:parseType="Resource">
|
| 64 |
+
<vCard:N rdf:parseType="Resource">
|
| 65 |
+
<vCard:Family>Shapiro</vCard:Family>
|
| 66 |
+
<vCard:Given>Bruce</vCard:Given>
|
| 67 |
+
</vCard:N>
|
| 68 |
+
<vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
|
| 69 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 70 |
+
<vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
|
| 71 |
+
</vCard:ORG>
|
| 72 |
+
</rdf:li>
|
| 73 |
+
<rdf:li rdf:parseType="Resource">
|
| 74 |
+
<vCard:N rdf:parseType="Resource">
|
| 75 |
+
<vCard:Family>Endler</vCard:Family>
|
| 76 |
+
<vCard:Given>Lukas</vCard:Given>
|
| 77 |
+
</vCard:N>
|
| 78 |
+
<vCard:EMAIL>lukas@ebi.ac.uk</vCard:EMAIL>
|
| 79 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 80 |
+
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
|
| 81 |
+
</vCard:ORG>
|
| 82 |
+
</rdf:li>
|
| 83 |
+
</rdf:Bag>
|
| 84 |
+
</dc:creator>
|
| 85 |
+
<dcterms:created rdf:parseType="Resource">
|
| 86 |
+
<dcterms:W3CDTF>2005-02-08T18:36:17Z</dcterms:W3CDTF>
|
| 87 |
+
</dcterms:created>
|
| 88 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 89 |
+
<dcterms:W3CDTF>2013-05-16T14:38:56Z</dcterms:W3CDTF>
|
| 90 |
+
</dcterms:modified>
|
| 91 |
+
<bqmodel:is>
|
| 92 |
+
<rdf:Bag>
|
| 93 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/MODEL6614715255"/>
|
| 94 |
+
</rdf:Bag>
|
| 95 |
+
</bqmodel:is>
|
| 96 |
+
<bqmodel:is>
|
| 97 |
+
<rdf:Bag>
|
| 98 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000006"/>
|
| 99 |
+
</rdf:Bag>
|
| 100 |
+
</bqmodel:is>
|
| 101 |
+
<bqmodel:isDescribedBy>
|
| 102 |
+
<rdf:Bag>
|
| 103 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/1831270"/>
|
| 104 |
+
</rdf:Bag>
|
| 105 |
+
</bqmodel:isDescribedBy>
|
| 106 |
+
<bqbiol:hasTaxon>
|
| 107 |
+
<rdf:Bag>
|
| 108 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/33154"/>
|
| 109 |
+
</rdf:Bag>
|
| 110 |
+
</bqbiol:hasTaxon>
|
| 111 |
+
<bqbiol:is>
|
| 112 |
+
<rdf:Bag>
|
| 113 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.pathway/sce04111"/>
|
| 114 |
+
</rdf:Bag>
|
| 115 |
+
</bqbiol:is>
|
| 116 |
+
<bqbiol:isVersionOf>
|
| 117 |
+
<rdf:Bag>
|
| 118 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000278"/>
|
| 119 |
+
</rdf:Bag>
|
| 120 |
+
</bqbiol:isVersionOf>
|
| 121 |
+
<bqbiol:hasVersion>
|
| 122 |
+
<rdf:Bag>
|
| 123 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_152"/>
|
| 124 |
+
</rdf:Bag>
|
| 125 |
+
</bqbiol:hasVersion>
|
| 126 |
+
<bqbiol:hasProperty>
|
| 127 |
+
<rdf:Bag>
|
| 128 |
+
<rdf:li rdf:resource="http://identifiers.org/mamo/MAMO_0000046"/>
|
| 129 |
+
</rdf:Bag>
|
| 130 |
+
</bqbiol:hasProperty>
|
| 131 |
+
</rdf:Description>
|
| 132 |
+
|
| 133 |
+
</rdf:RDF>
|
| 134 |
+
</annotation>
|
| 135 |
+
<listOfCompartments>
|
| 136 |
+
<compartment id="cell" metaid="_000002" size="1">
|
| 137 |
+
<annotation>
|
| 138 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 139 |
+
<rdf:Description rdf:about="#_000002">
|
| 140 |
+
<bqbiol:is>
|
| 141 |
+
<rdf:Bag>
|
| 142 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005623"/>
|
| 143 |
+
</rdf:Bag>
|
| 144 |
+
</bqbiol:is>
|
| 145 |
+
</rdf:Description>
|
| 146 |
+
|
| 147 |
+
</rdf:RDF>
|
| 148 |
+
</annotation>
|
| 149 |
+
</compartment>
|
| 150 |
+
</listOfCompartments>
|
| 151 |
+
<listOfSpecies>
|
| 152 |
+
<species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="EmptySet" initialAmount="1" metaid="_808249" sboTerm="SBO:0000291"/>
|
| 153 |
+
<species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="u" initialAmount="0" metaid="_808265" sboTerm="SBO:0000297">
|
| 154 |
+
<annotation>
|
| 155 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 156 |
+
<rdf:Description rdf:about="#_808265">
|
| 157 |
+
<bqbiol:hasProperty>
|
| 158 |
+
<rdf:Bag>
|
| 159 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004693"/>
|
| 160 |
+
</rdf:Bag>
|
| 161 |
+
</bqbiol:hasProperty>
|
| 162 |
+
|
| 163 |
+
<bqbiol:isVersionOf>
|
| 164 |
+
<rdf:Bag>
|
| 165 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031387"/>
|
| 166 |
+
</rdf:Bag>
|
| 167 |
+
</bqbiol:isVersionOf>
|
| 168 |
+
</rdf:Description>
|
| 169 |
+
|
| 170 |
+
</rdf:RDF>
|
| 171 |
+
</annotation>
|
| 172 |
+
</species>
|
| 173 |
+
<species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="z" initialAmount="0" metaid="_808285" sboTerm="SBO:0000297">
|
| 174 |
+
<annotation>
|
| 175 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 176 |
+
<rdf:Description rdf:about="#_808285">
|
| 177 |
+
<bqbiol:hasVersion>
|
| 178 |
+
<rdf:Bag>
|
| 179 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04551"/>
|
| 180 |
+
</rdf:Bag>
|
| 181 |
+
</bqbiol:hasVersion>
|
| 182 |
+
</rdf:Description>
|
| 183 |
+
|
| 184 |
+
</rdf:RDF>
|
| 185 |
+
</annotation>
|
| 186 |
+
</species>
|
| 187 |
+
<species boundaryCondition="true" compartment="cell" hasOnlySubstanceUnits="true" id="v" initialAmount="0" metaid="_175119" sboTerm="SBO:0000297">
|
| 188 |
+
<annotation>
|
| 189 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 190 |
+
<rdf:Description rdf:about="#_175119">
|
| 191 |
+
<bqbiol:hasVersion>
|
| 192 |
+
<rdf:Bag>
|
| 193 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04551"/>
|
| 194 |
+
</rdf:Bag>
|
| 195 |
+
</bqbiol:hasVersion>
|
| 196 |
+
<bqbiol:hasVersion>
|
| 197 |
+
<rdf:Bag>
|
| 198 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031387"/>
|
| 199 |
+
</rdf:Bag>
|
| 200 |
+
</bqbiol:hasVersion>
|
| 201 |
+
|
| 202 |
+
<bqbiol:hasProperty>
|
| 203 |
+
<rdf:Bag>
|
| 204 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004693"/>
|
| 205 |
+
</rdf:Bag>
|
| 206 |
+
</bqbiol:hasProperty>
|
| 207 |
+
</rdf:Description>
|
| 208 |
+
|
| 209 |
+
</rdf:RDF>
|
| 210 |
+
</annotation>
|
| 211 |
+
</species>
|
| 212 |
+
</listOfSpecies>
|
| 213 |
+
<listOfParameters>
|
| 214 |
+
<parameter id="kappa" metaid="_175134" value="0.015"/>
|
| 215 |
+
<parameter id="k6" metaid="_175135" value="1"/>
|
| 216 |
+
<parameter id="k4" metaid="_175136" value="180"/>
|
| 217 |
+
<parameter id="k4prime" metaid="_175139" value="0.018"/>
|
| 218 |
+
<parameter constant="false" id="alpha" metaid="_175140"/>
|
| 219 |
+
</listOfParameters>
|
| 220 |
+
<listOfRules>
|
| 221 |
+
<rateRule metaid="_175128" variable="u">
|
| 222 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 223 |
+
<apply>
|
| 224 |
+
<minus/>
|
| 225 |
+
<apply>
|
| 226 |
+
<times/>
|
| 227 |
+
<ci> k4 </ci>
|
| 228 |
+
<apply>
|
| 229 |
+
<minus/>
|
| 230 |
+
<ci> v </ci>
|
| 231 |
+
<ci> u </ci>
|
| 232 |
+
</apply>
|
| 233 |
+
<apply>
|
| 234 |
+
<plus/>
|
| 235 |
+
<ci> alpha </ci>
|
| 236 |
+
<apply>
|
| 237 |
+
<power/>
|
| 238 |
+
<ci> u </ci>
|
| 239 |
+
<cn type="integer"> 2 </cn>
|
| 240 |
+
</apply>
|
| 241 |
+
</apply>
|
| 242 |
+
</apply>
|
| 243 |
+
<apply>
|
| 244 |
+
<times/>
|
| 245 |
+
<ci> k6 </ci>
|
| 246 |
+
<ci> u </ci>
|
| 247 |
+
</apply>
|
| 248 |
+
</apply>
|
| 249 |
+
</math>
|
| 250 |
+
</rateRule>
|
| 251 |
+
<assignmentRule metaid="_175129" variable="z">
|
| 252 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 253 |
+
<apply>
|
| 254 |
+
<minus/>
|
| 255 |
+
<ci> v </ci>
|
| 256 |
+
<ci> u </ci>
|
| 257 |
+
</apply>
|
| 258 |
+
</math>
|
| 259 |
+
</assignmentRule>
|
| 260 |
+
<rateRule metaid="_175131" variable="v">
|
| 261 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 262 |
+
<apply>
|
| 263 |
+
<minus/>
|
| 264 |
+
<ci> kappa </ci>
|
| 265 |
+
<apply>
|
| 266 |
+
<times/>
|
| 267 |
+
<ci> k6 </ci>
|
| 268 |
+
<ci> u </ci>
|
| 269 |
+
</apply>
|
| 270 |
+
</apply>
|
| 271 |
+
</math>
|
| 272 |
+
</rateRule>
|
| 273 |
+
<assignmentRule metaid="_175132" variable="alpha">
|
| 274 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 275 |
+
<apply>
|
| 276 |
+
<divide/>
|
| 277 |
+
<ci> k4prime </ci>
|
| 278 |
+
<ci> k4 </ci>
|
| 279 |
+
</apply>
|
| 280 |
+
</math>
|
| 281 |
+
</assignmentRule>
|
| 282 |
+
</listOfRules>
|
| 283 |
+
<listOfReactions>
|
| 284 |
+
<reaction id="Reaction1" metaid="_175121" reversible="false" sboTerm="SBO:0000205">
|
| 285 |
+
<listOfReactants>
|
| 286 |
+
<speciesReference metaid="_372744" species="EmptySet"/>
|
| 287 |
+
</listOfReactants>
|
| 288 |
+
<listOfProducts>
|
| 289 |
+
<speciesReference metaid="_372756" species="z"/>
|
| 290 |
+
</listOfProducts>
|
| 291 |
+
<kineticLaw metaid="_372768">
|
| 292 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 293 |
+
<ci> kappa </ci>
|
| 294 |
+
</math>
|
| 295 |
+
</kineticLaw>
|
| 296 |
+
</reaction>
|
| 297 |
+
<reaction id="Reaction2" metaid="_175122" reversible="false" sboTerm="SBO:0000179">
|
| 298 |
+
<listOfReactants>
|
| 299 |
+
<speciesReference metaid="_372780" species="u"/>
|
| 300 |
+
</listOfReactants>
|
| 301 |
+
<listOfProducts>
|
| 302 |
+
<speciesReference metaid="_372792" species="EmptySet"/>
|
| 303 |
+
</listOfProducts>
|
| 304 |
+
<kineticLaw metaid="_372804">
|
| 305 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 306 |
+
<apply>
|
| 307 |
+
<times/>
|
| 308 |
+
<ci> k6 </ci>
|
| 309 |
+
<ci> u </ci>
|
| 310 |
+
</apply>
|
| 311 |
+
</math>
|
| 312 |
+
</kineticLaw>
|
| 313 |
+
</reaction>
|
| 314 |
+
<reaction id="Reaction3" metaid="_175123" reversible="false" sboTerm="SBO:0000176">
|
| 315 |
+
<listOfReactants>
|
| 316 |
+
<speciesReference metaid="_372816" species="z"/>
|
| 317 |
+
</listOfReactants>
|
| 318 |
+
<listOfProducts>
|
| 319 |
+
<speciesReference metaid="_372828" species="u"/>
|
| 320 |
+
</listOfProducts>
|
| 321 |
+
<kineticLaw metaid="_372840">
|
| 322 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 323 |
+
<apply>
|
| 324 |
+
<times/>
|
| 325 |
+
<ci> k4 </ci>
|
| 326 |
+
<ci> z </ci>
|
| 327 |
+
<apply>
|
| 328 |
+
<plus/>
|
| 329 |
+
<apply>
|
| 330 |
+
<divide/>
|
| 331 |
+
<ci> k4prime </ci>
|
| 332 |
+
<ci> k4 </ci>
|
| 333 |
+
</apply>
|
| 334 |
+
<apply>
|
| 335 |
+
<power/>
|
| 336 |
+
<ci> u </ci>
|
| 337 |
+
<cn type="integer"> 2 </cn>
|
| 338 |
+
</apply>
|
| 339 |
+
</apply>
|
| 340 |
+
</apply>
|
| 341 |
+
</math>
|
| 342 |
+
</kineticLaw>
|
| 343 |
+
</reaction>
|
| 344 |
+
</listOfReactions>
|
| 345 |
+
</model>
|
| 346 |
+
</sbml>
|
Data/BIOMD0000000006/Tyson1991_conditions.json
ADDED
|
@@ -0,0 +1,20 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"var_0": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.0,
|
| 7 |
+
0.1927371929929522
|
| 8 |
+
],
|
| 9 |
+
"period": 165.5
|
| 10 |
+
},
|
| 11 |
+
"var_1": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.0,
|
| 16 |
+
0.3243842768078514
|
| 17 |
+
],
|
| 18 |
+
"period": 165.0
|
| 19 |
+
}
|
| 20 |
+
}
|
Data/BIOMD0000000006/initial_conditions.json
ADDED
|
@@ -0,0 +1,7 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"var_0": 0.0,
|
| 5 |
+
"var_1": 0.0
|
| 6 |
+
}
|
| 7 |
+
}
|
Data/BIOMD0000000008/Gardner1998.csv
ADDED
|
@@ -0,0 +1,513 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
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|
|
|
|
|
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|
|
|
|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
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| 1 |
+
time,C,X,M,Y,Z
|
| 2 |
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0.0,0.20917378933088832,0.15128968711425134,0.35691624964283825,3.7071924859166465,0.41039731629530285
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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| 10 |
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| 11 |
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| 18 |
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| 26 |
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1.8786692759295498,0.2030153312811613,0.2198097262654161,0.4736715305549459,3.7031524384918426,0.43818374386940073
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| 27 |
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| 28 |
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| 29 |
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| 30 |
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| 31 |
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| 32 |
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| 33 |
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| 34 |
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| 39 |
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| 41 |
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3.0528375733855184,0.17250713534094345,0.2744937080901785,0.5134975303850612,3.706481063724847,0.449610081675827
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| 42 |
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| 43 |
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| 44 |
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3.287671232876712,0.16429102838268303,0.28560063286331644,0.5168290223479273,3.7080844058255034,0.4509153718322812
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| 45 |
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3.3659491193737767,0.16142272259622426,0.2892770376079656,0.5175427553850748,3.7086979897405796,0.45126658162276667
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| 46 |
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3.4442270058708413,0.15849426756731383,0.29293495434364153,0.5180510216264199,3.7093521185174843,0.45157463621834454
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| 47 |
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3.522504892367906,0.155508667776875,0.2965709780026232,0.5183495663164522,3.710047317063069,0.4518388661107948
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| 48 |
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3.6007827788649704,0.15246919402701617,0.30018167161931314,0.5184342400146105,3.7107840100699705,0.4520587051067738
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| 49 |
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3.679060665362035,0.14937930019847576,0.30376355092447305,0.5183009288067454,3.7115625618726416,0.4522336468424226
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| 50 |
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3.7573385518590996,0.14624241287400996,0.3073130454106605,0.517945377930479,3.712383377174399,0.45236313488393776
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| 51 |
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3.835616438356164,0.14306218487831956,0.3108265452550603,0.5173634043369205,3.71324677965404,0.452446695175247
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| 52 |
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3.9138943248532287,0.13984251069299045,0.31430041127883096,0.516551003697718,3.714153002495936,0.4524839464633575
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| 53 |
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3.9921722113502933,0.13658748946598448,0.3177309652605638,0.5155042817850921,3.7151022069360287,0.452474580026313
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| 54 |
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4.070450097847358,0.13330130458929634,0.32111445840181807,0.5142192310800173,3.716094542638206,0.4524182936777021
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| 55 |
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4.148727984344422,0.12998841431293126,0.3244471355859816,0.5126922183892473,3.7171300498897972,0.45231489889164
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| 56 |
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| 57 |
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4.305283757338552,0.12330108557043964,0.33094472957844195,0.5088975922784307,3.719330525517459,0.45196623362856453
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Data/BIOMD0000000008/Gardner1998.xml
ADDED
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@@ -0,0 +1,695 @@
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_000000" version="4">
|
| 3 |
+
<annotation>
|
| 4 |
+
<mathsbml:AuthorConfiguration xmlns:mathsbml="http://sbml.org/software/mathsbml/ns">
|
| 5 |
+
<mathsbml:date>2006-10-01T15:36:47</mathsbml:date>
|
| 6 |
+
<mathsbml:MachineDomain/>
|
| 7 |
+
<mathsbml:MachineID>5103-24185-26591</mathsbml:MachineID>
|
| 8 |
+
<mathsbml:MachineName>Dont-Even-Think-About-It</mathsbml:MachineName>
|
| 9 |
+
<mathsbml:MachineType>PC</mathsbml:MachineType>
|
| 10 |
+
<mathsbml:MathematicaVersion>5.2 for Mac OS X x86 (32-bit) (February 24, 2006)</mathsbml:MathematicaVersion>
|
| 11 |
+
<mathsbml:OperatingSystem>MacOSX</mathsbml:OperatingSystem>
|
| 12 |
+
<mathsbml:ProcessorType>x86</mathsbml:ProcessorType>
|
| 13 |
+
<mathsbml:ProductInformation mathsbml:ProductIDName="Mathematica" mathsbml:ProductKernelName="Mathematica 5.2 Kernel" mathsbml:ProductVersion="5.2 for Mac OS X x86 (32-bit) (February 24, 2006)" mathsbml:ProductVersionNumber="5.2"/>
|
| 14 |
+
<mathsbml:SoftwareVersion>2.6.0.p960929 (Prerelease Version of 29-Sept-2006)</mathsbml:SoftwareVersion>
|
| 15 |
+
<mathsbml:System>MacOSX-x86</mathsbml:System>
|
| 16 |
+
<mathsbml:UserName>mathman</mathsbml:UserName>
|
| 17 |
+
</mathsbml:AuthorConfiguration>
|
| 18 |
+
</annotation>
|
| 19 |
+
<model id="BIOMD0000000008" metaid="_000001" name="Gardner1998 - Cell Cycle Goldbeter">
|
| 20 |
+
<notes>
|
| 21 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 22 |
+
<div class="dc:title">Gardner1998 - Cell Cycle Goldbeter</div>
|
| 23 |
+
<div class="dc:description">
|
| 24 |
+
<p>Mathematical modeling of cell division cycle (CDC)
|
| 25 |
+
dynamics.</p>
|
| 26 |
+
</div>
|
| 27 |
+
<div class="dc:provenance">
|
| 28 |
+
<p>The SBML file has been generated by MathSBML 2.6.0.p960929
|
| 29 |
+
(Prerelease Version of 29-Sept-2006) 1-October-2006
|
| 30 |
+
15:36:36.076517.</p>
|
| 31 |
+
</div>
|
| 32 |
+
<div class="dc:bibliographicCitation">
|
| 33 |
+
<p>This model is described in the article:</p>
|
| 34 |
+
<div class="bibo:title">
|
| 35 |
+
<a href="http://identifiers.org/pubmed/9826676" title="Access to this publication">A theory for controlling
|
| 36 |
+
cell cycle dynamics using a reversibly binding inhibitor.</a>
|
| 37 |
+
</div>
|
| 38 |
+
<div class="bibo:authorList">Gardner TS, Dolnik M, Collins
|
| 39 |
+
JJ.</div>
|
| 40 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. U.S.A. 1998 Nov;
|
| 41 |
+
95(24): 14190-14195</div>
|
| 42 |
+
<p>Abstract:</p>
|
| 43 |
+
<div class="bibo:abstract">
|
| 44 |
+
<p>We demonstrate, by using mathematical modeling of cell
|
| 45 |
+
division cycle (CDC) dynamics, a potential mechanism for
|
| 46 |
+
precisely controlling the frequency of cell division and
|
| 47 |
+
regulating the size of a dividing cell. Control of the cell
|
| 48 |
+
cycle is achieved by artificially expressing a protein that
|
| 49 |
+
reversibly binds and inactivates any one of the CDC proteins.
|
| 50 |
+
In the simplest case, such as the checkpoint-free situation
|
| 51 |
+
encountered in early amphibian embryos, the frequency of CDC
|
| 52 |
+
oscillations can be increased or decreased by regulating the
|
| 53 |
+
rate of synthesis, the binding rate, or the equilibrium
|
| 54 |
+
constant of the binding protein. In a more complex model of
|
| 55 |
+
cell division, where size-control checkpoints are included, we
|
| 56 |
+
show that the same reversible binding reaction can alter the
|
| 57 |
+
mean cell mass in a continuously dividing cell. Because this
|
| 58 |
+
control scheme is general and requires only the expression of a
|
| 59 |
+
single protein, it provides a practical means for tuning the
|
| 60 |
+
characteristics of the cell cycle in vivo.</p>
|
| 61 |
+
</div>
|
| 62 |
+
</div>
|
| 63 |
+
<div class="dc:publisher">
|
| 64 |
+
<p>This model is hosted on
|
| 65 |
+
<a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 66 |
+
and identified by:
|
| 67 |
+
<a href="http://identifiers.org/biomodels.db/BIOMD0000000008">BIOMD0000000008</a>.</p>
|
| 68 |
+
<p>To cite BioModels Database, please use:
|
| 69 |
+
<a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database:
|
| 70 |
+
An enhanced, curated and annotated resource for published
|
| 71 |
+
quantitative kinetic models</a>.</p>
|
| 72 |
+
</div>
|
| 73 |
+
<div class="dc:license">
|
| 74 |
+
<p>To the extent possible under law, all copyright and related or
|
| 75 |
+
neighbouring rights to this encoded model have been dedicated to
|
| 76 |
+
the public domain worldwide. Please refer to
|
| 77 |
+
<a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0
|
| 78 |
+
Public Domain Dedication</a> for more information.</p>
|
| 79 |
+
</div>
|
| 80 |
+
</body>
|
| 81 |
+
</notes>
|
| 82 |
+
<annotation>
|
| 83 |
+
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|
| 84 |
+
<rdf:Description rdf:about="#_000001">
|
| 85 |
+
<dc:creator>
|
| 86 |
+
<rdf:Bag>
|
| 87 |
+
<rdf:li rdf:parseType="Resource">
|
| 88 |
+
<vCard:N rdf:parseType="Resource">
|
| 89 |
+
<vCard:Family>Shapiro</vCard:Family>
|
| 90 |
+
<vCard:Given>Bruce</vCard:Given>
|
| 91 |
+
</vCard:N>
|
| 92 |
+
<vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
|
| 93 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 94 |
+
<vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
|
| 95 |
+
</vCard:ORG>
|
| 96 |
+
</rdf:li>
|
| 97 |
+
</rdf:Bag>
|
| 98 |
+
</dc:creator>
|
| 99 |
+
<dcterms:created rdf:parseType="Resource">
|
| 100 |
+
<dcterms:W3CDTF>2005-01-30T13:02:57Z</dcterms:W3CDTF>
|
| 101 |
+
</dcterms:created>
|
| 102 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 103 |
+
<dcterms:W3CDTF>2014-06-03T14:33:39Z</dcterms:W3CDTF>
|
| 104 |
+
</dcterms:modified>
|
| 105 |
+
<bqmodel:is>
|
| 106 |
+
<rdf:Bag>
|
| 107 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/MODEL6614879888"/>
|
| 108 |
+
</rdf:Bag>
|
| 109 |
+
</bqmodel:is>
|
| 110 |
+
<bqmodel:is>
|
| 111 |
+
<rdf:Bag>
|
| 112 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000008"/>
|
| 113 |
+
</rdf:Bag>
|
| 114 |
+
</bqmodel:is>
|
| 115 |
+
<bqmodel:isDescribedBy>
|
| 116 |
+
<rdf:Bag>
|
| 117 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/9826676"/>
|
| 118 |
+
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|
| 119 |
+
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|
| 120 |
+
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|
| 121 |
+
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|
| 122 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000003"/>
|
| 123 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000004"/>
|
| 124 |
+
</rdf:Bag>
|
| 125 |
+
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|
| 126 |
+
<bqbiol:isVersionOf>
|
| 127 |
+
<rdf:Bag>
|
| 128 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000278"/>
|
| 129 |
+
</rdf:Bag>
|
| 130 |
+
</bqbiol:isVersionOf>
|
| 131 |
+
<bqbiol:hasTaxon>
|
| 132 |
+
<rdf:Bag>
|
| 133 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/8292"/>
|
| 134 |
+
</rdf:Bag>
|
| 135 |
+
</bqbiol:hasTaxon>
|
| 136 |
+
<bqbiol:isHomologTo>
|
| 137 |
+
<rdf:Bag>
|
| 138 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_152"/>
|
| 139 |
+
</rdf:Bag>
|
| 140 |
+
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|
| 141 |
+
<bqbiol:hasProperty>
|
| 142 |
+
<rdf:Bag>
|
| 143 |
+
<rdf:li rdf:resource="http://identifiers.org/mamo/MAMO_0000046"/>
|
| 144 |
+
</rdf:Bag>
|
| 145 |
+
</bqbiol:hasProperty>
|
| 146 |
+
</rdf:Description>
|
| 147 |
+
|
| 148 |
+
</rdf:RDF>
|
| 149 |
+
</annotation>
|
| 150 |
+
<listOfCompartments>
|
| 151 |
+
<compartment id="Cell" metaid="_202836" name="Cell" size="1" units="volume">
|
| 152 |
+
<annotation>
|
| 153 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 154 |
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<rdf:Description rdf:about="#_202836">
|
| 155 |
+
<bqbiol:is>
|
| 156 |
+
<rdf:Bag>
|
| 157 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005737"/>
|
| 158 |
+
</rdf:Bag>
|
| 159 |
+
</bqbiol:is>
|
| 160 |
+
</rdf:Description>
|
| 161 |
+
|
| 162 |
+
</rdf:RDF>
|
| 163 |
+
</annotation>
|
| 164 |
+
</compartment>
|
| 165 |
+
</listOfCompartments>
|
| 166 |
+
<listOfSpecies>
|
| 167 |
+
<species compartment="Cell" id="C" initialAmount="0" metaid="_202866" name="cyclin" substanceUnits="substance">
|
| 168 |
+
<annotation>
|
| 169 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 170 |
+
<rdf:Description rdf:about="#_202866">
|
| 171 |
+
<bqbiol:is>
|
| 172 |
+
<rdf:Bag>
|
| 173 |
+
<rdf:li rdf:resource="http://identifiers.org/interpro/IPR006670"/>
|
| 174 |
+
</rdf:Bag>
|
| 175 |
+
</bqbiol:is>
|
| 176 |
+
</rdf:Description>
|
| 177 |
+
|
| 178 |
+
</rdf:RDF>
|
| 179 |
+
</annotation>
|
| 180 |
+
</species>
|
| 181 |
+
<species compartment="Cell" id="X" initialAmount="0" metaid="_202906" name="protease" substanceUnits="substance">
|
| 182 |
+
<annotation>
|
| 183 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 184 |
+
<rdf:Description rdf:about="#_202906">
|
| 185 |
+
<bqbiol:hasProperty>
|
| 186 |
+
<rdf:Bag>
|
| 187 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0008233"/>
|
| 188 |
+
</rdf:Bag>
|
| 189 |
+
</bqbiol:hasProperty>
|
| 190 |
+
</rdf:Description>
|
| 191 |
+
|
| 192 |
+
</rdf:RDF>
|
| 193 |
+
</annotation>
|
| 194 |
+
</species>
|
| 195 |
+
<species compartment="Cell" id="M" initialAmount="0" metaid="_202886" name="cdc2k" substanceUnits="substance">
|
| 196 |
+
<annotation>
|
| 197 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 198 |
+
<rdf:Description rdf:about="#_202886">
|
| 199 |
+
<bqbiol:hasVersion>
|
| 200 |
+
<rdf:Bag>
|
| 201 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P35567"/>
|
| 202 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P24033"/>
|
| 203 |
+
</rdf:Bag>
|
| 204 |
+
</bqbiol:hasVersion>
|
| 205 |
+
</rdf:Description>
|
| 206 |
+
|
| 207 |
+
</rdf:RDF>
|
| 208 |
+
</annotation>
|
| 209 |
+
</species>
|
| 210 |
+
<species compartment="Cell" id="Y" initialAmount="1" metaid="_202926" name="cyclin inhibitor" substanceUnits="substance"/>
|
| 211 |
+
<species compartment="Cell" id="Z" initialAmount="1" metaid="_202946" name="complex inhibitor-cyclin" substanceUnits="substance">
|
| 212 |
+
<annotation>
|
| 213 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 214 |
+
<rdf:Description rdf:about="#_202946">
|
| 215 |
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<bqbiol:hasPart>
|
| 216 |
+
<rdf:Bag>
|
| 217 |
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<rdf:li rdf:resource="http://identifiers.org/interpro/IPR006670"/>
|
| 218 |
+
</rdf:Bag>
|
| 219 |
+
</bqbiol:hasPart>
|
| 220 |
+
</rdf:Description>
|
| 221 |
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|
| 222 |
+
</rdf:RDF>
|
| 223 |
+
</annotation>
|
| 224 |
+
</species>
|
| 225 |
+
</listOfSpecies>
|
| 226 |
+
<listOfParameters>
|
| 227 |
+
<parameter constant="false" id="V1" metaid="_324288" name="V1"/>
|
| 228 |
+
<parameter id="K6" metaid="_324289" name="K6" value="0.3"/>
|
| 229 |
+
<parameter id="V1p" metaid="_324291" name="V1p" value="0.75"/>
|
| 230 |
+
<parameter constant="false" id="V3" metaid="_324293" name="V3"/>
|
| 231 |
+
<parameter id="V3p" metaid="_324295" name="V3p" value="0.3"/>
|
| 232 |
+
</listOfParameters>
|
| 233 |
+
<listOfRules>
|
| 234 |
+
<assignmentRule metaid="rule1" variable="V1">
|
| 235 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 236 |
+
<apply>
|
| 237 |
+
<times/>
|
| 238 |
+
<ci> C </ci>
|
| 239 |
+
<ci> V1p </ci>
|
| 240 |
+
<apply>
|
| 241 |
+
<power/>
|
| 242 |
+
<apply>
|
| 243 |
+
<plus/>
|
| 244 |
+
<ci> C </ci>
|
| 245 |
+
<ci> K6 </ci>
|
| 246 |
+
</apply>
|
| 247 |
+
<cn type="integer"> -1 </cn>
|
| 248 |
+
</apply>
|
| 249 |
+
</apply>
|
| 250 |
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</math>
|
| 251 |
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</assignmentRule>
|
| 252 |
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<assignmentRule metaid="rule2" variable="V3">
|
| 253 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 254 |
+
<apply>
|
| 255 |
+
<times/>
|
| 256 |
+
<ci> M </ci>
|
| 257 |
+
<ci> V3p </ci>
|
| 258 |
+
</apply>
|
| 259 |
+
</math>
|
| 260 |
+
</assignmentRule>
|
| 261 |
+
</listOfRules>
|
| 262 |
+
<listOfReactions>
|
| 263 |
+
<reaction fast="false" id="reaction1" metaid="_202966" name="creation of cyclin" reversible="false">
|
| 264 |
+
<annotation>
|
| 265 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 266 |
+
<rdf:Description rdf:about="#_202966">
|
| 267 |
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<bqbiol:isVersionOf>
|
| 268 |
+
<rdf:Bag>
|
| 269 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006412"/>
|
| 270 |
+
</rdf:Bag>
|
| 271 |
+
</bqbiol:isVersionOf>
|
| 272 |
+
</rdf:Description>
|
| 273 |
+
|
| 274 |
+
</rdf:RDF>
|
| 275 |
+
</annotation>
|
| 276 |
+
<listOfProducts>
|
| 277 |
+
<speciesReference metaid="_655368" species="C"/>
|
| 278 |
+
</listOfProducts>
|
| 279 |
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<kineticLaw metaid="_655381">
|
| 280 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 281 |
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<ci> vi </ci>
|
| 282 |
+
</math>
|
| 283 |
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<listOfParameters>
|
| 284 |
+
<parameter id="vi" metaid="_324256" value="0.1"/>
|
| 285 |
+
</listOfParameters>
|
| 286 |
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</kineticLaw>
|
| 287 |
+
</reaction>
|
| 288 |
+
<reaction fast="false" id="reaction2" metaid="_203006" name="cdc2 kinase triggered degration of cyclin" reversible="false">
|
| 289 |
+
<annotation>
|
| 290 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 291 |
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<rdf:Description rdf:about="#_203006">
|
| 292 |
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<bqbiol:isVersionOf>
|
| 293 |
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<rdf:Bag>
|
| 294 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 295 |
+
</rdf:Bag>
|
| 296 |
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</bqbiol:isVersionOf>
|
| 297 |
+
</rdf:Description>
|
| 298 |
+
|
| 299 |
+
</rdf:RDF>
|
| 300 |
+
</annotation>
|
| 301 |
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<listOfReactants>
|
| 302 |
+
<speciesReference metaid="_655393" species="C"/>
|
| 303 |
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</listOfReactants>
|
| 304 |
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<listOfModifiers>
|
| 305 |
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<modifierSpeciesReference metaid="_655405" species="X"/>
|
| 306 |
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</listOfModifiers>
|
| 307 |
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<kineticLaw metaid="_655417">
|
| 308 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 309 |
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<apply>
|
| 310 |
+
<times/>
|
| 311 |
+
<ci> C </ci>
|
| 312 |
+
<ci> k1 </ci>
|
| 313 |
+
<ci> X </ci>
|
| 314 |
+
<apply>
|
| 315 |
+
<power/>
|
| 316 |
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<apply>
|
| 317 |
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<plus/>
|
| 318 |
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<ci> C </ci>
|
| 319 |
+
<ci> K5 </ci>
|
| 320 |
+
</apply>
|
| 321 |
+
<cn type="integer"> -1 </cn>
|
| 322 |
+
</apply>
|
| 323 |
+
</apply>
|
| 324 |
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</math>
|
| 325 |
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<listOfParameters>
|
| 326 |
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<parameter id="k1" metaid="_324258" value="0.5"/>
|
| 327 |
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<parameter id="K5" metaid="_324260" value="0.02"/>
|
| 328 |
+
</listOfParameters>
|
| 329 |
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</kineticLaw>
|
| 330 |
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</reaction>
|
| 331 |
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<reaction fast="false" id="reaction3" metaid="_202986" name="default degradation of cyclin" reversible="false">
|
| 332 |
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<annotation>
|
| 333 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 334 |
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<rdf:Description rdf:about="#_202986">
|
| 335 |
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<bqbiol:isVersionOf>
|
| 336 |
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<rdf:Bag>
|
| 337 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0008054"/>
|
| 338 |
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</rdf:Bag>
|
| 339 |
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</bqbiol:isVersionOf>
|
| 340 |
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</rdf:Description>
|
| 341 |
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|
| 342 |
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</rdf:RDF>
|
| 343 |
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</annotation>
|
| 344 |
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<listOfReactants>
|
| 345 |
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<speciesReference metaid="_655429" species="C"/>
|
| 346 |
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</listOfReactants>
|
| 347 |
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<kineticLaw metaid="_655441">
|
| 348 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 349 |
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<apply>
|
| 350 |
+
<times/>
|
| 351 |
+
<ci> C </ci>
|
| 352 |
+
<ci> kd </ci>
|
| 353 |
+
</apply>
|
| 354 |
+
</math>
|
| 355 |
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<listOfParameters>
|
| 356 |
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<parameter id="kd" metaid="_324262" value="0.02"/>
|
| 357 |
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</listOfParameters>
|
| 358 |
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</kineticLaw>
|
| 359 |
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</reaction>
|
| 360 |
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<reaction fast="false" id="reaction4" metaid="_203147" name="activation of cdc2 kinase" reversible="false">
|
| 361 |
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<annotation>
|
| 362 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 363 |
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<rdf:Description rdf:about="#_203147">
|
| 364 |
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<bqbiol:isVersionOf>
|
| 365 |
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<rdf:Bag>
|
| 366 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0045737"/>
|
| 367 |
+
</rdf:Bag>
|
| 368 |
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</bqbiol:isVersionOf>
|
| 369 |
+
</rdf:Description>
|
| 370 |
+
|
| 371 |
+
</rdf:RDF>
|
| 372 |
+
</annotation>
|
| 373 |
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<listOfProducts>
|
| 374 |
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<speciesReference metaid="_655453" species="M"/>
|
| 375 |
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</listOfProducts>
|
| 376 |
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<kineticLaw metaid="_655465">
|
| 377 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 378 |
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<apply>
|
| 379 |
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<times/>
|
| 380 |
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<apply>
|
| 381 |
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<plus/>
|
| 382 |
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<cn type="integer"> 1 </cn>
|
| 383 |
+
<apply>
|
| 384 |
+
<times/>
|
| 385 |
+
<cn type="integer"> -1 </cn>
|
| 386 |
+
<ci> M </ci>
|
| 387 |
+
</apply>
|
| 388 |
+
</apply>
|
| 389 |
+
<ci> V1 </ci>
|
| 390 |
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<apply>
|
| 391 |
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<power/>
|
| 392 |
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<apply>
|
| 393 |
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<plus/>
|
| 394 |
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<ci> K1 </ci>
|
| 395 |
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<apply>
|
| 396 |
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<times/>
|
| 397 |
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<cn type="integer"> -1 </cn>
|
| 398 |
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<ci> M </ci>
|
| 399 |
+
</apply>
|
| 400 |
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<cn type="integer"> 1 </cn>
|
| 401 |
+
</apply>
|
| 402 |
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<cn type="integer"> -1 </cn>
|
| 403 |
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</apply>
|
| 404 |
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|
| 405 |
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|
| 406 |
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|
| 407 |
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<parameter id="K1" metaid="_324263" value="0.1"/>
|
| 408 |
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</listOfParameters>
|
| 409 |
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</kineticLaw>
|
| 410 |
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|
| 411 |
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<reaction fast="false" id="reaction5" metaid="_203187" name="deactivation of cdc2 kinase" reversible="false">
|
| 412 |
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|
| 413 |
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|
| 414 |
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<rdf:Description rdf:about="#_203187">
|
| 415 |
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<bqbiol:isVersionOf>
|
| 416 |
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<rdf:Bag>
|
| 417 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0045736"/>
|
| 418 |
+
</rdf:Bag>
|
| 419 |
+
</bqbiol:isVersionOf>
|
| 420 |
+
</rdf:Description>
|
| 421 |
+
|
| 422 |
+
</rdf:RDF>
|
| 423 |
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</annotation>
|
| 424 |
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<listOfReactants>
|
| 425 |
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<speciesReference metaid="_655477" species="M"/>
|
| 426 |
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|
| 427 |
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<kineticLaw metaid="_655489">
|
| 428 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 429 |
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<apply>
|
| 430 |
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<times/>
|
| 431 |
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<ci> M </ci>
|
| 432 |
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<ci> V2 </ci>
|
| 433 |
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<apply>
|
| 434 |
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<power/>
|
| 435 |
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<apply>
|
| 436 |
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<plus/>
|
| 437 |
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<ci> K2 </ci>
|
| 438 |
+
<ci> M </ci>
|
| 439 |
+
</apply>
|
| 440 |
+
<cn type="integer"> -1 </cn>
|
| 441 |
+
</apply>
|
| 442 |
+
</apply>
|
| 443 |
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|
| 444 |
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<listOfParameters>
|
| 445 |
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<parameter id="V2" metaid="_324264" value="0.25"/>
|
| 446 |
+
<parameter id="K2" metaid="_324266" value="0.1"/>
|
| 447 |
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|
| 448 |
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</kineticLaw>
|
| 449 |
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</reaction>
|
| 450 |
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<reaction fast="false" id="reaction6" metaid="_203167" name="activation of cyclin protease" reversible="false">
|
| 451 |
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<listOfProducts>
|
| 452 |
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<speciesReference metaid="_655501" species="X"/>
|
| 453 |
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|
| 454 |
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<kineticLaw metaid="_655513">
|
| 455 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 456 |
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<apply>
|
| 457 |
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<times/>
|
| 458 |
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<ci> V3 </ci>
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| 459 |
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|
| 460 |
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<plus/>
|
| 461 |
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<cn type="integer"> 1 </cn>
|
| 462 |
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|
| 463 |
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<times/>
|
| 464 |
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<cn type="integer"> -1 </cn>
|
| 465 |
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<ci> X </ci>
|
| 466 |
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|
| 467 |
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|
| 468 |
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<apply>
|
| 469 |
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<power/>
|
| 470 |
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<apply>
|
| 471 |
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<plus/>
|
| 472 |
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<ci> K3 </ci>
|
| 473 |
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<apply>
|
| 474 |
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<times/>
|
| 475 |
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<cn type="integer"> -1 </cn>
|
| 476 |
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<ci> X </ci>
|
| 477 |
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|
| 478 |
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<cn type="integer"> 1 </cn>
|
| 479 |
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| 480 |
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<cn type="integer"> -1 </cn>
|
| 481 |
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|
| 482 |
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|
| 483 |
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| 484 |
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|
| 485 |
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|
| 486 |
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</listOfParameters>
|
| 487 |
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|
| 488 |
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| 489 |
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|
| 495 |
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|
| 496 |
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<times/>
|
| 497 |
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<ci> V4 </ci>
|
| 498 |
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<ci> X </ci>
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| 499 |
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|
| 500 |
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<power/>
|
| 501 |
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<apply>
|
| 502 |
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<plus/>
|
| 503 |
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|
| 504 |
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<ci> X </ci>
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| 505 |
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</apply>
|
| 506 |
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<cn type="integer"> -1 </cn>
|
| 507 |
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|
| 508 |
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| 509 |
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| 510 |
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<listOfParameters>
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| 511 |
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|
| 512 |
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<parameter id="V4" metaid="_324271" value="0.1"/>
|
| 513 |
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</listOfParameters>
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| 514 |
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</kineticLaw>
|
| 515 |
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|
| 516 |
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| 517 |
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|
| 518 |
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| 519 |
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| 520 |
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| 522 |
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| 523 |
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| 526 |
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|
| 527 |
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<times/>
|
| 528 |
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<ci> a1 </ci>
|
| 529 |
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<ci> C </ci>
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| 530 |
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<ci> Y </ci>
|
| 531 |
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|
| 532 |
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| 533 |
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|
| 534 |
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| 535 |
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| 536 |
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| 537 |
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| 545 |
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| 546 |
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| 547 |
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| 548 |
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|
| 549 |
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| 550 |
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| 551 |
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| 552 |
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| 553 |
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| 554 |
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| 555 |
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| 556 |
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| 559 |
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| 560 |
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<apply>
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| 561 |
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<times/>
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| 562 |
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<ci> a2 </ci>
|
| 563 |
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<ci> Z </ci>
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| 564 |
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| 565 |
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| 566 |
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| 567 |
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<parameter id="a2" metaid="_324275" value="0.05"/>
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| 568 |
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</listOfParameters>
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| 569 |
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| 570 |
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| 571 |
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| 572 |
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| 574 |
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<bqbiol:isVersionOf>
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| 576 |
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| 577 |
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| 578 |
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| 579 |
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</bqbiol:isVersionOf>
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| 580 |
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| 581 |
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|
| 582 |
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| 583 |
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| 584 |
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<listOfReactants>
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| 585 |
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<speciesReference metaid="_655646" species="Z"/>
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| 586 |
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| 587 |
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| 588 |
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| 589 |
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| 590 |
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| 591 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
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| 592 |
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<apply>
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| 593 |
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<times/>
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| 594 |
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<ci> alpha </ci>
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| 595 |
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<ci> d1 </ci>
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| 596 |
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<ci> Z </ci>
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| 597 |
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| 598 |
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| 599 |
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| 600 |
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<parameter id="alpha" metaid="_324276" value="0.1"/>
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| 601 |
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<parameter id="d1" metaid="_324278" value="0.05"/>
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| 602 |
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| 603 |
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| 604 |
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| 605 |
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| 606 |
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| 609 |
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| 610 |
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| 611 |
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| 612 |
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| 613 |
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| 614 |
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| 615 |
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| 616 |
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| 617 |
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| 618 |
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| 619 |
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<speciesReference metaid="_655682" species="Z"/>
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| 620 |
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| 621 |
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| 622 |
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<speciesReference metaid="_655694" species="Y"/>
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| 623 |
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| 624 |
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| 625 |
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| 626 |
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| 627 |
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<times/>
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| 628 |
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<ci> alpha </ci>
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| 629 |
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<ci> kd </ci>
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| 630 |
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<ci> Z </ci>
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| 631 |
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| 632 |
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</math>
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| 634 |
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<parameter id="alpha" metaid="_324282" value="0.1"/>
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| 636 |
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| 639 |
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| 640 |
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| 641 |
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| 644 |
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<rdf:Bag>
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| 645 |
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| 646 |
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| 647 |
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| 648 |
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| 649 |
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| 650 |
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| 651 |
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| 652 |
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<listOfProducts>
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| 653 |
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<speciesReference metaid="_655718" species="Y"/>
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| 654 |
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| 655 |
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<kineticLaw metaid="_655730">
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| 656 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 657 |
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<ci> vs </ci>
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| 658 |
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</math>
|
| 659 |
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<listOfParameters>
|
| 660 |
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<parameter id="vs" metaid="_324283" value="0.2"/>
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| 661 |
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| 662 |
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</kineticLaw>
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| 663 |
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| 664 |
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| 665 |
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<annotation>
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| 666 |
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| 667 |
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| 668 |
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<bqbiol:isVersionOf>
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| 669 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0044257"/>
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| 671 |
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</rdf:Bag>
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| 672 |
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| 673 |
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| 674 |
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| 675 |
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| 676 |
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| 677 |
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| 678 |
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<speciesReference metaid="_655742" species="Y"/>
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| 679 |
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| 680 |
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| 681 |
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| 682 |
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<apply>
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| 683 |
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<times/>
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| 684 |
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<ci> d1 </ci>
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| 685 |
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<ci> Y </ci>
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| 686 |
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</apply>
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| 687 |
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</math>
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| 688 |
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<listOfParameters>
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| 689 |
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<parameter id="d1" metaid="_324285" value="0.05"/>
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| 690 |
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| 693 |
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| 694 |
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| 695 |
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Data/BIOMD0000000008/Gardner1998_conditions.json
ADDED
|
@@ -0,0 +1,47 @@
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"C": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
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| 5 |
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"bounds": [
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| 6 |
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0.0351185300461486,
|
| 7 |
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0.2130975734004689
|
| 8 |
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],
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| 9 |
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| 10 |
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},
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| 11 |
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| 12 |
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| 13 |
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"trajectory_type_name": "oscillation",
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| 14 |
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"bounds": [
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| 15 |
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|
| 16 |
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|
| 17 |
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],
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| 18 |
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| 19 |
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},
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| 20 |
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| 21 |
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"trajectory_type": 3,
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| 22 |
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"trajectory_type_name": "oscillation",
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| 23 |
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"bounds": [
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| 24 |
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|
| 25 |
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0.5184342400146105
|
| 26 |
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],
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| 27 |
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"period": 205.0
|
| 28 |
+
},
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| 29 |
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"Y": {
|
| 30 |
+
"trajectory_type": 3,
|
| 31 |
+
"trajectory_type_name": "oscillation",
|
| 32 |
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"bounds": [
|
| 33 |
+
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|
| 34 |
+
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|
| 35 |
+
],
|
| 36 |
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|
| 37 |
+
},
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| 38 |
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|
| 39 |
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"trajectory_type": 3,
|
| 40 |
+
"trajectory_type_name": "oscillation",
|
| 41 |
+
"bounds": [
|
| 42 |
+
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|
| 43 |
+
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|
| 44 |
+
],
|
| 45 |
+
"period": 205.0
|
| 46 |
+
}
|
| 47 |
+
}
|
Data/BIOMD0000000008/initial_conditions.json
ADDED
|
@@ -0,0 +1,10 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
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"C": 0.20917378933088832,
|
| 5 |
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"X": 0.15128968711425134,
|
| 6 |
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"M": 0.35691624964283825,
|
| 7 |
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"Y": 3.7071924859166465,
|
| 8 |
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"Z": 0.41039731629530285
|
| 9 |
+
}
|
| 10 |
+
}
|
Data/BIOMD0000000009/Huang1996.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000009/Huang1996.xml
ADDED
|
@@ -0,0 +1,1429 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
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|
|
|
|
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|
|
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|
|
|
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|
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|
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|
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|
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|
|
|
|
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|
|
|
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|
|
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|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
|
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|
|
|
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|
|
|
|
|
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|
|
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|
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_770249" version="4">
|
| 3 |
+
<model id="BIOMD0000000009" metaid="_000001" name="Huang1996 - Ultrasensitivity in MAPK cascade">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Huang1996 - Ultrasensitivity in MAPK cascade</div>
|
| 7 |
+
<div class="dc:description"> <p>The temporal sequence of kinase activation, from MAPKKK (activated RAF) to the final effector MAPK (activated ERK), is described here. It is observed from the model that there is an increase in sensitivity along the levels of the cascade, where the activity of MAPK reaches its maximal before MAPKKK.</p>
|
| 8 |
+
</div>
|
| 9 |
+
<div class="dc:bibliographicCitation"> <p>This model is described in the article:</p>
|
| 10 |
+
<div class="bibo:title"> <a href="http://identifiers.org/pubmed/8816754" title="Access to this publication">Ultrasensitivity in the mitogen-activated protein kinase cascade.</a>
|
| 11 |
+
</div>
|
| 12 |
+
<div class="bibo:authorList">Huang CY, Ferrell JE Jr</div>
|
| 13 |
+
<div class="bibo:Journal">Proc. Natl. Acad. Sci. U.S.A. 1996:93(19):10078-83</div>
|
| 14 |
+
<p>Abstract:</p>
|
| 15 |
+
<div class="bibo:abstract"> <p>The mitogen-activated protein kinase (MAPK) cascade is a highly conserved series of three protein kinases implicated in diverse biological processes. Here we demonstrate that the cascade arrangement has unexpected consequences for the dynamics of MAPK signaling. We solved the rate equations for the cascade numerically and found that MAPK is predicted to behave like a highly cooperative enzyme, even though it was not assumed that any of the enzymes in the cascade were regulated cooperatively. Measurements of MAPK activation in Xenopus oocyte extracts confirmed this prediction. The stimulus/response curve of the MAPK was found to be as steep as that of a cooperative enzyme with a Hill coefficient of 4-5, well in excess of that of the classical allosteric protein hemoglobin. The shape of the MAPK stimulus/ response curve may make the cascade particularly appropriate for mediating processes like mitogenesis, cell fate induction, and oocyte maturation, where a cell switches from one discrete state to another.</p>
|
| 16 |
+
</div>
|
| 17 |
+
</div>
|
| 18 |
+
<div class="bm:curation"> <p>The species K_PP_norm, KKK_P_norm and KK_PP_norm are the relative concentrations of the active MAPK, MAPKK and MAPKKK, that is the double, or single resp. phophorylated forms divided by the total concentrations of each kinase. For MAPK additionally the also active MAPK divided by the maximal concentration of active MAPK is given by rel_K_PP_max. The parameter K_PP_norm_max, the maximal ratio of active MapK, has to be calculated for each change of parameters.</p>
|
| 19 |
+
</div>
|
| 20 |
+
<div class="dc:publisher"> <p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 21 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000009">BIOMD0000000009</a>
|
| 22 |
+
. </p>
|
| 23 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 24 |
+
. </p>
|
| 25 |
+
</div>
|
| 26 |
+
<div class="dc:license"> <p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 27 |
+
for more information. </p>
|
| 28 |
+
</div>
|
| 29 |
+
</body>
|
| 30 |
+
|
| 31 |
+
</notes>
|
| 32 |
+
<annotation>
|
| 33 |
+
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|
| 34 |
+
<rdf:Description rdf:about="#_000001">
|
| 35 |
+
<dc:creator>
|
| 36 |
+
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|
| 37 |
+
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|
| 38 |
+
<vCard:N rdf:parseType="Resource">
|
| 39 |
+
<vCard:Family>Machne</vCard:Family>
|
| 40 |
+
<vCard:Given>Rainer</vCard:Given>
|
| 41 |
+
</vCard:N>
|
| 42 |
+
<vCard:EMAIL>raim@tbi.univie.ac.at</vCard:EMAIL>
|
| 43 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 44 |
+
<vCard:Orgname>University of Vienna</vCard:Orgname>
|
| 45 |
+
</vCard:ORG>
|
| 46 |
+
</rdf:li>
|
| 47 |
+
</rdf:Bag>
|
| 48 |
+
</dc:creator>
|
| 49 |
+
<dcterms:created rdf:parseType="Resource">
|
| 50 |
+
<dcterms:W3CDTF>2005-02-10T23:39:30Z</dcterms:W3CDTF>
|
| 51 |
+
</dcterms:created>
|
| 52 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 53 |
+
<dcterms:W3CDTF>2015-06-02T12:02:44Z</dcterms:W3CDTF>
|
| 54 |
+
</dcterms:modified>
|
| 55 |
+
<bqmodel:is>
|
| 56 |
+
<rdf:Bag>
|
| 57 |
+
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|
| 58 |
+
</rdf:Bag>
|
| 59 |
+
</bqmodel:is>
|
| 60 |
+
<bqmodel:is>
|
| 61 |
+
<rdf:Bag>
|
| 62 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000009"/>
|
| 63 |
+
</rdf:Bag>
|
| 64 |
+
</bqmodel:is>
|
| 65 |
+
<bqmodel:isDescribedBy>
|
| 66 |
+
<rdf:Bag>
|
| 67 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/8816754"/>
|
| 68 |
+
</rdf:Bag>
|
| 69 |
+
</bqmodel:isDescribedBy>
|
| 70 |
+
<bqbiol:isHomologTo>
|
| 71 |
+
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|
| 72 |
+
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|
| 73 |
+
</rdf:Bag>
|
| 74 |
+
</bqbiol:isHomologTo>
|
| 75 |
+
<bqbiol:isVersionOf>
|
| 76 |
+
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|
| 77 |
+
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|
| 78 |
+
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|
| 79 |
+
</bqbiol:isVersionOf>
|
| 80 |
+
<bqbiol:hasTaxon>
|
| 81 |
+
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|
| 82 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/8355"/>
|
| 83 |
+
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|
| 84 |
+
</bqbiol:hasTaxon>
|
| 85 |
+
<bqbiol:hasProperty>
|
| 86 |
+
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|
| 87 |
+
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|
| 88 |
+
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|
| 89 |
+
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|
| 90 |
+
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|
| 91 |
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|
| 92 |
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|
| 93 |
+
</rdf:RDF>
|
| 94 |
+
</annotation>
|
| 95 |
+
<listOfUnitDefinitions>
|
| 96 |
+
<unitDefinition id="substance" metaid="metaid_0000046" name="micromole">
|
| 97 |
+
<listOfUnits>
|
| 98 |
+
<unit kind="mole" metaid="_396483" scale="-6"/>
|
| 99 |
+
</listOfUnits>
|
| 100 |
+
</unitDefinition>
|
| 101 |
+
</listOfUnitDefinitions>
|
| 102 |
+
<listOfCompartments>
|
| 103 |
+
<compartment id="compartment" metaid="_506358" size="4E-12"/>
|
| 104 |
+
</listOfCompartments>
|
| 105 |
+
<listOfSpecies>
|
| 106 |
+
<species compartment="compartment" id="E1" initialConcentration="3E-5" metaid="_506372" name="MAPKKK activator (Ras)">
|
| 107 |
+
<annotation>
|
| 108 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 109 |
+
<rdf:Description rdf:about="#_506372">
|
| 110 |
+
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|
| 111 |
+
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|
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|
| 113 |
+
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|
| 114 |
+
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|
| 115 |
+
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|
| 116 |
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|
| 117 |
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|
| 118 |
+
</rdf:RDF>
|
| 119 |
+
</annotation>
|
| 120 |
+
</species>
|
| 121 |
+
<species compartment="compartment" id="E2" initialConcentration="0.0003" metaid="_506392" name="MAPKKK inactivator"/>
|
| 122 |
+
<species compartment="compartment" id="KKK" initialConcentration="0.003" metaid="_506412" name="Mos">
|
| 123 |
+
<annotation>
|
| 124 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 125 |
+
<rdf:Description rdf:about="#_506412">
|
| 126 |
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|
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|
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|
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+
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|
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|
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+
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|
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|
| 133 |
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|
| 134 |
+
</rdf:RDF>
|
| 135 |
+
</annotation>
|
| 136 |
+
</species>
|
| 137 |
+
<species compartment="compartment" id="P_KKK" initialConcentration="0" metaid="_506432" name="Mos-P">
|
| 138 |
+
<annotation>
|
| 139 |
+
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|
| 140 |
+
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|
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|
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|
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|
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+
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|
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|
| 146 |
+
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|
| 147 |
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|
| 148 |
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|
| 149 |
+
</rdf:RDF>
|
| 150 |
+
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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</rdf:RDF>
|
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</annotation>
|
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</species>
|
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<species compartment="compartment" id="KPase" initialConcentration="0.12" metaid="_506572" name="MAPK-Pase">
|
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<annotation>
|
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
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|
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|
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|
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|
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|
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</rdf:RDF>
|
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</annotation>
|
| 256 |
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</species>
|
| 257 |
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<species compartment="compartment" id="KKPase" initialConcentration="0.0003" metaid="_506592" name="MAPKK-Pase"/>
|
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<species compartment="compartment" id="E1_KKK" initialConcentration="0" metaid="_506612" name="E1_Mos">
|
| 259 |
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<annotation>
|
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
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|
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|
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|
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P12965"/>
|
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<rdf:li rdf:resource="http://identifiers.org/interpro/IPR003577"/>
|
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</rdf:Bag>
|
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</bqbiol:hasPart>
|
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</rdf:Description>
|
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|
| 270 |
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|
| 271 |
+
</rdf:RDF>
|
| 272 |
+
</annotation>
|
| 273 |
+
</species>
|
| 274 |
+
<species compartment="compartment" id="E2_P_KKK" initialConcentration="0" metaid="_506632" name="E2_Mos-P">
|
| 275 |
+
<annotation>
|
| 276 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
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<rdf:Description rdf:about="#_506632">
|
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|
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|
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P12965"/>
|
| 281 |
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</rdf:Bag>
|
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</bqbiol:hasPart>
|
| 283 |
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</rdf:Description>
|
| 284 |
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|
| 285 |
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|
| 286 |
+
</rdf:RDF>
|
| 287 |
+
</annotation>
|
| 288 |
+
</species>
|
| 289 |
+
<species compartment="compartment" id="P_KKK_KK" initialConcentration="0" metaid="_506652" name="P-Mos_Mek1">
|
| 290 |
+
<annotation>
|
| 291 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 292 |
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<rdf:Description rdf:about="#_506652">
|
| 293 |
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<bqbiol:hasPart>
|
| 294 |
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<rdf:Bag>
|
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P12965"/>
|
| 296 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 297 |
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</rdf:Bag>
|
| 298 |
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</bqbiol:hasPart>
|
| 299 |
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</rdf:Description>
|
| 300 |
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|
| 301 |
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|
| 302 |
+
</rdf:RDF>
|
| 303 |
+
</annotation>
|
| 304 |
+
</species>
|
| 305 |
+
<species compartment="compartment" id="P_KKK_P_KK" initialConcentration="0" metaid="_506672" name="P-Mos_P-Mek1">
|
| 306 |
+
<annotation>
|
| 307 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 308 |
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<rdf:Description rdf:about="#_506672">
|
| 309 |
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<bqbiol:hasPart>
|
| 310 |
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<rdf:Bag>
|
| 311 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P12965"/>
|
| 312 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 313 |
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</rdf:Bag>
|
| 314 |
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</bqbiol:hasPart>
|
| 315 |
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</rdf:Description>
|
| 316 |
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|
| 317 |
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|
| 318 |
+
</rdf:RDF>
|
| 319 |
+
</annotation>
|
| 320 |
+
</species>
|
| 321 |
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<species compartment="compartment" id="PP_KK_K" initialConcentration="0" metaid="_506692" name="PP-Mek1_Erk2">
|
| 322 |
+
<annotation>
|
| 323 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 324 |
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<rdf:Description rdf:about="#_506692">
|
| 325 |
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<bqbiol:hasPart>
|
| 326 |
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<rdf:Bag>
|
| 327 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 328 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 329 |
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</rdf:Bag>
|
| 330 |
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</bqbiol:hasPart>
|
| 331 |
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</rdf:Description>
|
| 332 |
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|
| 333 |
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|
| 334 |
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</rdf:RDF>
|
| 335 |
+
</annotation>
|
| 336 |
+
</species>
|
| 337 |
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<species compartment="compartment" id="PP_KK_P_K" initialConcentration="0" metaid="_506712" name="PP-Mek1_P-Erk2">
|
| 338 |
+
<annotation>
|
| 339 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 340 |
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<rdf:Description rdf:about="#_506712">
|
| 341 |
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<bqbiol:hasPart>
|
| 342 |
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<rdf:Bag>
|
| 343 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 344 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 345 |
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</rdf:Bag>
|
| 346 |
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</bqbiol:hasPart>
|
| 347 |
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</rdf:Description>
|
| 348 |
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|
| 349 |
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|
| 350 |
+
</rdf:RDF>
|
| 351 |
+
</annotation>
|
| 352 |
+
</species>
|
| 353 |
+
<species compartment="compartment" id="KKPase_PP_KK" initialConcentration="0" metaid="_506732" name="MAPKK-Pase_PP-Mek1">
|
| 354 |
+
<annotation>
|
| 355 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 356 |
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<rdf:Description rdf:about="#_506732">
|
| 357 |
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<bqbiol:hasPart>
|
| 358 |
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<rdf:Bag>
|
| 359 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 360 |
+
</rdf:Bag>
|
| 361 |
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</bqbiol:hasPart>
|
| 362 |
+
</rdf:Description>
|
| 363 |
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|
| 364 |
+
|
| 365 |
+
</rdf:RDF>
|
| 366 |
+
</annotation>
|
| 367 |
+
</species>
|
| 368 |
+
<species compartment="compartment" id="KKPase_P_KK" initialConcentration="0" metaid="_506752" name="MAPKK-Pase_P-Mek1">
|
| 369 |
+
<annotation>
|
| 370 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 371 |
+
<rdf:Description rdf:about="#_506752">
|
| 372 |
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<bqbiol:hasPart>
|
| 373 |
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<rdf:Bag>
|
| 374 |
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<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 375 |
+
</rdf:Bag>
|
| 376 |
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</bqbiol:hasPart>
|
| 377 |
+
</rdf:Description>
|
| 378 |
+
|
| 379 |
+
|
| 380 |
+
</rdf:RDF>
|
| 381 |
+
</annotation>
|
| 382 |
+
</species>
|
| 383 |
+
<species compartment="compartment" id="KPase_PP_K" initialConcentration="0" metaid="_506772" name="MAPK-Pase_PP-Erk2">
|
| 384 |
+
<annotation>
|
| 385 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 386 |
+
<rdf:Description rdf:about="#_506772">
|
| 387 |
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<bqbiol:hasPart>
|
| 388 |
+
<rdf:Bag>
|
| 389 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q90W58"/>
|
| 390 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 391 |
+
</rdf:Bag>
|
| 392 |
+
</bqbiol:hasPart>
|
| 393 |
+
</rdf:Description>
|
| 394 |
+
|
| 395 |
+
|
| 396 |
+
</rdf:RDF>
|
| 397 |
+
</annotation>
|
| 398 |
+
</species>
|
| 399 |
+
<species compartment="compartment" id="KPase_P_K" initialConcentration="0" metaid="_506792" name="MAPK-Pase_P-Erk2">
|
| 400 |
+
<annotation>
|
| 401 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 402 |
+
<rdf:Description rdf:about="#_506792">
|
| 403 |
+
<bqbiol:hasPart>
|
| 404 |
+
<rdf:Bag>
|
| 405 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 406 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q90W58"/>
|
| 407 |
+
</rdf:Bag>
|
| 408 |
+
</bqbiol:hasPart>
|
| 409 |
+
</rdf:Description>
|
| 410 |
+
|
| 411 |
+
|
| 412 |
+
</rdf:RDF>
|
| 413 |
+
</annotation>
|
| 414 |
+
</species>
|
| 415 |
+
<species compartment="compartment" id="K_PP_norm" metaid="metaid_0000047" name="K_PP_norm"/>
|
| 416 |
+
<species compartment="compartment" id="KK_PP_norm" metaid="metaid_0000048" name="KK_PP_norm"/>
|
| 417 |
+
<species compartment="compartment" id="KKK_P_norm" metaid="metaid_0000049" name="KKK_P_norm"/>
|
| 418 |
+
<species compartment="compartment" id="rel_K_PP_max" metaid="metaid_0100049" name="relative maximal K_PP"/>
|
| 419 |
+
</listOfSpecies>
|
| 420 |
+
<listOfParameters>
|
| 421 |
+
<parameter id="K_PP_norm_max" metaid="metaid_0011050" value="0.900049">
|
| 422 |
+
<notes>
|
| 423 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 424 |
+
the maximal value of K_PP_norm at a stimulation conc. of 10.</p>
|
| 425 |
+
|
| 426 |
+
</notes>
|
| 427 |
+
</parameter>
|
| 428 |
+
</listOfParameters>
|
| 429 |
+
<listOfRules>
|
| 430 |
+
<assignmentRule metaid="metaid_0000050" variable="K_PP_norm">
|
| 431 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 432 |
+
<apply>
|
| 433 |
+
<divide/>
|
| 434 |
+
<apply>
|
| 435 |
+
<plus/>
|
| 436 |
+
<ci> PP_K </ci>
|
| 437 |
+
<ci> KPase_PP_K </ci>
|
| 438 |
+
</apply>
|
| 439 |
+
<apply>
|
| 440 |
+
<plus/>
|
| 441 |
+
<ci> PP_K </ci>
|
| 442 |
+
<ci> P_K </ci>
|
| 443 |
+
<ci> K </ci>
|
| 444 |
+
<ci> PP_KK_K </ci>
|
| 445 |
+
<ci> PP_KK_P_K </ci>
|
| 446 |
+
<ci> KPase_PP_K </ci>
|
| 447 |
+
<ci> KPase_P_K </ci>
|
| 448 |
+
</apply>
|
| 449 |
+
</apply>
|
| 450 |
+
</math>
|
| 451 |
+
</assignmentRule>
|
| 452 |
+
<assignmentRule metaid="met100050" variable="rel_K_PP_max">
|
| 453 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 454 |
+
<apply>
|
| 455 |
+
<divide/>
|
| 456 |
+
<ci> K_PP_norm </ci>
|
| 457 |
+
<ci> K_PP_norm_max </ci>
|
| 458 |
+
</apply>
|
| 459 |
+
</math>
|
| 460 |
+
</assignmentRule>
|
| 461 |
+
<assignmentRule metaid="metai0051" variable="KK_PP_norm">
|
| 462 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 463 |
+
<apply>
|
| 464 |
+
<divide/>
|
| 465 |
+
<apply>
|
| 466 |
+
<plus/>
|
| 467 |
+
<ci> PP_KK </ci>
|
| 468 |
+
<ci> PP_KK_K </ci>
|
| 469 |
+
<ci> PP_KK_P_K </ci>
|
| 470 |
+
<ci> KKPase_PP_KK </ci>
|
| 471 |
+
</apply>
|
| 472 |
+
<apply>
|
| 473 |
+
<plus/>
|
| 474 |
+
<ci> PP_KK </ci>
|
| 475 |
+
<ci> P_KK </ci>
|
| 476 |
+
<ci> KK </ci>
|
| 477 |
+
<ci> PP_KK_K </ci>
|
| 478 |
+
<ci> PP_KK_P_K </ci>
|
| 479 |
+
<ci> P_KKK_KK </ci>
|
| 480 |
+
<ci> P_KKK_P_KK </ci>
|
| 481 |
+
<ci> KKPase_PP_KK </ci>
|
| 482 |
+
<ci> KKPase_P_KK </ci>
|
| 483 |
+
</apply>
|
| 484 |
+
</apply>
|
| 485 |
+
</math>
|
| 486 |
+
</assignmentRule>
|
| 487 |
+
<assignmentRule metaid="metaid_0000052" variable="KKK_P_norm">
|
| 488 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 489 |
+
<apply>
|
| 490 |
+
<divide/>
|
| 491 |
+
<apply>
|
| 492 |
+
<plus/>
|
| 493 |
+
<ci> P_KKK </ci>
|
| 494 |
+
<ci> P_KKK_KK </ci>
|
| 495 |
+
<ci> P_KKK_P_KK </ci>
|
| 496 |
+
</apply>
|
| 497 |
+
<apply>
|
| 498 |
+
<plus/>
|
| 499 |
+
<ci> KKK </ci>
|
| 500 |
+
<ci> P_KKK </ci>
|
| 501 |
+
<ci> P_KKK_KK </ci>
|
| 502 |
+
<ci> P_KKK_P_KK </ci>
|
| 503 |
+
</apply>
|
| 504 |
+
</apply>
|
| 505 |
+
</math>
|
| 506 |
+
</assignmentRule>
|
| 507 |
+
</listOfRules>
|
| 508 |
+
<listOfReactions>
|
| 509 |
+
<reaction id="r1a" metaid="_506812" name="binding of MAPKKK activator">
|
| 510 |
+
<annotation>
|
| 511 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 512 |
+
<rdf:Description rdf:about="#_506812">
|
| 513 |
+
<bqbiol:isHomologTo>
|
| 514 |
+
<rdf:Bag>
|
| 515 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_996"/>
|
| 516 |
+
</rdf:Bag>
|
| 517 |
+
</bqbiol:isHomologTo>
|
| 518 |
+
|
| 519 |
+
<bqbiol:isVersionOf>
|
| 520 |
+
<rdf:Bag>
|
| 521 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031435"/>
|
| 522 |
+
</rdf:Bag>
|
| 523 |
+
</bqbiol:isVersionOf>
|
| 524 |
+
</rdf:Description>
|
| 525 |
+
|
| 526 |
+
|
| 527 |
+
</rdf:RDF>
|
| 528 |
+
</annotation>
|
| 529 |
+
<listOfReactants>
|
| 530 |
+
<speciesReference metaid="_396495" species="KKK"/>
|
| 531 |
+
<speciesReference metaid="_396507" species="E1"/>
|
| 532 |
+
</listOfReactants>
|
| 533 |
+
<listOfProducts>
|
| 534 |
+
<speciesReference metaid="_396519" species="E1_KKK"/>
|
| 535 |
+
</listOfProducts>
|
| 536 |
+
<kineticLaw metaid="_396531">
|
| 537 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 538 |
+
<apply>
|
| 539 |
+
<times/>
|
| 540 |
+
<ci> compartment </ci>
|
| 541 |
+
<apply>
|
| 542 |
+
<minus/>
|
| 543 |
+
<apply>
|
| 544 |
+
<times/>
|
| 545 |
+
<ci> a1 </ci>
|
| 546 |
+
<ci> E1 </ci>
|
| 547 |
+
<ci> KKK </ci>
|
| 548 |
+
</apply>
|
| 549 |
+
<apply>
|
| 550 |
+
<times/>
|
| 551 |
+
<ci> d1 </ci>
|
| 552 |
+
<ci> E1_KKK </ci>
|
| 553 |
+
</apply>
|
| 554 |
+
</apply>
|
| 555 |
+
</apply>
|
| 556 |
+
</math>
|
| 557 |
+
<listOfParameters>
|
| 558 |
+
<parameter id="a1" metaid="_815886" value="1000"/>
|
| 559 |
+
<parameter id="d1" metaid="_815887" value="150"/>
|
| 560 |
+
</listOfParameters>
|
| 561 |
+
</kineticLaw>
|
| 562 |
+
</reaction>
|
| 563 |
+
<reaction id="r1b" metaid="_506833" name="MAPKKK activation" reversible="false">
|
| 564 |
+
<annotation>
|
| 565 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 566 |
+
<rdf:Description rdf:about="#_506833">
|
| 567 |
+
<bqbiol:isHomologTo>
|
| 568 |
+
<rdf:Bag>
|
| 569 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_525"/>
|
| 570 |
+
</rdf:Bag>
|
| 571 |
+
</bqbiol:isHomologTo>
|
| 572 |
+
|
| 573 |
+
<bqbiol:isVersionOf>
|
| 574 |
+
<rdf:Bag>
|
| 575 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.11.1"/>
|
| 576 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0008349"/>
|
| 577 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000185"/>
|
| 578 |
+
</rdf:Bag>
|
| 579 |
+
</bqbiol:isVersionOf>
|
| 580 |
+
</rdf:Description>
|
| 581 |
+
|
| 582 |
+
|
| 583 |
+
</rdf:RDF>
|
| 584 |
+
</annotation>
|
| 585 |
+
<listOfReactants>
|
| 586 |
+
<speciesReference metaid="_396543" species="E1_KKK"/>
|
| 587 |
+
</listOfReactants>
|
| 588 |
+
<listOfProducts>
|
| 589 |
+
<speciesReference metaid="_396555" species="E1"/>
|
| 590 |
+
<speciesReference metaid="_396567" species="P_KKK"/>
|
| 591 |
+
</listOfProducts>
|
| 592 |
+
<kineticLaw metaid="_396579">
|
| 593 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 594 |
+
<apply>
|
| 595 |
+
<times/>
|
| 596 |
+
<ci> compartment </ci>
|
| 597 |
+
<ci> k2 </ci>
|
| 598 |
+
<ci> E1_KKK </ci>
|
| 599 |
+
</apply>
|
| 600 |
+
</math>
|
| 601 |
+
<listOfParameters>
|
| 602 |
+
<parameter id="k2" metaid="_815888" value="150"/>
|
| 603 |
+
</listOfParameters>
|
| 604 |
+
</kineticLaw>
|
| 605 |
+
</reaction>
|
| 606 |
+
<reaction id="r2a" metaid="_506853" name="binding of MAPKKK inactivator">
|
| 607 |
+
<annotation>
|
| 608 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 609 |
+
<rdf:Description rdf:about="#_506853">
|
| 610 |
+
<bqbiol:isVersionOf>
|
| 611 |
+
<rdf:Bag>
|
| 612 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031435"/>
|
| 613 |
+
</rdf:Bag>
|
| 614 |
+
</bqbiol:isVersionOf>
|
| 615 |
+
</rdf:Description>
|
| 616 |
+
|
| 617 |
+
|
| 618 |
+
</rdf:RDF>
|
| 619 |
+
</annotation>
|
| 620 |
+
<listOfReactants>
|
| 621 |
+
<speciesReference metaid="_396591" species="P_KKK"/>
|
| 622 |
+
<speciesReference metaid="_396603" species="E2"/>
|
| 623 |
+
</listOfReactants>
|
| 624 |
+
<listOfProducts>
|
| 625 |
+
<speciesReference metaid="_396615" species="E2_P_KKK"/>
|
| 626 |
+
</listOfProducts>
|
| 627 |
+
<kineticLaw metaid="_396627">
|
| 628 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 629 |
+
<apply>
|
| 630 |
+
<times/>
|
| 631 |
+
<ci> compartment </ci>
|
| 632 |
+
<apply>
|
| 633 |
+
<minus/>
|
| 634 |
+
<apply>
|
| 635 |
+
<times/>
|
| 636 |
+
<ci> a2 </ci>
|
| 637 |
+
<ci> E2 </ci>
|
| 638 |
+
<ci> P_KKK </ci>
|
| 639 |
+
</apply>
|
| 640 |
+
<apply>
|
| 641 |
+
<times/>
|
| 642 |
+
<ci> d2 </ci>
|
| 643 |
+
<ci> E2_P_KKK </ci>
|
| 644 |
+
</apply>
|
| 645 |
+
</apply>
|
| 646 |
+
</apply>
|
| 647 |
+
</math>
|
| 648 |
+
<listOfParameters>
|
| 649 |
+
<parameter id="a2" metaid="_815889" value="1000"/>
|
| 650 |
+
<parameter id="d2" metaid="_815890" value="150"/>
|
| 651 |
+
</listOfParameters>
|
| 652 |
+
</kineticLaw>
|
| 653 |
+
</reaction>
|
| 654 |
+
<reaction id="r2b" metaid="_506873" name="MAPKKK inactivation" reversible="false">
|
| 655 |
+
<annotation>
|
| 656 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 657 |
+
<rdf:Description rdf:about="#_506873">
|
| 658 |
+
<bqbiol:isVersionOf>
|
| 659 |
+
<rdf:Bag>
|
| 660 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 661 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051390"/>
|
| 662 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 663 |
+
</rdf:Bag>
|
| 664 |
+
</bqbiol:isVersionOf>
|
| 665 |
+
</rdf:Description>
|
| 666 |
+
|
| 667 |
+
|
| 668 |
+
</rdf:RDF>
|
| 669 |
+
</annotation>
|
| 670 |
+
<listOfReactants>
|
| 671 |
+
<speciesReference metaid="_396639" species="E2_P_KKK"/>
|
| 672 |
+
</listOfReactants>
|
| 673 |
+
<listOfProducts>
|
| 674 |
+
<speciesReference metaid="_396651" species="E2"/>
|
| 675 |
+
<speciesReference metaid="_396663" species="KKK"/>
|
| 676 |
+
</listOfProducts>
|
| 677 |
+
<kineticLaw metaid="_396675">
|
| 678 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 679 |
+
<apply>
|
| 680 |
+
<times/>
|
| 681 |
+
<ci> compartment </ci>
|
| 682 |
+
<ci> k2 </ci>
|
| 683 |
+
<ci> E2_P_KKK </ci>
|
| 684 |
+
</apply>
|
| 685 |
+
</math>
|
| 686 |
+
<listOfParameters>
|
| 687 |
+
<parameter id="k2" metaid="_815891" value="150"/>
|
| 688 |
+
</listOfParameters>
|
| 689 |
+
</kineticLaw>
|
| 690 |
+
</reaction>
|
| 691 |
+
<reaction id="r3a" metaid="_506893" name="binding P-MAPKKK and MAPKK">
|
| 692 |
+
<annotation>
|
| 693 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 694 |
+
<rdf:Description rdf:about="#_506893">
|
| 695 |
+
<bqbiol:isHomologTo>
|
| 696 |
+
<rdf:Bag>
|
| 697 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_143"/>
|
| 698 |
+
</rdf:Bag>
|
| 699 |
+
</bqbiol:isHomologTo>
|
| 700 |
+
|
| 701 |
+
<bqbiol:isVersionOf>
|
| 702 |
+
<rdf:Bag>
|
| 703 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 704 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031435"/>
|
| 705 |
+
</rdf:Bag>
|
| 706 |
+
</bqbiol:isVersionOf>
|
| 707 |
+
</rdf:Description>
|
| 708 |
+
|
| 709 |
+
|
| 710 |
+
</rdf:RDF>
|
| 711 |
+
</annotation>
|
| 712 |
+
<listOfReactants>
|
| 713 |
+
<speciesReference metaid="_396687" species="KK"/>
|
| 714 |
+
<speciesReference metaid="_396699" species="P_KKK"/>
|
| 715 |
+
</listOfReactants>
|
| 716 |
+
<listOfProducts>
|
| 717 |
+
<speciesReference metaid="_396712" species="P_KKK_KK"/>
|
| 718 |
+
</listOfProducts>
|
| 719 |
+
<kineticLaw metaid="_396724">
|
| 720 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 721 |
+
<apply>
|
| 722 |
+
<times/>
|
| 723 |
+
<ci> compartment </ci>
|
| 724 |
+
<apply>
|
| 725 |
+
<minus/>
|
| 726 |
+
<apply>
|
| 727 |
+
<times/>
|
| 728 |
+
<ci> a3 </ci>
|
| 729 |
+
<ci> KK </ci>
|
| 730 |
+
<ci> P_KKK </ci>
|
| 731 |
+
</apply>
|
| 732 |
+
<apply>
|
| 733 |
+
<times/>
|
| 734 |
+
<ci> d3 </ci>
|
| 735 |
+
<ci> P_KKK_KK </ci>
|
| 736 |
+
</apply>
|
| 737 |
+
</apply>
|
| 738 |
+
</apply>
|
| 739 |
+
</math>
|
| 740 |
+
<listOfParameters>
|
| 741 |
+
<parameter id="a3" metaid="_815892" value="1000"/>
|
| 742 |
+
<parameter id="d3" metaid="_815893" value="150"/>
|
| 743 |
+
</listOfParameters>
|
| 744 |
+
</kineticLaw>
|
| 745 |
+
</reaction>
|
| 746 |
+
<reaction id="r3b" metaid="_506913" name="phosphorylation of MAPKK" reversible="false">
|
| 747 |
+
<annotation>
|
| 748 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 749 |
+
<rdf:Description rdf:about="#_506913">
|
| 750 |
+
<bqbiol:isHomologTo>
|
| 751 |
+
<rdf:Bag>
|
| 752 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_614"/>
|
| 753 |
+
</rdf:Bag>
|
| 754 |
+
</bqbiol:isHomologTo>
|
| 755 |
+
|
| 756 |
+
<bqbiol:isVersionOf>
|
| 757 |
+
<rdf:Bag>
|
| 758 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.11.25"/>
|
| 759 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 760 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004709"/>
|
| 761 |
+
</rdf:Bag>
|
| 762 |
+
</bqbiol:isVersionOf>
|
| 763 |
+
</rdf:Description>
|
| 764 |
+
|
| 765 |
+
|
| 766 |
+
</rdf:RDF>
|
| 767 |
+
</annotation>
|
| 768 |
+
<listOfReactants>
|
| 769 |
+
<speciesReference metaid="_396736" species="P_KKK_KK"/>
|
| 770 |
+
</listOfReactants>
|
| 771 |
+
<listOfProducts>
|
| 772 |
+
<speciesReference metaid="_396748" species="P_KK"/>
|
| 773 |
+
<speciesReference metaid="_396760" species="P_KKK"/>
|
| 774 |
+
</listOfProducts>
|
| 775 |
+
<kineticLaw metaid="_396772">
|
| 776 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 777 |
+
<apply>
|
| 778 |
+
<times/>
|
| 779 |
+
<ci> compartment </ci>
|
| 780 |
+
<ci> k3 </ci>
|
| 781 |
+
<ci> P_KKK_KK </ci>
|
| 782 |
+
</apply>
|
| 783 |
+
</math>
|
| 784 |
+
<listOfParameters>
|
| 785 |
+
<parameter id="k3" metaid="_815894" value="150"/>
|
| 786 |
+
</listOfParameters>
|
| 787 |
+
</kineticLaw>
|
| 788 |
+
</reaction>
|
| 789 |
+
<reaction id="r4a" metaid="_506933" name="binding MAPKK-Pase and P-MAPKK">
|
| 790 |
+
<annotation>
|
| 791 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 792 |
+
<rdf:Description rdf:about="#_506933">
|
| 793 |
+
<bqbiol:isVersionOf>
|
| 794 |
+
<rdf:Bag>
|
| 795 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 796 |
+
</rdf:Bag>
|
| 797 |
+
</bqbiol:isVersionOf>
|
| 798 |
+
</rdf:Description>
|
| 799 |
+
|
| 800 |
+
|
| 801 |
+
</rdf:RDF>
|
| 802 |
+
</annotation>
|
| 803 |
+
<listOfReactants>
|
| 804 |
+
<speciesReference metaid="_396784" species="P_KK"/>
|
| 805 |
+
<speciesReference metaid="_396796" species="KKPase"/>
|
| 806 |
+
</listOfReactants>
|
| 807 |
+
<listOfProducts>
|
| 808 |
+
<speciesReference metaid="_396808" species="KKPase_P_KK"/>
|
| 809 |
+
</listOfProducts>
|
| 810 |
+
<kineticLaw metaid="_396820">
|
| 811 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 812 |
+
<apply>
|
| 813 |
+
<times/>
|
| 814 |
+
<ci> compartment </ci>
|
| 815 |
+
<apply>
|
| 816 |
+
<minus/>
|
| 817 |
+
<apply>
|
| 818 |
+
<times/>
|
| 819 |
+
<ci> a4 </ci>
|
| 820 |
+
<ci> P_KK </ci>
|
| 821 |
+
<ci> KKPase </ci>
|
| 822 |
+
</apply>
|
| 823 |
+
<apply>
|
| 824 |
+
<times/>
|
| 825 |
+
<ci> d4 </ci>
|
| 826 |
+
<ci> KKPase_P_KK </ci>
|
| 827 |
+
</apply>
|
| 828 |
+
</apply>
|
| 829 |
+
</apply>
|
| 830 |
+
</math>
|
| 831 |
+
<listOfParameters>
|
| 832 |
+
<parameter id="a4" metaid="_815895" value="1000"/>
|
| 833 |
+
<parameter id="d4" metaid="_815896" value="150"/>
|
| 834 |
+
</listOfParameters>
|
| 835 |
+
</kineticLaw>
|
| 836 |
+
</reaction>
|
| 837 |
+
<reaction id="r4b" metaid="_506953" name="dephosphorylation of P-MAPKK" reversible="false">
|
| 838 |
+
<annotation>
|
| 839 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 840 |
+
<rdf:Description rdf:about="#_506953">
|
| 841 |
+
<bqbiol:isVersionOf>
|
| 842 |
+
<rdf:Bag>
|
| 843 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 844 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 845 |
+
</rdf:Bag>
|
| 846 |
+
</bqbiol:isVersionOf>
|
| 847 |
+
</rdf:Description>
|
| 848 |
+
|
| 849 |
+
|
| 850 |
+
</rdf:RDF>
|
| 851 |
+
</annotation>
|
| 852 |
+
<listOfReactants>
|
| 853 |
+
<speciesReference metaid="_396832" species="KKPase_P_KK"/>
|
| 854 |
+
</listOfReactants>
|
| 855 |
+
<listOfProducts>
|
| 856 |
+
<speciesReference metaid="_396844" species="KK"/>
|
| 857 |
+
<speciesReference metaid="_396856" species="KKPase"/>
|
| 858 |
+
</listOfProducts>
|
| 859 |
+
<kineticLaw metaid="_396868">
|
| 860 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 861 |
+
<apply>
|
| 862 |
+
<times/>
|
| 863 |
+
<ci> compartment </ci>
|
| 864 |
+
<ci> k4 </ci>
|
| 865 |
+
<ci> KKPase_P_KK </ci>
|
| 866 |
+
</apply>
|
| 867 |
+
</math>
|
| 868 |
+
<listOfParameters>
|
| 869 |
+
<parameter id="k4" metaid="_815897" value="150"/>
|
| 870 |
+
</listOfParameters>
|
| 871 |
+
</kineticLaw>
|
| 872 |
+
</reaction>
|
| 873 |
+
<reaction id="r5a" metaid="_506973" name="binding P-MAPKKK and P-MAPKK">
|
| 874 |
+
<annotation>
|
| 875 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 876 |
+
<rdf:Description rdf:about="#_506973">
|
| 877 |
+
<bqbiol:isHomologTo>
|
| 878 |
+
<rdf:Bag>
|
| 879 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_143"/>
|
| 880 |
+
</rdf:Bag>
|
| 881 |
+
</bqbiol:isHomologTo>
|
| 882 |
+
|
| 883 |
+
<bqbiol:isVersionOf>
|
| 884 |
+
<rdf:Bag>
|
| 885 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031435"/>
|
| 886 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 887 |
+
</rdf:Bag>
|
| 888 |
+
</bqbiol:isVersionOf>
|
| 889 |
+
</rdf:Description>
|
| 890 |
+
|
| 891 |
+
|
| 892 |
+
</rdf:RDF>
|
| 893 |
+
</annotation>
|
| 894 |
+
<listOfReactants>
|
| 895 |
+
<speciesReference metaid="_396880" species="P_KK"/>
|
| 896 |
+
<speciesReference metaid="_396892" species="P_KKK"/>
|
| 897 |
+
</listOfReactants>
|
| 898 |
+
<listOfProducts>
|
| 899 |
+
<speciesReference metaid="_396904" species="P_KKK_P_KK"/>
|
| 900 |
+
</listOfProducts>
|
| 901 |
+
<kineticLaw metaid="_396916">
|
| 902 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 903 |
+
<apply>
|
| 904 |
+
<times/>
|
| 905 |
+
<ci> compartment </ci>
|
| 906 |
+
<apply>
|
| 907 |
+
<minus/>
|
| 908 |
+
<apply>
|
| 909 |
+
<times/>
|
| 910 |
+
<ci> a5 </ci>
|
| 911 |
+
<ci> P_KK </ci>
|
| 912 |
+
<ci> P_KKK </ci>
|
| 913 |
+
</apply>
|
| 914 |
+
<apply>
|
| 915 |
+
<times/>
|
| 916 |
+
<ci> d5 </ci>
|
| 917 |
+
<ci> P_KKK_P_KK </ci>
|
| 918 |
+
</apply>
|
| 919 |
+
</apply>
|
| 920 |
+
</apply>
|
| 921 |
+
</math>
|
| 922 |
+
<listOfParameters>
|
| 923 |
+
<parameter id="a5" metaid="_815899" value="1000"/>
|
| 924 |
+
<parameter id="d5" metaid="_815901" value="150"/>
|
| 925 |
+
</listOfParameters>
|
| 926 |
+
</kineticLaw>
|
| 927 |
+
</reaction>
|
| 928 |
+
<reaction id="r5b" metaid="_506993" name="phosphorylation of P-MAPKK" reversible="false">
|
| 929 |
+
<annotation>
|
| 930 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 931 |
+
<rdf:Description rdf:about="#_506993">
|
| 932 |
+
<bqbiol:isHomologTo>
|
| 933 |
+
<rdf:Bag>
|
| 934 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_614"/>
|
| 935 |
+
</rdf:Bag>
|
| 936 |
+
</bqbiol:isHomologTo>
|
| 937 |
+
|
| 938 |
+
<bqbiol:isVersionOf>
|
| 939 |
+
<rdf:Bag>
|
| 940 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.11.25"/>
|
| 941 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 942 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004709"/>
|
| 943 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000186"/>
|
| 944 |
+
</rdf:Bag>
|
| 945 |
+
</bqbiol:isVersionOf>
|
| 946 |
+
</rdf:Description>
|
| 947 |
+
|
| 948 |
+
|
| 949 |
+
</rdf:RDF>
|
| 950 |
+
</annotation>
|
| 951 |
+
<listOfReactants>
|
| 952 |
+
<speciesReference metaid="_396928" species="P_KKK_P_KK"/>
|
| 953 |
+
</listOfReactants>
|
| 954 |
+
<listOfProducts>
|
| 955 |
+
<speciesReference metaid="_396940" species="PP_KK"/>
|
| 956 |
+
<speciesReference metaid="_396952" species="P_KKK"/>
|
| 957 |
+
</listOfProducts>
|
| 958 |
+
<kineticLaw metaid="_396965">
|
| 959 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 960 |
+
<apply>
|
| 961 |
+
<times/>
|
| 962 |
+
<ci> compartment </ci>
|
| 963 |
+
<ci> k5 </ci>
|
| 964 |
+
<ci> P_KKK_P_KK </ci>
|
| 965 |
+
</apply>
|
| 966 |
+
</math>
|
| 967 |
+
<listOfParameters>
|
| 968 |
+
<parameter id="k5" metaid="_815902" value="150"/>
|
| 969 |
+
</listOfParameters>
|
| 970 |
+
</kineticLaw>
|
| 971 |
+
</reaction>
|
| 972 |
+
<reaction id="r6a" metaid="_507013" name="binding MAPKK-Pase and PP-MAPKK">
|
| 973 |
+
<annotation>
|
| 974 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 975 |
+
<rdf:Description rdf:about="#_507013">
|
| 976 |
+
<bqbiol:isVersionOf>
|
| 977 |
+
<rdf:Bag>
|
| 978 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 979 |
+
</rdf:Bag>
|
| 980 |
+
</bqbiol:isVersionOf>
|
| 981 |
+
</rdf:Description>
|
| 982 |
+
|
| 983 |
+
|
| 984 |
+
</rdf:RDF>
|
| 985 |
+
</annotation>
|
| 986 |
+
<listOfReactants>
|
| 987 |
+
<speciesReference metaid="_396977" species="PP_KK"/>
|
| 988 |
+
<speciesReference metaid="_396989" species="KKPase"/>
|
| 989 |
+
</listOfReactants>
|
| 990 |
+
<listOfProducts>
|
| 991 |
+
<speciesReference metaid="_397001" species="KKPase_PP_KK"/>
|
| 992 |
+
</listOfProducts>
|
| 993 |
+
<kineticLaw metaid="_397013">
|
| 994 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 995 |
+
<apply>
|
| 996 |
+
<times/>
|
| 997 |
+
<ci> compartment </ci>
|
| 998 |
+
<apply>
|
| 999 |
+
<minus/>
|
| 1000 |
+
<apply>
|
| 1001 |
+
<times/>
|
| 1002 |
+
<ci> a6 </ci>
|
| 1003 |
+
<ci> PP_KK </ci>
|
| 1004 |
+
<ci> KKPase </ci>
|
| 1005 |
+
</apply>
|
| 1006 |
+
<apply>
|
| 1007 |
+
<times/>
|
| 1008 |
+
<ci> d6 </ci>
|
| 1009 |
+
<ci> KKPase_PP_KK </ci>
|
| 1010 |
+
</apply>
|
| 1011 |
+
</apply>
|
| 1012 |
+
</apply>
|
| 1013 |
+
</math>
|
| 1014 |
+
<listOfParameters>
|
| 1015 |
+
<parameter id="a6" metaid="_815903" value="1000"/>
|
| 1016 |
+
<parameter id="d6" metaid="_815904" value="150"/>
|
| 1017 |
+
</listOfParameters>
|
| 1018 |
+
</kineticLaw>
|
| 1019 |
+
</reaction>
|
| 1020 |
+
<reaction id="r6b" metaid="_507033" name="dephosphorylation of PP-MAPKK" reversible="false">
|
| 1021 |
+
<annotation>
|
| 1022 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1023 |
+
<rdf:Description rdf:about="#_507033">
|
| 1024 |
+
<bqbiol:isVersionOf>
|
| 1025 |
+
<rdf:Bag>
|
| 1026 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 1027 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 1028 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051389"/>
|
| 1029 |
+
</rdf:Bag>
|
| 1030 |
+
</bqbiol:isVersionOf>
|
| 1031 |
+
</rdf:Description>
|
| 1032 |
+
|
| 1033 |
+
|
| 1034 |
+
</rdf:RDF>
|
| 1035 |
+
</annotation>
|
| 1036 |
+
<listOfReactants>
|
| 1037 |
+
<speciesReference metaid="_397025" species="KKPase_PP_KK"/>
|
| 1038 |
+
</listOfReactants>
|
| 1039 |
+
<listOfProducts>
|
| 1040 |
+
<speciesReference metaid="_397037" species="P_KK"/>
|
| 1041 |
+
<speciesReference metaid="_397049" species="KKPase"/>
|
| 1042 |
+
</listOfProducts>
|
| 1043 |
+
<kineticLaw metaid="_397061">
|
| 1044 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1045 |
+
<apply>
|
| 1046 |
+
<times/>
|
| 1047 |
+
<ci> compartment </ci>
|
| 1048 |
+
<ci> k6 </ci>
|
| 1049 |
+
<ci> KKPase_PP_KK </ci>
|
| 1050 |
+
</apply>
|
| 1051 |
+
</math>
|
| 1052 |
+
<listOfParameters>
|
| 1053 |
+
<parameter id="k6" metaid="_815905" value="150"/>
|
| 1054 |
+
</listOfParameters>
|
| 1055 |
+
</kineticLaw>
|
| 1056 |
+
</reaction>
|
| 1057 |
+
<reaction id="r7a" metaid="_507053" name="binding MAPK and PP-MAPKK">
|
| 1058 |
+
<annotation>
|
| 1059 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1060 |
+
<rdf:Description rdf:about="#_507053">
|
| 1061 |
+
<bqbiol:hasVersion>
|
| 1062 |
+
<rdf:Bag>
|
| 1063 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1780"/>
|
| 1064 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_495"/>
|
| 1065 |
+
</rdf:Bag>
|
| 1066 |
+
</bqbiol:hasVersion>
|
| 1067 |
+
|
| 1068 |
+
<bqbiol:isVersionOf>
|
| 1069 |
+
<rdf:Bag>
|
| 1070 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 1071 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1072 |
+
</rdf:Bag>
|
| 1073 |
+
</bqbiol:isVersionOf>
|
| 1074 |
+
</rdf:Description>
|
| 1075 |
+
|
| 1076 |
+
|
| 1077 |
+
</rdf:RDF>
|
| 1078 |
+
</annotation>
|
| 1079 |
+
<listOfReactants>
|
| 1080 |
+
<speciesReference metaid="_397073" species="K"/>
|
| 1081 |
+
<speciesReference metaid="_397085" species="PP_KK"/>
|
| 1082 |
+
</listOfReactants>
|
| 1083 |
+
<listOfProducts>
|
| 1084 |
+
<speciesReference metaid="_397097" species="PP_KK_K"/>
|
| 1085 |
+
</listOfProducts>
|
| 1086 |
+
<kineticLaw metaid="_397109">
|
| 1087 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1088 |
+
<apply>
|
| 1089 |
+
<times/>
|
| 1090 |
+
<ci> compartment </ci>
|
| 1091 |
+
<apply>
|
| 1092 |
+
<minus/>
|
| 1093 |
+
<apply>
|
| 1094 |
+
<times/>
|
| 1095 |
+
<ci> a7 </ci>
|
| 1096 |
+
<ci> K </ci>
|
| 1097 |
+
<ci> PP_KK </ci>
|
| 1098 |
+
</apply>
|
| 1099 |
+
<apply>
|
| 1100 |
+
<times/>
|
| 1101 |
+
<ci> d7 </ci>
|
| 1102 |
+
<ci> PP_KK_K </ci>
|
| 1103 |
+
</apply>
|
| 1104 |
+
</apply>
|
| 1105 |
+
</apply>
|
| 1106 |
+
</math>
|
| 1107 |
+
<listOfParameters>
|
| 1108 |
+
<parameter id="a7" metaid="_815906" value="1000"/>
|
| 1109 |
+
<parameter id="d7" metaid="_815907" value="150"/>
|
| 1110 |
+
</listOfParameters>
|
| 1111 |
+
</kineticLaw>
|
| 1112 |
+
</reaction>
|
| 1113 |
+
<reaction id="r7b" metaid="_507073" name="phosphorylation of MAPK" reversible="false">
|
| 1114 |
+
<annotation>
|
| 1115 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1116 |
+
<rdf:Description rdf:about="#_507073">
|
| 1117 |
+
<bqbiol:hasVersion>
|
| 1118 |
+
<rdf:Bag>
|
| 1119 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 1120 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 1121 |
+
</rdf:Bag>
|
| 1122 |
+
</bqbiol:hasVersion>
|
| 1123 |
+
|
| 1124 |
+
<bqbiol:isVersionOf>
|
| 1125 |
+
<rdf:Bag>
|
| 1126 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 1127 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 1128 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 1129 |
+
</rdf:Bag>
|
| 1130 |
+
</bqbiol:isVersionOf>
|
| 1131 |
+
</rdf:Description>
|
| 1132 |
+
|
| 1133 |
+
|
| 1134 |
+
</rdf:RDF>
|
| 1135 |
+
</annotation>
|
| 1136 |
+
<listOfReactants>
|
| 1137 |
+
<speciesReference metaid="_397121" species="PP_KK_K"/>
|
| 1138 |
+
</listOfReactants>
|
| 1139 |
+
<listOfProducts>
|
| 1140 |
+
<speciesReference metaid="_397133" species="P_K"/>
|
| 1141 |
+
<speciesReference metaid="_397145" species="PP_KK"/>
|
| 1142 |
+
</listOfProducts>
|
| 1143 |
+
<kineticLaw metaid="_397158">
|
| 1144 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1145 |
+
<apply>
|
| 1146 |
+
<times/>
|
| 1147 |
+
<ci> compartment </ci>
|
| 1148 |
+
<ci> k7 </ci>
|
| 1149 |
+
<ci> PP_KK_K </ci>
|
| 1150 |
+
</apply>
|
| 1151 |
+
</math>
|
| 1152 |
+
<listOfParameters>
|
| 1153 |
+
<parameter id="k7" metaid="_815908" value="150"/>
|
| 1154 |
+
</listOfParameters>
|
| 1155 |
+
</kineticLaw>
|
| 1156 |
+
</reaction>
|
| 1157 |
+
<reaction id="r8a" metaid="_507093" name="binding MAPK-Pase and P-MAPK">
|
| 1158 |
+
<annotation>
|
| 1159 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1160 |
+
<rdf:Description rdf:about="#_507093">
|
| 1161 |
+
<bqbiol:isVersionOf>
|
| 1162 |
+
<rdf:Bag>
|
| 1163 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1164 |
+
</rdf:Bag>
|
| 1165 |
+
</bqbiol:isVersionOf>
|
| 1166 |
+
</rdf:Description>
|
| 1167 |
+
|
| 1168 |
+
|
| 1169 |
+
</rdf:RDF>
|
| 1170 |
+
</annotation>
|
| 1171 |
+
<listOfReactants>
|
| 1172 |
+
<speciesReference metaid="_397170" species="P_K"/>
|
| 1173 |
+
<speciesReference metaid="_397182" species="KPase"/>
|
| 1174 |
+
</listOfReactants>
|
| 1175 |
+
<listOfProducts>
|
| 1176 |
+
<speciesReference metaid="_397194" species="KPase_P_K"/>
|
| 1177 |
+
</listOfProducts>
|
| 1178 |
+
<kineticLaw metaid="_397206">
|
| 1179 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1180 |
+
<apply>
|
| 1181 |
+
<times/>
|
| 1182 |
+
<ci> compartment </ci>
|
| 1183 |
+
<apply>
|
| 1184 |
+
<minus/>
|
| 1185 |
+
<apply>
|
| 1186 |
+
<times/>
|
| 1187 |
+
<ci> a8 </ci>
|
| 1188 |
+
<ci> P_K </ci>
|
| 1189 |
+
<ci> KPase </ci>
|
| 1190 |
+
</apply>
|
| 1191 |
+
<apply>
|
| 1192 |
+
<times/>
|
| 1193 |
+
<ci> d8 </ci>
|
| 1194 |
+
<ci> KPase_P_K </ci>
|
| 1195 |
+
</apply>
|
| 1196 |
+
</apply>
|
| 1197 |
+
</apply>
|
| 1198 |
+
</math>
|
| 1199 |
+
<listOfParameters>
|
| 1200 |
+
<parameter id="a8" metaid="_815909" value="1000"/>
|
| 1201 |
+
<parameter id="d8" metaid="_815910" value="150"/>
|
| 1202 |
+
</listOfParameters>
|
| 1203 |
+
</kineticLaw>
|
| 1204 |
+
</reaction>
|
| 1205 |
+
<reaction id="r8b" metaid="_507113" name="dephosphorylation of P-MAPK" reversible="false">
|
| 1206 |
+
<annotation>
|
| 1207 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1208 |
+
<rdf:Description rdf:about="#_507113">
|
| 1209 |
+
<bqbiol:isVersionOf>
|
| 1210 |
+
<rdf:Bag>
|
| 1211 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 1212 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 1213 |
+
</rdf:Bag>
|
| 1214 |
+
</bqbiol:isVersionOf>
|
| 1215 |
+
</rdf:Description>
|
| 1216 |
+
|
| 1217 |
+
|
| 1218 |
+
</rdf:RDF>
|
| 1219 |
+
</annotation>
|
| 1220 |
+
<listOfReactants>
|
| 1221 |
+
<speciesReference metaid="_397218" species="KPase_P_K"/>
|
| 1222 |
+
</listOfReactants>
|
| 1223 |
+
<listOfProducts>
|
| 1224 |
+
<speciesReference metaid="_397230" species="K"/>
|
| 1225 |
+
<speciesReference metaid="_397242" species="KPase"/>
|
| 1226 |
+
</listOfProducts>
|
| 1227 |
+
<kineticLaw metaid="_397254">
|
| 1228 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1229 |
+
<apply>
|
| 1230 |
+
<times/>
|
| 1231 |
+
<ci> compartment </ci>
|
| 1232 |
+
<ci> k8 </ci>
|
| 1233 |
+
<ci> KPase_P_K </ci>
|
| 1234 |
+
</apply>
|
| 1235 |
+
</math>
|
| 1236 |
+
<listOfParameters>
|
| 1237 |
+
<parameter id="k8" metaid="_815911" value="150"/>
|
| 1238 |
+
</listOfParameters>
|
| 1239 |
+
</kineticLaw>
|
| 1240 |
+
</reaction>
|
| 1241 |
+
<reaction id="r9a" metaid="_507133" name="binding PP-MAPKK and P-MAPK">
|
| 1242 |
+
<annotation>
|
| 1243 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1244 |
+
<rdf:Description rdf:about="#_507133">
|
| 1245 |
+
<bqbiol:hasVersion>
|
| 1246 |
+
<rdf:Bag>
|
| 1247 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1780"/>
|
| 1248 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_495"/>
|
| 1249 |
+
</rdf:Bag>
|
| 1250 |
+
</bqbiol:hasVersion>
|
| 1251 |
+
|
| 1252 |
+
<bqbiol:isVersionOf>
|
| 1253 |
+
<rdf:Bag>
|
| 1254 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1255 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 1256 |
+
</rdf:Bag>
|
| 1257 |
+
</bqbiol:isVersionOf>
|
| 1258 |
+
</rdf:Description>
|
| 1259 |
+
|
| 1260 |
+
|
| 1261 |
+
</rdf:RDF>
|
| 1262 |
+
</annotation>
|
| 1263 |
+
<listOfReactants>
|
| 1264 |
+
<speciesReference metaid="_397266" species="P_K"/>
|
| 1265 |
+
<speciesReference metaid="_397278" species="PP_KK"/>
|
| 1266 |
+
</listOfReactants>
|
| 1267 |
+
<listOfProducts>
|
| 1268 |
+
<speciesReference metaid="_397291" species="PP_KK_P_K"/>
|
| 1269 |
+
</listOfProducts>
|
| 1270 |
+
<kineticLaw metaid="_397303">
|
| 1271 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1272 |
+
<apply>
|
| 1273 |
+
<times/>
|
| 1274 |
+
<ci> compartment </ci>
|
| 1275 |
+
<apply>
|
| 1276 |
+
<minus/>
|
| 1277 |
+
<apply>
|
| 1278 |
+
<times/>
|
| 1279 |
+
<ci> a9 </ci>
|
| 1280 |
+
<ci> P_K </ci>
|
| 1281 |
+
<ci> PP_KK </ci>
|
| 1282 |
+
</apply>
|
| 1283 |
+
<apply>
|
| 1284 |
+
<times/>
|
| 1285 |
+
<ci> d9 </ci>
|
| 1286 |
+
<ci> PP_KK_P_K </ci>
|
| 1287 |
+
</apply>
|
| 1288 |
+
</apply>
|
| 1289 |
+
</apply>
|
| 1290 |
+
</math>
|
| 1291 |
+
<listOfParameters>
|
| 1292 |
+
<parameter id="a9" metaid="_815912" value="1000"/>
|
| 1293 |
+
<parameter id="d9" metaid="_815913" value="150"/>
|
| 1294 |
+
</listOfParameters>
|
| 1295 |
+
</kineticLaw>
|
| 1296 |
+
</reaction>
|
| 1297 |
+
<reaction id="r9b" metaid="_507153" name="phosphorylation of P-MAPK" reversible="false">
|
| 1298 |
+
<annotation>
|
| 1299 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1300 |
+
<rdf:Description rdf:about="#_507153">
|
| 1301 |
+
<bqbiol:isVersionOf>
|
| 1302 |
+
<rdf:Bag>
|
| 1303 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 1304 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 1305 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 1306 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000187"/>
|
| 1307 |
+
</rdf:Bag>
|
| 1308 |
+
</bqbiol:isVersionOf>
|
| 1309 |
+
|
| 1310 |
+
<bqbiol:hasVersion>
|
| 1311 |
+
<rdf:Bag>
|
| 1312 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 1313 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 1314 |
+
</rdf:Bag>
|
| 1315 |
+
</bqbiol:hasVersion>
|
| 1316 |
+
</rdf:Description>
|
| 1317 |
+
|
| 1318 |
+
|
| 1319 |
+
</rdf:RDF>
|
| 1320 |
+
</annotation>
|
| 1321 |
+
<listOfReactants>
|
| 1322 |
+
<speciesReference metaid="_397315" species="PP_KK_P_K"/>
|
| 1323 |
+
</listOfReactants>
|
| 1324 |
+
<listOfProducts>
|
| 1325 |
+
<speciesReference metaid="_397327" species="PP_KK"/>
|
| 1326 |
+
<speciesReference metaid="_397339" species="PP_K"/>
|
| 1327 |
+
</listOfProducts>
|
| 1328 |
+
<kineticLaw metaid="_397351">
|
| 1329 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1330 |
+
<apply>
|
| 1331 |
+
<times/>
|
| 1332 |
+
<ci> compartment </ci>
|
| 1333 |
+
<ci> k9 </ci>
|
| 1334 |
+
<ci> PP_KK_P_K </ci>
|
| 1335 |
+
</apply>
|
| 1336 |
+
</math>
|
| 1337 |
+
<listOfParameters>
|
| 1338 |
+
<parameter id="k9" metaid="_815914" value="150"/>
|
| 1339 |
+
</listOfParameters>
|
| 1340 |
+
</kineticLaw>
|
| 1341 |
+
</reaction>
|
| 1342 |
+
<reaction id="r10a" metaid="_507173" name="binding MAPK-Pase and PP-MAPK">
|
| 1343 |
+
<annotation>
|
| 1344 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1345 |
+
<rdf:Description rdf:about="#_507173">
|
| 1346 |
+
<bqbiol:isVersionOf>
|
| 1347 |
+
<rdf:Bag>
|
| 1348 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1349 |
+
</rdf:Bag>
|
| 1350 |
+
</bqbiol:isVersionOf>
|
| 1351 |
+
</rdf:Description>
|
| 1352 |
+
|
| 1353 |
+
|
| 1354 |
+
</rdf:RDF>
|
| 1355 |
+
</annotation>
|
| 1356 |
+
<listOfReactants>
|
| 1357 |
+
<speciesReference metaid="_397363" species="PP_K"/>
|
| 1358 |
+
<speciesReference metaid="_397376" species="KPase"/>
|
| 1359 |
+
</listOfReactants>
|
| 1360 |
+
<listOfProducts>
|
| 1361 |
+
<speciesReference metaid="_397388" species="KPase_PP_K"/>
|
| 1362 |
+
</listOfProducts>
|
| 1363 |
+
<kineticLaw metaid="_397400">
|
| 1364 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1365 |
+
<apply>
|
| 1366 |
+
<times/>
|
| 1367 |
+
<ci> compartment </ci>
|
| 1368 |
+
<apply>
|
| 1369 |
+
<minus/>
|
| 1370 |
+
<apply>
|
| 1371 |
+
<times/>
|
| 1372 |
+
<ci> a10 </ci>
|
| 1373 |
+
<ci> PP_K </ci>
|
| 1374 |
+
<ci> KPase </ci>
|
| 1375 |
+
</apply>
|
| 1376 |
+
<apply>
|
| 1377 |
+
<times/>
|
| 1378 |
+
<ci> d10 </ci>
|
| 1379 |
+
<ci> KPase_PP_K </ci>
|
| 1380 |
+
</apply>
|
| 1381 |
+
</apply>
|
| 1382 |
+
</apply>
|
| 1383 |
+
</math>
|
| 1384 |
+
<listOfParameters>
|
| 1385 |
+
<parameter id="a10" metaid="_815916" value="1000"/>
|
| 1386 |
+
<parameter id="d10" metaid="_815918" value="150"/>
|
| 1387 |
+
</listOfParameters>
|
| 1388 |
+
</kineticLaw>
|
| 1389 |
+
</reaction>
|
| 1390 |
+
<reaction id="r10b" metaid="_507193" name="dephosphorylation of PP-MAPK" reversible="false">
|
| 1391 |
+
<annotation>
|
| 1392 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1393 |
+
<rdf:Description rdf:about="#_507193">
|
| 1394 |
+
<bqbiol:isVersionOf>
|
| 1395 |
+
<rdf:Bag>
|
| 1396 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 1397 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 1398 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000188"/>
|
| 1399 |
+
</rdf:Bag>
|
| 1400 |
+
</bqbiol:isVersionOf>
|
| 1401 |
+
</rdf:Description>
|
| 1402 |
+
|
| 1403 |
+
|
| 1404 |
+
</rdf:RDF>
|
| 1405 |
+
</annotation>
|
| 1406 |
+
<listOfReactants>
|
| 1407 |
+
<speciesReference metaid="_397412" species="KPase_PP_K"/>
|
| 1408 |
+
</listOfReactants>
|
| 1409 |
+
<listOfProducts>
|
| 1410 |
+
<speciesReference metaid="_397424" species="P_K"/>
|
| 1411 |
+
<speciesReference metaid="_397436" species="KPase"/>
|
| 1412 |
+
</listOfProducts>
|
| 1413 |
+
<kineticLaw metaid="_397448">
|
| 1414 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1415 |
+
<apply>
|
| 1416 |
+
<times/>
|
| 1417 |
+
<ci> compartment </ci>
|
| 1418 |
+
<ci> k10 </ci>
|
| 1419 |
+
<ci> KPase_PP_K </ci>
|
| 1420 |
+
</apply>
|
| 1421 |
+
</math>
|
| 1422 |
+
<listOfParameters>
|
| 1423 |
+
<parameter id="k10" metaid="_815919" value="150"/>
|
| 1424 |
+
</listOfParameters>
|
| 1425 |
+
</kineticLaw>
|
| 1426 |
+
</reaction>
|
| 1427 |
+
</listOfReactions>
|
| 1428 |
+
</model>
|
| 1429 |
+
</sbml>
|
Data/BIOMD0000000009/Huang1996_conditions.json
ADDED
|
@@ -0,0 +1,236 @@
|
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|
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|
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|
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|
|
|
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|
|
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|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
|
|
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|
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|
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|
|
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|
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|
|
|
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|
|
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|
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| 1 |
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 11 |
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| 12 |
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| 13 |
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| 14 |
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| 15 |
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| 16 |
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| 21 |
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| 39 |
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| 41 |
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| 43 |
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|
Data/BIOMD0000000009/initial_conditions.json
ADDED
|
@@ -0,0 +1,31 @@
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|
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|
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|
| 1 |
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{
|
| 2 |
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| 3 |
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| 4 |
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|
| 5 |
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|
| 6 |
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|
| 7 |
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| 8 |
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| 9 |
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| 10 |
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| 13 |
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|
| 14 |
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|
| 15 |
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|
| 16 |
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|
| 17 |
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|
| 18 |
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|
| 24 |
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|
| 25 |
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| 26 |
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| 28 |
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|
| 29 |
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|
| 30 |
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}
|
| 31 |
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|
Data/BIOMD0000000010/Kholodenko2000.csv
ADDED
|
@@ -0,0 +1,513 @@
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|
| 1 |
+
time,MKKK,MKKK_P,MKK,MKK_P,MKK_PP,MAPK,MAPK_P,MAPK_PP
|
| 2 |
+
0.0,90.08385428882094,9.916145711179064,144.57213516674292,85.64791460162257,69.77995023163557,1.0520392514669576,4.986659513603995,293.9613012349261
|
| 3 |
+
6.8493150684931505,90.56289778604634,9.437102213953658,147.44103537717726,85.58210981513226,66.97685480769158,1.1276151326111679,5.202000062205229,293.6703848051806
|
| 4 |
+
13.698630136986301,91.02016632181252,8.979833678187488,150.37938467200354,85.48288784292944,64.1377274850681,1.2124172191728793,5.437509159745501,293.3500736210787
|
| 5 |
+
20.54794520547945,91.45550261345396,8.544497386546036,153.3838252894457,85.34770181848619,61.26847289206923,1.307778333981963,5.6952621787176945,292.9969594872974
|
| 6 |
+
27.397260273972602,91.86883460156628,8.13116539843371,156.4509197838799,85.17378576815041,58.37529444797079,1.4152349077595197,5.977518767529485,292.607246324708
|
| 7 |
+
34.24657534246575,92.26017099889829,7.739829001101709,159.57718254005798,84.9581008500706,55.464716609872546,1.5365724862761647,6.28674378500817,292.1766837287126
|
| 8 |
+
41.0958904109589,92.62960184443638,7.3703981555636195,162.75908746867984,84.6973080601885,52.5436044711328,1.673855006266079,6.62559743761082,291.7005475561199
|
| 9 |
+
47.945205479452056,92.9773048038011,7.022695196198893,165.99307472577792,84.38771525604639,49.619210018176844,1.8294910953241081,6.996928951040273,291.1735799536323
|
| 10 |
+
54.794520547945204,93.30354484697432,6.69645515302567,169.2755611821976,84.02523379738597,46.6992050204176,2.006272335731005,7.403747585604275,290.58998007866137
|
| 11 |
+
61.64383561643835,93.60866975207792,6.391330247922079,172.60294982624362,83.60534430611274,43.791705867644836,2.2074095434857877,7.84917153608077,289.9434189204301
|
| 12 |
+
68.4931506849315,93.89310722530085,6.106892774699143,175.971636498099,83.1230443756433,40.90531912625888,2.436601507779499,8.336347548442498,289.22705094377454
|
| 13 |
+
75.34246575342466,94.15736011798407,5.842639882015931,179.37801496270058,82.5727990574116,38.049185979889,2.6980846242532364,8.86835614236409,288.4335592333791
|
| 14 |
+
82.1917808219178,94.40199923526606,5.598000764733949,182.81848048038478,81.94849578148266,35.23302373813374,2.9966717912828402,9.44808618348283,287.55524202523077
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| 15 |
+
89.04109589041096,94.62765465616293,5.372345343837085,186.2894307133103,81.24340688141571,32.46716240527513,3.3377872437514777,10.078065218780308,286.5841475374646
|
| 16 |
+
95.89041095890411,94.83500639516114,5.164993604838881,189.78726343757884,80.4501684438135,29.762568118608833,3.72747632322159,10.760269953659991,285.5122537231148
|
| 17 |
+
102.73972602739725,95.02477388218115,4.975226117818868,193.30837070741185,79.56078419805719,27.13084509453209,4.172377314149523,11.495912876783459,284.3317098090634
|
| 18 |
+
109.58904109589041,95.19770591551949,4.802294084480521,196.84912959046713,78.56667060006617,24.584199809467858,4.679649099522104,12.285234101930158,283.0351167985442
|
| 19 |
+
116.43835616438356,95.35456986425517,4.645430135744847,200.40588815195122,77.45876644651187,22.135345401538046,5.256831152724031,13.127290196204237,281.6158786510684
|
| 20 |
+
123.2876712328767,95.49614253178981,4.503857468210212,203.97494868827246,76.22771693831278,19.797334373415925,5.911631975704066,14.019817958316896,280.0685500659758
|
| 21 |
+
130.13698630136986,95.62320071920855,4.376799280791466,207.55254523913575,74.8641919669984,17.583262793867018,6.651630908168559,14.959149542764463,278.38921954906385
|
| 22 |
+
136.986301369863,95.7365141515136,4.263485848486429,211.13482026768037,73.3593045767829,15.505875155537899,7.483922248781329,15.940239263286545,276.57583848792916
|
| 23 |
+
143.83561643835617,95.83683865727193,4.163161342728117,214.71779602189622,71.70523234926222,13.57697162884272,8.41467901287166,16.956800411416094,274.6285205757096
|
| 24 |
+
150.68493150684932,95.92491154116112,4.075088458838922,218.29734768063412,69.89591691589473,11.80673540347232,9.448673925382437,18.001635027755967,272.54969104685944
|
| 25 |
+
157.53424657534245,96.0014475626148,3.9985524373852557,221.8691744124979,67.92792017302676,10.202905414476513,10.588885759766377,19.066998446352216,270.34411579387955
|
| 26 |
+
164.3835616438356,96.06713633228374,3.9328636677163167,225.42877395032338,65.80124445418087,8.769981595496912,11.836239874559878,20.14496485354885,268.01879527188964
|
| 27 |
+
171.23287671232876,96.12264049371693,3.877359506283127,228.9714203087252,63.52002548912028,7.508554202155684,13.1894410669294,21.227907206627247,265.5826517264419
|
| 28 |
+
178.08219178082192,96.16859439123226,3.8314056087678,232.492145431174,61.092938577798094,6.414915991029038,14.645022285159666,22.308918774764148,263.0460589400746
|
| 29 |
+
184.93150684931507,96.20560309826502,3.794396901735027,235.98572536797883,58.53316566526498,5.481108966757337,16.197639008557186,23.382029795293775,260.4203311961472
|
| 30 |
+
191.78082191780823,96.23424148999591,3.7657585100041318,239.44666739759427,55.85790173540163,4.695430867005245,17.840511275087177,24.442359110751553,257.71712961415903
|
| 31 |
+
198.63013698630135,96.25505337511844,3.7449466248815972,242.86919790319266,53.087520019308926,4.043282077499572,19.565902742545422,25.48616726392639,254.94792999352592
|
| 32 |
+
205.4794520547945,96.26855047399685,3.7314495260031757,246.24724674696844,50.24427301670324,3.508480236329479,21.365645986083486,26.51084413617261,252.1235098777416
|
| 33 |
+
212.32876712328766,96.2752114009599,3.724788599040109,249.57442243984528,47.351283861164184,3.0742936989917253,23.231631526256667,27.51470167027391,249.253666803467
|
| 34 |
+
219.17808219178082,96.27548088708303,3.7245191129169855,252.84398365472268,44.43156539512124,2.72445095015725,25.15616660929334,28.496799988096306,246.34703340260788
|
| 35 |
+
226.02739726027397,96.26976916917233,3.730230830827697,256.04880389546247,41.507290463621395,2.443905640917332,27.13222128564276,29.45678297235513,243.41099574199959
|
| 36 |
+
232.87671232876713,96.25845169581851,3.741548304181529,259.1813335326872,38.599398150719104,2.219268316594926,29.153562779300273,30.39471332757247,240.4517238931247
|
| 37 |
+
239.72602739726028,96.24186922164118,3.758130778358853,262.2335634387202,35.72745388352167,2.0389826777593267,31.21479901412478,31.310931908266795,237.47426907760584
|
| 38 |
+
246.5753424657534,96.22032819121921,3.77967180878083,265.19700297553914,32.909683597589186,1.8933134268728056,33.31136338232409,32.20596152416361,234.4826750935097
|
| 39 |
+
253.42465753424656,96.194101249601,3.805898750399034,268.0626784694591,30.16309425269314,1.774227277848906,35.43946713695084,33.08044920316112,231.48008365988542
|
| 40 |
+
260.2739726027397,96.16342855173698,3.836571448263059,270.82115085226246,27.50370786107385,1.6751412866648483,37.59599820888451,33.935052418911866,228.46894937220108
|
| 41 |
+
267.12328767123284,96.1285187257532,3.871481274246838,273.46260011377063,24.946657327102738,1.5907425591277256,39.77845409055422,34.77044035422419,225.45110555521913
|
| 42 |
+
273.972602739726,96.0895501500636,3.9104498499364357,275.97697137542775,22.506254119946906,1.5167745046264054,41.98485538941988,35.587267408687815,222.42787720188994
|
| 43 |
+
280.82191780821915,96.04667226560179,3.953327734398253,278.3542001787304,20.195942772469987,1.4498570488006295,44.21366598311337,36.38615188598302,219.40018213090136
|
| 44 |
+
287.67123287671234,96.00000691086922,3.999993089130828,280.5845452776272,18.028111946059813,1.3873427763139026,46.4637195625554,37.16766806343667,216.36861237400572
|
| 45 |
+
294.52054794520546,95.94964961522298,4.050350384777063,282.65903579624666,16.01375093987002,1.327213263884265,48.73415258749103,37.93234361454967,213.33350379795712
|
| 46 |
+
301.36986301369865,95.8956708057635,4.104329194236537,284.5700027543031,14.161989748838876,1.2680074968589323,51.02434172120964,38.680659160726954,210.29499911806124
|
| 47 |
+
308.2191780821918,95.83811700212807,4.161882997871975,286.31170197060925,12.47952656753649,1.2087714618552206,53.333840237455114,39.41305052195565,207.25310924058712
|
| 48 |
+
315.0684931506849,95.77701189519367,4.222988104806365,287.8809161036041,10.970059861977585,1.1490240344192921,55.66231780234603,40.12991295902829,204.2077692386236
|
| 49 |
+
321.9178082191781,95.7123573752033,4.287642624796745,289.2774663956659,9.633812209201587,1.088721395133501,58.00950082773435,40.83160654204304,201.15889263022055
|
| 50 |
+
328.7671232876712,95.64413452924504,4.355865470754994,290.50453139201835,8.467261721039241,1.0282068869433107,60.37511416924795,41.518462465572846,198.10642336517716
|
| 51 |
+
335.6164383561644,95.57230454897255,4.4276954510274615,291.56865885202694,7.463200556870028,0.9681405911039124,62.758831583294516,42.190789210785184,195.0503792059183
|
| 52 |
+
342.4657534246575,95.49680960975606,4.50319039024397,292.4794513269664,6.611148256624357,0.9094004164101256,65.16023365616992,42.84887875175835,191.9908875920697
|
| 53 |
+
349.3150684931507,95.4175736771956,4.582426322804407,293.24893704210257,5.8980945463984,0.8529684114998494,67.5787815202167,43.49301138529492,188.92820709448642
|
| 54 |
+
356.16438356164383,95.33450320664622,4.665496793353802,293.89078401936575,5.309394324475737,0.7998216561593079,70.01380671778583,44.123458708737594,185.8627345734747
|
| 55 |
+
363.01369863013696,95.247487730457,4.752512269543022,294.4193897217978,4.829783436083768,0.7508268421191733,72.46451501637924,44.74048563422306,182.7949993493959
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| 56 |
+
369.86301369863014,95.15640026386328,4.843599736136748,294.8490857631023,4.444242251337289,0.7066719855611397,74.93000438747572,45.3443504105682,179.72564520195434
|
| 57 |
+
376.71232876712327,95.06109753920431,4.9389024607957195,295.19349499437334,4.138674101735634,0.6678309038917339,77.40929097413803,45.935303415075005,176.65540561078524
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| 58 |
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383.56164383561645,94.96142002980072,5.038579970199311,295.46508452698345,3.900354898030807,0.6345605749864084,79.90133949444485,46.51358509754611,173.58507540800733
|
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Data/BIOMD0000000010/Kholodenko2000.xml
ADDED
|
@@ -0,0 +1,733 @@
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| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_492719" version="4">
|
| 3 |
+
<model id="BIOMD0000000010" metaid="_000001" name="Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Kholodenko2000 - Ultrasensitivity and negative feedback bring oscillations in MAPK cascade</div>
|
| 7 |
+
<div class="dc:description">
|
| 8 |
+
<p>The combination of ultrasensitivity and negative feedback bring sustained oscillations in the mitogen-activated protein kinase cascades.</p>
|
| 9 |
+
</div>
|
| 10 |
+
<div class="dc:bibliographicCitation">
|
| 11 |
+
<p>This model is described in the article:</p>
|
| 12 |
+
<div class="bibo:title">
|
| 13 |
+
<a href="http://identifiers.org/pubmed/10712587" title="Access to this publication">Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades.</a>
|
| 14 |
+
</div>
|
| 15 |
+
<div class="bibo:authorList">Kholodenko BN</div>
|
| 16 |
+
<div class="bibo:Journal">Eur. J. Biochem. 2000; 267(6):1583-8</div>
|
| 17 |
+
<p>Abstract:</p>
|
| 18 |
+
<div class="bibo:abstract">
|
| 19 |
+
<p>Functional organization of signal transduction into protein phosphorylation cascades, such as the mitogen-activated protein kinase (MAPK) cascades, greatly enhances the sensitivity of cellular targets to external stimuli. The sensitivity increases multiplicatively with the number of cascade levels, so that a tiny change in a stimulus results in a large change in the response, the phenomenon referred to as ultrasensitivity. In a variety of cell types, the MAPK cascades are imbedded in long feedback loops, positive or negative, depending on whether the terminal kinase stimulates or inhibits the activation of the initial level. Here we demonstrate that a negative feedback loop combined with intrinsic ultrasensitivity of the MAPK cascade can bring about sustained oscillations in MAPK phosphorylation. Based on recent kinetic data on the MAPK cascades, we predict that the period of oscillations can range from minutes to hours. The phosphorylation level can vary between the base level and almost 100% of the total protein. The oscillations of the phosphorylation cascades and slow protein diffusion in the cytoplasm can lead to intracellular waves of phospho-proteins.</p>
|
| 20 |
+
</div>
|
| 21 |
+
</div>
|
| 22 |
+
<div class="dc:publisher">
|
| 23 |
+
<p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 24 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000010">BIOMD0000000010</a>
|
| 25 |
+
. </p>
|
| 26 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 27 |
+
. </p>
|
| 28 |
+
</div>
|
| 29 |
+
<div class="dc:license">
|
| 30 |
+
<p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 31 |
+
for more information. </p>
|
| 32 |
+
</div>
|
| 33 |
+
</body>
|
| 34 |
+
</notes>
|
| 35 |
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|
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|
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<vCard:EMAIL>Herbert_Sauro@kgi.edu</vCard:EMAIL>
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|
| 278 |
+
<plus/>
|
| 279 |
+
<ci> K1 </ci>
|
| 280 |
+
<ci> MKKK </ci>
|
| 281 |
+
</apply>
|
| 282 |
+
</apply>
|
| 283 |
+
</apply>
|
| 284 |
+
</math>
|
| 285 |
+
<listOfParameters>
|
| 286 |
+
<parameter id="V1" metaid="_001327" value="2.5"/>
|
| 287 |
+
<parameter id="Ki" metaid="_001328" value="9"/>
|
| 288 |
+
<parameter id="n" metaid="_001329" value="1"/>
|
| 289 |
+
<parameter id="K1" metaid="_001331" value="10"/>
|
| 290 |
+
</listOfParameters>
|
| 291 |
+
</kineticLaw>
|
| 292 |
+
</reaction>
|
| 293 |
+
<reaction id="J1" metaid="_584655" name="MAPKKK inactivation" reversible="false">
|
| 294 |
+
<annotation>
|
| 295 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 296 |
+
<rdf:Description rdf:about="#_584655">
|
| 297 |
+
<bqbiol:isVersionOf>
|
| 298 |
+
<rdf:Bag>
|
| 299 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 300 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051390"/>
|
| 301 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 302 |
+
</rdf:Bag>
|
| 303 |
+
</bqbiol:isVersionOf>
|
| 304 |
+
</rdf:Description>
|
| 305 |
+
|
| 306 |
+
</rdf:RDF>
|
| 307 |
+
</annotation>
|
| 308 |
+
<listOfReactants>
|
| 309 |
+
<speciesReference metaid="_653209" species="MKKK_P"/>
|
| 310 |
+
</listOfReactants>
|
| 311 |
+
<listOfProducts>
|
| 312 |
+
<speciesReference metaid="_653221" species="MKKK"/>
|
| 313 |
+
</listOfProducts>
|
| 314 |
+
<kineticLaw metaid="_653233">
|
| 315 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 316 |
+
<apply>
|
| 317 |
+
<divide/>
|
| 318 |
+
<apply>
|
| 319 |
+
<times/>
|
| 320 |
+
<ci> uVol </ci>
|
| 321 |
+
<ci> V2 </ci>
|
| 322 |
+
<ci> MKKK_P </ci>
|
| 323 |
+
</apply>
|
| 324 |
+
<apply>
|
| 325 |
+
<plus/>
|
| 326 |
+
<ci> KK2 </ci>
|
| 327 |
+
<ci> MKKK_P </ci>
|
| 328 |
+
</apply>
|
| 329 |
+
</apply>
|
| 330 |
+
</math>
|
| 331 |
+
<listOfParameters>
|
| 332 |
+
<parameter id="V2" metaid="_001333" value="0.25"/>
|
| 333 |
+
<parameter id="KK2" metaid="_001335" value="8"/>
|
| 334 |
+
</listOfParameters>
|
| 335 |
+
</kineticLaw>
|
| 336 |
+
</reaction>
|
| 337 |
+
<reaction id="J2" metaid="_584675" name="phosphorylation of MAPKK" reversible="false">
|
| 338 |
+
<annotation>
|
| 339 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 340 |
+
<rdf:Description rdf:about="#_584675">
|
| 341 |
+
<bqbiol:isHomologTo>
|
| 342 |
+
<rdf:Bag>
|
| 343 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_614"/>
|
| 344 |
+
</rdf:Bag>
|
| 345 |
+
</bqbiol:isHomologTo>
|
| 346 |
+
|
| 347 |
+
<bqbiol:isVersionOf>
|
| 348 |
+
<rdf:Bag>
|
| 349 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.11.25"/>
|
| 350 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004709"/>
|
| 351 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 352 |
+
</rdf:Bag>
|
| 353 |
+
</bqbiol:isVersionOf>
|
| 354 |
+
</rdf:Description>
|
| 355 |
+
|
| 356 |
+
</rdf:RDF>
|
| 357 |
+
</annotation>
|
| 358 |
+
<listOfReactants>
|
| 359 |
+
<speciesReference metaid="_653245" species="MKK"/>
|
| 360 |
+
</listOfReactants>
|
| 361 |
+
<listOfProducts>
|
| 362 |
+
<speciesReference metaid="_653257" species="MKK_P"/>
|
| 363 |
+
</listOfProducts>
|
| 364 |
+
<listOfModifiers>
|
| 365 |
+
<modifierSpeciesReference metaid="_653269" species="MKKK_P"/>
|
| 366 |
+
</listOfModifiers>
|
| 367 |
+
<kineticLaw metaid="_653281">
|
| 368 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 369 |
+
<apply>
|
| 370 |
+
<divide/>
|
| 371 |
+
<apply>
|
| 372 |
+
<times/>
|
| 373 |
+
<ci> uVol </ci>
|
| 374 |
+
<ci> k3 </ci>
|
| 375 |
+
<ci> MKKK_P </ci>
|
| 376 |
+
<ci> MKK </ci>
|
| 377 |
+
</apply>
|
| 378 |
+
<apply>
|
| 379 |
+
<plus/>
|
| 380 |
+
<ci> KK3 </ci>
|
| 381 |
+
<ci> MKK </ci>
|
| 382 |
+
</apply>
|
| 383 |
+
</apply>
|
| 384 |
+
</math>
|
| 385 |
+
<listOfParameters>
|
| 386 |
+
<parameter id="k3" metaid="_001337" value="0.025"/>
|
| 387 |
+
<parameter id="KK3" metaid="_001339" value="15"/>
|
| 388 |
+
</listOfParameters>
|
| 389 |
+
</kineticLaw>
|
| 390 |
+
</reaction>
|
| 391 |
+
<reaction id="J3" metaid="_584695" name="phosphorylation of MAPKK-P" reversible="false">
|
| 392 |
+
<annotation>
|
| 393 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 394 |
+
<rdf:Description rdf:about="#_584695">
|
| 395 |
+
<bqbiol:isHomologTo>
|
| 396 |
+
<rdf:Bag>
|
| 397 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_614"/>
|
| 398 |
+
</rdf:Bag>
|
| 399 |
+
</bqbiol:isHomologTo>
|
| 400 |
+
|
| 401 |
+
<bqbiol:isVersionOf>
|
| 402 |
+
<rdf:Bag>
|
| 403 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.11.25"/>
|
| 404 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000186"/>
|
| 405 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 406 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004709"/>
|
| 407 |
+
</rdf:Bag>
|
| 408 |
+
</bqbiol:isVersionOf>
|
| 409 |
+
</rdf:Description>
|
| 410 |
+
|
| 411 |
+
</rdf:RDF>
|
| 412 |
+
</annotation>
|
| 413 |
+
<listOfReactants>
|
| 414 |
+
<speciesReference metaid="_653293" species="MKK_P"/>
|
| 415 |
+
</listOfReactants>
|
| 416 |
+
<listOfProducts>
|
| 417 |
+
<speciesReference metaid="_653305" species="MKK_PP"/>
|
| 418 |
+
</listOfProducts>
|
| 419 |
+
<listOfModifiers>
|
| 420 |
+
<modifierSpeciesReference metaid="_653317" species="MKKK_P"/>
|
| 421 |
+
</listOfModifiers>
|
| 422 |
+
<kineticLaw metaid="_653329">
|
| 423 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 424 |
+
<apply>
|
| 425 |
+
<divide/>
|
| 426 |
+
<apply>
|
| 427 |
+
<times/>
|
| 428 |
+
<ci> uVol </ci>
|
| 429 |
+
<ci> k4 </ci>
|
| 430 |
+
<ci> MKKK_P </ci>
|
| 431 |
+
<ci> MKK_P </ci>
|
| 432 |
+
</apply>
|
| 433 |
+
<apply>
|
| 434 |
+
<plus/>
|
| 435 |
+
<ci> KK4 </ci>
|
| 436 |
+
<ci> MKK_P </ci>
|
| 437 |
+
</apply>
|
| 438 |
+
</apply>
|
| 439 |
+
</math>
|
| 440 |
+
<listOfParameters>
|
| 441 |
+
<parameter id="k4" metaid="_001341" value="0.025"/>
|
| 442 |
+
<parameter id="KK4" metaid="_001343" value="15"/>
|
| 443 |
+
</listOfParameters>
|
| 444 |
+
</kineticLaw>
|
| 445 |
+
</reaction>
|
| 446 |
+
<reaction id="J4" metaid="_584715" name="dephosphorylation of MAPKK-PP" reversible="false">
|
| 447 |
+
<annotation>
|
| 448 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 449 |
+
<rdf:Description rdf:about="#_584715">
|
| 450 |
+
<bqbiol:isVersionOf>
|
| 451 |
+
<rdf:Bag>
|
| 452 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 453 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 454 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051389"/>
|
| 455 |
+
</rdf:Bag>
|
| 456 |
+
</bqbiol:isVersionOf>
|
| 457 |
+
</rdf:Description>
|
| 458 |
+
|
| 459 |
+
</rdf:RDF>
|
| 460 |
+
</annotation>
|
| 461 |
+
<listOfReactants>
|
| 462 |
+
<speciesReference metaid="_653341" species="MKK_PP"/>
|
| 463 |
+
</listOfReactants>
|
| 464 |
+
<listOfProducts>
|
| 465 |
+
<speciesReference metaid="_653353" species="MKK_P"/>
|
| 466 |
+
</listOfProducts>
|
| 467 |
+
<kineticLaw metaid="_653365">
|
| 468 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 469 |
+
<apply>
|
| 470 |
+
<divide/>
|
| 471 |
+
<apply>
|
| 472 |
+
<times/>
|
| 473 |
+
<ci> uVol </ci>
|
| 474 |
+
<ci> V5 </ci>
|
| 475 |
+
<ci> MKK_PP </ci>
|
| 476 |
+
</apply>
|
| 477 |
+
<apply>
|
| 478 |
+
<plus/>
|
| 479 |
+
<ci> KK5 </ci>
|
| 480 |
+
<ci> MKK_PP </ci>
|
| 481 |
+
</apply>
|
| 482 |
+
</apply>
|
| 483 |
+
</math>
|
| 484 |
+
<listOfParameters>
|
| 485 |
+
<parameter id="V5" metaid="_001345" value="0.75"/>
|
| 486 |
+
<parameter id="KK5" metaid="_001347" value="15"/>
|
| 487 |
+
</listOfParameters>
|
| 488 |
+
</kineticLaw>
|
| 489 |
+
</reaction>
|
| 490 |
+
<reaction id="J5" metaid="_584735" name="dephosphorylation of MAPKK-P" reversible="false">
|
| 491 |
+
<annotation>
|
| 492 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 493 |
+
<rdf:Description rdf:about="#_584735">
|
| 494 |
+
<bqbiol:isVersionOf>
|
| 495 |
+
<rdf:Bag>
|
| 496 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 497 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 498 |
+
</rdf:Bag>
|
| 499 |
+
</bqbiol:isVersionOf>
|
| 500 |
+
</rdf:Description>
|
| 501 |
+
|
| 502 |
+
</rdf:RDF>
|
| 503 |
+
</annotation>
|
| 504 |
+
<listOfReactants>
|
| 505 |
+
<speciesReference metaid="_653377" species="MKK_P"/>
|
| 506 |
+
</listOfReactants>
|
| 507 |
+
<listOfProducts>
|
| 508 |
+
<speciesReference metaid="_653389" species="MKK"/>
|
| 509 |
+
</listOfProducts>
|
| 510 |
+
<kineticLaw metaid="_653402">
|
| 511 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 512 |
+
<apply>
|
| 513 |
+
<divide/>
|
| 514 |
+
<apply>
|
| 515 |
+
<times/>
|
| 516 |
+
<ci> uVol </ci>
|
| 517 |
+
<ci> V6 </ci>
|
| 518 |
+
<ci> MKK_P </ci>
|
| 519 |
+
</apply>
|
| 520 |
+
<apply>
|
| 521 |
+
<plus/>
|
| 522 |
+
<ci> KK6 </ci>
|
| 523 |
+
<ci> MKK_P </ci>
|
| 524 |
+
</apply>
|
| 525 |
+
</apply>
|
| 526 |
+
</math>
|
| 527 |
+
<listOfParameters>
|
| 528 |
+
<parameter id="V6" metaid="_001349" value="0.75"/>
|
| 529 |
+
<parameter id="KK6" metaid="_001351" value="15"/>
|
| 530 |
+
</listOfParameters>
|
| 531 |
+
</kineticLaw>
|
| 532 |
+
</reaction>
|
| 533 |
+
<reaction id="J6" metaid="_584755" name="phosphorylation of MAPK" reversible="false">
|
| 534 |
+
<annotation>
|
| 535 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 536 |
+
<rdf:Description rdf:about="#_584755">
|
| 537 |
+
<bqbiol:hasVersion>
|
| 538 |
+
<rdf:Bag>
|
| 539 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 540 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 541 |
+
</rdf:Bag>
|
| 542 |
+
</bqbiol:hasVersion>
|
| 543 |
+
|
| 544 |
+
<bqbiol:isVersionOf>
|
| 545 |
+
<rdf:Bag>
|
| 546 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 547 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 548 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 549 |
+
</rdf:Bag>
|
| 550 |
+
</bqbiol:isVersionOf>
|
| 551 |
+
</rdf:Description>
|
| 552 |
+
|
| 553 |
+
</rdf:RDF>
|
| 554 |
+
</annotation>
|
| 555 |
+
<listOfReactants>
|
| 556 |
+
<speciesReference metaid="_653414" species="MAPK"/>
|
| 557 |
+
</listOfReactants>
|
| 558 |
+
<listOfProducts>
|
| 559 |
+
<speciesReference metaid="_653426" species="MAPK_P"/>
|
| 560 |
+
</listOfProducts>
|
| 561 |
+
<listOfModifiers>
|
| 562 |
+
<modifierSpeciesReference metaid="_653438" species="MKK_PP"/>
|
| 563 |
+
</listOfModifiers>
|
| 564 |
+
<kineticLaw metaid="_653450">
|
| 565 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 566 |
+
<apply>
|
| 567 |
+
<divide/>
|
| 568 |
+
<apply>
|
| 569 |
+
<times/>
|
| 570 |
+
<ci> uVol </ci>
|
| 571 |
+
<ci> k7 </ci>
|
| 572 |
+
<ci> MKK_PP </ci>
|
| 573 |
+
<ci> MAPK </ci>
|
| 574 |
+
</apply>
|
| 575 |
+
<apply>
|
| 576 |
+
<plus/>
|
| 577 |
+
<ci> KK7 </ci>
|
| 578 |
+
<ci> MAPK </ci>
|
| 579 |
+
</apply>
|
| 580 |
+
</apply>
|
| 581 |
+
</math>
|
| 582 |
+
<listOfParameters>
|
| 583 |
+
<parameter id="k7" metaid="_001353" value="0.025"/>
|
| 584 |
+
<parameter id="KK7" metaid="_001355" value="15"/>
|
| 585 |
+
</listOfParameters>
|
| 586 |
+
</kineticLaw>
|
| 587 |
+
</reaction>
|
| 588 |
+
<reaction id="J7" metaid="_584775" name="phosphorylation of MAPK-P" reversible="false">
|
| 589 |
+
<annotation>
|
| 590 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 591 |
+
<rdf:Description rdf:about="#_584775">
|
| 592 |
+
<bqbiol:hasVersion>
|
| 593 |
+
<rdf:Bag>
|
| 594 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 595 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 596 |
+
</rdf:Bag>
|
| 597 |
+
</bqbiol:hasVersion>
|
| 598 |
+
|
| 599 |
+
<bqbiol:isVersionOf>
|
| 600 |
+
<rdf:Bag>
|
| 601 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 602 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 603 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 604 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000187"/>
|
| 605 |
+
</rdf:Bag>
|
| 606 |
+
</bqbiol:isVersionOf>
|
| 607 |
+
</rdf:Description>
|
| 608 |
+
|
| 609 |
+
</rdf:RDF>
|
| 610 |
+
</annotation>
|
| 611 |
+
<listOfReactants>
|
| 612 |
+
<speciesReference metaid="_653463" species="MAPK_P"/>
|
| 613 |
+
</listOfReactants>
|
| 614 |
+
<listOfProducts>
|
| 615 |
+
<speciesReference metaid="_653475" species="MAPK_PP"/>
|
| 616 |
+
</listOfProducts>
|
| 617 |
+
<listOfModifiers>
|
| 618 |
+
<modifierSpeciesReference metaid="_653487" species="MKK_PP"/>
|
| 619 |
+
</listOfModifiers>
|
| 620 |
+
<kineticLaw metaid="_653499">
|
| 621 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 622 |
+
<apply>
|
| 623 |
+
<divide/>
|
| 624 |
+
<apply>
|
| 625 |
+
<times/>
|
| 626 |
+
<ci> uVol </ci>
|
| 627 |
+
<ci> k8 </ci>
|
| 628 |
+
<ci> MKK_PP </ci>
|
| 629 |
+
<ci> MAPK_P </ci>
|
| 630 |
+
</apply>
|
| 631 |
+
<apply>
|
| 632 |
+
<plus/>
|
| 633 |
+
<ci> KK8 </ci>
|
| 634 |
+
<ci> MAPK_P </ci>
|
| 635 |
+
</apply>
|
| 636 |
+
</apply>
|
| 637 |
+
</math>
|
| 638 |
+
<listOfParameters>
|
| 639 |
+
<parameter id="k8" metaid="_001357" value="0.025"/>
|
| 640 |
+
<parameter id="KK8" metaid="_001359" value="15"/>
|
| 641 |
+
</listOfParameters>
|
| 642 |
+
</kineticLaw>
|
| 643 |
+
</reaction>
|
| 644 |
+
<reaction id="J8" metaid="_584795" name="dephosphorylation of MAPK-PP" reversible="false">
|
| 645 |
+
<annotation>
|
| 646 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 647 |
+
<rdf:Description rdf:about="#_584795">
|
| 648 |
+
<bqbiol:isVersionOf>
|
| 649 |
+
<rdf:Bag>
|
| 650 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 651 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000188"/>
|
| 652 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 653 |
+
</rdf:Bag>
|
| 654 |
+
</bqbiol:isVersionOf>
|
| 655 |
+
</rdf:Description>
|
| 656 |
+
|
| 657 |
+
</rdf:RDF>
|
| 658 |
+
</annotation>
|
| 659 |
+
<listOfReactants>
|
| 660 |
+
<speciesReference metaid="_653511" species="MAPK_PP"/>
|
| 661 |
+
</listOfReactants>
|
| 662 |
+
<listOfProducts>
|
| 663 |
+
<speciesReference metaid="_653523" species="MAPK_P"/>
|
| 664 |
+
</listOfProducts>
|
| 665 |
+
<kineticLaw metaid="_653535">
|
| 666 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 667 |
+
<apply>
|
| 668 |
+
<divide/>
|
| 669 |
+
<apply>
|
| 670 |
+
<times/>
|
| 671 |
+
<ci> uVol </ci>
|
| 672 |
+
<ci> V9 </ci>
|
| 673 |
+
<ci> MAPK_PP </ci>
|
| 674 |
+
</apply>
|
| 675 |
+
<apply>
|
| 676 |
+
<plus/>
|
| 677 |
+
<ci> KK9 </ci>
|
| 678 |
+
<ci> MAPK_PP </ci>
|
| 679 |
+
</apply>
|
| 680 |
+
</apply>
|
| 681 |
+
</math>
|
| 682 |
+
<listOfParameters>
|
| 683 |
+
<parameter id="V9" metaid="_001361" value="0.5"/>
|
| 684 |
+
<parameter id="KK9" metaid="_001363" value="15"/>
|
| 685 |
+
</listOfParameters>
|
| 686 |
+
</kineticLaw>
|
| 687 |
+
</reaction>
|
| 688 |
+
<reaction id="J9" metaid="_584815" name="dephosphorylation of MAPK-P" reversible="false">
|
| 689 |
+
<annotation>
|
| 690 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 691 |
+
<rdf:Description rdf:about="#_584815">
|
| 692 |
+
<bqbiol:isVersionOf>
|
| 693 |
+
<rdf:Bag>
|
| 694 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 695 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 696 |
+
</rdf:Bag>
|
| 697 |
+
</bqbiol:isVersionOf>
|
| 698 |
+
</rdf:Description>
|
| 699 |
+
|
| 700 |
+
</rdf:RDF>
|
| 701 |
+
</annotation>
|
| 702 |
+
<listOfReactants>
|
| 703 |
+
<speciesReference metaid="_653547" species="MAPK_P"/>
|
| 704 |
+
</listOfReactants>
|
| 705 |
+
<listOfProducts>
|
| 706 |
+
<speciesReference metaid="_653559" species="MAPK"/>
|
| 707 |
+
</listOfProducts>
|
| 708 |
+
<kineticLaw metaid="_653571">
|
| 709 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 710 |
+
<apply>
|
| 711 |
+
<divide/>
|
| 712 |
+
<apply>
|
| 713 |
+
<times/>
|
| 714 |
+
<ci> uVol </ci>
|
| 715 |
+
<ci> V10 </ci>
|
| 716 |
+
<ci> MAPK_P </ci>
|
| 717 |
+
</apply>
|
| 718 |
+
<apply>
|
| 719 |
+
<plus/>
|
| 720 |
+
<ci> KK10 </ci>
|
| 721 |
+
<ci> MAPK_P </ci>
|
| 722 |
+
</apply>
|
| 723 |
+
</apply>
|
| 724 |
+
</math>
|
| 725 |
+
<listOfParameters>
|
| 726 |
+
<parameter id="V10" metaid="_001365" value="0.5"/>
|
| 727 |
+
<parameter id="KK10" metaid="_001367" value="15"/>
|
| 728 |
+
</listOfParameters>
|
| 729 |
+
</kineticLaw>
|
| 730 |
+
</reaction>
|
| 731 |
+
</listOfReactions>
|
| 732 |
+
</model>
|
| 733 |
+
</sbml>
|
Data/BIOMD0000000010/Kholodenko2000_conditions.json
ADDED
|
@@ -0,0 +1,74 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"MKKK": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
46.05208726855047,
|
| 7 |
+
96.27610635735368
|
| 8 |
+
],
|
| 9 |
+
"period": 189.5
|
| 10 |
+
},
|
| 11 |
+
"MKKK_P": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
3.7238936426464,
|
| 16 |
+
53.947912731449534
|
| 17 |
+
],
|
| 18 |
+
"period": 189.5
|
| 19 |
+
},
|
| 20 |
+
"MKK": {
|
| 21 |
+
"trajectory_type": 3,
|
| 22 |
+
"trajectory_type_name": "oscillation",
|
| 23 |
+
"bounds": [
|
| 24 |
+
103.63767429900304,
|
| 25 |
+
296.08736608340195
|
| 26 |
+
],
|
| 27 |
+
"period": 190.0
|
| 28 |
+
},
|
| 29 |
+
"MKK_P": {
|
| 30 |
+
"trajectory_type": 3,
|
| 31 |
+
"trajectory_type_name": "oscillation",
|
| 32 |
+
"bounds": [
|
| 33 |
+
3.3659051525695376,
|
| 34 |
+
85.68937162869928
|
| 35 |
+
],
|
| 36 |
+
"period": 190.0
|
| 37 |
+
},
|
| 38 |
+
"MKK_PP": {
|
| 39 |
+
"trajectory_type": 3,
|
| 40 |
+
"trajectory_type_name": "oscillation",
|
| 41 |
+
"bounds": [
|
| 42 |
+
0.5467287640254573,
|
| 43 |
+
116.57912970302178
|
| 44 |
+
],
|
| 45 |
+
"period": 190.0
|
| 46 |
+
},
|
| 47 |
+
"MAPK": {
|
| 48 |
+
"trajectory_type": 3,
|
| 49 |
+
"trajectory_type_name": "oscillation",
|
| 50 |
+
"bounds": [
|
| 51 |
+
0.4366306499181546,
|
| 52 |
+
204.23284915620783
|
| 53 |
+
],
|
| 54 |
+
"period": 190.0
|
| 55 |
+
},
|
| 56 |
+
"MAPK_P": {
|
| 57 |
+
"trajectory_type": 3,
|
| 58 |
+
"trajectory_type_name": "oscillation",
|
| 59 |
+
"bounds": [
|
| 60 |
+
2.9433479589393348,
|
| 61 |
+
76.51427116822963
|
| 62 |
+
],
|
| 63 |
+
"period": 190.0
|
| 64 |
+
},
|
| 65 |
+
"MAPK_PP": {
|
| 66 |
+
"trajectory_type": 3,
|
| 67 |
+
"trajectory_type_name": "oscillation",
|
| 68 |
+
"bounds": [
|
| 69 |
+
35.80441809122079,
|
| 70 |
+
296.62002139114094
|
| 71 |
+
],
|
| 72 |
+
"period": 190.0
|
| 73 |
+
}
|
| 74 |
+
}
|
Data/BIOMD0000000010/initial_conditions.json
ADDED
|
@@ -0,0 +1,13 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"MKKK": 90.08385428882094,
|
| 5 |
+
"MKKK_P": 9.916145711179064,
|
| 6 |
+
"MKK": 144.57213516674292,
|
| 7 |
+
"MKK_P": 85.64791460162257,
|
| 8 |
+
"MKK_PP": 69.77995023163557,
|
| 9 |
+
"MAPK": 1.0520392514669576,
|
| 10 |
+
"MAPK_P": 4.986659513603995,
|
| 11 |
+
"MAPK_PP": 293.9613012349261
|
| 12 |
+
}
|
| 13 |
+
}
|
Data/BIOMD0000000011/Levchenko2000.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000011/Levchenko2000.xml
ADDED
|
@@ -0,0 +1,1780 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
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|
|
|
|
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|
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version4" level="2" metaid="_350618" version="4">
|
| 3 |
+
<model id="MAPK_in_Solution" metaid="_350630" name="Levchenko2000_MAPK_noScaffold">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<h1>MAPK cascade in solution (no scaffold)</h1>
|
| 7 |
+
<table border="0" cellpadding="2" cellspacing="0"> <thead> <tr> <th align="left" bgcolor="#eeeeee" valign="middle">Description</th>
|
| 8 |
+
</tr>
|
| 9 |
+
</thead>
|
| 10 |
+
<tbody> <tr> <td>This model describes a basic 3-
|
| 11 |
+
stage Mitogen Activated Protein Kinase (MAPK)
|
| 12 |
+
cascade in solution. This cascade is typically expressed as RAF=
|
| 13 |
+
=>MEK==>MAPK (alternative forms are K3==>K2==>
|
| 14 |
+
K1 and KKK==>KK==>K)
|
| 15 |
+
. The input signal is RAFK (RAF Kinase)
|
| 16 |
+
and the output signal is MAPKpp (
|
| 17 |
+
doubly phosphorylated form of MAPK)
|
| 18 |
+
. RAFK phosphorylates RAF once to RAFp. RAFp,
|
| 19 |
+
the phosphorylated form of RAF induces two phoshporylations of MEK,
|
| 20 |
+
to MEKp and MEKpp. MEKpp,
|
| 21 |
+
the doubly phosphorylated form of MEK,
|
| 22 |
+
induces two phosphorylations of MAPK to MAPKp and MAPKpp.</td>
|
| 23 |
+
</tr>
|
| 24 |
+
</tbody>
|
| 25 |
+
</table>
|
| 26 |
+
<table border="0" cellpadding="2" cellspacing="0"> <thead> <tr> <th align="left" bgcolor="#eeeeee" valign="middle">Rate constant </th>
|
| 27 |
+
<th align="left" bgcolor="#eeeeee" valign="middle">Reaction</th>
|
| 28 |
+
</tr>
|
| 29 |
+
</thead>
|
| 30 |
+
<tbody> <tr> <td>a10 = 5.</td>
|
| 31 |
+
<td>MAPKPH + MAPKpp -> MAPKppMAPKPH</td>
|
| 32 |
+
</tr>
|
| 33 |
+
<tr> <td>a1 = 1.</td>
|
| 34 |
+
<td>RAF + RAFK -> RAFRAFK</td>
|
| 35 |
+
</tr>
|
| 36 |
+
<tr> <td>a2 = 0.5</td>
|
| 37 |
+
<td>RAFp + RAFPH -> RAFpRAFPH</td>
|
| 38 |
+
</tr>
|
| 39 |
+
<tr> <td>a3 = 3.3</td>
|
| 40 |
+
<td>MEK + RAFp -> MEKRAFp</td>
|
| 41 |
+
</tr>
|
| 42 |
+
<tr> <td>a4 = 10.</td>
|
| 43 |
+
<td>MEKp + MEKPH -> MEKpMEKPH</td>
|
| 44 |
+
</tr>
|
| 45 |
+
<tr> <td>a5 = 3.3</td>
|
| 46 |
+
<td>MEKp + RAFp -> MEKpRAFp</td>
|
| 47 |
+
</tr>
|
| 48 |
+
<tr> <td>a6 = 10.</td>
|
| 49 |
+
<td>MEKPH + MEKpp -> MEKppMEKPH</td>
|
| 50 |
+
</tr>
|
| 51 |
+
<tr> <td>a7 = 20.</td>
|
| 52 |
+
<td>MAPK + MEKpp -> MAPKMEKpp</td>
|
| 53 |
+
</tr>
|
| 54 |
+
<tr> <td>a8 = 5.</td>
|
| 55 |
+
<td>MAPKp + MAPKPH -> MAPKpMAPKPH</td>
|
| 56 |
+
</tr>
|
| 57 |
+
<tr> <td>a9 = 20.</td>
|
| 58 |
+
<td>MAPKp + MEKpp -> MAPKpMEKpp</td>
|
| 59 |
+
</tr>
|
| 60 |
+
<tr> <td>d10 = 0.4</td>
|
| 61 |
+
<td>MAPKppMAPKPH -> MAPKPH + MAPKpp</td>
|
| 62 |
+
</tr>
|
| 63 |
+
<tr> <td>d1 = 0.4</td>
|
| 64 |
+
<td>RAFRAFK -> RAF + RAFK</td>
|
| 65 |
+
</tr>
|
| 66 |
+
<tr> <td>d2 = 0.5</td>
|
| 67 |
+
<td>RAFpRAFPH -> RAFp + RAFPH</td>
|
| 68 |
+
</tr>
|
| 69 |
+
<tr> <td>d3 = 0.42</td>
|
| 70 |
+
<td>MEKRAFp -> MEK + RAFp</td>
|
| 71 |
+
</tr>
|
| 72 |
+
<tr> <td>d4 = 0.8</td>
|
| 73 |
+
<td>MEKpMEKPH -> MEKp + MEKPH</td>
|
| 74 |
+
</tr>
|
| 75 |
+
<tr> <td>d5 = 0.4</td>
|
| 76 |
+
<td>MEKpRAFp -> MEKp + RAFp</td>
|
| 77 |
+
</tr>
|
| 78 |
+
<tr> <td>d6 = 0.8</td>
|
| 79 |
+
<td>MEKppMEKPH -> MEKPH + MEKpp</td>
|
| 80 |
+
</tr>
|
| 81 |
+
<tr> <td>d7 = 0.6</td>
|
| 82 |
+
<td>MAPKMEKpp -> MAPK + MEKpp</td>
|
| 83 |
+
</tr>
|
| 84 |
+
<tr> <td>d8 = 0.4</td>
|
| 85 |
+
<td>MAPKpMAPKPH -> MAPKp + MAPKPH</td>
|
| 86 |
+
</tr>
|
| 87 |
+
<tr> <td>d9 = 0.6</td>
|
| 88 |
+
<td>MAPKpMEKpp -> MAPKp + MEKpp</td>
|
| 89 |
+
</tr>
|
| 90 |
+
<tr> <td>k10 = 0.1</td>
|
| 91 |
+
<td>MAPKppMAPKPH -> MAPKp + MAPKPH</td>
|
| 92 |
+
</tr>
|
| 93 |
+
<tr> <td>k1 = 0.1</td>
|
| 94 |
+
<td>RAFRAFK -> RAFK + RAFp</td>
|
| 95 |
+
</tr>
|
| 96 |
+
<tr> <td>k2 = 0.1</td>
|
| 97 |
+
<td>RAFpRAFPH -> RAF + RAFPH</td>
|
| 98 |
+
</tr>
|
| 99 |
+
<tr> <td>k3 = 0.1</td>
|
| 100 |
+
<td>MEKRAFp -> MEKp + RAFp</td>
|
| 101 |
+
</tr>
|
| 102 |
+
<tr> <td>k4 = 0.1</td>
|
| 103 |
+
<td>MEKpMEKPH -> MEK + MEKPH</td>
|
| 104 |
+
</tr>
|
| 105 |
+
<tr> <td>k5 = 0.1</td>
|
| 106 |
+
<td>MEKpRAFp -> MEKpp + RAFp</td>
|
| 107 |
+
</tr>
|
| 108 |
+
<tr> <td>k6 = 0.1</td>
|
| 109 |
+
<td>MEKppMEKPH -> MEKp + MEKPH</td>
|
| 110 |
+
</tr>
|
| 111 |
+
<tr> <td>k7 = 0.1</td>
|
| 112 |
+
<td>MAPKMEKpp -> MAPKp + MEKpp</td>
|
| 113 |
+
</tr>
|
| 114 |
+
<tr> <td>k8 = 0.1</td>
|
| 115 |
+
<td>MAPKpMAPKPH -> MAPK + MAPKPH</td>
|
| 116 |
+
</tr>
|
| 117 |
+
<tr> <td>k9 = 0.1</td>
|
| 118 |
+
<td>MAPKpMEKpp -> MAPKpp + MEKpp</td>
|
| 119 |
+
</tr>
|
| 120 |
+
</tbody>
|
| 121 |
+
</table>
|
| 122 |
+
<table border="0" cellpadding="2" cellspacing="0"> <thead> <tr> <th align="left" bgcolor="#eeeeee" valign="middle">Variable</th>
|
| 123 |
+
<th align="left" bgcolor="#eeeeee" valign="middle">IC </th>
|
| 124 |
+
<th align="left" bgcolor="#eeeeee" valign="middle">ODE</th>
|
| 125 |
+
</tr>
|
| 126 |
+
</thead>
|
| 127 |
+
<tbody> <tr> <td>MAPK</td>
|
| 128 |
+
<td>0.3</td>
|
| 129 |
+
<td>MAPK'[t] == d7*MAPKMEKpp[t] + k8*MAPKpMAPKPH[t] -
|
| 130 |
+
a7*MAPK[t]*MEKpp[t]</td>
|
| 131 |
+
</tr>
|
| 132 |
+
<tr> <td>MAPKMEKpp</td>
|
| 133 |
+
<td>0</td>
|
| 134 |
+
<td>MAPKMEKpp'[t] == -(d7*MAPKMEKpp[t]) - k7*MAPKMEKpp[t]
|
| 135 |
+
+ a7*MAPK[t]*MEKpp[t]</td>
|
| 136 |
+
</tr>
|
| 137 |
+
<tr> <td>MAPKp</td>
|
| 138 |
+
<td>0</td>
|
| 139 |
+
<td>MAPKp'[t] == k7*MAPKMEKpp[t] - a8*MAPKp[t]*MAPKPH[t]
|
| 140 |
+
+ d8*MAPKpMAPKPH[t] + d9*MAPKpMEKpp[t] + k10*
|
| 141 |
+
MAPKppMAPKPH[t] - a9*MAPKp[t]*MEKpp[t]</td>
|
| 142 |
+
</tr>
|
| 143 |
+
<tr> <td>MAPKPH</td>
|
| 144 |
+
<td>0.3</td>
|
| 145 |
+
<td>MAPKPH'[t] == -(a8*MAPKp[t]*MAPKPH[t]) + d8*MAPKpMAPKPH[
|
| 146 |
+
t] + k8*MAPKpMAPKPH[t] - a10*MAPKPH[t]*MAPKpp[t] +
|
| 147 |
+
d10*MAPKppMAPKPH[t] + k10*MAPKppMAPKPH[t]</td>
|
| 148 |
+
</tr>
|
| 149 |
+
<tr> <td>MAPKpMAPKPH</td>
|
| 150 |
+
<td>0</td>
|
| 151 |
+
<td>MAPKpMAPKPH'[t] == a8*MAPKp[t]*MAPKPH[t] - d8*
|
| 152 |
+
MAPKpMAPKPH[t] - k8*MAPKpMAPKPH[t]</td>
|
| 153 |
+
</tr>
|
| 154 |
+
<tr> <td>MAPKpMEKpp</td>
|
| 155 |
+
<td>0</td>
|
| 156 |
+
<td>MAPKpMEKpp'[t] == -(d9*MAPKpMEKpp[t]) - k9*MAPKpMEKpp[t]
|
| 157 |
+
+ a9*MAPKp[t]*MEKpp[t]</td>
|
| 158 |
+
</tr>
|
| 159 |
+
<tr> <td>MAPKpp</td>
|
| 160 |
+
<td>0</td>
|
| 161 |
+
<td>MAPKpp'[t] == k9*MAPKpMEKpp[t] - a10*MAPKPH[t]*MAPKpp[t]
|
| 162 |
+
+ d10*MAPKppMAPKPH[t]</td>
|
| 163 |
+
</tr>
|
| 164 |
+
<tr> <td>MAPKppMAPKPH</td>
|
| 165 |
+
<td>0</td>
|
| 166 |
+
<td>MAPKppMAPKPH'[t] == a10*MAPKPH[t]*MAPKpp[t] - d10*
|
| 167 |
+
MAPKppMAPKPH[t] - k10*MAPKppMAPKPH[t]</td>
|
| 168 |
+
</tr>
|
| 169 |
+
<tr> <td>MEK</td>
|
| 170 |
+
<td>0.2</td>
|
| 171 |
+
<td>MEK'[t] == k4*MEKpMEKPH[t] + d3*MEKRAFp[t] -
|
| 172 |
+
a3*MEK[t]*RAFp[t]</td>
|
| 173 |
+
</tr>
|
| 174 |
+
<tr> <td>MEKp</td>
|
| 175 |
+
<td>0</td>
|
| 176 |
+
<td>MEKp'[t] == -(a4*MEKp[t]*MEKPH[t]) + d4*MEKpMEKPH[t]
|
| 177 |
+
+ k6*MEKppMEKPH[t] + d5*MEKpRAFp[t] + k3*MEKRAFp[
|
| 178 |
+
t] - a5*MEKp[t]*RAFp[t]</td>
|
| 179 |
+
</tr>
|
| 180 |
+
<tr> <td>MEKPH</td>
|
| 181 |
+
<td>0.2</td>
|
| 182 |
+
<td>MEKPH'[t] == -(a4*MEKp[t]*MEKPH[t]) + d4*MEKpMEKPH[t]
|
| 183 |
+
+ k4*MEKpMEKPH[t] - a6*MEKPH[t]*MEKpp[t] + d6*
|
| 184 |
+
MEKppMEKPH[t] + k6*MEKppMEKPH[t]</td>
|
| 185 |
+
</tr>
|
| 186 |
+
<tr> <td>MEKpMEKPH</td>
|
| 187 |
+
<td>0</td>
|
| 188 |
+
<td>MEKpMEKPH'[t] == a4*MEKp[t]*MEKPH[t] - d4*MEKpMEKPH[t]
|
| 189 |
+
- k4*MEKpMEKPH[t]</td>
|
| 190 |
+
</tr>
|
| 191 |
+
<tr> <td>MEKpp</td>
|
| 192 |
+
<td>0</td>
|
| 193 |
+
<td>MEKpp'[t] == d7*MAPKMEKpp[t] + k7*MAPKMEKpp[t] +
|
| 194 |
+
d9*MAPKpMEKpp[t] + k9*MAPKpMEKpp[t] - a7*MAPK[t]*
|
| 195 |
+
MEKpp[t] - a9*MAPKp[t]*MEKpp[t] - a6*MEKPH[t]*MEKpp[t]
|
| 196 |
+
+ d6*MEKppMEKPH[t] + k5*MEKpRAFp[t]</td>
|
| 197 |
+
</tr>
|
| 198 |
+
<tr> <td>MEKppMEKPH</td>
|
| 199 |
+
<td>0</td>
|
| 200 |
+
<td>MEKppMEKPH'[t] == a6*MEKPH[t]*MEKpp[t] - d6*MEKppMEKPH[
|
| 201 |
+
t] - k6*MEKppMEKPH[t]</td>
|
| 202 |
+
</tr>
|
| 203 |
+
<tr> <td>MEKpRAFp</td>
|
| 204 |
+
<td>0</td>
|
| 205 |
+
<td>MEKpRAFp'[t] == -(d5*MEKpRAFp[t]) - k5*MEKpRAFp[t]
|
| 206 |
+
+ a5*MEKp[t]*RAFp[t]</td>
|
| 207 |
+
</tr>
|
| 208 |
+
<tr> <td>MEKRAFp</td>
|
| 209 |
+
<td>0</td>
|
| 210 |
+
<td>MEKRAFp'[t] == -(d3*MEKRAFp[t]) - k3*MEKRAFp[t] +
|
| 211 |
+
a3*MEK[t]*RAFp[t]</td>
|
| 212 |
+
</tr>
|
| 213 |
+
<tr> <td>RAF</td>
|
| 214 |
+
<td>0.4</td>
|
| 215 |
+
<td>RAF'[t] == -(a1*RAF[t]*RAFK[t]) + k2*RAFpRAFPH[t] +
|
| 216 |
+
d1*RAFRAFK[t]</td>
|
| 217 |
+
</tr>
|
| 218 |
+
<tr> <td>RAFK</td>
|
| 219 |
+
<td>0.1</td>
|
| 220 |
+
<td>RAFK'[t] == -(a1*RAF[t]*RAFK[t]) + d1*RAFRAFK[t] +
|
| 221 |
+
k1*RAFRAFK[t]</td>
|
| 222 |
+
</tr>
|
| 223 |
+
<tr> <td>RAFp</td>
|
| 224 |
+
<td>0</td>
|
| 225 |
+
<td>RAFp'[t] == d5*MEKpRAFp[t] + k5*MEKpRAFp[t] +
|
| 226 |
+
d3*MEKRAFp[t] + k3*MEKRAFp[t] - a3*MEK[t]*RAFp[t]
|
| 227 |
+
- a5*MEKp[t]*RAFp[t] - a2*RAFp[t]*RAFPH[t] + d2*
|
| 228 |
+
RAFpRAFPH[t] + k1*RAFRAFK[t]</td>
|
| 229 |
+
</tr>
|
| 230 |
+
<tr> <td>RAFPH</td>
|
| 231 |
+
<td>0.3</td>
|
| 232 |
+
<td>RAFPH'[t] == -(a2*RAFp[t]*RAFPH[t]) + d2*RAFpRAFPH[t]
|
| 233 |
+
+ k2*RAFpRAFPH[t]</td>
|
| 234 |
+
</tr>
|
| 235 |
+
<tr> <td>RAFpRAFPH</td>
|
| 236 |
+
<td>0</td>
|
| 237 |
+
<td>RAFpRAFPH'[t] == a2*RAFp[t]*RAFPH[t] - d2*RAFpRAFPH[t]
|
| 238 |
+
- k2*RAFpRAFPH[t]</td>
|
| 239 |
+
</tr>
|
| 240 |
+
<tr> <td>RAFRAFK</td>
|
| 241 |
+
<td>0</td>
|
| 242 |
+
<td>RAFRAFK'[t] == a1*RAF[t]*RAFK[t] - d1*RAFRAFK[t] -
|
| 243 |
+
k1*RAFRAFK[t]</td>
|
| 244 |
+
</tr>
|
| 245 |
+
</tbody>
|
| 246 |
+
</table>
|
| 247 |
+
<p>Generated by Cellerator Version 1.4.3 (6-March-2004) using Mathematica 5.0
|
| 248 |
+
for Mac OS X (November 19, 2003), March 6, 2004 12:18:07, using (PowerMac,
|
| 249 |
+
PowerPC,Mac OS X,MacOSX,Darwin)</p>
|
| 250 |
+
<p>author=B.E.Shapiro</p>
|
| 251 |
+
<p>This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2010 The BioModels.net Team. <br/>
|
| 252 |
+
For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>
|
| 253 |
+
. <br/>
|
| 254 |
+
To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a>
|
| 255 |
+
</p>
|
| 256 |
+
</body>
|
| 257 |
+
|
| 258 |
+
</notes>
|
| 259 |
+
<annotation>
|
| 260 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 261 |
+
<rdf:Description rdf:about="#_350630">
|
| 262 |
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<dc:creator>
|
| 263 |
+
<rdf:Bag>
|
| 264 |
+
<rdf:li rdf:parseType="Resource">
|
| 265 |
+
<vCard:N rdf:parseType="Resource">
|
| 266 |
+
<vCard:Family>Shapiro</vCard:Family>
|
| 267 |
+
<vCard:Given>Bruce</vCard:Given>
|
| 268 |
+
</vCard:N>
|
| 269 |
+
<vCard:EMAIL>bshapiro@jpl.nasa.gov</vCard:EMAIL>
|
| 270 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 271 |
+
<vCard:Orgname>NASA Jet Propulsion Laboratory</vCard:Orgname>
|
| 272 |
+
</vCard:ORG>
|
| 273 |
+
</rdf:li>
|
| 274 |
+
</rdf:Bag>
|
| 275 |
+
</dc:creator>
|
| 276 |
+
<dcterms:created rdf:parseType="Resource">
|
| 277 |
+
<dcterms:W3CDTF>2005-02-15T00:12:30Z</dcterms:W3CDTF>
|
| 278 |
+
</dcterms:created>
|
| 279 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 280 |
+
<dcterms:W3CDTF>2013-06-03T13:36:09Z</dcterms:W3CDTF>
|
| 281 |
+
</dcterms:modified>
|
| 282 |
+
<bqmodel:is>
|
| 283 |
+
<rdf:Bag>
|
| 284 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/MODEL6615234250"/>
|
| 285 |
+
</rdf:Bag>
|
| 286 |
+
</bqmodel:is>
|
| 287 |
+
<bqmodel:is>
|
| 288 |
+
<rdf:Bag>
|
| 289 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000011"/>
|
| 290 |
+
</rdf:Bag>
|
| 291 |
+
</bqmodel:is>
|
| 292 |
+
<bqmodel:isDescribedBy>
|
| 293 |
+
<rdf:Bag>
|
| 294 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/10823939"/>
|
| 295 |
+
</rdf:Bag>
|
| 296 |
+
</bqmodel:isDescribedBy>
|
| 297 |
+
<bqmodel:isDerivedFrom>
|
| 298 |
+
<rdf:Bag>
|
| 299 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000009"/>
|
| 300 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/6501300"/>
|
| 301 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/6947258"/>
|
| 302 |
+
</rdf:Bag>
|
| 303 |
+
</bqmodel:isDerivedFrom>
|
| 304 |
+
<bqbiol:isHomologTo>
|
| 305 |
+
<rdf:Bag>
|
| 306 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_634"/>
|
| 307 |
+
</rdf:Bag>
|
| 308 |
+
</bqbiol:isHomologTo>
|
| 309 |
+
<bqbiol:isVersionOf>
|
| 310 |
+
<rdf:Bag>
|
| 311 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000165"/>
|
| 312 |
+
</rdf:Bag>
|
| 313 |
+
</bqbiol:isVersionOf>
|
| 314 |
+
<bqbiol:hasTaxon>
|
| 315 |
+
<rdf:Bag>
|
| 316 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/8355"/>
|
| 317 |
+
</rdf:Bag>
|
| 318 |
+
</bqbiol:hasTaxon>
|
| 319 |
+
<bqbiol:hasProperty>
|
| 320 |
+
<rdf:Bag>
|
| 321 |
+
<rdf:li rdf:resource="http://identifiers.org/mamo/MAMO_0000046"/>
|
| 322 |
+
</rdf:Bag>
|
| 323 |
+
</bqbiol:hasProperty>
|
| 324 |
+
</rdf:Description>
|
| 325 |
+
|
| 326 |
+
|
| 327 |
+
</rdf:RDF>
|
| 328 |
+
</annotation>
|
| 329 |
+
<listOfUnitDefinitions>
|
| 330 |
+
<unitDefinition id="substance" metaid="metaid_0000030" name="micromole">
|
| 331 |
+
<listOfUnits>
|
| 332 |
+
<unit kind="mole" metaid="_8a70cde2_1bca_4245_89b5_c24cf879196d" scale="-6"/>
|
| 333 |
+
</listOfUnits>
|
| 334 |
+
</unitDefinition>
|
| 335 |
+
</listOfUnitDefinitions>
|
| 336 |
+
<listOfCompartments>
|
| 337 |
+
<compartment id="Cytoplasm" metaid="_191248" size="1">
|
| 338 |
+
<annotation>
|
| 339 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 340 |
+
<rdf:Description rdf:about="#_191248">
|
| 341 |
+
<bqbiol:is>
|
| 342 |
+
<rdf:Bag>
|
| 343 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005737"/>
|
| 344 |
+
</rdf:Bag>
|
| 345 |
+
</bqbiol:is>
|
| 346 |
+
</rdf:Description>
|
| 347 |
+
|
| 348 |
+
|
| 349 |
+
</rdf:RDF>
|
| 350 |
+
</annotation>
|
| 351 |
+
</compartment>
|
| 352 |
+
</listOfCompartments>
|
| 353 |
+
<listOfSpecies>
|
| 354 |
+
<species compartment="Cytoplasm" hasOnlySubstanceUnits="true" id="MAPK" initialAmount="0.4" metaid="_191261" name="MAPK">
|
| 355 |
+
<annotation>
|
| 356 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 357 |
+
<rdf:Description rdf:about="#_191261">
|
| 358 |
+
<bqbiol:isVersionOf>
|
| 359 |
+
<rdf:Bag>
|
| 360 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 361 |
+
</rdf:Bag>
|
| 362 |
+
</bqbiol:isVersionOf>
|
| 363 |
+
</rdf:Description>
|
| 364 |
+
|
| 365 |
+
|
| 366 |
+
</rdf:RDF>
|
| 367 |
+
</annotation>
|
| 368 |
+
</species>
|
| 369 |
+
<species compartment="Cytoplasm" hasOnlySubstanceUnits="true" id="MAPKMEKpp" initialAmount="0" metaid="_191281" name="MAPK_MEK-PP">
|
| 370 |
+
<annotation>
|
| 371 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 372 |
+
<rdf:Description rdf:about="#_191281">
|
| 373 |
+
<bqbiol:hasPart>
|
| 374 |
+
<rdf:Bag>
|
| 375 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 376 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q05116"/>
|
| 377 |
+
</rdf:Bag>
|
| 378 |
+
</bqbiol:hasPart>
|
| 379 |
+
</rdf:Description>
|
| 380 |
+
|
| 381 |
+
|
| 382 |
+
</rdf:RDF>
|
| 383 |
+
</annotation>
|
| 384 |
+
</species>
|
| 385 |
+
<species compartment="Cytoplasm" hasOnlySubstanceUnits="true" id="MAPKp" initialAmount="0" metaid="_191301" name="MAPK-P">
|
| 386 |
+
<annotation>
|
| 387 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 388 |
+
<rdf:Description rdf:about="#_191301">
|
| 389 |
+
<bqbiol:isVersionOf>
|
| 390 |
+
<rdf:Bag>
|
| 391 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P26696"/>
|
| 392 |
+
</rdf:Bag>
|
| 393 |
+
</bqbiol:isVersionOf>
|
| 394 |
+
</rdf:Description>
|
| 395 |
+
|
| 396 |
+
|
| 397 |
+
</rdf:RDF>
|
| 398 |
+
</annotation>
|
| 399 |
+
</species>
|
| 400 |
+
<species compartment="Cytoplasm" hasOnlySubstanceUnits="true" id="MAPKPH" initialAmount="0.3" metaid="_191321" name="MAPK phosphatase">
|
| 401 |
+
<annotation>
|
| 402 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 403 |
+
<rdf:Description rdf:about="#_191321">
|
| 404 |
+
<bqbiol:is>
|
| 405 |
+
<rdf:Bag>
|
| 406 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/Q90W58"/>
|
| 407 |
+
</rdf:Bag>
|
| 408 |
+
</bqbiol:is>
|
| 409 |
+
</rdf:Description>
|
| 410 |
+
|
| 411 |
+
|
| 412 |
+
</rdf:RDF>
|
| 413 |
+
</annotation>
|
| 414 |
+
</species>
|
| 415 |
+
<species compartment="Cytoplasm" hasOnlySubstanceUnits="true" id="MAPKpMAPKPH" initialAmount="0" metaid="_191341" name="MAPK-P_MAPKPase">
|
| 416 |
+
<annotation>
|
| 417 |
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|
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|
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|
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|
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|
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|
| 631 |
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|
| 632 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 662 |
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|
| 663 |
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|
| 664 |
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|
| 665 |
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|
| 666 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 678 |
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
| 698 |
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|
| 699 |
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|
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|
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|
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|
| 703 |
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|
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|
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|
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|
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|
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|
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|
| 717 |
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|
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|
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<times/>
|
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<ci> a5 </ci>
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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<times/>
|
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<ci> a6 </ci>
|
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|
| 1250 |
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|
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| 1255 |
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| 1317 |
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<apply>
|
| 1318 |
+
<times/>
|
| 1319 |
+
<ci> k6 </ci>
|
| 1320 |
+
<ci> MEKppMEKPH </ci>
|
| 1321 |
+
</apply>
|
| 1322 |
+
</math>
|
| 1323 |
+
<listOfParameters>
|
| 1324 |
+
<parameter id="k6" metaid="_972069" value="0.1"/>
|
| 1325 |
+
</listOfParameters>
|
| 1326 |
+
</kineticLaw>
|
| 1327 |
+
</reaction>
|
| 1328 |
+
<reaction id="Reaction19" metaid="_192063" name="binding of MAPK and MEK-PP" reversible="false">
|
| 1329 |
+
<annotation>
|
| 1330 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1331 |
+
<rdf:Description rdf:about="#_192063">
|
| 1332 |
+
<bqbiol:isHomologTo>
|
| 1333 |
+
<rdf:Bag>
|
| 1334 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_495"/>
|
| 1335 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1780"/>
|
| 1336 |
+
</rdf:Bag>
|
| 1337 |
+
</bqbiol:isHomologTo>
|
| 1338 |
+
|
| 1339 |
+
<bqbiol:is>
|
| 1340 |
+
<rdf:Bag>
|
| 1341 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1342 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 1343 |
+
</rdf:Bag>
|
| 1344 |
+
</bqbiol:is>
|
| 1345 |
+
</rdf:Description>
|
| 1346 |
+
|
| 1347 |
+
|
| 1348 |
+
</rdf:RDF>
|
| 1349 |
+
</annotation>
|
| 1350 |
+
<listOfReactants>
|
| 1351 |
+
<speciesReference metaid="_15746a2a_a0d8_470f_aa80_e7a19095bfc8" species="MAPK"/>
|
| 1352 |
+
<speciesReference metaid="eb27fc68_9837_4e12_996a_cb26ab997ca8" species="MEKpp"/>
|
| 1353 |
+
</listOfReactants>
|
| 1354 |
+
<listOfProducts>
|
| 1355 |
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<speciesReference metaid="_9a07be9f_b2dd_4b5c_89ef_f0dccf7c4aeb" species="MAPKMEKpp"/>
|
| 1356 |
+
</listOfProducts>
|
| 1357 |
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<kineticLaw metaid="e8251e72_35b0_4f47_be5d_23b333fdbf23">
|
| 1358 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1359 |
+
<apply>
|
| 1360 |
+
<times/>
|
| 1361 |
+
<ci> a7 </ci>
|
| 1362 |
+
<ci> MAPK </ci>
|
| 1363 |
+
<ci> MEKpp </ci>
|
| 1364 |
+
</apply>
|
| 1365 |
+
</math>
|
| 1366 |
+
<listOfParameters>
|
| 1367 |
+
<parameter id="a7" metaid="_972071" value="20"/>
|
| 1368 |
+
</listOfParameters>
|
| 1369 |
+
</kineticLaw>
|
| 1370 |
+
</reaction>
|
| 1371 |
+
<reaction id="Reaction20" metaid="_192083" name="dissociation of MAPK_MEK-PP" reversible="false">
|
| 1372 |
+
<annotation>
|
| 1373 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1374 |
+
<rdf:Description rdf:about="#_192083">
|
| 1375 |
+
<bqbiol:isVersionOf>
|
| 1376 |
+
<rdf:Bag>
|
| 1377 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0043241"/>
|
| 1378 |
+
</rdf:Bag>
|
| 1379 |
+
</bqbiol:isVersionOf>
|
| 1380 |
+
</rdf:Description>
|
| 1381 |
+
|
| 1382 |
+
|
| 1383 |
+
</rdf:RDF>
|
| 1384 |
+
</annotation>
|
| 1385 |
+
<listOfReactants>
|
| 1386 |
+
<speciesReference metaid="a98a6414_1c44_4051_9ff5_6aa6ffb9dd76" species="MAPKMEKpp"/>
|
| 1387 |
+
</listOfReactants>
|
| 1388 |
+
<listOfProducts>
|
| 1389 |
+
<speciesReference metaid="_76a756c1_9b69_4295_ad1d_54d2ccf40f4f" species="MAPK"/>
|
| 1390 |
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<speciesReference metaid="c23c39e7_8eee_45d0_88e1_5c27e8c1ab19" species="MEKpp"/>
|
| 1391 |
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</listOfProducts>
|
| 1392 |
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<kineticLaw metaid="_90ab6137_7d0b_4ed0_b99a_9c4fe425b503">
|
| 1393 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1394 |
+
<apply>
|
| 1395 |
+
<times/>
|
| 1396 |
+
<ci> d7 </ci>
|
| 1397 |
+
<ci> MAPKMEKpp </ci>
|
| 1398 |
+
</apply>
|
| 1399 |
+
</math>
|
| 1400 |
+
<listOfParameters>
|
| 1401 |
+
<parameter id="d7" metaid="_972073" value="0.6"/>
|
| 1402 |
+
</listOfParameters>
|
| 1403 |
+
</kineticLaw>
|
| 1404 |
+
</reaction>
|
| 1405 |
+
<reaction id="Reaction21" metaid="_192102" name="phosphorylation of MAPK" reversible="false">
|
| 1406 |
+
<annotation>
|
| 1407 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1408 |
+
<rdf:Description rdf:about="#_192102">
|
| 1409 |
+
<bqbiol:isHomologTo>
|
| 1410 |
+
<rdf:Bag>
|
| 1411 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 1412 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 1413 |
+
</rdf:Bag>
|
| 1414 |
+
</bqbiol:isHomologTo>
|
| 1415 |
+
|
| 1416 |
+
<bqbiol:isVersionOf>
|
| 1417 |
+
<rdf:Bag>
|
| 1418 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 1419 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 1420 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 1421 |
+
</rdf:Bag>
|
| 1422 |
+
</bqbiol:isVersionOf>
|
| 1423 |
+
</rdf:Description>
|
| 1424 |
+
|
| 1425 |
+
|
| 1426 |
+
</rdf:RDF>
|
| 1427 |
+
</annotation>
|
| 1428 |
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<listOfReactants>
|
| 1429 |
+
<speciesReference metaid="_8106062d_5d4f_4a6f_9112_ec383728cdc3" species="MAPKMEKpp"/>
|
| 1430 |
+
</listOfReactants>
|
| 1431 |
+
<listOfProducts>
|
| 1432 |
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<speciesReference metaid="_65bdcf07_bd09_4843_bb9c_190d451a0657" species="MAPKp"/>
|
| 1433 |
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<speciesReference metaid="_12e24e20_6562_4c4b_9d25_456fcbdf5e8a" species="MEKpp"/>
|
| 1434 |
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</listOfProducts>
|
| 1435 |
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<kineticLaw metaid="_7208daaf_abec_4d1a_af3a_70aebb4cebb6">
|
| 1436 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1437 |
+
<apply>
|
| 1438 |
+
<times/>
|
| 1439 |
+
<ci> k7 </ci>
|
| 1440 |
+
<ci> MAPKMEKpp </ci>
|
| 1441 |
+
</apply>
|
| 1442 |
+
</math>
|
| 1443 |
+
<listOfParameters>
|
| 1444 |
+
<parameter id="k7" metaid="_972075" value="0.1"/>
|
| 1445 |
+
</listOfParameters>
|
| 1446 |
+
</kineticLaw>
|
| 1447 |
+
</reaction>
|
| 1448 |
+
<reaction id="Reaction22" metaid="_192122" name="binding of MAPK-P and MAPK phosphatase" reversible="false">
|
| 1449 |
+
<annotation>
|
| 1450 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1451 |
+
<rdf:Description rdf:about="#_192122">
|
| 1452 |
+
<bqbiol:isVersionOf>
|
| 1453 |
+
<rdf:Bag>
|
| 1454 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1455 |
+
</rdf:Bag>
|
| 1456 |
+
</bqbiol:isVersionOf>
|
| 1457 |
+
</rdf:Description>
|
| 1458 |
+
|
| 1459 |
+
|
| 1460 |
+
</rdf:RDF>
|
| 1461 |
+
</annotation>
|
| 1462 |
+
<listOfReactants>
|
| 1463 |
+
<speciesReference metaid="fd39b9fa_6c90_4a82_a283_0676d9e8a39f" species="MAPKp"/>
|
| 1464 |
+
<speciesReference metaid="_482d3fbe_023e_4339_ba5d_16420b52191b" species="MAPKPH"/>
|
| 1465 |
+
</listOfReactants>
|
| 1466 |
+
<listOfProducts>
|
| 1467 |
+
<speciesReference metaid="_899522a9_ca1e_4d99_b7f0_bcc1621cd6c4" species="MAPKpMAPKPH"/>
|
| 1468 |
+
</listOfProducts>
|
| 1469 |
+
<kineticLaw metaid="a1136704_bfb0_425d_95b0_9778c446e62a">
|
| 1470 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1471 |
+
<apply>
|
| 1472 |
+
<times/>
|
| 1473 |
+
<ci> a8 </ci>
|
| 1474 |
+
<ci> MAPKp </ci>
|
| 1475 |
+
<ci> MAPKPH </ci>
|
| 1476 |
+
</apply>
|
| 1477 |
+
</math>
|
| 1478 |
+
<listOfParameters>
|
| 1479 |
+
<parameter id="a8" metaid="_972077" value="5"/>
|
| 1480 |
+
</listOfParameters>
|
| 1481 |
+
</kineticLaw>
|
| 1482 |
+
</reaction>
|
| 1483 |
+
<reaction id="Reaction23" metaid="_192142" name="dissociation of MAPK-P_MAPKPase" reversible="false">
|
| 1484 |
+
<annotation>
|
| 1485 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1486 |
+
<rdf:Description rdf:about="#_192142">
|
| 1487 |
+
<bqbiol:isVersionOf>
|
| 1488 |
+
<rdf:Bag>
|
| 1489 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0043241"/>
|
| 1490 |
+
</rdf:Bag>
|
| 1491 |
+
</bqbiol:isVersionOf>
|
| 1492 |
+
</rdf:Description>
|
| 1493 |
+
|
| 1494 |
+
|
| 1495 |
+
</rdf:RDF>
|
| 1496 |
+
</annotation>
|
| 1497 |
+
<listOfReactants>
|
| 1498 |
+
<speciesReference metaid="_13d29e4d_cdb0_4759_b52a_b3c3f06a5b6d" species="MAPKpMAPKPH"/>
|
| 1499 |
+
</listOfReactants>
|
| 1500 |
+
<listOfProducts>
|
| 1501 |
+
<speciesReference metaid="_4ca6c421_0ed5_4b91_9a97_086ee4fdb771" species="MAPKp"/>
|
| 1502 |
+
<speciesReference metaid="be93d9bc_9f9b_4e7c_b009_44abf972e709" species="MAPKPH"/>
|
| 1503 |
+
</listOfProducts>
|
| 1504 |
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<kineticLaw metaid="_17133747_8da3_422d_8f84_200b14ddb39d">
|
| 1505 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1506 |
+
<apply>
|
| 1507 |
+
<times/>
|
| 1508 |
+
<ci> d8 </ci>
|
| 1509 |
+
<ci> MAPKpMAPKPH </ci>
|
| 1510 |
+
</apply>
|
| 1511 |
+
</math>
|
| 1512 |
+
<listOfParameters>
|
| 1513 |
+
<parameter id="d8" metaid="_972079" value="0.4"/>
|
| 1514 |
+
</listOfParameters>
|
| 1515 |
+
</kineticLaw>
|
| 1516 |
+
</reaction>
|
| 1517 |
+
<reaction id="Reaction24" metaid="_192162" name="dephosphorylation of MAPK-P" reversible="false">
|
| 1518 |
+
<annotation>
|
| 1519 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1520 |
+
<rdf:Description rdf:about="#_192162">
|
| 1521 |
+
<bqbiol:isVersionOf>
|
| 1522 |
+
<rdf:Bag>
|
| 1523 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 1524 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 1525 |
+
</rdf:Bag>
|
| 1526 |
+
</bqbiol:isVersionOf>
|
| 1527 |
+
</rdf:Description>
|
| 1528 |
+
|
| 1529 |
+
|
| 1530 |
+
</rdf:RDF>
|
| 1531 |
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</annotation>
|
| 1532 |
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<listOfReactants>
|
| 1533 |
+
<speciesReference metaid="fa9eb5a3_ff62_4991_adf4_7756c3571836" species="MAPKpMAPKPH"/>
|
| 1534 |
+
</listOfReactants>
|
| 1535 |
+
<listOfProducts>
|
| 1536 |
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<speciesReference metaid="_35792aaa_8124_4fca_8915_c6eb4f8aa31c" species="MAPK"/>
|
| 1537 |
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<speciesReference metaid="af2512de_407f_4da4_9ed1_dd84745c0937" species="MAPKPH"/>
|
| 1538 |
+
</listOfProducts>
|
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|
| 1540 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1541 |
+
<apply>
|
| 1542 |
+
<times/>
|
| 1543 |
+
<ci> k8 </ci>
|
| 1544 |
+
<ci> MAPKpMAPKPH </ci>
|
| 1545 |
+
</apply>
|
| 1546 |
+
</math>
|
| 1547 |
+
<listOfParameters>
|
| 1548 |
+
<parameter id="k8" metaid="_972081" value="0.1"/>
|
| 1549 |
+
</listOfParameters>
|
| 1550 |
+
</kineticLaw>
|
| 1551 |
+
</reaction>
|
| 1552 |
+
<reaction id="Reaction25" metaid="_192182" name="binding of MAPK-P and MEK-PP" reversible="false">
|
| 1553 |
+
<annotation>
|
| 1554 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1555 |
+
<rdf:Description rdf:about="#_192182">
|
| 1556 |
+
<bqbiol:isHomologTo>
|
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+
<rdf:Bag>
|
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+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_495"/>
|
| 1559 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1780"/>
|
| 1560 |
+
</rdf:Bag>
|
| 1561 |
+
</bqbiol:isHomologTo>
|
| 1562 |
+
|
| 1563 |
+
<bqbiol:isVersionOf>
|
| 1564 |
+
<rdf:Bag>
|
| 1565 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1566 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0031434"/>
|
| 1567 |
+
</rdf:Bag>
|
| 1568 |
+
</bqbiol:isVersionOf>
|
| 1569 |
+
</rdf:Description>
|
| 1570 |
+
|
| 1571 |
+
|
| 1572 |
+
</rdf:RDF>
|
| 1573 |
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|
| 1574 |
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<listOfReactants>
|
| 1575 |
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<speciesReference metaid="_4c8cdcc8_81f2_4769_9ff5_4dfe9018b263" species="MAPKp"/>
|
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<speciesReference metaid="_1df91187_f25b_4db1_867f_16980e077efd" species="MEKpp"/>
|
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|
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<listOfProducts>
|
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<speciesReference metaid="_897eefeb_6f1f_4083_a689_50771f166cb3" species="MAPKpMEKpp"/>
|
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|
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|
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
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+
<apply>
|
| 1584 |
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<times/>
|
| 1585 |
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<ci> a9 </ci>
|
| 1586 |
+
<ci> MAPKp </ci>
|
| 1587 |
+
<ci> MEKpp </ci>
|
| 1588 |
+
</apply>
|
| 1589 |
+
</math>
|
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<listOfParameters>
|
| 1591 |
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<parameter id="a9" metaid="_972083" value="20"/>
|
| 1592 |
+
</listOfParameters>
|
| 1593 |
+
</kineticLaw>
|
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+
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|
| 1595 |
+
<reaction id="Reaction26" metaid="_192203" name="dissociation of MAPK-P_MEK-PP" reversible="false">
|
| 1596 |
+
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|
| 1597 |
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|
| 1598 |
+
<rdf:Description rdf:about="#_192203">
|
| 1599 |
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<bqbiol:isVersionOf>
|
| 1600 |
+
<rdf:Bag>
|
| 1601 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0043241"/>
|
| 1602 |
+
</rdf:Bag>
|
| 1603 |
+
</bqbiol:isVersionOf>
|
| 1604 |
+
</rdf:Description>
|
| 1605 |
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|
| 1606 |
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|
| 1607 |
+
</rdf:RDF>
|
| 1608 |
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|
| 1609 |
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<listOfReactants>
|
| 1610 |
+
<speciesReference metaid="_0fc1497b_c76b_4900_9655_80a7d6470eb3" species="MAPKpMEKpp"/>
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| 1611 |
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<listOfProducts>
|
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<speciesReference metaid="_0e9b0421_2a6a_429e_ad80_3469882ac6aa" species="MAPKp"/>
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<speciesReference metaid="_8577ea4e_2644_4023_b39b_6e6c4aeded3e" species="MEKpp"/>
|
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|
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| 1618 |
+
<apply>
|
| 1619 |
+
<times/>
|
| 1620 |
+
<ci> d9 </ci>
|
| 1621 |
+
<ci> MAPKpMEKpp </ci>
|
| 1622 |
+
</apply>
|
| 1623 |
+
</math>
|
| 1624 |
+
<listOfParameters>
|
| 1625 |
+
<parameter id="d9" metaid="_972085" value="0.6"/>
|
| 1626 |
+
</listOfParameters>
|
| 1627 |
+
</kineticLaw>
|
| 1628 |
+
</reaction>
|
| 1629 |
+
<reaction id="Reaction27" metaid="_192223" name="phosphorylation of MAPK-P" reversible="false">
|
| 1630 |
+
<annotation>
|
| 1631 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1632 |
+
<rdf:Description rdf:about="#_192223">
|
| 1633 |
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<bqbiol:isVersionOf>
|
| 1634 |
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<rdf:Bag>
|
| 1635 |
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<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.12.2"/>
|
| 1636 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000187"/>
|
| 1637 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006468"/>
|
| 1638 |
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<rdf:li rdf:resource="http://identifiers.org/go/GO:0004708"/>
|
| 1639 |
+
</rdf:Bag>
|
| 1640 |
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</bqbiol:isVersionOf>
|
| 1641 |
+
|
| 1642 |
+
<bqbiol:isHomologTo>
|
| 1643 |
+
<rdf:Bag>
|
| 1644 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_136"/>
|
| 1645 |
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<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2247"/>
|
| 1646 |
+
</rdf:Bag>
|
| 1647 |
+
</bqbiol:isHomologTo>
|
| 1648 |
+
</rdf:Description>
|
| 1649 |
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|
| 1650 |
+
|
| 1651 |
+
</rdf:RDF>
|
| 1652 |
+
</annotation>
|
| 1653 |
+
<listOfReactants>
|
| 1654 |
+
<speciesReference metaid="a4556bf5_9cc7_4f6d_b2df_62aa6027f691" species="MAPKpMEKpp"/>
|
| 1655 |
+
</listOfReactants>
|
| 1656 |
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<listOfProducts>
|
| 1657 |
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<speciesReference metaid="_1a541711_e8d4_4ae4_833f_599bb0dd8f16" species="MAPKpp"/>
|
| 1658 |
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<speciesReference metaid="cbc099ed_dfbc_42d5_a5f2_1df1f065444c" species="MEKpp"/>
|
| 1659 |
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</listOfProducts>
|
| 1660 |
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<kineticLaw metaid="_468de039_8381_4b45_b096_776869b5e7b4">
|
| 1661 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1662 |
+
<apply>
|
| 1663 |
+
<times/>
|
| 1664 |
+
<ci> k9 </ci>
|
| 1665 |
+
<ci> MAPKpMEKpp </ci>
|
| 1666 |
+
</apply>
|
| 1667 |
+
</math>
|
| 1668 |
+
<listOfParameters>
|
| 1669 |
+
<parameter id="k9" metaid="_972087" value="0.1"/>
|
| 1670 |
+
</listOfParameters>
|
| 1671 |
+
</kineticLaw>
|
| 1672 |
+
</reaction>
|
| 1673 |
+
<reaction id="Reaction28" metaid="_192243" name="binding of MAPK-PP and MAPK phosphatase" reversible="false">
|
| 1674 |
+
<annotation>
|
| 1675 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1676 |
+
<rdf:Description rdf:about="#_192243">
|
| 1677 |
+
<bqbiol:isVersionOf>
|
| 1678 |
+
<rdf:Bag>
|
| 1679 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051019"/>
|
| 1680 |
+
</rdf:Bag>
|
| 1681 |
+
</bqbiol:isVersionOf>
|
| 1682 |
+
</rdf:Description>
|
| 1683 |
+
|
| 1684 |
+
|
| 1685 |
+
</rdf:RDF>
|
| 1686 |
+
</annotation>
|
| 1687 |
+
<listOfReactants>
|
| 1688 |
+
<speciesReference metaid="_3fa5c6d3_438b_4e36_90e1_42175153d4cf" species="MAPKPH"/>
|
| 1689 |
+
<speciesReference metaid="_0f809334_a7dd_4376_af7a_1ca8fd21b03c" species="MAPKpp"/>
|
| 1690 |
+
</listOfReactants>
|
| 1691 |
+
<listOfProducts>
|
| 1692 |
+
<speciesReference metaid="e01c2e92_69dc_46e1_a3aa_88657b0e3ccb" species="MAPKppMAPKPH"/>
|
| 1693 |
+
</listOfProducts>
|
| 1694 |
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<kineticLaw metaid="d3dd457b_3c33_44c8_bbcf_a800c44d38c2">
|
| 1695 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1696 |
+
<apply>
|
| 1697 |
+
<times/>
|
| 1698 |
+
<ci> a10 </ci>
|
| 1699 |
+
<ci> MAPKPH </ci>
|
| 1700 |
+
<ci> MAPKpp </ci>
|
| 1701 |
+
</apply>
|
| 1702 |
+
</math>
|
| 1703 |
+
<listOfParameters>
|
| 1704 |
+
<parameter id="a10" metaid="_972089" value="5"/>
|
| 1705 |
+
</listOfParameters>
|
| 1706 |
+
</kineticLaw>
|
| 1707 |
+
</reaction>
|
| 1708 |
+
<reaction id="Reaction29" metaid="_192262" name="dissociation of MAPK-PP_MAPKPase" reversible="false">
|
| 1709 |
+
<annotation>
|
| 1710 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1711 |
+
<rdf:Description rdf:about="#_192262">
|
| 1712 |
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<bqbiol:isVersionOf>
|
| 1713 |
+
<rdf:Bag>
|
| 1714 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0043241"/>
|
| 1715 |
+
</rdf:Bag>
|
| 1716 |
+
</bqbiol:isVersionOf>
|
| 1717 |
+
</rdf:Description>
|
| 1718 |
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|
| 1719 |
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|
| 1720 |
+
</rdf:RDF>
|
| 1721 |
+
</annotation>
|
| 1722 |
+
<listOfReactants>
|
| 1723 |
+
<speciesReference metaid="_07eb2587_6ee8_4658_8151_f664e2f3b08f" species="MAPKppMAPKPH"/>
|
| 1724 |
+
</listOfReactants>
|
| 1725 |
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<listOfProducts>
|
| 1726 |
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<speciesReference metaid="_2fe6bebc_9e69_49ee_a025_3f3244778f2a" species="MAPKPH"/>
|
| 1727 |
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<speciesReference metaid="c01fe4e9_ff2b_4975_a93f_6c1b60eaa720" species="MAPKpp"/>
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| 1728 |
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</listOfProducts>
|
| 1729 |
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<kineticLaw metaid="_78164f9b_ca1d_49fa_9a35_c6328dc0f778">
|
| 1730 |
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<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1731 |
+
<apply>
|
| 1732 |
+
<times/>
|
| 1733 |
+
<ci> d10 </ci>
|
| 1734 |
+
<ci> MAPKppMAPKPH </ci>
|
| 1735 |
+
</apply>
|
| 1736 |
+
</math>
|
| 1737 |
+
<listOfParameters>
|
| 1738 |
+
<parameter id="d10" metaid="_972091" value="0.4"/>
|
| 1739 |
+
</listOfParameters>
|
| 1740 |
+
</kineticLaw>
|
| 1741 |
+
</reaction>
|
| 1742 |
+
<reaction id="Reaction30" metaid="_192283" name="dephosphorylation of MAPK-PP" reversible="false">
|
| 1743 |
+
<annotation>
|
| 1744 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1745 |
+
<rdf:Description rdf:about="#_192283">
|
| 1746 |
+
<bqbiol:isVersionOf>
|
| 1747 |
+
<rdf:Bag>
|
| 1748 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.16"/>
|
| 1749 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006470"/>
|
| 1750 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0000188"/>
|
| 1751 |
+
</rdf:Bag>
|
| 1752 |
+
</bqbiol:isVersionOf>
|
| 1753 |
+
</rdf:Description>
|
| 1754 |
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|
| 1755 |
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|
| 1756 |
+
</rdf:RDF>
|
| 1757 |
+
</annotation>
|
| 1758 |
+
<listOfReactants>
|
| 1759 |
+
<speciesReference metaid="_2aeba255_b065_44c3_8ed2_e74c59ee90ce" species="MAPKppMAPKPH"/>
|
| 1760 |
+
</listOfReactants>
|
| 1761 |
+
<listOfProducts>
|
| 1762 |
+
<speciesReference metaid="_6d47de5a_dc61_43f0_9711_57d53e5082c4" species="MAPKp"/>
|
| 1763 |
+
<speciesReference metaid="f4be023a_0c16_4d16_aaeb_d2fc0545a1ad" species="MAPKPH"/>
|
| 1764 |
+
</listOfProducts>
|
| 1765 |
+
<kineticLaw metaid="fd0736ff_bc5a_413b_b05a_52181401f973">
|
| 1766 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1767 |
+
<apply>
|
| 1768 |
+
<times/>
|
| 1769 |
+
<ci> k10 </ci>
|
| 1770 |
+
<ci> MAPKppMAPKPH </ci>
|
| 1771 |
+
</apply>
|
| 1772 |
+
</math>
|
| 1773 |
+
<listOfParameters>
|
| 1774 |
+
<parameter id="k10" metaid="_972093" value="0.1"/>
|
| 1775 |
+
</listOfParameters>
|
| 1776 |
+
</kineticLaw>
|
| 1777 |
+
</reaction>
|
| 1778 |
+
</listOfReactions>
|
| 1779 |
+
</model>
|
| 1780 |
+
</sbml>
|
Data/BIOMD0000000011/Levchenko2000_conditions.json
ADDED
|
@@ -0,0 +1,200 @@
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|
|
|
|
|
|
|
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|
|
|
|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"MAPK": {
|
| 3 |
+
"trajectory_type": 2,
|
| 4 |
+
"trajectory_type_name": "dec_stable",
|
| 5 |
+
"bounds": [
|
| 6 |
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|
| 7 |
+
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|
| 8 |
+
],
|
| 9 |
+
"period": 0.0
|
| 10 |
+
},
|
| 11 |
+
"MAPKMEKpp": {
|
| 12 |
+
"trajectory_type": 1,
|
| 13 |
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"trajectory_type_name": "inc_stable",
|
| 14 |
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"bounds": [
|
| 15 |
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0.0,
|
| 16 |
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|
| 17 |
+
],
|
| 18 |
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"period": 0.0
|
| 19 |
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},
|
| 20 |
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"MAPKp": {
|
| 21 |
+
"trajectory_type": 1,
|
| 22 |
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"trajectory_type_name": "inc_stable",
|
| 23 |
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"bounds": [
|
| 24 |
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0.0,
|
| 25 |
+
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|
| 26 |
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],
|
| 27 |
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"period": 0.0
|
| 28 |
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},
|
| 29 |
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"MAPKPH": {
|
| 30 |
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"trajectory_type": 2,
|
| 31 |
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"trajectory_type_name": "dec_stable",
|
| 32 |
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"bounds": [
|
| 33 |
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|
| 34 |
+
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|
| 35 |
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],
|
| 36 |
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"period": 0.0
|
| 37 |
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},
|
| 38 |
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"MAPKpMAPKPH": {
|
| 39 |
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"trajectory_type": 1,
|
| 40 |
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"trajectory_type_name": "inc_stable",
|
| 41 |
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"bounds": [
|
| 42 |
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0.0,
|
| 43 |
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|
| 44 |
+
],
|
| 45 |
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"period": 0.0
|
| 46 |
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},
|
| 47 |
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"MAPKpMEKpp": {
|
| 48 |
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"trajectory_type": 1,
|
| 49 |
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"trajectory_type_name": "inc_stable",
|
| 50 |
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"bounds": [
|
| 51 |
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0.0,
|
| 52 |
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|
| 53 |
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],
|
| 54 |
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"period": 0.0
|
| 55 |
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},
|
| 56 |
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"MAPKpp": {
|
| 57 |
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"trajectory_type": 1,
|
| 58 |
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"trajectory_type_name": "inc_stable",
|
| 59 |
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"bounds": [
|
| 60 |
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0.0,
|
| 61 |
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|
| 62 |
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],
|
| 63 |
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"period": 0.0
|
| 64 |
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},
|
| 65 |
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"MAPKppMAPKPH": {
|
| 66 |
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"trajectory_type": 1,
|
| 67 |
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"trajectory_type_name": "inc_stable",
|
| 68 |
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"bounds": [
|
| 69 |
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0.0,
|
| 70 |
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|
| 71 |
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],
|
| 72 |
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"period": 0.0
|
| 73 |
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},
|
| 74 |
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"MEK": {
|
| 75 |
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"trajectory_type": 2,
|
| 76 |
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"trajectory_type_name": "dec_stable",
|
| 77 |
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"bounds": [
|
| 78 |
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|
| 79 |
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0.2
|
| 80 |
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],
|
| 81 |
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"period": 0.0
|
| 82 |
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},
|
| 83 |
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"MEKp": {
|
| 84 |
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"trajectory_type": 1,
|
| 85 |
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"trajectory_type_name": "inc_stable",
|
| 86 |
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"bounds": [
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| 87 |
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|
| 88 |
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|
| 89 |
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],
|
| 90 |
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"period": 0.0
|
| 91 |
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},
|
| 92 |
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"MEKPH": {
|
| 93 |
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|
| 94 |
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"trajectory_type_name": "dec_stable",
|
| 95 |
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"bounds": [
|
| 96 |
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|
| 97 |
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|
| 98 |
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],
|
| 99 |
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"period": 0.0
|
| 100 |
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},
|
| 101 |
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"MEKpMEKPH": {
|
| 102 |
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| 200 |
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|
Data/BIOMD0000000011/initial_conditions.json
ADDED
|
@@ -0,0 +1,27 @@
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| 1 |
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{
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| 2 |
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| 26 |
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| 27 |
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|
Data/BIOMD0000000012/Elowitz2000.csv
ADDED
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@@ -0,0 +1,513 @@
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| 1 |
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time,PX,PY,PZ,X,Y,Z
|
| 2 |
+
0.0,0.0,0.0,0.0,0.0,20.0,0.0
|
| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 7 |
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| 8 |
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| 9 |
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|
| 10 |
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|
| 11 |
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|
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Data/BIOMD0000000012/Elowitz2000.xml
ADDED
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2/version3" level="2" metaid="_153818" version="3">
|
| 3 |
+
<model id="BIOMD0000000012" metaid="_000001" name="Elowitz2000 - Repressilator">
|
| 4 |
+
<notes>
|
| 5 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 6 |
+
<div class="dc:title">Elowitz2000 - Repressilator</div>
|
| 7 |
+
<div class="dc:description">
|
| 8 |
+
<p>This model describes the deterministic version of the repressilator system.</p>
|
| 9 |
+
<p>The authors of this model (see reference) use three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network that they called the repressilator. The model system was induced in Escherichia coli.</p>
|
| 10 |
+
<p>In this system, LacI (variable X is the mRNA, variable PX is the protein) inhibits the tetracycline-resistance transposon tetR (Y, PY describe mRNA and protein). Protein tetR inhibits the gene Cl from phage Lambda (Z, PZ: mRNA, protein),and protein Cl inhibits lacI expression. With the appropriate parameter values this system oscillates.</p>
|
| 11 |
+
</div>
|
| 12 |
+
<div class="dc:bibliographicCitation">
|
| 13 |
+
<p>This model is described in the article:</p>
|
| 14 |
+
<div class="bibo:title">
|
| 15 |
+
<a href="http://identifiers.org/pubmed/10659856" title="Access to this publication">A synthetic oscillatory network of transcriptional regulators.</a>
|
| 16 |
+
</div>
|
| 17 |
+
<div class="bibo:authorList">Elowitz MB, Leibler S.</div>
|
| 18 |
+
<div class="bibo:Journal">Nature. 2000 Jan; 403(6767):335-338</div>
|
| 19 |
+
<p>Abstract:</p>
|
| 20 |
+
<div class="bibo:abstract">
|
| 21 |
+
<p>Networks of interacting biomolecules carry out many essential functions in living cells, but the 'design principles' underlying the functioning of such intracellular networks remain poorly understood, despite intensive efforts including quantitative analysis of relatively simple systems. Here we present a complementary approach to this problem: the design and construction of a synthetic network to implement a particular function. We used three transcriptional repressor systems that are not part of any natural biological clock to build an oscillating network, termed the repressilator, in Escherichia coli. The network periodically induces the synthesis of green fluorescent protein as a readout of its state in individual cells. The resulting oscillations, with typical periods of hours, are slower than the cell-division cycle, so the state of the oscillator has to be transmitted from generation to generation. This artificial clock displays noisy behaviour, possibly because of stochastic fluctuations of its components. Such 'rational network design may lead both to the engineering of new cellular behaviours and to an improved understanding of naturally occurring networks.</p>
|
| 22 |
+
</div>
|
| 23 |
+
</div>
|
| 24 |
+
<div class="bm:curation">
|
| 25 |
+
<p>The model is based upon the equations in Box 1 of the paper; however, these equations as printed are dimensionless, and the correct dimensions have been returned to the equations, and the parameters set to reproduce Figure 1C (left).</p>
|
| 26 |
+
</div>
|
| 27 |
+
<div class="bm:modification">
|
| 28 |
+
<p>The original model was generated by B.E. Shapiro using Cellerator version 1.0 update 2.1127 using Mathematica 4.2 for Mac OS X (June 4, 2002), November 27, 2002 12:15:32, using (PowerMac,PowerPC, Mac OS X,MacOSX,Darwin).</p>
|
| 29 |
+
<p>Nicolas Le Novere provided a corrected version generated by SBMLeditor on Sun Aug 20 00:44:05 BST 2006. This removed the EmptySet species. Ran fine on COPASI 4.0 build 18.</p>
|
| 30 |
+
<p>Bruce Shapiro revised the model with SBMLeditor on 23 October 2006 20:39 PST. This defines default units and correct reactions. The original Cellerator reactions while being mathematically correct did not accurately reflect the intent of the authors. The original notes were mostly removed because they were mostly incorrect in the revised version. Tested with MathSBML 2.6.0.</p>
|
| 31 |
+
<p>Nicolas Le Novere changed the volume to 1 cubic micrometre, to allow for stochastic simulation.</p>
|
| 32 |
+
<p>Changed by Lukas Endler to use the average livetime of mRNA instead of its halflife and a corrected value of alpha and alpha0.</p>
|
| 33 |
+
<p>Moreover, the equations used in this model were clarified, cf. below.</p>
|
| 34 |
+
<p>The equations given in <b>box 1</b>
|
| 35 |
+
of the original publication are rescaled in three respects (lowercase letters denote the rescaled, uppercase letters the unscaled number of molecules per cell): </p>
|
| 36 |
+
<ul>
|
| 37 |
+
<li>the time is rescaled to the average mRNA lifetime, <em>t_ave: τ = t/t_ave</em></li>
|
| 38 |
+
<li>the mRNA concentration is rescaled to the translation efficiency <em>eff: m = M/eff</em></li>
|
| 39 |
+
<li>the protein concentration is rescaled to <em>Km: p = P/Km</em></li>
|
| 40 |
+
</ul>
|
| 41 |
+
<p>
|
| 42 |
+
<em>α</em>
|
| 43 |
+
in the equations should be in units of rescaled proteins per promotor and cell, and <em>β</em>
|
| 44 |
+
is the ratio of the protein to the mRNA decay rates or the ratio of the mRNA to the protein halflife. </p>
|
| 45 |
+
<p>In this version of the model <em>α</em>
|
| 46 |
+
and <em>β</em>
|
| 47 |
+
are calculated correspondingly to the article, while <em>p</em>
|
| 48 |
+
and <em>m</em>
|
| 49 |
+
where just replaced by <em>P/Km</em>
|
| 50 |
+
resp. <em>M/eff</em>
|
| 51 |
+
and all equations multiplied by <em>1/t_ave</em>
|
| 52 |
+
. Also, to make the equations easier to read, commonly used variables derived from the parameters given in the article by simple rules were introduced. </p>
|
| 53 |
+
<p>The parameters given in the article were:</p>
|
| 54 |
+
<table>
|
| 55 |
+
<tr>
|
| 56 |
+
<td>promotor strength (repressed) ( <em>tps_repr</em>
|
| 57 |
+
): </td>
|
| 58 |
+
<td>5*10 <sup>-4</sup></td>
|
| 59 |
+
<td>transcripts/(promotor*s)</td>
|
| 60 |
+
</tr>
|
| 61 |
+
<tr>
|
| 62 |
+
<td>promotor strength (full) ( <em>tps_active</em>
|
| 63 |
+
): </td>
|
| 64 |
+
<td>0.5</td>
|
| 65 |
+
<td>transcripts/(promotor*s)</td>
|
| 66 |
+
</tr>
|
| 67 |
+
<tr>
|
| 68 |
+
<td>mRNA half life, τ <sub>1/2,mRNA</sub>
|
| 69 |
+
: </td>
|
| 70 |
+
<td>2</td>
|
| 71 |
+
<td>min</td>
|
| 72 |
+
</tr>
|
| 73 |
+
<tr>
|
| 74 |
+
<td>protein half life, τ <sub>1/2,prot</sub>
|
| 75 |
+
: </td>
|
| 76 |
+
<td>10</td>
|
| 77 |
+
<td>min</td>
|
| 78 |
+
</tr>
|
| 79 |
+
<tr>
|
| 80 |
+
<td>K <sub>M</sub>
|
| 81 |
+
: </td>
|
| 82 |
+
<td>40</td>
|
| 83 |
+
<td>monomers/cell</td>
|
| 84 |
+
</tr>
|
| 85 |
+
<tr>
|
| 86 |
+
<td>Hill coefficient n:</td>
|
| 87 |
+
<td>2</td>
|
| 88 |
+
<td/>
|
| 89 |
+
</tr>
|
| 90 |
+
</table>
|
| 91 |
+
<p>From these the following constants can be derived:</p>
|
| 92 |
+
<table>
|
| 93 |
+
<tr>
|
| 94 |
+
<td>average mRNA lifetime ( <em>t_ave</em>
|
| 95 |
+
): </td>
|
| 96 |
+
<td>
|
| 97 |
+
<em>τ <sub>1/2,mRNA</sub>
|
| 98 |
+
/ln(2) </em>
|
| 99 |
+
</td>
|
| 100 |
+
<td>= 2.89 min</td>
|
| 101 |
+
</tr>
|
| 102 |
+
<tr>
|
| 103 |
+
<td>mRNA decay rate ( <em>kd_mRNA</em>
|
| 104 |
+
): </td>
|
| 105 |
+
<td>
|
| 106 |
+
<em>ln(2)/ τ <sub>1/2,mRNA</sub></em>
|
| 107 |
+
</td>
|
| 108 |
+
<td>= 0.347 min <sup>-1</sup></td>
|
| 109 |
+
</tr>
|
| 110 |
+
<tr>
|
| 111 |
+
<td>protein decay rate ( <em>kd_prot</em>
|
| 112 |
+
): </td>
|
| 113 |
+
<td>
|
| 114 |
+
<em>ln(2)/ τ <sub>1/2,prot</sub></em>
|
| 115 |
+
</td>
|
| 116 |
+
</tr>
|
| 117 |
+
<tr>
|
| 118 |
+
<td>transcription rate ( <em>a_tr</em>
|
| 119 |
+
): </td>
|
| 120 |
+
<td>
|
| 121 |
+
<em>tps_active*60</em>
|
| 122 |
+
</td>
|
| 123 |
+
<td>= 29.97 transcripts/min</td>
|
| 124 |
+
</tr>
|
| 125 |
+
<tr>
|
| 126 |
+
<td>transcription rate (repressed) ( <em>a0_tr</em>
|
| 127 |
+
): </td>
|
| 128 |
+
<td>
|
| 129 |
+
<em>tps_repr*60</em>
|
| 130 |
+
</td>
|
| 131 |
+
<td>= 0.03 transcripts/min</td>
|
| 132 |
+
</tr>
|
| 133 |
+
<tr>
|
| 134 |
+
<td>translation rate ( <em>k_tl</em>
|
| 135 |
+
): </td>
|
| 136 |
+
<td>
|
| 137 |
+
<em>eff*kd_mRNA</em>
|
| 138 |
+
</td>
|
| 139 |
+
<td>= 6.93 proteins/(mRNA*min)</td>
|
| 140 |
+
</tr>
|
| 141 |
+
<tr>
|
| 142 |
+
<td>α :</td>
|
| 143 |
+
<td>
|
| 144 |
+
<em>a_tr*eff*τ <sub>1/2,prot</sub>
|
| 145 |
+
/(ln(2)*K <sub>M</sub>
|
| 146 |
+
) </em>
|
| 147 |
+
</td>
|
| 148 |
+
<td>= 216.4 proteins/(promotor*cell*Km)</td>
|
| 149 |
+
</tr>
|
| 150 |
+
<tr>
|
| 151 |
+
<td>α <sub>0</sub>
|
| 152 |
+
: </td>
|
| 153 |
+
<td>
|
| 154 |
+
<em>a0_tr*eff*τ <sub>1/2,prot</sub>
|
| 155 |
+
/(ln(2)*K <sub>M</sub>
|
| 156 |
+
) </em>
|
| 157 |
+
</td>
|
| 158 |
+
<td>= 0.2164 proteins/(promotor*cell*Km)</td>
|
| 159 |
+
</tr>
|
| 160 |
+
<tr>
|
| 161 |
+
<td>β :</td>
|
| 162 |
+
<td>
|
| 163 |
+
<em>k_dp/k_dm</em>
|
| 164 |
+
</td>
|
| 165 |
+
<td>= 0.2</td>
|
| 166 |
+
</tr>
|
| 167 |
+
</table>
|
| 168 |
+
<br/>
|
| 169 |
+
<p>Annotation by the Kinetic Simulation Algorithm Ontology (KiSAO):</p>
|
| 170 |
+
<p>To reproduce the simulations run published by the authors, the model has to be simulated with any of two different approaches. First, one could use a deterministic method ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000035" title="Access to: KISAO_0000035">KISAO_0000035</a>
|
| 171 |
+
) with continuous variables ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000018" title="Access to: KISAO_0000018">KISAO_0000018</a>
|
| 172 |
+
). One sample algorithm to use is the CVODE solver ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000019" title="Access to: KISAO_0000019">KISAO_0000019</a>
|
| 173 |
+
). Second, one could simulate the system using Gillespie's direct method ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000029" title="Access to: KISAO_0000029">KISAO_0000029</a>
|
| 174 |
+
), which is a stochastic method ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000036" title="Access to: KISAO_0000036">KISAO_0000036</a>
|
| 175 |
+
) supporting adaptive timesteps ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000041" title="Access to: KISAO_0000041">KISAO_0000041</a>
|
| 176 |
+
) and using discrete variables ( <a href="http://identifiers.org/biomodels.kisao/KISAO_0000016" title="Access to: KISAO_0000016">KISAO_0000016</a>
|
| 177 |
+
). </p>
|
| 178 |
+
</div>
|
| 179 |
+
<div class="dc:publisher">
|
| 180 |
+
<p>This model is hosted on <a href="http://www.ebi.ac.uk/biomodels/">BioModels Database</a>
|
| 181 |
+
and identified by: <a href="http://identifiers.org/biomodels.db/BIOMD0000000012">BIOMD0000000012</a>
|
| 182 |
+
. </p>
|
| 183 |
+
<p>To cite BioModels Database, please use: <a href="http://identifiers.org/pubmed/20587024" title="Latest BioModels Database publication">BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models</a>
|
| 184 |
+
. </p>
|
| 185 |
+
</div>
|
| 186 |
+
<div class="dc:license">
|
| 187 |
+
<p>To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to <a href="http://creativecommons.org/publicdomain/zero/1.0/" title="Access to: CC0 1.0 Universal (CC0 1.0), Public Domain Dedication">CC0 Public Domain Dedication</a>
|
| 188 |
+
for more information. </p>
|
| 189 |
+
</div>
|
| 190 |
+
</body>
|
| 191 |
+
</notes>
|
| 192 |
+
<annotation>
|
| 193 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:vCard="http://www.w3.org/2001/vcard-rdf/3.0#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:dcterms="http://purl.org/dc/terms/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 194 |
+
<rdf:Description rdf:about="#_000001">
|
| 195 |
+
<dc:creator>
|
| 196 |
+
<rdf:Bag>
|
| 197 |
+
<rdf:li rdf:parseType="Resource">
|
| 198 |
+
<vCard:N rdf:parseType="Resource">
|
| 199 |
+
<vCard:Family>Le Novère</vCard:Family>
|
| 200 |
+
<vCard:Given>Nicolas</vCard:Given>
|
| 201 |
+
</vCard:N>
|
| 202 |
+
<vCard:EMAIL>lenov@ebi.ac.uk</vCard:EMAIL>
|
| 203 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 204 |
+
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
|
| 205 |
+
</vCard:ORG>
|
| 206 |
+
</rdf:li>
|
| 207 |
+
|
| 208 |
+
|
| 209 |
+
|
| 210 |
+
<rdf:li rdf:parseType="Resource">
|
| 211 |
+
<vCard:N rdf:parseType="Resource">
|
| 212 |
+
<vCard:Family>Shapiro</vCard:Family>
|
| 213 |
+
<vCard:Given>Bruce</vCard:Given>
|
| 214 |
+
</vCard:N>
|
| 215 |
+
<vCard:EMAIL>bshapiro@caltech.edu</vCard:EMAIL>
|
| 216 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 217 |
+
<vCard:Orgname>Jet Propulsion Laboratory</vCard:Orgname>
|
| 218 |
+
</vCard:ORG>
|
| 219 |
+
</rdf:li>
|
| 220 |
+
<rdf:li rdf:parseType="Resource">
|
| 221 |
+
<vCard:N rdf:parseType="Resource">
|
| 222 |
+
<vCard:Family>Juty</vCard:Family>
|
| 223 |
+
<vCard:Given>Nick</vCard:Given>
|
| 224 |
+
</vCard:N>
|
| 225 |
+
<vCard:EMAIL>juty@ebi.ac.uk</vCard:EMAIL>
|
| 226 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 227 |
+
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
|
| 228 |
+
</vCard:ORG>
|
| 229 |
+
</rdf:li>
|
| 230 |
+
<rdf:li rdf:parseType="Resource">
|
| 231 |
+
<vCard:N rdf:parseType="Resource">
|
| 232 |
+
<vCard:Family>Endler</vCard:Family>
|
| 233 |
+
<vCard:Given>Lukas</vCard:Given>
|
| 234 |
+
</vCard:N>
|
| 235 |
+
<vCard:EMAIL>lukas@ebi.ac.uk</vCard:EMAIL>
|
| 236 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 237 |
+
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
|
| 238 |
+
</vCard:ORG>
|
| 239 |
+
</rdf:li>
|
| 240 |
+
<rdf:li rdf:parseType="Resource">
|
| 241 |
+
<vCard:N rdf:parseType="Resource">
|
| 242 |
+
<vCard:Family>Chelliah</vCard:Family>
|
| 243 |
+
<vCard:Given>Vijayalakshmi</vCard:Given>
|
| 244 |
+
</vCard:N>
|
| 245 |
+
<vCard:EMAIL>viji@ebi.ac.uk</vCard:EMAIL>
|
| 246 |
+
<vCard:ORG rdf:parseType="Resource">
|
| 247 |
+
<vCard:Orgname>EMBL-EBI</vCard:Orgname>
|
| 248 |
+
</vCard:ORG>
|
| 249 |
+
</rdf:li>
|
| 250 |
+
</rdf:Bag>
|
| 251 |
+
</dc:creator>
|
| 252 |
+
<dcterms:created rdf:parseType="Resource">
|
| 253 |
+
<dcterms:W3CDTF>2009-01-20T14:03:56Z</dcterms:W3CDTF>
|
| 254 |
+
</dcterms:created>
|
| 255 |
+
<dcterms:modified rdf:parseType="Resource">
|
| 256 |
+
<dcterms:W3CDTF>2013-07-10T10:59:30Z</dcterms:W3CDTF>
|
| 257 |
+
</dcterms:modified>
|
| 258 |
+
<bqmodel:is>
|
| 259 |
+
<rdf:Bag>
|
| 260 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/MODEL6615351360"/>
|
| 261 |
+
</rdf:Bag>
|
| 262 |
+
</bqmodel:is>
|
| 263 |
+
<bqmodel:is>
|
| 264 |
+
<rdf:Bag>
|
| 265 |
+
<rdf:li rdf:resource="http://identifiers.org/biomodels.db/BIOMD0000000012"/>
|
| 266 |
+
</rdf:Bag>
|
| 267 |
+
</bqmodel:is>
|
| 268 |
+
<bqmodel:isDescribedBy>
|
| 269 |
+
<rdf:Bag>
|
| 270 |
+
<rdf:li rdf:resource="http://identifiers.org/pubmed/10659856"/>
|
| 271 |
+
</rdf:Bag>
|
| 272 |
+
</bqmodel:isDescribedBy>
|
| 273 |
+
<bqbiol:hasTaxon>
|
| 274 |
+
<rdf:Bag>
|
| 275 |
+
<rdf:li rdf:resource="http://identifiers.org/taxonomy/562"/>
|
| 276 |
+
</rdf:Bag>
|
| 277 |
+
</bqbiol:hasTaxon>
|
| 278 |
+
<bqbiol:isVersionOf>
|
| 279 |
+
<rdf:Bag>
|
| 280 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0040029"/>
|
| 281 |
+
</rdf:Bag>
|
| 282 |
+
</bqbiol:isVersionOf>
|
| 283 |
+
<bqbiol:hasProperty>
|
| 284 |
+
<rdf:Bag>
|
| 285 |
+
<rdf:li rdf:resource="http://identifiers.org/mamo/MAMO_0000046"/>
|
| 286 |
+
</rdf:Bag>
|
| 287 |
+
</bqbiol:hasProperty>
|
| 288 |
+
</rdf:Description>
|
| 289 |
+
|
| 290 |
+
</rdf:RDF>
|
| 291 |
+
</annotation>
|
| 292 |
+
<listOfUnitDefinitions>
|
| 293 |
+
<unitDefinition id="volume" metaid="metaid_0000029" name="cubic microns">
|
| 294 |
+
<listOfUnits>
|
| 295 |
+
<unit kind="litre" metaid="_420934" scale="-15"/>
|
| 296 |
+
</listOfUnits>
|
| 297 |
+
</unitDefinition>
|
| 298 |
+
<unitDefinition id="substance" metaid="metaid_1000000" name="item">
|
| 299 |
+
<listOfUnits>
|
| 300 |
+
<unit kind="item" metaid="_420947"/>
|
| 301 |
+
</listOfUnits>
|
| 302 |
+
</unitDefinition>
|
| 303 |
+
<unitDefinition id="time" metaid="metaid_0000030" name="minute">
|
| 304 |
+
<listOfUnits>
|
| 305 |
+
<unit kind="second" metaid="_420960" multiplier="60"/>
|
| 306 |
+
</listOfUnits>
|
| 307 |
+
</unitDefinition>
|
| 308 |
+
</listOfUnitDefinitions>
|
| 309 |
+
<listOfCompartments>
|
| 310 |
+
<compartment id="cell" metaid="_000002" sboTerm="SBO:0000290" size="1">
|
| 311 |
+
<annotation>
|
| 312 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 313 |
+
<rdf:Description rdf:about="#_000002">
|
| 314 |
+
<bqbiol:is>
|
| 315 |
+
<rdf:Bag>
|
| 316 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0005623"/>
|
| 317 |
+
</rdf:Bag>
|
| 318 |
+
</bqbiol:is>
|
| 319 |
+
</rdf:Description>
|
| 320 |
+
|
| 321 |
+
</rdf:RDF>
|
| 322 |
+
</annotation>
|
| 323 |
+
</compartment>
|
| 324 |
+
</listOfCompartments>
|
| 325 |
+
<listOfSpecies>
|
| 326 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="PX" initialAmount="0" metaid="PX" name="LacI protein" sboTerm="SBO:0000252">
|
| 327 |
+
<notes>
|
| 328 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 329 |
+
lacI inhibitor</p>
|
| 330 |
+
</notes>
|
| 331 |
+
<annotation>
|
| 332 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 333 |
+
<rdf:Description rdf:about="#PX">
|
| 334 |
+
<bqbiol:is>
|
| 335 |
+
<rdf:Bag>
|
| 336 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03023"/>
|
| 337 |
+
</rdf:Bag>
|
| 338 |
+
</bqbiol:is>
|
| 339 |
+
</rdf:Description>
|
| 340 |
+
|
| 341 |
+
</rdf:RDF>
|
| 342 |
+
</annotation>
|
| 343 |
+
</species>
|
| 344 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="PY" initialAmount="0" metaid="PY" name="TetR protein" sboTerm="SBO:0000252">
|
| 345 |
+
<notes>
|
| 346 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 347 |
+
Tet repressor protein</p>
|
| 348 |
+
</notes>
|
| 349 |
+
<annotation>
|
| 350 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 351 |
+
<rdf:Description rdf:about="#PY">
|
| 352 |
+
<bqbiol:is>
|
| 353 |
+
<rdf:Bag>
|
| 354 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04483"/>
|
| 355 |
+
</rdf:Bag>
|
| 356 |
+
</bqbiol:is>
|
| 357 |
+
</rdf:Description>
|
| 358 |
+
|
| 359 |
+
</rdf:RDF>
|
| 360 |
+
</annotation>
|
| 361 |
+
</species>
|
| 362 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="PZ" initialAmount="0" metaid="PZ" name="cI protein" sboTerm="SBO:0000252">
|
| 363 |
+
<notes>
|
| 364 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 365 |
+
lambda repressor</p>
|
| 366 |
+
</notes>
|
| 367 |
+
<annotation>
|
| 368 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 369 |
+
<rdf:Description rdf:about="#PZ">
|
| 370 |
+
<bqbiol:is>
|
| 371 |
+
<rdf:Bag>
|
| 372 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03034"/>
|
| 373 |
+
</rdf:Bag>
|
| 374 |
+
</bqbiol:is>
|
| 375 |
+
</rdf:Description>
|
| 376 |
+
|
| 377 |
+
</rdf:RDF>
|
| 378 |
+
</annotation>
|
| 379 |
+
</species>
|
| 380 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="X" initialAmount="0" metaid="_905769" name="LacI mRNA" sboTerm="SBO:0000250">
|
| 381 |
+
<annotation>
|
| 382 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 383 |
+
<rdf:Description rdf:about="#_905769">
|
| 384 |
+
<bqbiol:isVersionOf>
|
| 385 |
+
<rdf:Bag>
|
| 386 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:33699"/>
|
| 387 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
|
| 388 |
+
</rdf:Bag>
|
| 389 |
+
</bqbiol:isVersionOf>
|
| 390 |
+
|
| 391 |
+
<bqbiol:encodes>
|
| 392 |
+
<rdf:Bag>
|
| 393 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03023"/>
|
| 394 |
+
</rdf:Bag>
|
| 395 |
+
</bqbiol:encodes>
|
| 396 |
+
</rdf:Description>
|
| 397 |
+
|
| 398 |
+
</rdf:RDF>
|
| 399 |
+
</annotation>
|
| 400 |
+
</species>
|
| 401 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="Y" initialAmount="20" metaid="_905781" name="TetR mRNA" sboTerm="SBO:0000250">
|
| 402 |
+
<annotation>
|
| 403 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 404 |
+
<rdf:Description rdf:about="#_905781">
|
| 405 |
+
<bqbiol:isVersionOf>
|
| 406 |
+
<rdf:Bag>
|
| 407 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:33699"/>
|
| 408 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
|
| 409 |
+
</rdf:Bag>
|
| 410 |
+
</bqbiol:isVersionOf>
|
| 411 |
+
|
| 412 |
+
<bqbiol:encodes>
|
| 413 |
+
<rdf:Bag>
|
| 414 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P04483"/>
|
| 415 |
+
</rdf:Bag>
|
| 416 |
+
</bqbiol:encodes>
|
| 417 |
+
</rdf:Description>
|
| 418 |
+
|
| 419 |
+
</rdf:RDF>
|
| 420 |
+
</annotation>
|
| 421 |
+
</species>
|
| 422 |
+
<species compartment="cell" hasOnlySubstanceUnits="true" id="Z" initialAmount="0" metaid="_905802" name="cI mRNA" sboTerm="SBO:0000250">
|
| 423 |
+
<annotation>
|
| 424 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 425 |
+
<rdf:Description rdf:about="#_905802">
|
| 426 |
+
<bqbiol:isVersionOf>
|
| 427 |
+
<rdf:Bag>
|
| 428 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:33699"/>
|
| 429 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00046"/>
|
| 430 |
+
</rdf:Bag>
|
| 431 |
+
</bqbiol:isVersionOf>
|
| 432 |
+
|
| 433 |
+
<bqbiol:encodes>
|
| 434 |
+
<rdf:Bag>
|
| 435 |
+
<rdf:li rdf:resource="http://identifiers.org/uniprot/P03034"/>
|
| 436 |
+
</rdf:Bag>
|
| 437 |
+
</bqbiol:encodes>
|
| 438 |
+
</rdf:Description>
|
| 439 |
+
|
| 440 |
+
</rdf:RDF>
|
| 441 |
+
</annotation>
|
| 442 |
+
</species>
|
| 443 |
+
</listOfSpecies>
|
| 444 |
+
<listOfParameters>
|
| 445 |
+
<parameter constant="false" id="beta" metaid="metaid_0000022" name="beta" value="0.2">
|
| 446 |
+
<notes>
|
| 447 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 448 |
+
ratio of protein to mRNA decay rates</p>
|
| 449 |
+
</notes>
|
| 450 |
+
</parameter>
|
| 451 |
+
<parameter constant="false" id="alpha0" metaid="metaid_0000023" name="alpha0" sboTerm="SBO:0000485" value="0.2164">
|
| 452 |
+
<notes>
|
| 453 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 454 |
+
Leakiness in protein copies per promoter and cell</p>
|
| 455 |
+
</notes>
|
| 456 |
+
</parameter>
|
| 457 |
+
<parameter constant="false" id="alpha" metaid="metaid_0000024" name="alpha" sboTerm="SBO:0000186" value="216.404">
|
| 458 |
+
<notes>
|
| 459 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 460 |
+
Protein copies per promoter and cell</p>
|
| 461 |
+
</notes>
|
| 462 |
+
</parameter>
|
| 463 |
+
<parameter id="eff" metaid="metaid_0000025" name="translation efficiency" value="20">
|
| 464 |
+
<notes>
|
| 465 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 466 |
+
Average number of proteins per transcript</p>
|
| 467 |
+
</notes>
|
| 468 |
+
</parameter>
|
| 469 |
+
<parameter id="n" metaid="metaid_0000026" name="n" sboTerm="SBO:0000190" value="2">
|
| 470 |
+
<notes>
|
| 471 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 472 |
+
Hill coefficient</p>
|
| 473 |
+
</notes>
|
| 474 |
+
</parameter>
|
| 475 |
+
<parameter id="KM" metaid="metaid_0000027" name="KM" sboTerm="SBO:0000288" value="40">
|
| 476 |
+
<notes>
|
| 477 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 478 |
+
Number of repressor molecules per cell giving half maximal repression, in monomers per cell</p>
|
| 479 |
+
</notes>
|
| 480 |
+
</parameter>
|
| 481 |
+
<parameter id="tau_mRNA" metaid="metaid_0000028" name="mRNA half life" sboTerm="SBO:0000332" value="2"/>
|
| 482 |
+
<parameter id="tau_prot" metaid="metaid_0000128" name="protein half life" sboTerm="SBO:0000332" value="10"/>
|
| 483 |
+
<parameter constant="false" id="t_ave" metaid="metaid_0000032" name="average mRNA life time" sboTerm="SBO:0000348"/>
|
| 484 |
+
<parameter constant="false" id="kd_mRNA" metaid="metaid_0000132" name="kd_mRNA" sboTerm="SBO:0000356">
|
| 485 |
+
<notes>
|
| 486 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 487 |
+
mRNA decay rate constant</p>
|
| 488 |
+
</notes>
|
| 489 |
+
</parameter>
|
| 490 |
+
<parameter constant="false" id="kd_prot" metaid="metaid_0000133" name="kd_prot" sboTerm="SBO:0000356">
|
| 491 |
+
<notes>
|
| 492 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 493 |
+
Protein decay rate costant</p>
|
| 494 |
+
</notes>
|
| 495 |
+
</parameter>
|
| 496 |
+
<parameter constant="false" id="k_tl" metaid="metaid_0000233" name="k_tl" sboTerm="SBO:0000016">
|
| 497 |
+
<notes>
|
| 498 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 499 |
+
Translation rate constant</p>
|
| 500 |
+
</notes>
|
| 501 |
+
</parameter>
|
| 502 |
+
<parameter constant="false" id="a_tr" metaid="metaid_0900235" name="a_tr" sboTerm="SBO:0000186">
|
| 503 |
+
<notes>
|
| 504 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 505 |
+
Transcription rate from free promotor minus a0_tr</p>
|
| 506 |
+
</notes>
|
| 507 |
+
</parameter>
|
| 508 |
+
<parameter id="ps_a" metaid="metaid_0800235" name="tps_active" sboTerm="SBO:0000186" value="0.5">
|
| 509 |
+
<notes>
|
| 510 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 511 |
+
Transcrition from free promotor in transcripts per second and promotor</p>
|
| 512 |
+
</notes>
|
| 513 |
+
</parameter>
|
| 514 |
+
<parameter id="ps_0" metaid="metaid_0500235" name="tps_repr" sboTerm="SBO:0000485" value="0.0005">
|
| 515 |
+
<notes>
|
| 516 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 517 |
+
Transcrition from fully repressed promotor in transcripts per second and promotor</p>
|
| 518 |
+
</notes>
|
| 519 |
+
</parameter>
|
| 520 |
+
<parameter constant="false" id="a0_tr" metaid="metaid_0000234" name="a0_tr" sboTerm="SBO:0000485">
|
| 521 |
+
<notes>
|
| 522 |
+
<p xmlns="http://www.w3.org/1999/xhtml">
|
| 523 |
+
Transcription rate from fully repressed promotor</p>
|
| 524 |
+
</notes>
|
| 525 |
+
</parameter>
|
| 526 |
+
</listOfParameters>
|
| 527 |
+
<listOfRules>
|
| 528 |
+
<assignmentRule metaid="metaid_0500035" variable="t_ave">
|
| 529 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 530 |
+
<apply>
|
| 531 |
+
<divide/>
|
| 532 |
+
<ci> tau_mRNA </ci>
|
| 533 |
+
<apply>
|
| 534 |
+
<ln/>
|
| 535 |
+
<cn> 2 </cn>
|
| 536 |
+
</apply>
|
| 537 |
+
</apply>
|
| 538 |
+
</math>
|
| 539 |
+
</assignmentRule>
|
| 540 |
+
<assignmentRule metaid="metaid_0240045" variable="beta">
|
| 541 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 542 |
+
<apply>
|
| 543 |
+
<divide/>
|
| 544 |
+
<ci> tau_mRNA </ci>
|
| 545 |
+
<ci> tau_prot </ci>
|
| 546 |
+
</apply>
|
| 547 |
+
</math>
|
| 548 |
+
</assignmentRule>
|
| 549 |
+
<assignmentRule metaid="metaid_0400235" variable="k_tl">
|
| 550 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 551 |
+
<apply>
|
| 552 |
+
<divide/>
|
| 553 |
+
<ci> eff </ci>
|
| 554 |
+
<ci> t_ave </ci>
|
| 555 |
+
</apply>
|
| 556 |
+
</math>
|
| 557 |
+
</assignmentRule>
|
| 558 |
+
<assignmentRule metaid="metaid_1000237" variable="a_tr">
|
| 559 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 560 |
+
<apply>
|
| 561 |
+
<times/>
|
| 562 |
+
<apply>
|
| 563 |
+
<minus/>
|
| 564 |
+
<ci> ps_a </ci>
|
| 565 |
+
<ci> ps_0 </ci>
|
| 566 |
+
</apply>
|
| 567 |
+
<cn> 60 </cn>
|
| 568 |
+
</apply>
|
| 569 |
+
</math>
|
| 570 |
+
</assignmentRule>
|
| 571 |
+
<assignmentRule metaid="metaid_0100236" variable="a0_tr">
|
| 572 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 573 |
+
<apply>
|
| 574 |
+
<times/>
|
| 575 |
+
<ci> ps_0 </ci>
|
| 576 |
+
<cn> 60 </cn>
|
| 577 |
+
</apply>
|
| 578 |
+
</math>
|
| 579 |
+
</assignmentRule>
|
| 580 |
+
<assignmentRule metaid="metaid_0010335" variable="kd_prot">
|
| 581 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 582 |
+
<apply>
|
| 583 |
+
<divide/>
|
| 584 |
+
<apply>
|
| 585 |
+
<ln/>
|
| 586 |
+
<cn> 2 </cn>
|
| 587 |
+
</apply>
|
| 588 |
+
<ci> tau_prot </ci>
|
| 589 |
+
</apply>
|
| 590 |
+
</math>
|
| 591 |
+
</assignmentRule>
|
| 592 |
+
<assignmentRule metaid="metaid_0020435" variable="kd_mRNA">
|
| 593 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 594 |
+
<apply>
|
| 595 |
+
<divide/>
|
| 596 |
+
<apply>
|
| 597 |
+
<ln/>
|
| 598 |
+
<cn> 2 </cn>
|
| 599 |
+
</apply>
|
| 600 |
+
<ci> tau_mRNA </ci>
|
| 601 |
+
</apply>
|
| 602 |
+
</math>
|
| 603 |
+
</assignmentRule>
|
| 604 |
+
<assignmentRule metaid="metaid_0230035" variable="alpha">
|
| 605 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 606 |
+
<apply>
|
| 607 |
+
<divide/>
|
| 608 |
+
<apply>
|
| 609 |
+
<times/>
|
| 610 |
+
<ci> a_tr </ci>
|
| 611 |
+
<ci> eff </ci>
|
| 612 |
+
<ci> tau_prot </ci>
|
| 613 |
+
</apply>
|
| 614 |
+
<apply>
|
| 615 |
+
<times/>
|
| 616 |
+
<apply>
|
| 617 |
+
<ln/>
|
| 618 |
+
<cn> 2 </cn>
|
| 619 |
+
</apply>
|
| 620 |
+
<ci> KM </ci>
|
| 621 |
+
</apply>
|
| 622 |
+
</apply>
|
| 623 |
+
</math>
|
| 624 |
+
</assignmentRule>
|
| 625 |
+
<assignmentRule metaid="metaid_0240035" variable="alpha0">
|
| 626 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 627 |
+
<apply>
|
| 628 |
+
<divide/>
|
| 629 |
+
<apply>
|
| 630 |
+
<times/>
|
| 631 |
+
<ci> a0_tr </ci>
|
| 632 |
+
<ci> eff </ci>
|
| 633 |
+
<ci> tau_prot </ci>
|
| 634 |
+
</apply>
|
| 635 |
+
<apply>
|
| 636 |
+
<times/>
|
| 637 |
+
<apply>
|
| 638 |
+
<ln/>
|
| 639 |
+
<cn> 2 </cn>
|
| 640 |
+
</apply>
|
| 641 |
+
<ci> KM </ci>
|
| 642 |
+
</apply>
|
| 643 |
+
</apply>
|
| 644 |
+
</math>
|
| 645 |
+
</assignmentRule>
|
| 646 |
+
</listOfRules>
|
| 647 |
+
<listOfReactions>
|
| 648 |
+
<reaction id="Reaction1" metaid="_905823" name="degradation of LacI transcripts" reversible="false" sboTerm="SBO:0000179">
|
| 649 |
+
<annotation>
|
| 650 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 651 |
+
<rdf:Description rdf:about="#_905823">
|
| 652 |
+
<bqbiol:isVersionOf>
|
| 653 |
+
<rdf:Bag>
|
| 654 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006402"/>
|
| 655 |
+
</rdf:Bag>
|
| 656 |
+
</bqbiol:isVersionOf>
|
| 657 |
+
</rdf:Description>
|
| 658 |
+
|
| 659 |
+
</rdf:RDF>
|
| 660 |
+
</annotation>
|
| 661 |
+
<listOfReactants>
|
| 662 |
+
<speciesReference metaid="_420973" species="X"/>
|
| 663 |
+
</listOfReactants>
|
| 664 |
+
<kineticLaw metaid="_420986" sboTerm="SBO:0000049">
|
| 665 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 666 |
+
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqmodel="http://biomodels.net/model-qualifiers/" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1000 |
+
<rdf:Description rdf:about="#_906042">
|
| 1001 |
+
<bqbiol:isVersionOf>
|
| 1002 |
+
<rdf:Bag>
|
| 1003 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006351"/>
|
| 1004 |
+
</rdf:Bag>
|
| 1005 |
+
</bqbiol:isVersionOf>
|
| 1006 |
+
</rdf:Description>
|
| 1007 |
+
|
| 1008 |
+
</rdf:RDF>
|
| 1009 |
+
</annotation>
|
| 1010 |
+
<listOfProducts>
|
| 1011 |
+
<speciesReference metaid="_421304" species="Z"/>
|
| 1012 |
+
</listOfProducts>
|
| 1013 |
+
<listOfModifiers>
|
| 1014 |
+
<modifierSpeciesReference metaid="_421317" sboTerm="SBO:0000536" species="PY"/>
|
| 1015 |
+
</listOfModifiers>
|
| 1016 |
+
<kineticLaw metaid="_421329">
|
| 1017 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1018 |
+
<apply>
|
| 1019 |
+
<plus/>
|
| 1020 |
+
<ci> a0_tr </ci>
|
| 1021 |
+
<apply>
|
| 1022 |
+
<divide/>
|
| 1023 |
+
<apply>
|
| 1024 |
+
<times/>
|
| 1025 |
+
<ci> a_tr </ci>
|
| 1026 |
+
<apply>
|
| 1027 |
+
<power/>
|
| 1028 |
+
<ci> KM </ci>
|
| 1029 |
+
<ci> n </ci>
|
| 1030 |
+
</apply>
|
| 1031 |
+
</apply>
|
| 1032 |
+
<apply>
|
| 1033 |
+
<plus/>
|
| 1034 |
+
<apply>
|
| 1035 |
+
<power/>
|
| 1036 |
+
<ci> KM </ci>
|
| 1037 |
+
<ci> n </ci>
|
| 1038 |
+
</apply>
|
| 1039 |
+
<apply>
|
| 1040 |
+
<power/>
|
| 1041 |
+
<ci> PY </ci>
|
| 1042 |
+
<ci> n </ci>
|
| 1043 |
+
</apply>
|
| 1044 |
+
</apply>
|
| 1045 |
+
</apply>
|
| 1046 |
+
</apply>
|
| 1047 |
+
</math>
|
| 1048 |
+
</kineticLaw>
|
| 1049 |
+
</reaction>
|
| 1050 |
+
</listOfReactions>
|
| 1051 |
+
</model>
|
| 1052 |
+
</sbml>
|
Data/BIOMD0000000012/Elowitz2000_conditions.json
ADDED
|
@@ -0,0 +1,56 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"PX": {
|
| 3 |
+
"trajectory_type": 3,
|
| 4 |
+
"trajectory_type_name": "oscillation",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.0,
|
| 7 |
+
2338.2136679163223
|
| 8 |
+
],
|
| 9 |
+
"period": 136.5
|
| 10 |
+
},
|
| 11 |
+
"PY": {
|
| 12 |
+
"trajectory_type": 3,
|
| 13 |
+
"trajectory_type_name": "oscillation",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.0,
|
| 16 |
+
2358.865680254101
|
| 17 |
+
],
|
| 18 |
+
"period": 133.0
|
| 19 |
+
},
|
| 20 |
+
"PZ": {
|
| 21 |
+
"trajectory_type": 3,
|
| 22 |
+
"trajectory_type_name": "oscillation",
|
| 23 |
+
"bounds": [
|
| 24 |
+
0.0,
|
| 25 |
+
2351.9987800003887
|
| 26 |
+
],
|
| 27 |
+
"period": 132.33333333333334
|
| 28 |
+
},
|
| 29 |
+
"X": {
|
| 30 |
+
"trajectory_type": 3,
|
| 31 |
+
"trajectory_type_name": "oscillation",
|
| 32 |
+
"bounds": [
|
| 33 |
+
0.0,
|
| 34 |
+
32.352744773377715
|
| 35 |
+
],
|
| 36 |
+
"period": 130.0
|
| 37 |
+
},
|
| 38 |
+
"Y": {
|
| 39 |
+
"trajectory_type": 3,
|
| 40 |
+
"trajectory_type_name": "oscillation",
|
| 41 |
+
"bounds": [
|
| 42 |
+
0.1135612005885983,
|
| 43 |
+
32.61751364690126
|
| 44 |
+
],
|
| 45 |
+
"period": 123.0
|
| 46 |
+
},
|
| 47 |
+
"Z": {
|
| 48 |
+
"trajectory_type": 3,
|
| 49 |
+
"trajectory_type_name": "oscillation",
|
| 50 |
+
"bounds": [
|
| 51 |
+
0.0,
|
| 52 |
+
32.532654511860954
|
| 53 |
+
],
|
| 54 |
+
"period": 137.5
|
| 55 |
+
}
|
| 56 |
+
}
|
Data/BIOMD0000000012/initial_conditions.json
ADDED
|
@@ -0,0 +1,11 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"PX": 0.0,
|
| 5 |
+
"PY": 0.0,
|
| 6 |
+
"PZ": 0.0,
|
| 7 |
+
"X": 0.0,
|
| 8 |
+
"Y": 20.0,
|
| 9 |
+
"Z": 0.0
|
| 10 |
+
}
|
| 11 |
+
}
|
Data/BIOMD0000000013/Poolman2004.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000013/Poolman2004.xml
ADDED
|
@@ -0,0 +1,2559 @@
|
|
|
|
|
|
|
|
|
|
|
|
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|
| 1 |
+
<?xml version='1.0' encoding='UTF-8' standalone='no'?>
|
| 2 |
+
<sbml xmlns="http://www.sbml.org/sbml/level2" level="2" metaid="metaid_000001" version="1" xmlns:jd="http://www.sys-bio.org/sbml">
|
| 3 |
+
<annotation>
|
| 4 |
+
<jd:header>
|
| 5 |
+
<jd:VersionHeader SBMLVersion="1.0"/>
|
| 6 |
+
<jd:ModelHeader Author="Mark Poolman, Oxford Brookes University" ModelTitle="Calvin Cycle" ModelVersion="??"/>
|
| 7 |
+
</jd:header>
|
| 8 |
+
<jd:display>
|
| 9 |
+
<jd:SBMLGraphicsHeader BackGroundColor="15728639"/>
|
| 10 |
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</jd:display>
|
| 11 |
+
</annotation>
|
| 12 |
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<model id="untitled" metaid="metaid_0000002" name="Poolman2004_CalvinCycle">
|
| 13 |
+
<notes>
|
| 14 |
+
<body xmlns="http://www.w3.org/1999/xhtml">
|
| 15 |
+
<p>
|
| 16 |
+
This a model from the article:
|
| 17 |
+
<br/>
|
| 18 |
+
<strong> Applications of metabolic modelling to plant metabolism.
|
| 19 |
+
</strong>
|
| 20 |
+
<br/>
|
| 21 |
+
Poolman MG ,Assmus HE, Fell DA
|
| 22 |
+
<em>J. Exp. Bot.</em>[2004 May; Volume: 55 (Issue: 400 )]: 1177-86
|
| 23 |
+
<a href="http://www.ncbi.nlm.nih.gov/pubmed/15073223">15073223</a>,
|
| 24 |
+
<br/>
|
| 25 |
+
<strong>Abstract:</strong>
|
| 26 |
+
<br/>
|
| 27 |
+
In this paper some of the general concepts underpinning the computer modelling of metabolic systems are introduced. The difference between kinetic and structural modelling is emphasized, and the more important techniques from both, along with the physiological implications, are described. These approaches are then illustrated by descriptions of other work, in which they have been applied to models of the Calvin cycle, sucrose metabolism in sugar cane, and starch metabolism in potatoes.
|
| 28 |
+
</p>
|
| 29 |
+
<br/>
|
| 30 |
+
<br/>
|
| 31 |
+
<p> This model describes the non oxidative Calvin cycle as depicted in Poolman et al; J Exp Bot (2004) 55:1177-1186, fig 2. Reaction E20: E4P + F6P ↔ S7P + GAP, is depicted in the figure, but not included in the model. The light reaction: ADP + P
|
| 32 |
+
<sub>i</sub> → ATP, is included in the model, but only mentioned in the figure caption. The parameters and initial concentrations are the same as in Poolman, 1999, Computer Modelling Applied to the Calvin Cycle, PhD Thesis, Oxford Brookes University, Appendix A (available at at
|
| 33 |
+
<a href="http://mudshark.brookes.ac.uk/index.php/Publications/Theses/Mark">http://mudshark.brookes.ac.uk/index.php/Publications/Theses/Mark</a>) </p>
|
| 34 |
+
<p> © Mark Poolman (mgpoolman@brookes.ac.uk) 1995-2002
|
| 35 |
+
<br/>
|
| 36 |
+
Based on a description by Pettersson 1988, Eur. J. Biochem. 175, 661-672
|
| 37 |
+
<br/>
|
| 38 |
+
Differences are:
|
| 39 |
+
<br/>
|
| 40 |
+
1 - Reactions assumed by Pettersson to be in equilibrium have fast mass action kinetics.
|
| 41 |
+
<br/>
|
| 42 |
+
2 - Introduction of the parameter PGAxpMult to modulate PGA export through TPT.
|
| 43 |
+
<br/>
|
| 44 |
+
3 - Introduction of Starch phosphorylase reaction.
|
| 45 |
+
<br/>
|
| 46 |
+
|
| 47 |
+
This file may be freely copied or translated into other formats provided:
|
| 48 |
+
<br/>
|
| 49 |
+
1 - This notice is reproduced in its entirety
|
| 50 |
+
<br/>
|
| 51 |
+
2 - Published material making use of (information gained from) this model cites at least:
|
| 52 |
+
<br/>
|
| 53 |
+
(a) Poolman, 1999, Computer Modelling Applied to the Calvin Cycle, PhD Thesis, Oxford Brookes University
|
| 54 |
+
<br/>
|
| 55 |
+
(b) Poolman, Fell, and Thomas. 2000, Modelling Photosynthesis and its control, J. Exp. Bot. 51, 319-328
|
| 56 |
+
<br/>
|
| 57 |
+
or
|
| 58 |
+
<br/>
|
| 59 |
+
(c) Poolman et al. 2001, Computer modelling and experimental evidence for two steady states in the photosynthetic Calvin cycle. Eur. J. Biochem. 268, 2810-2816
|
| 60 |
+
<br/>
|
| 61 |
+
Further related information may be found at
|
| 62 |
+
<a href="http://mudshark.brookes.ac.uk">http://mudshark.brookes.ac.uk</a>.
|
| 63 |
+
</p>
|
| 64 |
+
<p>This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2012 The BioModels.net Team.<br/>
|
| 65 |
+
For more information see the <a href="http://www.ebi.ac.uk/biomodels/legal.html" target="_blank">terms of use</a>.<br/>
|
| 66 |
+
To cite BioModels Database, please use: <a href="http://www.ncbi.nlm.nih.gov/pubmed/20587024" target="_blank">Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.</a>
|
| 67 |
+
</p>
|
| 68 |
+
</body>
|
| 69 |
+
</notes>
|
| 70 |
+
<annotation>
|
| 71 |
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<jd:notes type="ASCII">
|
| 72 |
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<jd:note value="// Calvin cycle model"/>
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| 73 |
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<jd:note value="// (c) Mark Poolman (mgpoolman@brookes.ac.uk) 1995-2002"/>
|
| 74 |
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<jd:note value="// Based description by Pettersson 1988, Eur. J. Biochem. 175, 661--672"/>
|
| 75 |
+
<jd:note value="//"/>
|
| 76 |
+
<jd:note value="//Differences are:"/>
|
| 77 |
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<jd:note value="// 1 - Reactions assumed by Pettersson to be in equilibrium have fast mass action kinetics."/>
|
| 78 |
+
<jd:note value="//"/>
|
| 79 |
+
<jd:note value="// 2 - Introduction of the parameter PGAxpMult to modulate PGA export through TPT."/>
|
| 80 |
+
<jd:note value="//"/>
|
| 81 |
+
<jd:note value="// 3 - Introduction of Starch phosphorylase reaction."/>
|
| 82 |
+
<jd:note value="//"/>
|
| 83 |
+
<jd:note value="//"/>
|
| 84 |
+
<jd:note value="//This file may be freely copied or translated into other formats provided:"/>
|
| 85 |
+
<jd:note value="//"/>
|
| 86 |
+
<jd:note value="// 1 - This notice is reproduced in its entirety"/>
|
| 87 |
+
<jd:note value="//"/>
|
| 88 |
+
<jd:note value="// 2 - Published material making use of (information gained from) this model cites at least:"/>
|
| 89 |
+
<jd:note value="//"/>
|
| 90 |
+
<jd:note value="// (a) Poolman, 1999, Computer Modelling Applied to the Calvin Cycle, PhD Thesis, Oxford Brookes University"/>
|
| 91 |
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<jd:note value="//"/>
|
| 92 |
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<jd:note value="// and:"/>
|
| 93 |
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<jd:note value="// (b) Poolman, Fell, and Thomas. 2000, Modelling Photosynthesis and its control,"/>
|
| 94 |
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<jd:note value="// J. Exp. Bot. 51, 319--328"/>
|
| 95 |
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<jd:note value="//"/>
|
| 96 |
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<jd:note value="// or"/>
|
| 97 |
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<jd:note value="//"/>
|
| 98 |
+
<jd:note value="// (c) Poolman et al. 2001, Computer modelling and experimental evidence for two steady states in"/>
|
| 99 |
+
<jd:note value="// the photosynthetic Calvin cycle. Eur. J. Biochem. 268, 2810--2816 "/>
|
| 100 |
+
<jd:note value="//"/>
|
| 101 |
+
<jd:note value="//Further related information may be found at http://mudshark.brookes.ac.uk"/>
|
| 102 |
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</jd:notes>
|
| 103 |
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|
| 244 |
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|
| 245 |
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|
| 246 |
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|
| 247 |
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|
| 248 |
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|
| 249 |
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|
| 250 |
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<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16526"/>
|
| 251 |
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|
| 252 |
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|
| 253 |
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|
| 254 |
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|
| 255 |
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|
| 256 |
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|
| 257 |
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|
| 258 |
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|
| 259 |
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</rdf:RDF>
|
| 260 |
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|
| 261 |
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|
| 262 |
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|
| 263 |
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<annotation>
|
| 264 |
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|
| 265 |
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|
| 266 |
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|
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|
| 268 |
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|
| 269 |
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|
| 270 |
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<rdf:Bag>
|
| 271 |
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|
| 272 |
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|
| 273 |
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|
| 274 |
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|
| 275 |
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|
| 276 |
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|
| 277 |
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|
| 278 |
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|
| 279 |
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|
| 280 |
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|
| 281 |
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|
| 282 |
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|
| 283 |
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|
| 284 |
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|
| 285 |
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|
| 286 |
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|
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|
| 288 |
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|
| 289 |
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|
| 290 |
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|
| 291 |
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|
| 292 |
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|
| 293 |
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|
| 294 |
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|
| 295 |
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|
| 296 |
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|
| 297 |
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|
| 298 |
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|
| 299 |
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</rdf:RDF>
|
| 300 |
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|
| 301 |
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|
| 302 |
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|
| 303 |
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<annotation>
|
| 304 |
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|
| 305 |
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|
| 306 |
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|
| 307 |
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|
| 308 |
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|
| 309 |
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<jd:shadow name="___ATP_ch_1" x="864" y="441"/>
|
| 310 |
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<jd:shadow name="___ATP_ch_2" x="23" y="246"/>
|
| 311 |
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</jd:listOfShadows>
|
| 312 |
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|
| 313 |
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|
| 314 |
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|
| 315 |
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|
| 316 |
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|
| 317 |
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|
| 318 |
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|
| 319 |
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|
| 320 |
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|
| 321 |
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|
| 322 |
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|
| 323 |
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|
| 324 |
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|
| 325 |
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|
| 326 |
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|
| 327 |
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|
| 328 |
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|
| 329 |
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|
| 330 |
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|
| 331 |
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|
| 332 |
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|
| 333 |
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|
| 334 |
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|
| 335 |
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|
| 336 |
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|
| 337 |
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|
| 338 |
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</rdf:Bag>
|
| 339 |
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|
| 340 |
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|
| 341 |
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|
| 342 |
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|
| 343 |
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|
| 344 |
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|
| 345 |
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</rdf:RDF>
|
| 346 |
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</annotation>
|
| 347 |
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</species>
|
| 348 |
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|
| 349 |
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<annotation>
|
| 350 |
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|
| 351 |
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|
| 352 |
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|
| 353 |
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|
| 354 |
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|
| 355 |
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|
| 356 |
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|
| 357 |
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|
| 358 |
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|
| 359 |
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</rdf:Bag>
|
| 360 |
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|
| 361 |
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|
| 362 |
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|
| 363 |
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|
| 364 |
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|
| 365 |
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|
| 366 |
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</rdf:RDF>
|
| 367 |
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</annotation>
|
| 368 |
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|
| 369 |
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|
| 370 |
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<annotation>
|
| 371 |
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|
| 372 |
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|
| 373 |
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|
| 374 |
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|
| 375 |
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|
| 376 |
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|
| 377 |
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<rdf:Bag>
|
| 378 |
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|
| 379 |
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<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00118"/>
|
| 380 |
+
</rdf:Bag>
|
| 381 |
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</bqbiol:is>
|
| 382 |
+
</rdf:Description>
|
| 383 |
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|
| 384 |
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|
| 385 |
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|
| 386 |
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|
| 387 |
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</rdf:RDF>
|
| 388 |
+
</annotation>
|
| 389 |
+
</species>
|
| 390 |
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|
| 391 |
+
<annotation>
|
| 392 |
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|
| 393 |
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|
| 394 |
+
</jd:display>
|
| 395 |
+
<jd:listOfShadows>
|
| 396 |
+
<jd:shadow name="___Pi_ch_0" x="22" y="140"/>
|
| 397 |
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<jd:shadow name="___Pi_ch_1" x="241" y="124"/>
|
| 398 |
+
<jd:shadow name="___Pi_ch_2" x="426" y="428"/>
|
| 399 |
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<jd:shadow name="___Pi_ch_3" x="175" y="633"/>
|
| 400 |
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<jd:shadow name="___Pi_ch_4" x="535" y="554"/>
|
| 401 |
+
<jd:shadow name="___Pi_ch_5" x="693" y="25"/>
|
| 402 |
+
</jd:listOfShadows>
|
| 403 |
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|
| 404 |
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<rdf:Description rdf:about="#metaid_0000011">
|
| 405 |
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<bqbiol:is>
|
| 406 |
+
<rdf:Bag>
|
| 407 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:18367"/>
|
| 408 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00009"/>
|
| 409 |
+
</rdf:Bag>
|
| 410 |
+
</bqbiol:is>
|
| 411 |
+
</rdf:Description>
|
| 412 |
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|
| 413 |
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|
| 414 |
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|
| 415 |
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|
| 416 |
+
</rdf:RDF>
|
| 417 |
+
</annotation>
|
| 418 |
+
</species>
|
| 419 |
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<species compartment="chloroplast" id="DHAP_ch" initialConcentration="0.29345" metaid="metaid_0000012">
|
| 420 |
+
<annotation>
|
| 421 |
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|
| 422 |
+
<jd:font fontColor="0" fontName="Arial" fontSize="8"/>
|
| 423 |
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</jd:display>
|
| 424 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 425 |
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<rdf:Description rdf:about="#metaid_0000012">
|
| 426 |
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<bqbiol:is>
|
| 427 |
+
<rdf:Bag>
|
| 428 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16108"/>
|
| 429 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00111"/>
|
| 430 |
+
</rdf:Bag>
|
| 431 |
+
</bqbiol:is>
|
| 432 |
+
</rdf:Description>
|
| 433 |
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|
| 434 |
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|
| 435 |
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|
| 436 |
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|
| 437 |
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</rdf:RDF>
|
| 438 |
+
</annotation>
|
| 439 |
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</species>
|
| 440 |
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<species compartment="chloroplast" id="FBP_ch" initialConcentration="0.02776" metaid="metaid_0000013">
|
| 441 |
+
<annotation>
|
| 442 |
+
<jd:display borderType="ntRound" edgeColor="0" edgeThickness="1" fillColor="16777215" iconIndex="-1" selectedEdgeColor="255" x="354" y="429">
|
| 443 |
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|
| 444 |
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</jd:display>
|
| 445 |
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|
| 446 |
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<rdf:Description rdf:about="#metaid_0000013">
|
| 447 |
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<bqbiol:is>
|
| 448 |
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<rdf:Bag>
|
| 449 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:28013"/>
|
| 450 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C05378"/>
|
| 451 |
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</rdf:Bag>
|
| 452 |
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</bqbiol:is>
|
| 453 |
+
</rdf:Description>
|
| 454 |
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|
| 455 |
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|
| 456 |
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|
| 457 |
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|
| 458 |
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</rdf:RDF>
|
| 459 |
+
</annotation>
|
| 460 |
+
</species>
|
| 461 |
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<species compartment="chloroplast" id="F6P_ch" initialConcentration="1.36481" metaid="metaid_0000014">
|
| 462 |
+
<annotation>
|
| 463 |
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|
| 464 |
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|
| 465 |
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</jd:display>
|
| 466 |
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|
| 467 |
+
<rdf:Description rdf:about="#metaid_0000014">
|
| 468 |
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<bqbiol:isVersionOf>
|
| 469 |
+
<rdf:Bag>
|
| 470 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:57634"/>
|
| 471 |
+
</rdf:Bag>
|
| 472 |
+
</bqbiol:isVersionOf>
|
| 473 |
+
</rdf:Description>
|
| 474 |
+
|
| 475 |
+
|
| 476 |
+
|
| 477 |
+
|
| 478 |
+
</rdf:RDF>
|
| 479 |
+
</annotation>
|
| 480 |
+
</species>
|
| 481 |
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<species compartment="chloroplast" id="E4P_ch" initialConcentration="0.41021" metaid="metaid_0000015">
|
| 482 |
+
<annotation>
|
| 483 |
+
<jd:display borderType="ntRound" edgeColor="0" edgeThickness="1" fillColor="16777215" iconIndex="-1" selectedEdgeColor="255" x="354" y="165">
|
| 484 |
+
<jd:font fontColor="0" fontName="Arial" fontSize="8"/>
|
| 485 |
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</jd:display>
|
| 486 |
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|
| 487 |
+
<rdf:Description rdf:about="#metaid_0000015">
|
| 488 |
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<bqbiol:is>
|
| 489 |
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<rdf:Bag>
|
| 490 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:48153"/>
|
| 491 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00279"/>
|
| 492 |
+
</rdf:Bag>
|
| 493 |
+
</bqbiol:is>
|
| 494 |
+
</rdf:Description>
|
| 495 |
+
|
| 496 |
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|
| 497 |
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|
| 498 |
+
|
| 499 |
+
</rdf:RDF>
|
| 500 |
+
</annotation>
|
| 501 |
+
</species>
|
| 502 |
+
<species compartment="chloroplast" id="X5P_ch" initialConcentration="0.00363" metaid="metaid_0000016">
|
| 503 |
+
<annotation>
|
| 504 |
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<jd:display borderType="ntRound" edgeColor="0" edgeThickness="1" fillColor="16777215" iconIndex="-1" selectedEdgeColor="255" x="828" y="164">
|
| 505 |
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|
| 506 |
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</jd:display>
|
| 507 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 508 |
+
<rdf:Description rdf:about="#metaid_0000016">
|
| 509 |
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<bqbiol:is>
|
| 510 |
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<rdf:Bag>
|
| 511 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:16332"/>
|
| 512 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00231"/>
|
| 513 |
+
</rdf:Bag>
|
| 514 |
+
</bqbiol:is>
|
| 515 |
+
</rdf:Description>
|
| 516 |
+
|
| 517 |
+
|
| 518 |
+
|
| 519 |
+
|
| 520 |
+
</rdf:RDF>
|
| 521 |
+
</annotation>
|
| 522 |
+
</species>
|
| 523 |
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<species compartment="chloroplast" id="SBP_ch" initialConcentration="1.56486" metaid="metaid_0000017">
|
| 524 |
+
<annotation>
|
| 525 |
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<jd:display borderType="ntRound" edgeColor="0" edgeThickness="1" fillColor="16777215" iconIndex="-1" selectedEdgeColor="255" x="515" y="70">
|
| 526 |
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|
| 527 |
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</jd:display>
|
| 528 |
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|
| 529 |
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<rdf:Description rdf:about="#metaid_0000017">
|
| 530 |
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<bqbiol:is>
|
| 531 |
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<rdf:Bag>
|
| 532 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:17969"/>
|
| 533 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C00447"/>
|
| 534 |
+
</rdf:Bag>
|
| 535 |
+
</bqbiol:is>
|
| 536 |
+
</rdf:Description>
|
| 537 |
+
|
| 538 |
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|
| 539 |
+
|
| 540 |
+
|
| 541 |
+
</rdf:RDF>
|
| 542 |
+
</annotation>
|
| 543 |
+
</species>
|
| 544 |
+
<species compartment="chloroplast" id="S7P_ch" initialConcentration="0.00541" metaid="metaid_0000018">
|
| 545 |
+
<annotation>
|
| 546 |
+
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|
| 547 |
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<jd:font fontColor="0" fontName="Arial" fontSize="8"/>
|
| 548 |
+
</jd:display>
|
| 549 |
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<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 550 |
+
<rdf:Description rdf:about="#metaid_0000018">
|
| 551 |
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<bqbiol:is>
|
| 552 |
+
<rdf:Bag>
|
| 553 |
+
<rdf:li rdf:resource="http://identifiers.org/chebi/CHEBI:15721"/>
|
| 554 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.compound/C05382"/>
|
| 555 |
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|
| 557 |
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| 559 |
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| 560 |
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|
| 561 |
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|
| 562 |
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| 563 |
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|
| 564 |
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|
| 565 |
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|
| 566 |
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|
| 567 |
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|
| 571 |
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|
| 572 |
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|
| 573 |
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|
| 574 |
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|
| 575 |
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|
| 576 |
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|
| 577 |
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|
| 578 |
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| 580 |
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| 582 |
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|
| 583 |
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|
| 584 |
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|
| 585 |
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|
| 586 |
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|
| 587 |
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|
| 588 |
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|
| 592 |
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|
| 593 |
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|
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|
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|
| 596 |
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|
| 597 |
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|
| 598 |
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|
| 599 |
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| 600 |
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|
| 601 |
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|
| 602 |
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|
| 603 |
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|
| 604 |
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|
| 605 |
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|
| 606 |
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|
| 607 |
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|
| 608 |
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|
| 609 |
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|
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|
| 611 |
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|
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|
| 613 |
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|
| 614 |
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|
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|
| 616 |
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|
| 617 |
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|
| 618 |
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|
| 619 |
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|
| 620 |
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|
| 621 |
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|
| 622 |
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|
| 623 |
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|
| 624 |
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|
| 625 |
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|
| 626 |
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|
| 627 |
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|
| 628 |
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|
| 629 |
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|
| 630 |
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|
| 631 |
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|
| 632 |
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|
| 633 |
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|
| 634 |
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| 635 |
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|
| 637 |
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|
| 638 |
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|
| 639 |
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|
| 640 |
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|
| 641 |
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|
| 642 |
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|
| 643 |
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|
| 644 |
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| 645 |
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|
| 646 |
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|
| 647 |
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|
| 648 |
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|
| 649 |
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|
| 650 |
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|
| 651 |
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|
| 652 |
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|
| 653 |
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|
| 654 |
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|
| 655 |
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| 656 |
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|
| 658 |
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|
| 659 |
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|
| 660 |
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|
| 661 |
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|
| 662 |
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|
| 663 |
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|
| 664 |
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|
| 665 |
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|
| 666 |
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|
| 667 |
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|
| 668 |
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|
| 669 |
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|
| 670 |
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|
| 671 |
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|
| 672 |
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|
| 673 |
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|
| 674 |
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|
| 675 |
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|
| 676 |
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| 677 |
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|
| 679 |
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|
| 680 |
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|
| 681 |
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|
| 682 |
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|
| 683 |
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|
| 684 |
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|
| 685 |
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|
| 686 |
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|
| 687 |
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|
| 688 |
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|
| 689 |
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|
| 690 |
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|
| 691 |
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|
| 692 |
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|
| 693 |
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|
| 694 |
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|
| 695 |
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|
| 696 |
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| 697 |
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| 698 |
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| 699 |
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|
| 700 |
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|
| 701 |
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|
| 702 |
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|
| 703 |
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|
| 704 |
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</rdf:Bag>
|
| 705 |
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</bqbiol:is>
|
| 706 |
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|
| 707 |
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|
| 708 |
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|
| 709 |
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|
| 710 |
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|
| 711 |
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</rdf:RDF>
|
| 712 |
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|
| 713 |
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|
| 714 |
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|
| 715 |
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|
| 716 |
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|
| 717 |
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|
| 718 |
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|
| 719 |
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|
| 720 |
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|
| 721 |
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|
| 722 |
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|
| 723 |
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|
| 724 |
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|
| 725 |
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|
| 726 |
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|
| 727 |
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|
| 728 |
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|
| 729 |
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|
| 730 |
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|
| 731 |
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|
| 732 |
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|
| 733 |
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|
| 734 |
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|
| 735 |
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|
| 736 |
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|
| 737 |
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|
| 738 |
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|
| 739 |
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|
| 740 |
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|
| 741 |
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|
| 742 |
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|
| 743 |
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|
| 744 |
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| 745 |
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|
| 746 |
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|
| 747 |
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|
| 748 |
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|
| 749 |
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|
| 750 |
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|
| 751 |
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|
| 752 |
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|
| 753 |
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|
| 754 |
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|
| 755 |
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|
| 756 |
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|
| 757 |
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|
| 758 |
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|
| 759 |
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|
| 760 |
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|
| 761 |
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|
| 762 |
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|
| 763 |
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|
| 764 |
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| 765 |
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| 766 |
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|
| 767 |
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|
| 768 |
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|
| 769 |
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|
| 770 |
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|
| 771 |
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|
| 772 |
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|
| 773 |
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|
| 774 |
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|
| 775 |
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|
| 776 |
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|
| 777 |
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|
| 778 |
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|
| 779 |
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|
| 780 |
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|
| 781 |
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|
| 782 |
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|
| 783 |
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|
| 784 |
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|
| 785 |
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| 786 |
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|
| 787 |
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|
| 788 |
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|
| 789 |
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|
| 790 |
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|
| 791 |
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|
| 792 |
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|
| 793 |
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|
| 794 |
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|
| 795 |
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|
| 796 |
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|
| 797 |
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|
| 798 |
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|
| 799 |
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|
| 800 |
+
</annotation>
|
| 801 |
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|
| 802 |
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|
| 803 |
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|
| 804 |
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|
| 805 |
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| 806 |
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|
| 808 |
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|
| 809 |
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|
| 810 |
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|
| 811 |
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|
| 812 |
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|
| 813 |
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|
| 814 |
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|
| 815 |
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|
| 816 |
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|
| 817 |
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|
| 818 |
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|
| 819 |
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|
| 820 |
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|
| 821 |
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|
| 822 |
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|
| 823 |
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|
| 824 |
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|
| 825 |
+
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|
| 826 |
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|
| 827 |
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|
| 828 |
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|
| 829 |
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|
| 830 |
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|
| 831 |
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|
| 832 |
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|
| 833 |
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|
| 834 |
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|
| 835 |
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|
| 836 |
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|
| 837 |
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| 838 |
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|
| 839 |
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|
| 840 |
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|
| 841 |
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|
| 842 |
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|
| 843 |
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|
| 844 |
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|
| 845 |
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|
| 846 |
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|
| 847 |
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|
| 848 |
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|
| 849 |
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|
| 850 |
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|
| 851 |
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|
| 852 |
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|
| 853 |
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|
| 854 |
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|
| 855 |
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|
| 856 |
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|
| 857 |
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|
| 858 |
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|
| 859 |
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|
| 860 |
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|
| 861 |
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|
| 862 |
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|
| 863 |
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|
| 864 |
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|
| 865 |
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|
| 866 |
+
<modifierSpeciesReference metaid="_3a3320bc-acf8-46e0-9ae7-106ee344f7f5" species="FBP_ch"/>
|
| 867 |
+
<modifierSpeciesReference metaid="db8b266b-57d6-41b2-835c-64daed84fbdb" species="SBP_ch"/>
|
| 868 |
+
<modifierSpeciesReference metaid="f4798b06-8e11-43c6-8883-7bd1be7d8e50" species="Pi_ch"/>
|
| 869 |
+
<modifierSpeciesReference metaid="_64b351ca-ce3b-45c1-9057-d50c24eab5f7" species="x_NADPH_ch"/>
|
| 870 |
+
</listOfModifiers>
|
| 871 |
+
<kineticLaw metaid="_56bf45a9-2b37-43d9-b483-a2ef7d332e21">
|
| 872 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 873 |
+
<apply>
|
| 874 |
+
<divide/>
|
| 875 |
+
<apply>
|
| 876 |
+
<times/>
|
| 877 |
+
<ci> Light_on </ci>
|
| 878 |
+
<ci> Rbco_vm </ci>
|
| 879 |
+
<ci> RuBP_ch </ci>
|
| 880 |
+
<ci> chloroplast </ci>
|
| 881 |
+
</apply>
|
| 882 |
+
<apply>
|
| 883 |
+
<plus/>
|
| 884 |
+
<ci> RuBP_ch </ci>
|
| 885 |
+
<apply>
|
| 886 |
+
<times/>
|
| 887 |
+
<ci> Rbco_km </ci>
|
| 888 |
+
<apply>
|
| 889 |
+
<plus/>
|
| 890 |
+
<cn type="integer"> 1 </cn>
|
| 891 |
+
<apply>
|
| 892 |
+
<divide/>
|
| 893 |
+
<ci> PGA_ch </ci>
|
| 894 |
+
<ci> Rbco_KiPGA </ci>
|
| 895 |
+
</apply>
|
| 896 |
+
<apply>
|
| 897 |
+
<divide/>
|
| 898 |
+
<ci> FBP_ch </ci>
|
| 899 |
+
<ci> Rbco_KiFBP </ci>
|
| 900 |
+
</apply>
|
| 901 |
+
<apply>
|
| 902 |
+
<divide/>
|
| 903 |
+
<ci> SBP_ch </ci>
|
| 904 |
+
<ci> Rbco_KiSBP </ci>
|
| 905 |
+
</apply>
|
| 906 |
+
<apply>
|
| 907 |
+
<divide/>
|
| 908 |
+
<ci> Pi_ch </ci>
|
| 909 |
+
<ci> Rbco_KiPi </ci>
|
| 910 |
+
</apply>
|
| 911 |
+
<apply>
|
| 912 |
+
<divide/>
|
| 913 |
+
<ci> x_NADPH_ch </ci>
|
| 914 |
+
<ci> Rbco_KiNADPH </ci>
|
| 915 |
+
</apply>
|
| 916 |
+
</apply>
|
| 917 |
+
</apply>
|
| 918 |
+
</apply>
|
| 919 |
+
</apply>
|
| 920 |
+
</math>
|
| 921 |
+
<listOfParameters>
|
| 922 |
+
<parameter id="Rbco_vm" metaid="_513822" value="340"/>
|
| 923 |
+
<parameter id="Rbco_km" metaid="_513823" value="0.02"/>
|
| 924 |
+
<parameter id="Rbco_KiPGA" metaid="_513824" value="0.84"/>
|
| 925 |
+
<parameter id="Rbco_KiFBP" metaid="_513825" value="0.04"/>
|
| 926 |
+
<parameter id="Rbco_KiSBP" metaid="_513827" value="0.075"/>
|
| 927 |
+
<parameter id="Rbco_KiPi" metaid="_513828" value="0.9"/>
|
| 928 |
+
<parameter id="Rbco_KiNADPH" metaid="_513829" value="0.07"/>
|
| 929 |
+
</listOfParameters>
|
| 930 |
+
</kineticLaw>
|
| 931 |
+
</reaction>
|
| 932 |
+
<reaction id="E2" metaid="metaid_0000045" reversible="false">
|
| 933 |
+
<annotation>
|
| 934 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 935 |
+
<jd:pt x="857" y="525"/>
|
| 936 |
+
<jd:pt x="880" y="525"/>
|
| 937 |
+
<jd:pt x="904" y="526"/>
|
| 938 |
+
<jd:pt x="887" y="491"/>
|
| 939 |
+
<jd:pt x="904" y="526"/>
|
| 940 |
+
<jd:pt x="810" y="524"/>
|
| 941 |
+
<jd:pt x="797" y="523"/>
|
| 942 |
+
<jd:pt x="810" y="524"/>
|
| 943 |
+
<jd:pt x="810" y="498"/>
|
| 944 |
+
</jd:arcSeg>
|
| 945 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 946 |
+
<rdf:Description rdf:about="#metaid_0000045">
|
| 947 |
+
<bqbiol:isVersionOf>
|
| 948 |
+
<rdf:Bag>
|
| 949 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.2.3"/>
|
| 950 |
+
</rdf:Bag>
|
| 951 |
+
</bqbiol:isVersionOf>
|
| 952 |
+
|
| 953 |
+
<bqbiol:is>
|
| 954 |
+
<rdf:Bag>
|
| 955 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01512"/>
|
| 956 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1186"/>
|
| 957 |
+
</rdf:Bag>
|
| 958 |
+
</bqbiol:is>
|
| 959 |
+
</rdf:Description>
|
| 960 |
+
|
| 961 |
+
|
| 962 |
+
|
| 963 |
+
|
| 964 |
+
</rdf:RDF>
|
| 965 |
+
</annotation>
|
| 966 |
+
<listOfReactants>
|
| 967 |
+
<speciesReference metaid="_34615088-a9fc-4e4a-b28e-2de94e36142e" species="PGA_ch"/>
|
| 968 |
+
<speciesReference metaid="_3420cd85-d136-4dbd-8ef3-2e14bc1f26e6" species="ATP_ch">
|
| 969 |
+
<annotation>
|
| 970 |
+
<jd:shadowRef shadowRef="___ATP_ch_1"/>
|
| 971 |
+
</annotation>
|
| 972 |
+
</speciesReference>
|
| 973 |
+
</listOfReactants>
|
| 974 |
+
<listOfProducts>
|
| 975 |
+
<speciesReference metaid="_0161c9fd-0db0-4538-9cea-32a04ca9be38" species="BPGA_ch"/>
|
| 976 |
+
<speciesReference metaid="_9e279344-990e-495e-82c5-4f7ebc230b51" species="ADP_ch">
|
| 977 |
+
<annotation>
|
| 978 |
+
<jd:shadowRef shadowRef="___ADP_ch_1"/>
|
| 979 |
+
</annotation>
|
| 980 |
+
</speciesReference>
|
| 981 |
+
</listOfProducts>
|
| 982 |
+
<kineticLaw metaid="_359c1ba8-deae-42a0-9da3-9ca492e8a884">
|
| 983 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 984 |
+
<apply>
|
| 985 |
+
<times/>
|
| 986 |
+
<ci> Light_on </ci>
|
| 987 |
+
<ci> PGK_v </ci>
|
| 988 |
+
<ci> chloroplast </ci>
|
| 989 |
+
<apply>
|
| 990 |
+
<minus/>
|
| 991 |
+
<apply>
|
| 992 |
+
<times/>
|
| 993 |
+
<ci> PGA_ch </ci>
|
| 994 |
+
<ci> ATP_ch </ci>
|
| 995 |
+
</apply>
|
| 996 |
+
<apply>
|
| 997 |
+
<divide/>
|
| 998 |
+
<apply>
|
| 999 |
+
<times/>
|
| 1000 |
+
<ci> BPGA_ch </ci>
|
| 1001 |
+
<ci> ADP_ch </ci>
|
| 1002 |
+
</apply>
|
| 1003 |
+
<ci> q2 </ci>
|
| 1004 |
+
</apply>
|
| 1005 |
+
</apply>
|
| 1006 |
+
</apply>
|
| 1007 |
+
</math>
|
| 1008 |
+
<listOfParameters>
|
| 1009 |
+
<parameter id="PGK_v" metaid="_513830" value="500000000"/>
|
| 1010 |
+
<parameter id="q2" metaid="_513831" value="0.00031"/>
|
| 1011 |
+
</listOfParameters>
|
| 1012 |
+
</kineticLaw>
|
| 1013 |
+
</reaction>
|
| 1014 |
+
<reaction id="E3" metaid="metaid_0000050" reversible="false">
|
| 1015 |
+
<annotation>
|
| 1016 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 1017 |
+
<jd:pt x="610" y="521"/>
|
| 1018 |
+
<jd:pt x="653" y="526"/>
|
| 1019 |
+
<jd:pt x="649" y="521"/>
|
| 1020 |
+
<jd:pt x="651" y="522"/>
|
| 1021 |
+
<jd:pt x="649" y="521"/>
|
| 1022 |
+
<jd:pt x="649" y="488"/>
|
| 1023 |
+
<jd:pt x="649" y="521"/>
|
| 1024 |
+
<jd:pt x="571" y="521"/>
|
| 1025 |
+
<jd:pt x="575" y="493"/>
|
| 1026 |
+
<jd:pt x="571" y="521"/>
|
| 1027 |
+
<jd:pt x="550" y="520"/>
|
| 1028 |
+
<jd:pt x="571" y="521"/>
|
| 1029 |
+
<jd:pt x="576" y="524"/>
|
| 1030 |
+
</jd:arcSeg>
|
| 1031 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1032 |
+
<rdf:Description rdf:about="#metaid_0000050">
|
| 1033 |
+
<bqbiol:isVersionOf>
|
| 1034 |
+
<rdf:Bag>
|
| 1035 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/1.2.1.13"/>
|
| 1036 |
+
</rdf:Bag>
|
| 1037 |
+
</bqbiol:isVersionOf>
|
| 1038 |
+
|
| 1039 |
+
<bqbiol:is>
|
| 1040 |
+
<rdf:Bag>
|
| 1041 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01063"/>
|
| 1042 |
+
</rdf:Bag>
|
| 1043 |
+
</bqbiol:is>
|
| 1044 |
+
</rdf:Description>
|
| 1045 |
+
|
| 1046 |
+
|
| 1047 |
+
|
| 1048 |
+
|
| 1049 |
+
</rdf:RDF>
|
| 1050 |
+
</annotation>
|
| 1051 |
+
<listOfReactants>
|
| 1052 |
+
<speciesReference metaid="dbe6284c-afa3-4bdd-9119-fd42f902730c" species="x_NADPH_ch"/>
|
| 1053 |
+
<speciesReference metaid="_5caecc97-51ca-41a0-8be2-584f05049a40" species="BPGA_ch"/>
|
| 1054 |
+
<speciesReference metaid="_33d4393d-8cf3-4aeb-9e64-3b96adb33962" species="x_Proton_ch"/>
|
| 1055 |
+
</listOfReactants>
|
| 1056 |
+
<listOfProducts>
|
| 1057 |
+
<speciesReference metaid="_017af2be-072c-45a1-811c-c657e677a40b" species="x_NADP_ch"/>
|
| 1058 |
+
<speciesReference metaid="_3b7a2511-f775-48f6-8ca8-7bca886908ce" species="GAP_ch"/>
|
| 1059 |
+
<speciesReference metaid="_06cd5f96-499c-4cdf-bd72-dfe3f41ac749" species="Pi_ch">
|
| 1060 |
+
<annotation>
|
| 1061 |
+
<jd:shadowRef shadowRef="___Pi_ch_4"/>
|
| 1062 |
+
</annotation>
|
| 1063 |
+
</speciesReference>
|
| 1064 |
+
</listOfProducts>
|
| 1065 |
+
<kineticLaw metaid="_2fc2cc49-ed52-4775-bfac-75b89efe723c">
|
| 1066 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1067 |
+
<apply>
|
| 1068 |
+
<times/>
|
| 1069 |
+
<ci> Light_on </ci>
|
| 1070 |
+
<ci> G3Pdh_v </ci>
|
| 1071 |
+
<ci> chloroplast </ci>
|
| 1072 |
+
<apply>
|
| 1073 |
+
<minus/>
|
| 1074 |
+
<apply>
|
| 1075 |
+
<times/>
|
| 1076 |
+
<ci> BPGA_ch </ci>
|
| 1077 |
+
<ci> x_NADPH_ch </ci>
|
| 1078 |
+
<ci> x_Proton_ch </ci>
|
| 1079 |
+
</apply>
|
| 1080 |
+
<apply>
|
| 1081 |
+
<divide/>
|
| 1082 |
+
<apply>
|
| 1083 |
+
<times/>
|
| 1084 |
+
<ci> x_NADP_ch </ci>
|
| 1085 |
+
<ci> GAP_ch </ci>
|
| 1086 |
+
<ci> Pi_ch </ci>
|
| 1087 |
+
</apply>
|
| 1088 |
+
<ci> q3 </ci>
|
| 1089 |
+
</apply>
|
| 1090 |
+
</apply>
|
| 1091 |
+
</apply>
|
| 1092 |
+
</math>
|
| 1093 |
+
<listOfParameters>
|
| 1094 |
+
<parameter id="G3Pdh_v" metaid="_513832" value="500000000"/>
|
| 1095 |
+
<parameter id="q3" metaid="_513833" value="16000000"/>
|
| 1096 |
+
</listOfParameters>
|
| 1097 |
+
</kineticLaw>
|
| 1098 |
+
</reaction>
|
| 1099 |
+
<reaction id="E4" metaid="metaid_0000032">
|
| 1100 |
+
<annotation>
|
| 1101 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1102 |
+
<jd:pt x="380" y="522"/>
|
| 1103 |
+
<jd:pt x="378" y="523"/>
|
| 1104 |
+
<jd:pt x="378" y="523"/>
|
| 1105 |
+
</jd:arcSeg>
|
| 1106 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1107 |
+
<rdf:Description rdf:about="#metaid_0000032">
|
| 1108 |
+
<bqbiol:isVersionOf>
|
| 1109 |
+
<rdf:Bag>
|
| 1110 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.1"/>
|
| 1111 |
+
</rdf:Bag>
|
| 1112 |
+
</bqbiol:isVersionOf>
|
| 1113 |
+
|
| 1114 |
+
<bqbiol:is>
|
| 1115 |
+
<rdf:Bag>
|
| 1116 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01015"/>
|
| 1117 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_775"/>
|
| 1118 |
+
</rdf:Bag>
|
| 1119 |
+
</bqbiol:is>
|
| 1120 |
+
</rdf:Description>
|
| 1121 |
+
|
| 1122 |
+
|
| 1123 |
+
|
| 1124 |
+
|
| 1125 |
+
</rdf:RDF>
|
| 1126 |
+
</annotation>
|
| 1127 |
+
<listOfReactants>
|
| 1128 |
+
<speciesReference metaid="_21be7544-ccd8-4f61-8fa1-6a02cb48ef42" species="GAP_ch"/>
|
| 1129 |
+
</listOfReactants>
|
| 1130 |
+
<listOfProducts>
|
| 1131 |
+
<speciesReference metaid="_4dee9985-b72c-4048-91a6-7beac299c0db" species="DHAP_ch"/>
|
| 1132 |
+
</listOfProducts>
|
| 1133 |
+
<kineticLaw metaid="faca373b-a5b5-4517-be27-d1bdd4c01337">
|
| 1134 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1135 |
+
<apply>
|
| 1136 |
+
<times/>
|
| 1137 |
+
<ci> chloroplast </ci>
|
| 1138 |
+
<ci> TPI_v </ci>
|
| 1139 |
+
<apply>
|
| 1140 |
+
<minus/>
|
| 1141 |
+
<ci> GAP_ch </ci>
|
| 1142 |
+
<apply>
|
| 1143 |
+
<divide/>
|
| 1144 |
+
<ci> DHAP_ch </ci>
|
| 1145 |
+
<ci> q4 </ci>
|
| 1146 |
+
</apply>
|
| 1147 |
+
</apply>
|
| 1148 |
+
</apply>
|
| 1149 |
+
</math>
|
| 1150 |
+
<listOfParameters>
|
| 1151 |
+
<parameter id="TPI_v" metaid="_513834" value="500000000"/>
|
| 1152 |
+
<parameter id="q4" metaid="_513835" value="22"/>
|
| 1153 |
+
</listOfParameters>
|
| 1154 |
+
</kineticLaw>
|
| 1155 |
+
</reaction>
|
| 1156 |
+
<reaction id="E5" metaid="metaid_0000033">
|
| 1157 |
+
<annotation>
|
| 1158 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1159 |
+
<jd:pt x="372" y="487"/>
|
| 1160 |
+
<jd:pt x="380" y="495"/>
|
| 1161 |
+
<jd:pt x="372" y="502"/>
|
| 1162 |
+
<jd:pt x="355" y="493"/>
|
| 1163 |
+
<jd:pt x="372" y="502"/>
|
| 1164 |
+
<jd:pt x="372" y="472"/>
|
| 1165 |
+
<jd:pt x="372" y="472"/>
|
| 1166 |
+
</jd:arcSeg>
|
| 1167 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1168 |
+
<rdf:Description rdf:about="#metaid_0000033">
|
| 1169 |
+
<bqbiol:isVersionOf>
|
| 1170 |
+
<rdf:Bag>
|
| 1171 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.13"/>
|
| 1172 |
+
</rdf:Bag>
|
| 1173 |
+
</bqbiol:isVersionOf>
|
| 1174 |
+
|
| 1175 |
+
<bqbiol:is>
|
| 1176 |
+
<rdf:Bag>
|
| 1177 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01070"/>
|
| 1178 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1602"/>
|
| 1179 |
+
</rdf:Bag>
|
| 1180 |
+
</bqbiol:is>
|
| 1181 |
+
</rdf:Description>
|
| 1182 |
+
|
| 1183 |
+
|
| 1184 |
+
|
| 1185 |
+
|
| 1186 |
+
</rdf:RDF>
|
| 1187 |
+
</annotation>
|
| 1188 |
+
<listOfReactants>
|
| 1189 |
+
<speciesReference metaid="_8d026924-d6e9-4766-ab66-4c3374c2b5ef" species="GAP_ch"/>
|
| 1190 |
+
<speciesReference metaid="_79d617ff-680b-4b6f-aab9-ac07095fc225" species="DHAP_ch"/>
|
| 1191 |
+
</listOfReactants>
|
| 1192 |
+
<listOfProducts>
|
| 1193 |
+
<speciesReference metaid="_8a3e809c-3580-465f-8f8d-98b07ff93aa7" species="FBP_ch"/>
|
| 1194 |
+
</listOfProducts>
|
| 1195 |
+
<kineticLaw metaid="_31f86627-f454-45d1-9910-f20e7a42f53c">
|
| 1196 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1197 |
+
<apply>
|
| 1198 |
+
<times/>
|
| 1199 |
+
<ci> F_Aldo_v </ci>
|
| 1200 |
+
<ci> chloroplast </ci>
|
| 1201 |
+
<apply>
|
| 1202 |
+
<minus/>
|
| 1203 |
+
<apply>
|
| 1204 |
+
<times/>
|
| 1205 |
+
<ci> DHAP_ch </ci>
|
| 1206 |
+
<ci> GAP_ch </ci>
|
| 1207 |
+
</apply>
|
| 1208 |
+
<apply>
|
| 1209 |
+
<divide/>
|
| 1210 |
+
<ci> FBP_ch </ci>
|
| 1211 |
+
<ci> q5 </ci>
|
| 1212 |
+
</apply>
|
| 1213 |
+
</apply>
|
| 1214 |
+
</apply>
|
| 1215 |
+
</math>
|
| 1216 |
+
<listOfParameters>
|
| 1217 |
+
<parameter id="F_Aldo_v" metaid="_513837" value="500000000"/>
|
| 1218 |
+
<parameter id="q5" metaid="_513839" value="7.1"/>
|
| 1219 |
+
</listOfParameters>
|
| 1220 |
+
</kineticLaw>
|
| 1221 |
+
</reaction>
|
| 1222 |
+
<reaction id="E6" metaid="metaid_0000048" reversible="false">
|
| 1223 |
+
<annotation>
|
| 1224 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 1225 |
+
<jd:pt x="371" y="374"/>
|
| 1226 |
+
<jd:pt x="372" y="398"/>
|
| 1227 |
+
<jd:pt x="371" y="389"/>
|
| 1228 |
+
<jd:pt x="405" y="367"/>
|
| 1229 |
+
<jd:pt x="371" y="389"/>
|
| 1230 |
+
<jd:pt x="371" y="359"/>
|
| 1231 |
+
<jd:pt x="370" y="371"/>
|
| 1232 |
+
</jd:arcSeg>
|
| 1233 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1234 |
+
<rdf:Description rdf:about="#metaid_0000048">
|
| 1235 |
+
<bqbiol:isVersionOf>
|
| 1236 |
+
<rdf:Bag>
|
| 1237 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.11"/>
|
| 1238 |
+
</rdf:Bag>
|
| 1239 |
+
</bqbiol:isVersionOf>
|
| 1240 |
+
|
| 1241 |
+
<bqbiol:is>
|
| 1242 |
+
<rdf:Bag>
|
| 1243 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R04780"/>
|
| 1244 |
+
</rdf:Bag>
|
| 1245 |
+
</bqbiol:is>
|
| 1246 |
+
</rdf:Description>
|
| 1247 |
+
|
| 1248 |
+
|
| 1249 |
+
|
| 1250 |
+
|
| 1251 |
+
</rdf:RDF>
|
| 1252 |
+
</annotation>
|
| 1253 |
+
<listOfReactants>
|
| 1254 |
+
<speciesReference metaid="b3887ca6-4357-4bc7-ac76-8074a49f6af7" species="FBP_ch"/>
|
| 1255 |
+
</listOfReactants>
|
| 1256 |
+
<listOfProducts>
|
| 1257 |
+
<speciesReference metaid="_08bf9bea-f91a-4100-a264-77216c9c55d9" species="F6P_ch"/>
|
| 1258 |
+
<speciesReference metaid="_0feefa56-70b5-40a5-9295-34cf3d6657cc" species="Pi_ch"/>
|
| 1259 |
+
</listOfProducts>
|
| 1260 |
+
<kineticLaw metaid="_8371f015-f0f2-4ee7-b689-758367e7e2c5">
|
| 1261 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1262 |
+
<apply>
|
| 1263 |
+
<divide/>
|
| 1264 |
+
<apply>
|
| 1265 |
+
<times/>
|
| 1266 |
+
<ci> Light_on </ci>
|
| 1267 |
+
<ci> FBPase_ch_vm </ci>
|
| 1268 |
+
<ci> FBP_ch </ci>
|
| 1269 |
+
<ci> chloroplast </ci>
|
| 1270 |
+
</apply>
|
| 1271 |
+
<apply>
|
| 1272 |
+
<plus/>
|
| 1273 |
+
<ci> FBP_ch </ci>
|
| 1274 |
+
<apply>
|
| 1275 |
+
<times/>
|
| 1276 |
+
<ci> FBPase_ch_km </ci>
|
| 1277 |
+
<apply>
|
| 1278 |
+
<plus/>
|
| 1279 |
+
<cn type="integer"> 1 </cn>
|
| 1280 |
+
<apply>
|
| 1281 |
+
<divide/>
|
| 1282 |
+
<ci> F6P_ch </ci>
|
| 1283 |
+
<ci> FBPase_ch_KiF6P </ci>
|
| 1284 |
+
</apply>
|
| 1285 |
+
<apply>
|
| 1286 |
+
<divide/>
|
| 1287 |
+
<ci> Pi_ch </ci>
|
| 1288 |
+
<ci> FBPase_ch_KiPi </ci>
|
| 1289 |
+
</apply>
|
| 1290 |
+
</apply>
|
| 1291 |
+
</apply>
|
| 1292 |
+
</apply>
|
| 1293 |
+
</apply>
|
| 1294 |
+
</math>
|
| 1295 |
+
<listOfParameters>
|
| 1296 |
+
<parameter id="FBPase_ch_vm" metaid="_513841" value="200"/>
|
| 1297 |
+
<parameter id="FBPase_ch_km" metaid="_513843" value="0.03"/>
|
| 1298 |
+
<parameter id="FBPase_ch_KiF6P" metaid="_513844" value="0.7"/>
|
| 1299 |
+
<parameter id="FBPase_ch_KiPi" metaid="_513845" value="12"/>
|
| 1300 |
+
</listOfParameters>
|
| 1301 |
+
</kineticLaw>
|
| 1302 |
+
</reaction>
|
| 1303 |
+
<reaction id="E7" metaid="metaid_0000034">
|
| 1304 |
+
<annotation>
|
| 1305 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1306 |
+
<jd:pt x="371" y="249"/>
|
| 1307 |
+
<jd:pt x="492" y="200"/>
|
| 1308 |
+
<jd:pt x="371" y="278"/>
|
| 1309 |
+
<jd:pt x="372" y="277"/>
|
| 1310 |
+
<jd:pt x="371" y="278"/>
|
| 1311 |
+
<jd:pt x="371" y="220"/>
|
| 1312 |
+
<jd:pt x="406" y="171"/>
|
| 1313 |
+
<jd:pt x="371" y="220"/>
|
| 1314 |
+
<jd:pt x="372" y="219"/>
|
| 1315 |
+
</jd:arcSeg>
|
| 1316 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1317 |
+
<rdf:Description rdf:about="#metaid_0000034">
|
| 1318 |
+
<bqbiol:isVersionOf>
|
| 1319 |
+
<rdf:Bag>
|
| 1320 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/>
|
| 1321 |
+
</rdf:Bag>
|
| 1322 |
+
</bqbiol:isVersionOf>
|
| 1323 |
+
|
| 1324 |
+
<bqbiol:is>
|
| 1325 |
+
<rdf:Bag>
|
| 1326 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01830"/>
|
| 1327 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1811"/>
|
| 1328 |
+
</rdf:Bag>
|
| 1329 |
+
</bqbiol:is>
|
| 1330 |
+
</rdf:Description>
|
| 1331 |
+
|
| 1332 |
+
|
| 1333 |
+
|
| 1334 |
+
|
| 1335 |
+
</rdf:RDF>
|
| 1336 |
+
</annotation>
|
| 1337 |
+
<listOfReactants>
|
| 1338 |
+
<speciesReference metaid="_11eb98fa-f85c-4e2a-9b86-edb2d2313924" species="GAP_ch"/>
|
| 1339 |
+
<speciesReference metaid="_8730be87-bfe0-4530-88fa-565ddbe959e9" species="F6P_ch"/>
|
| 1340 |
+
</listOfReactants>
|
| 1341 |
+
<listOfProducts>
|
| 1342 |
+
<speciesReference metaid="_0fcc129d-8f3f-47d8-83d2-544b561e5219" species="X5P_ch"/>
|
| 1343 |
+
<speciesReference metaid="a28b9972-62f3-450c-b321-a7424feebfcc" species="E4P_ch"/>
|
| 1344 |
+
</listOfProducts>
|
| 1345 |
+
<kineticLaw metaid="fd107a5c-d95d-4248-8306-0916f8eaf86c">
|
| 1346 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1347 |
+
<apply>
|
| 1348 |
+
<times/>
|
| 1349 |
+
<ci> chloroplast </ci>
|
| 1350 |
+
<ci> F_TKL_v </ci>
|
| 1351 |
+
<apply>
|
| 1352 |
+
<minus/>
|
| 1353 |
+
<apply>
|
| 1354 |
+
<times/>
|
| 1355 |
+
<ci> F6P_ch </ci>
|
| 1356 |
+
<ci> GAP_ch </ci>
|
| 1357 |
+
</apply>
|
| 1358 |
+
<apply>
|
| 1359 |
+
<divide/>
|
| 1360 |
+
<apply>
|
| 1361 |
+
<times/>
|
| 1362 |
+
<ci> E4P_ch </ci>
|
| 1363 |
+
<ci> X5P_ch </ci>
|
| 1364 |
+
</apply>
|
| 1365 |
+
<ci> q7 </ci>
|
| 1366 |
+
</apply>
|
| 1367 |
+
</apply>
|
| 1368 |
+
</apply>
|
| 1369 |
+
</math>
|
| 1370 |
+
<listOfParameters>
|
| 1371 |
+
<parameter id="F_TKL_v" metaid="_513846" value="500000000"/>
|
| 1372 |
+
<parameter id="q7" metaid="_513847" value="0.084"/>
|
| 1373 |
+
</listOfParameters>
|
| 1374 |
+
</kineticLaw>
|
| 1375 |
+
</reaction>
|
| 1376 |
+
<reaction id="E8" metaid="metaid_0000035">
|
| 1377 |
+
<annotation>
|
| 1378 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1379 |
+
<jd:pt x="405" y="80"/>
|
| 1380 |
+
<jd:pt x="250" y="53"/>
|
| 1381 |
+
<jd:pt x="372" y="82"/>
|
| 1382 |
+
<jd:pt x="371" y="69"/>
|
| 1383 |
+
<jd:pt x="372" y="82"/>
|
| 1384 |
+
<jd:pt x="438" y="78"/>
|
| 1385 |
+
<jd:pt x="456" y="78"/>
|
| 1386 |
+
</jd:arcSeg>
|
| 1387 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1388 |
+
<rdf:Description rdf:about="#metaid_0000035">
|
| 1389 |
+
<bqbiol:isVersionOf>
|
| 1390 |
+
<rdf:Bag>
|
| 1391 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/4.1.2.13"/>
|
| 1392 |
+
</rdf:Bag>
|
| 1393 |
+
</bqbiol:isVersionOf>
|
| 1394 |
+
|
| 1395 |
+
<bqbiol:is>
|
| 1396 |
+
<rdf:Bag>
|
| 1397 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01829"/>
|
| 1398 |
+
</rdf:Bag>
|
| 1399 |
+
</bqbiol:is>
|
| 1400 |
+
</rdf:Description>
|
| 1401 |
+
|
| 1402 |
+
|
| 1403 |
+
|
| 1404 |
+
|
| 1405 |
+
</rdf:RDF>
|
| 1406 |
+
</annotation>
|
| 1407 |
+
<listOfReactants>
|
| 1408 |
+
<speciesReference metaid="_57c6ec74-716f-456d-8200-e870ad9a5ed1" species="DHAP_ch"/>
|
| 1409 |
+
<speciesReference metaid="_37c8cd01-41d9-44f3-ac1a-24a9ac83eec0" species="E4P_ch"/>
|
| 1410 |
+
</listOfReactants>
|
| 1411 |
+
<listOfProducts>
|
| 1412 |
+
<speciesReference metaid="db341bfa-709e-4efe-b101-c0012d44ba00" species="SBP_ch"/>
|
| 1413 |
+
</listOfProducts>
|
| 1414 |
+
<kineticLaw metaid="_32da8053-ae0c-4d31-a40a-35553120fbf4">
|
| 1415 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1416 |
+
<apply>
|
| 1417 |
+
<times/>
|
| 1418 |
+
<ci> chloroplast </ci>
|
| 1419 |
+
<ci> E_Aldo_v </ci>
|
| 1420 |
+
<apply>
|
| 1421 |
+
<minus/>
|
| 1422 |
+
<apply>
|
| 1423 |
+
<times/>
|
| 1424 |
+
<ci> E4P_ch </ci>
|
| 1425 |
+
<ci> DHAP_ch </ci>
|
| 1426 |
+
</apply>
|
| 1427 |
+
<apply>
|
| 1428 |
+
<divide/>
|
| 1429 |
+
<ci> SBP_ch </ci>
|
| 1430 |
+
<ci> q8 </ci>
|
| 1431 |
+
</apply>
|
| 1432 |
+
</apply>
|
| 1433 |
+
</apply>
|
| 1434 |
+
</math>
|
| 1435 |
+
<listOfParameters>
|
| 1436 |
+
<parameter id="E_Aldo_v" metaid="_513848" value="500000000"/>
|
| 1437 |
+
<parameter id="q8" metaid="_513849" value="13"/>
|
| 1438 |
+
</listOfParameters>
|
| 1439 |
+
</kineticLaw>
|
| 1440 |
+
</reaction>
|
| 1441 |
+
<reaction id="E9" metaid="metaid_0000051" reversible="false">
|
| 1442 |
+
<annotation>
|
| 1443 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 1444 |
+
<jd:pt x="620" y="77"/>
|
| 1445 |
+
<jd:pt x="585" y="77"/>
|
| 1446 |
+
<jd:pt x="596" y="77"/>
|
| 1447 |
+
<jd:pt x="644" y="77"/>
|
| 1448 |
+
<jd:pt x="652" y="72"/>
|
| 1449 |
+
<jd:pt x="644" y="77"/>
|
| 1450 |
+
<jd:pt x="648" y="76"/>
|
| 1451 |
+
</jd:arcSeg>
|
| 1452 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1453 |
+
<rdf:Description rdf:about="#metaid_0000051">
|
| 1454 |
+
<bqbiol:isVersionOf>
|
| 1455 |
+
<rdf:Bag>
|
| 1456 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/3.1.3.37"/>
|
| 1457 |
+
</rdf:Bag>
|
| 1458 |
+
</bqbiol:isVersionOf>
|
| 1459 |
+
|
| 1460 |
+
<bqbiol:is>
|
| 1461 |
+
<rdf:Bag>
|
| 1462 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01845"/>
|
| 1463 |
+
</rdf:Bag>
|
| 1464 |
+
</bqbiol:is>
|
| 1465 |
+
</rdf:Description>
|
| 1466 |
+
|
| 1467 |
+
|
| 1468 |
+
|
| 1469 |
+
|
| 1470 |
+
</rdf:RDF>
|
| 1471 |
+
</annotation>
|
| 1472 |
+
<listOfReactants>
|
| 1473 |
+
<speciesReference metaid="_98d68b1d-103a-43de-b8b4-872b9a881aaf" species="SBP_ch"/>
|
| 1474 |
+
</listOfReactants>
|
| 1475 |
+
<listOfProducts>
|
| 1476 |
+
<speciesReference metaid="_7fdf5915-7f9f-4283-a061-ddbe3eb77504" species="Pi_ch">
|
| 1477 |
+
<annotation>
|
| 1478 |
+
<jd:shadowRef shadowRef="___Pi_ch_5"/>
|
| 1479 |
+
</annotation>
|
| 1480 |
+
</speciesReference>
|
| 1481 |
+
<speciesReference metaid="_1b2d3cf4-fe77-4dc8-8e3b-00f4c996c5ad" species="S7P_ch"/>
|
| 1482 |
+
</listOfProducts>
|
| 1483 |
+
<kineticLaw metaid="dfa60ac3-3b00-4a28-8056-61a4456708bb">
|
| 1484 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1485 |
+
<apply>
|
| 1486 |
+
<divide/>
|
| 1487 |
+
<apply>
|
| 1488 |
+
<times/>
|
| 1489 |
+
<ci> Light_on </ci>
|
| 1490 |
+
<ci> SBPase_ch_vm </ci>
|
| 1491 |
+
<ci> SBP_ch </ci>
|
| 1492 |
+
<ci> chloroplast </ci>
|
| 1493 |
+
</apply>
|
| 1494 |
+
<apply>
|
| 1495 |
+
<plus/>
|
| 1496 |
+
<ci> SBP_ch </ci>
|
| 1497 |
+
<apply>
|
| 1498 |
+
<times/>
|
| 1499 |
+
<ci> SBPase_ch_km </ci>
|
| 1500 |
+
<apply>
|
| 1501 |
+
<plus/>
|
| 1502 |
+
<cn type="integer"> 1 </cn>
|
| 1503 |
+
<apply>
|
| 1504 |
+
<divide/>
|
| 1505 |
+
<ci> Pi_ch </ci>
|
| 1506 |
+
<ci> SBPase_ch_KiPi </ci>
|
| 1507 |
+
</apply>
|
| 1508 |
+
</apply>
|
| 1509 |
+
</apply>
|
| 1510 |
+
</apply>
|
| 1511 |
+
</apply>
|
| 1512 |
+
</math>
|
| 1513 |
+
<listOfParameters>
|
| 1514 |
+
<parameter id="SBPase_ch_vm" metaid="_513850" value="40"/>
|
| 1515 |
+
<parameter id="SBPase_ch_km" metaid="_513851" value="0.013"/>
|
| 1516 |
+
<parameter id="SBPase_ch_KiPi" metaid="_513852" value="12"/>
|
| 1517 |
+
</listOfParameters>
|
| 1518 |
+
</kineticLaw>
|
| 1519 |
+
</reaction>
|
| 1520 |
+
<reaction id="E10" metaid="metaid_0000036">
|
| 1521 |
+
<annotation>
|
| 1522 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1523 |
+
<jd:pt x="859" y="81"/>
|
| 1524 |
+
<jd:pt x="811" y="77"/>
|
| 1525 |
+
<jd:pt x="815" y="78"/>
|
| 1526 |
+
<jd:pt x="615" y="116"/>
|
| 1527 |
+
<jd:pt x="815" y="78"/>
|
| 1528 |
+
<jd:pt x="903" y="84"/>
|
| 1529 |
+
<jd:pt x="893" y="92"/>
|
| 1530 |
+
<jd:pt x="903" y="84"/>
|
| 1531 |
+
<jd:pt x="893" y="92"/>
|
| 1532 |
+
</jd:arcSeg>
|
| 1533 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1534 |
+
<rdf:Description rdf:about="#metaid_0000036">
|
| 1535 |
+
<bqbiol:isVersionOf>
|
| 1536 |
+
<rdf:Bag>
|
| 1537 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.2.1.1"/>
|
| 1538 |
+
</rdf:Bag>
|
| 1539 |
+
</bqbiol:isVersionOf>
|
| 1540 |
+
|
| 1541 |
+
<bqbiol:is>
|
| 1542 |
+
<rdf:Bag>
|
| 1543 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01641"/>
|
| 1544 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1629"/>
|
| 1545 |
+
</rdf:Bag>
|
| 1546 |
+
</bqbiol:is>
|
| 1547 |
+
</rdf:Description>
|
| 1548 |
+
|
| 1549 |
+
|
| 1550 |
+
|
| 1551 |
+
|
| 1552 |
+
</rdf:RDF>
|
| 1553 |
+
</annotation>
|
| 1554 |
+
<listOfReactants>
|
| 1555 |
+
<speciesReference metaid="a499b8d1-2083-4ad7-b897-303d35b3a1f7" species="S7P_ch"/>
|
| 1556 |
+
<speciesReference metaid="_2bde77ac-f86a-4339-9afb-501cdd27532c" species="GAP_ch"/>
|
| 1557 |
+
</listOfReactants>
|
| 1558 |
+
<listOfProducts>
|
| 1559 |
+
<speciesReference metaid="_48d45e29-5439-438f-8c77-0366b91a864d" species="R5P_ch"/>
|
| 1560 |
+
<speciesReference metaid="e610266d-6475-488b-a3b2-af5ec138a6a2" species="X5P_ch"/>
|
| 1561 |
+
</listOfProducts>
|
| 1562 |
+
<kineticLaw metaid="_5faf995e-49ca-4546-b19f-3149c1b1a548">
|
| 1563 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1564 |
+
<apply>
|
| 1565 |
+
<times/>
|
| 1566 |
+
<ci> chloroplast </ci>
|
| 1567 |
+
<ci> G_TKL_v </ci>
|
| 1568 |
+
<apply>
|
| 1569 |
+
<minus/>
|
| 1570 |
+
<apply>
|
| 1571 |
+
<times/>
|
| 1572 |
+
<ci> GAP_ch </ci>
|
| 1573 |
+
<ci> S7P_ch </ci>
|
| 1574 |
+
</apply>
|
| 1575 |
+
<apply>
|
| 1576 |
+
<divide/>
|
| 1577 |
+
<apply>
|
| 1578 |
+
<times/>
|
| 1579 |
+
<ci> X5P_ch </ci>
|
| 1580 |
+
<ci> R5P_ch </ci>
|
| 1581 |
+
</apply>
|
| 1582 |
+
<ci> q10 </ci>
|
| 1583 |
+
</apply>
|
| 1584 |
+
</apply>
|
| 1585 |
+
</apply>
|
| 1586 |
+
</math>
|
| 1587 |
+
<listOfParameters>
|
| 1588 |
+
<parameter id="G_TKL_v" metaid="_513853" value="500000000"/>
|
| 1589 |
+
<parameter id="q10" metaid="_513854" value="0.85"/>
|
| 1590 |
+
</listOfParameters>
|
| 1591 |
+
</kineticLaw>
|
| 1592 |
+
</reaction>
|
| 1593 |
+
<reaction id="E11" metaid="metaid_0000037">
|
| 1594 |
+
<annotation>
|
| 1595 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1596 |
+
<jd:pt x="949" y="215"/>
|
| 1597 |
+
<jd:pt x="950" y="216"/>
|
| 1598 |
+
<jd:pt x="950" y="216"/>
|
| 1599 |
+
</jd:arcSeg>
|
| 1600 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1601 |
+
<rdf:Description rdf:about="#metaid_0000037">
|
| 1602 |
+
<bqbiol:isVersionOf>
|
| 1603 |
+
<rdf:Bag>
|
| 1604 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.6"/>
|
| 1605 |
+
</rdf:Bag>
|
| 1606 |
+
</bqbiol:isVersionOf>
|
| 1607 |
+
|
| 1608 |
+
<bqbiol:is>
|
| 1609 |
+
<rdf:Bag>
|
| 1610 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01056"/>
|
| 1611 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_2033"/>
|
| 1612 |
+
</rdf:Bag>
|
| 1613 |
+
</bqbiol:is>
|
| 1614 |
+
</rdf:Description>
|
| 1615 |
+
|
| 1616 |
+
|
| 1617 |
+
|
| 1618 |
+
|
| 1619 |
+
</rdf:RDF>
|
| 1620 |
+
</annotation>
|
| 1621 |
+
<listOfReactants>
|
| 1622 |
+
<speciesReference metaid="_3390fba3-f962-44c2-bebf-ffbb66f4c686" species="R5P_ch"/>
|
| 1623 |
+
</listOfReactants>
|
| 1624 |
+
<listOfProducts>
|
| 1625 |
+
<speciesReference metaid="e5ae66af-8879-4a8c-ba2f-4352ac7e18ef" species="Ru5P_ch"/>
|
| 1626 |
+
</listOfProducts>
|
| 1627 |
+
<kineticLaw metaid="_68c2e85d-6bc3-4f89-a502-8791cf6b27a6">
|
| 1628 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1629 |
+
<apply>
|
| 1630 |
+
<times/>
|
| 1631 |
+
<ci> R5Piso_v </ci>
|
| 1632 |
+
<ci> chloroplast </ci>
|
| 1633 |
+
<apply>
|
| 1634 |
+
<minus/>
|
| 1635 |
+
<ci> R5P_ch </ci>
|
| 1636 |
+
<apply>
|
| 1637 |
+
<divide/>
|
| 1638 |
+
<ci> Ru5P_ch </ci>
|
| 1639 |
+
<ci> q11 </ci>
|
| 1640 |
+
</apply>
|
| 1641 |
+
</apply>
|
| 1642 |
+
</apply>
|
| 1643 |
+
</math>
|
| 1644 |
+
<listOfParameters>
|
| 1645 |
+
<parameter id="R5Piso_v" metaid="_513855" value="500000000"/>
|
| 1646 |
+
<parameter id="q11" metaid="_513857" value="0.4"/>
|
| 1647 |
+
</listOfParameters>
|
| 1648 |
+
</kineticLaw>
|
| 1649 |
+
</reaction>
|
| 1650 |
+
<reaction id="E12" metaid="metaid_0000038">
|
| 1651 |
+
<annotation>
|
| 1652 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1653 |
+
<jd:pt x="887" y="209"/>
|
| 1654 |
+
<jd:pt x="884" y="203"/>
|
| 1655 |
+
<jd:pt x="888" y="215"/>
|
| 1656 |
+
</jd:arcSeg>
|
| 1657 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1658 |
+
<rdf:Description rdf:about="#metaid_0000038">
|
| 1659 |
+
<bqbiol:isVersionOf>
|
| 1660 |
+
<rdf:Bag>
|
| 1661 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/5.1.3.1"/>
|
| 1662 |
+
</rdf:Bag>
|
| 1663 |
+
</bqbiol:isVersionOf>
|
| 1664 |
+
|
| 1665 |
+
<bqbiol:is>
|
| 1666 |
+
<rdf:Bag>
|
| 1667 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01429"/>
|
| 1668 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1522"/>
|
| 1669 |
+
</rdf:Bag>
|
| 1670 |
+
</bqbiol:is>
|
| 1671 |
+
</rdf:Description>
|
| 1672 |
+
|
| 1673 |
+
|
| 1674 |
+
|
| 1675 |
+
|
| 1676 |
+
</rdf:RDF>
|
| 1677 |
+
</annotation>
|
| 1678 |
+
<listOfReactants>
|
| 1679 |
+
<speciesReference metaid="f7d62e70-ad64-4598-ad00-6189b07d3b63" species="X5P_ch"/>
|
| 1680 |
+
</listOfReactants>
|
| 1681 |
+
<listOfProducts>
|
| 1682 |
+
<speciesReference metaid="_888fd6e0-9151-4a18-9a54-8655d7c1040d" species="Ru5P_ch"/>
|
| 1683 |
+
</listOfProducts>
|
| 1684 |
+
<kineticLaw metaid="dacdcce7-6c9a-4a32-b112-8d65b358d4c1">
|
| 1685 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1686 |
+
<apply>
|
| 1687 |
+
<times/>
|
| 1688 |
+
<ci> chloroplast </ci>
|
| 1689 |
+
<ci> X5Pepi_v </ci>
|
| 1690 |
+
<apply>
|
| 1691 |
+
<minus/>
|
| 1692 |
+
<ci> X5P_ch </ci>
|
| 1693 |
+
<apply>
|
| 1694 |
+
<divide/>
|
| 1695 |
+
<ci> Ru5P_ch </ci>
|
| 1696 |
+
<ci> q12 </ci>
|
| 1697 |
+
</apply>
|
| 1698 |
+
</apply>
|
| 1699 |
+
</apply>
|
| 1700 |
+
</math>
|
| 1701 |
+
<listOfParameters>
|
| 1702 |
+
<parameter id="X5Pepi_v" metaid="_513859" value="500000000"/>
|
| 1703 |
+
<parameter id="q12" metaid="_513860" value="0.67"/>
|
| 1704 |
+
</listOfParameters>
|
| 1705 |
+
</kineticLaw>
|
| 1706 |
+
</reaction>
|
| 1707 |
+
<reaction id="E13" metaid="metaid_0000044" reversible="false">
|
| 1708 |
+
<annotation>
|
| 1709 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 1710 |
+
<jd:pt x="951" y="319"/>
|
| 1711 |
+
<jd:pt x="950" y="292"/>
|
| 1712 |
+
<jd:pt x="950" y="301"/>
|
| 1713 |
+
<jd:pt x="909" y="290"/>
|
| 1714 |
+
<jd:pt x="950" y="301"/>
|
| 1715 |
+
<jd:pt x="952" y="337"/>
|
| 1716 |
+
<jd:pt x="952" y="324"/>
|
| 1717 |
+
<jd:pt x="952" y="337"/>
|
| 1718 |
+
<jd:pt x="924" y="336"/>
|
| 1719 |
+
</jd:arcSeg>
|
| 1720 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1721 |
+
<rdf:Description rdf:about="#metaid_0000044">
|
| 1722 |
+
<bqbiol:isVersionOf>
|
| 1723 |
+
<rdf:Bag>
|
| 1724 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.7.1.19"/>
|
| 1725 |
+
</rdf:Bag>
|
| 1726 |
+
</bqbiol:isVersionOf>
|
| 1727 |
+
|
| 1728 |
+
<bqbiol:is>
|
| 1729 |
+
<rdf:Bag>
|
| 1730 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R01423"/>
|
| 1731 |
+
</rdf:Bag>
|
| 1732 |
+
</bqbiol:is>
|
| 1733 |
+
</rdf:Description>
|
| 1734 |
+
|
| 1735 |
+
|
| 1736 |
+
|
| 1737 |
+
|
| 1738 |
+
</rdf:RDF>
|
| 1739 |
+
</annotation>
|
| 1740 |
+
<listOfReactants>
|
| 1741 |
+
<speciesReference metaid="dd5847de-0446-43c0-876c-998c11c5bfea" species="Ru5P_ch"/>
|
| 1742 |
+
<speciesReference metaid="_76e5371e-1d44-4083-8101-d1548cf39004" species="ATP_ch">
|
| 1743 |
+
<annotation>
|
| 1744 |
+
<jd:shadowRef shadowRef="___ATP_ch_0"/>
|
| 1745 |
+
</annotation>
|
| 1746 |
+
</speciesReference>
|
| 1747 |
+
</listOfReactants>
|
| 1748 |
+
<listOfProducts>
|
| 1749 |
+
<speciesReference metaid="e2444a4d-291d-4c52-8deb-00e1e3e4b804" species="RuBP_ch"/>
|
| 1750 |
+
<speciesReference metaid="_6a7d6d4a-42c0-486e-aace-2303c57e6fd0" species="ADP_ch">
|
| 1751 |
+
<annotation>
|
| 1752 |
+
<jd:shadowRef shadowRef="___ADP_ch_0"/>
|
| 1753 |
+
</annotation>
|
| 1754 |
+
</speciesReference>
|
| 1755 |
+
</listOfProducts>
|
| 1756 |
+
<listOfModifiers>
|
| 1757 |
+
<modifierSpeciesReference metaid="_0994aefd-c509-4169-bcc7-698e6c6fc73c" species="PGA_ch"/>
|
| 1758 |
+
<modifierSpeciesReference metaid="_5bec8216-10c5-43aa-9279-12255e8fb9d1" species="Pi_ch"/>
|
| 1759 |
+
</listOfModifiers>
|
| 1760 |
+
<kineticLaw metaid="_5c698391-634e-4316-8ea7-5984063b3ba9">
|
| 1761 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1762 |
+
<apply>
|
| 1763 |
+
<divide/>
|
| 1764 |
+
<apply>
|
| 1765 |
+
<times/>
|
| 1766 |
+
<ci> Light_on </ci>
|
| 1767 |
+
<ci> Ru5Pk_ch_vm </ci>
|
| 1768 |
+
<ci> Ru5P_ch </ci>
|
| 1769 |
+
<ci> chloroplast </ci>
|
| 1770 |
+
<ci> ATP_ch </ci>
|
| 1771 |
+
</apply>
|
| 1772 |
+
<apply>
|
| 1773 |
+
<times/>
|
| 1774 |
+
<apply>
|
| 1775 |
+
<plus/>
|
| 1776 |
+
<ci> Ru5P_ch </ci>
|
| 1777 |
+
<apply>
|
| 1778 |
+
<times/>
|
| 1779 |
+
<ci> Ru5Pk_ch_km1 </ci>
|
| 1780 |
+
<apply>
|
| 1781 |
+
<plus/>
|
| 1782 |
+
<cn type="integer"> 1 </cn>
|
| 1783 |
+
<apply>
|
| 1784 |
+
<divide/>
|
| 1785 |
+
<ci> PGA_ch </ci>
|
| 1786 |
+
<ci> Ru5Pk_ch_KiPGA </ci>
|
| 1787 |
+
</apply>
|
| 1788 |
+
<apply>
|
| 1789 |
+
<divide/>
|
| 1790 |
+
<ci> RuBP_ch </ci>
|
| 1791 |
+
<ci> Ru5Pk_ch_KiRuBP </ci>
|
| 1792 |
+
</apply>
|
| 1793 |
+
<apply>
|
| 1794 |
+
<divide/>
|
| 1795 |
+
<ci> Pi_ch </ci>
|
| 1796 |
+
<ci> Ru5Pk_ch_KiPi </ci>
|
| 1797 |
+
</apply>
|
| 1798 |
+
</apply>
|
| 1799 |
+
</apply>
|
| 1800 |
+
</apply>
|
| 1801 |
+
<apply>
|
| 1802 |
+
<plus/>
|
| 1803 |
+
<apply>
|
| 1804 |
+
<times/>
|
| 1805 |
+
<ci> ATP_ch </ci>
|
| 1806 |
+
<apply>
|
| 1807 |
+
<plus/>
|
| 1808 |
+
<cn type="integer"> 1 </cn>
|
| 1809 |
+
<apply>
|
| 1810 |
+
<divide/>
|
| 1811 |
+
<ci> ADP_ch </ci>
|
| 1812 |
+
<ci> Ru5Pk_ch_KiADP1 </ci>
|
| 1813 |
+
</apply>
|
| 1814 |
+
</apply>
|
| 1815 |
+
</apply>
|
| 1816 |
+
<apply>
|
| 1817 |
+
<times/>
|
| 1818 |
+
<ci> Ru5Pk_ch_km2 </ci>
|
| 1819 |
+
<apply>
|
| 1820 |
+
<plus/>
|
| 1821 |
+
<cn type="integer"> 1 </cn>
|
| 1822 |
+
<apply>
|
| 1823 |
+
<divide/>
|
| 1824 |
+
<ci> ADP_ch </ci>
|
| 1825 |
+
<ci> Ru5Pk_ch_KiADP2 </ci>
|
| 1826 |
+
</apply>
|
| 1827 |
+
</apply>
|
| 1828 |
+
</apply>
|
| 1829 |
+
</apply>
|
| 1830 |
+
</apply>
|
| 1831 |
+
</apply>
|
| 1832 |
+
</math>
|
| 1833 |
+
<listOfParameters>
|
| 1834 |
+
<parameter id="Ru5Pk_ch_vm" metaid="_513861" value="10000"/>
|
| 1835 |
+
<parameter id="Ru5Pk_ch_km1" metaid="_513862" value="0.05"/>
|
| 1836 |
+
<parameter id="Ru5Pk_ch_KiPGA" metaid="_513864" value="2"/>
|
| 1837 |
+
<parameter id="Ru5Pk_ch_KiRuBP" metaid="_513865" value="0.7"/>
|
| 1838 |
+
<parameter id="Ru5Pk_ch_KiPi" metaid="_513866" value="4"/>
|
| 1839 |
+
<parameter id="Ru5Pk_ch_KiADP1" metaid="_513868" value="2.5"/>
|
| 1840 |
+
<parameter id="Ru5Pk_ch_km2" metaid="_513869" value="0.05"/>
|
| 1841 |
+
<parameter id="Ru5Pk_ch_KiADP2" metaid="_513870" value="0.4"/>
|
| 1842 |
+
</listOfParameters>
|
| 1843 |
+
</kineticLaw>
|
| 1844 |
+
</reaction>
|
| 1845 |
+
<reaction id="E14" metaid="metaid_0000041">
|
| 1846 |
+
<annotation>
|
| 1847 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1848 |
+
<jd:pt x="261" y="333"/>
|
| 1849 |
+
<jd:pt x="259" y="334"/>
|
| 1850 |
+
<jd:pt x="259" y="334"/>
|
| 1851 |
+
</jd:arcSeg>
|
| 1852 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1853 |
+
<rdf:Description rdf:about="#metaid_0000041">
|
| 1854 |
+
<bqbiol:isVersionOf>
|
| 1855 |
+
<rdf:Bag>
|
| 1856 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/5.3.1.9"/>
|
| 1857 |
+
</rdf:Bag>
|
| 1858 |
+
</bqbiol:isVersionOf>
|
| 1859 |
+
|
| 1860 |
+
<bqbiol:is>
|
| 1861 |
+
<rdf:Bag>
|
| 1862 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00771"/>
|
| 1863 |
+
<rdf:li rdf:resource="http://identifiers.org/reactome/REACT_1164"/>
|
| 1864 |
+
</rdf:Bag>
|
| 1865 |
+
</bqbiol:is>
|
| 1866 |
+
</rdf:Description>
|
| 1867 |
+
|
| 1868 |
+
|
| 1869 |
+
|
| 1870 |
+
|
| 1871 |
+
</rdf:RDF>
|
| 1872 |
+
</annotation>
|
| 1873 |
+
<listOfReactants>
|
| 1874 |
+
<speciesReference metaid="_63c7e015-d0d7-456a-aca3-f4a9e7c489b2" species="F6P_ch"/>
|
| 1875 |
+
</listOfReactants>
|
| 1876 |
+
<listOfProducts>
|
| 1877 |
+
<speciesReference metaid="_54e63d56-e40d-4475-95cb-433d0f6b20d1" species="G6P_ch"/>
|
| 1878 |
+
</listOfProducts>
|
| 1879 |
+
<kineticLaw metaid="_7753ebc6-096e-4a13-8b27-2d3a01f2218b">
|
| 1880 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1881 |
+
<apply>
|
| 1882 |
+
<times/>
|
| 1883 |
+
<ci> PGI_v </ci>
|
| 1884 |
+
<ci> chloroplast </ci>
|
| 1885 |
+
<apply>
|
| 1886 |
+
<minus/>
|
| 1887 |
+
<ci> F6P_ch </ci>
|
| 1888 |
+
<apply>
|
| 1889 |
+
<divide/>
|
| 1890 |
+
<ci> G6P_ch </ci>
|
| 1891 |
+
<ci> q14 </ci>
|
| 1892 |
+
</apply>
|
| 1893 |
+
</apply>
|
| 1894 |
+
</apply>
|
| 1895 |
+
</math>
|
| 1896 |
+
<listOfParameters>
|
| 1897 |
+
<parameter id="PGI_v" metaid="_513871" value="500000000"/>
|
| 1898 |
+
<parameter id="q14" metaid="_513872" value="2.3"/>
|
| 1899 |
+
</listOfParameters>
|
| 1900 |
+
</kineticLaw>
|
| 1901 |
+
</reaction>
|
| 1902 |
+
<reaction id="E15" metaid="metaid_0000042">
|
| 1903 |
+
<annotation>
|
| 1904 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1905 |
+
<jd:pt x="147" y="304"/>
|
| 1906 |
+
<jd:pt x="148" y="306"/>
|
| 1907 |
+
<jd:pt x="148" y="306"/>
|
| 1908 |
+
</jd:arcSeg>
|
| 1909 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1910 |
+
<rdf:Description rdf:about="#metaid_0000042">
|
| 1911 |
+
<bqbiol:is>
|
| 1912 |
+
<rdf:Bag>
|
| 1913 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R00959"/>
|
| 1914 |
+
</rdf:Bag>
|
| 1915 |
+
</bqbiol:is>
|
| 1916 |
+
|
| 1917 |
+
<bqbiol:isVersionOf>
|
| 1918 |
+
<rdf:Bag>
|
| 1919 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/5.4.2.2"/>
|
| 1920 |
+
</rdf:Bag>
|
| 1921 |
+
</bqbiol:isVersionOf>
|
| 1922 |
+
</rdf:Description>
|
| 1923 |
+
|
| 1924 |
+
|
| 1925 |
+
|
| 1926 |
+
|
| 1927 |
+
</rdf:RDF>
|
| 1928 |
+
</annotation>
|
| 1929 |
+
<listOfReactants>
|
| 1930 |
+
<speciesReference metaid="c2a4e187-d30c-4ee9-a449-eabc09a34d5b" species="G6P_ch"/>
|
| 1931 |
+
</listOfReactants>
|
| 1932 |
+
<listOfProducts>
|
| 1933 |
+
<speciesReference metaid="_7179704b-4056-4252-a35d-c27ce6fd52ad" species="G1P_ch"/>
|
| 1934 |
+
</listOfProducts>
|
| 1935 |
+
<kineticLaw metaid="c2137e50-d098-4895-a634-6bd4e20fe245">
|
| 1936 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1937 |
+
<apply>
|
| 1938 |
+
<times/>
|
| 1939 |
+
<ci> PGM_v </ci>
|
| 1940 |
+
<ci> chloroplast </ci>
|
| 1941 |
+
<apply>
|
| 1942 |
+
<minus/>
|
| 1943 |
+
<ci> G6P_ch </ci>
|
| 1944 |
+
<apply>
|
| 1945 |
+
<divide/>
|
| 1946 |
+
<ci> G1P_ch </ci>
|
| 1947 |
+
<ci> q15 </ci>
|
| 1948 |
+
</apply>
|
| 1949 |
+
</apply>
|
| 1950 |
+
</apply>
|
| 1951 |
+
</math>
|
| 1952 |
+
<listOfParameters>
|
| 1953 |
+
<parameter id="PGM_v" metaid="_513873" value="500000000"/>
|
| 1954 |
+
<parameter id="q15" metaid="_513874" value="0.058"/>
|
| 1955 |
+
</listOfParameters>
|
| 1956 |
+
</kineticLaw>
|
| 1957 |
+
</reaction>
|
| 1958 |
+
<reaction id="light_reaction" metaid="metaid_0000043" reversible="false">
|
| 1959 |
+
<annotation>
|
| 1960 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 1961 |
+
<jd:pt x="783" y="765"/>
|
| 1962 |
+
<jd:pt x="854" y="748"/>
|
| 1963 |
+
<jd:pt x="817" y="763"/>
|
| 1964 |
+
<jd:pt x="829" y="774"/>
|
| 1965 |
+
<jd:pt x="817" y="763"/>
|
| 1966 |
+
<jd:pt x="749" y="767"/>
|
| 1967 |
+
<jd:pt x="751" y="765"/>
|
| 1968 |
+
</jd:arcSeg>
|
| 1969 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 1970 |
+
<rdf:Description rdf:about="#metaid_0000043">
|
| 1971 |
+
<bqbiol:isVersionOf>
|
| 1972 |
+
<rdf:Bag>
|
| 1973 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0006176"/>
|
| 1974 |
+
</rdf:Bag>
|
| 1975 |
+
</bqbiol:isVersionOf>
|
| 1976 |
+
</rdf:Description>
|
| 1977 |
+
|
| 1978 |
+
|
| 1979 |
+
|
| 1980 |
+
|
| 1981 |
+
</rdf:RDF>
|
| 1982 |
+
</annotation>
|
| 1983 |
+
<listOfReactants>
|
| 1984 |
+
<speciesReference metaid="f79deada-d2cd-4cca-93ce-516d860cedd9" species="Pi_ch"/>
|
| 1985 |
+
<speciesReference metaid="_1a44a885-3917-4f0b-8de4-7285dbc14c97" species="ADP_ch"/>
|
| 1986 |
+
</listOfReactants>
|
| 1987 |
+
<listOfProducts>
|
| 1988 |
+
<speciesReference metaid="_8c14724c-4014-4fe6-a2dd-d46c69293676" species="ATP_ch"/>
|
| 1989 |
+
</listOfProducts>
|
| 1990 |
+
<kineticLaw metaid="_8567e768-c8c0-4b75-abd0-bb524f76c949">
|
| 1991 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 1992 |
+
<apply>
|
| 1993 |
+
<divide/>
|
| 1994 |
+
<apply>
|
| 1995 |
+
<times/>
|
| 1996 |
+
<ci> Light_on </ci>
|
| 1997 |
+
<ci> LR_vm </ci>
|
| 1998 |
+
<ci> ADP_ch </ci>
|
| 1999 |
+
<ci> Pi_ch </ci>
|
| 2000 |
+
<ci> chloroplast </ci>
|
| 2001 |
+
</apply>
|
| 2002 |
+
<apply>
|
| 2003 |
+
<times/>
|
| 2004 |
+
<apply>
|
| 2005 |
+
<plus/>
|
| 2006 |
+
<ci> ADP_ch </ci>
|
| 2007 |
+
<ci> LR_kmADP </ci>
|
| 2008 |
+
</apply>
|
| 2009 |
+
<apply>
|
| 2010 |
+
<plus/>
|
| 2011 |
+
<ci> Pi_ch </ci>
|
| 2012 |
+
<ci> LR_kmPi </ci>
|
| 2013 |
+
</apply>
|
| 2014 |
+
</apply>
|
| 2015 |
+
</apply>
|
| 2016 |
+
</math>
|
| 2017 |
+
<listOfParameters>
|
| 2018 |
+
<parameter id="LR_vm" metaid="_513875" value="3500"/>
|
| 2019 |
+
<parameter id="LR_kmADP" metaid="_513876" value="0.014"/>
|
| 2020 |
+
<parameter id="LR_kmPi" metaid="_513877" value="0.3"/>
|
| 2021 |
+
</listOfParameters>
|
| 2022 |
+
</kineticLaw>
|
| 2023 |
+
</reaction>
|
| 2024 |
+
<reaction id="E16" metaid="metaid_0000046" reversible="false">
|
| 2025 |
+
<annotation>
|
| 2026 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 2027 |
+
<jd:pt x="109" y="171"/>
|
| 2028 |
+
<jd:pt x="96" y="192"/>
|
| 2029 |
+
<jd:pt x="108" y="189"/>
|
| 2030 |
+
<jd:pt x="129" y="229"/>
|
| 2031 |
+
<jd:pt x="108" y="189"/>
|
| 2032 |
+
<jd:pt x="110" y="153"/>
|
| 2033 |
+
<jd:pt x="109" y="135"/>
|
| 2034 |
+
<jd:pt x="110" y="153"/>
|
| 2035 |
+
<jd:pt x="83" y="123"/>
|
| 2036 |
+
<jd:pt x="110" y="153"/>
|
| 2037 |
+
<jd:pt x="85" y="147"/>
|
| 2038 |
+
</jd:arcSeg>
|
| 2039 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 2040 |
+
<rdf:Description rdf:about="#metaid_0000046">
|
| 2041 |
+
<bqbiol:is>
|
| 2042 |
+
<rdf:Bag>
|
| 2043 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02111"/>
|
| 2044 |
+
</rdf:Bag>
|
| 2045 |
+
</bqbiol:is>
|
| 2046 |
+
|
| 2047 |
+
<bqbiol:isVersionOf>
|
| 2048 |
+
<rdf:Bag>
|
| 2049 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/>
|
| 2050 |
+
</rdf:Bag>
|
| 2051 |
+
</bqbiol:isVersionOf>
|
| 2052 |
+
</rdf:Description>
|
| 2053 |
+
|
| 2054 |
+
|
| 2055 |
+
|
| 2056 |
+
|
| 2057 |
+
</rdf:RDF>
|
| 2058 |
+
</annotation>
|
| 2059 |
+
<listOfReactants>
|
| 2060 |
+
<speciesReference metaid="e38789da-2bc0-4eeb-aace-036f4824ec09" species="ATP_ch">
|
| 2061 |
+
<annotation>
|
| 2062 |
+
<jd:shadowRef shadowRef="___ATP_ch_2"/>
|
| 2063 |
+
</annotation>
|
| 2064 |
+
</speciesReference>
|
| 2065 |
+
<speciesReference metaid="_1d93a465-1b02-4f28-8d5f-068ffae8b988" species="G1P_ch"/>
|
| 2066 |
+
</listOfReactants>
|
| 2067 |
+
<listOfProducts>
|
| 2068 |
+
<speciesReference metaid="f5778da6-5472-4d4f-b5f2-b4fb3d47aba4" species="x_Starch_ch"/>
|
| 2069 |
+
<speciesReference metaid="ca4e57ef-3a70-4744-ae5d-5ad229b8e25f" species="ADP_ch">
|
| 2070 |
+
<annotation>
|
| 2071 |
+
<jd:shadowRef shadowRef="___ADP_ch_2"/>
|
| 2072 |
+
</annotation>
|
| 2073 |
+
</speciesReference>
|
| 2074 |
+
<speciesReference metaid="_412b9538-4ea9-4841-ac92-86c289485806" species="Pi_ch" stoichiometry="2">
|
| 2075 |
+
<annotation>
|
| 2076 |
+
<jd:shadowRef shadowRef="___Pi_ch_0"/>
|
| 2077 |
+
</annotation>
|
| 2078 |
+
</speciesReference>
|
| 2079 |
+
</listOfProducts>
|
| 2080 |
+
<listOfModifiers>
|
| 2081 |
+
<modifierSpeciesReference metaid="_74c30b7b-38be-4164-9d75-1caf47a51848" species="PGA_ch"/>
|
| 2082 |
+
<modifierSpeciesReference metaid="f2f8be82-a5f0-414a-8a1d-477b870d5712" species="F6P_ch"/>
|
| 2083 |
+
<modifierSpeciesReference metaid="eaf3b284-fcad-4ab5-8b72-a73ab5ac1b03" species="FBP_ch"/>
|
| 2084 |
+
</listOfModifiers>
|
| 2085 |
+
<kineticLaw metaid="_3967a4a3-7661-4cf1-8539-3ed1dccdb870">
|
| 2086 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 2087 |
+
<apply>
|
| 2088 |
+
<divide/>
|
| 2089 |
+
<apply>
|
| 2090 |
+
<times/>
|
| 2091 |
+
<ci> StSyn_vm </ci>
|
| 2092 |
+
<ci> G1P_ch </ci>
|
| 2093 |
+
<ci> ATP_ch </ci>
|
| 2094 |
+
<ci> chloroplast </ci>
|
| 2095 |
+
</apply>
|
| 2096 |
+
<apply>
|
| 2097 |
+
<plus/>
|
| 2098 |
+
<apply>
|
| 2099 |
+
<times/>
|
| 2100 |
+
<apply>
|
| 2101 |
+
<plus/>
|
| 2102 |
+
<ci> G1P_ch </ci>
|
| 2103 |
+
<ci> stsyn_ch_km1 </ci>
|
| 2104 |
+
</apply>
|
| 2105 |
+
<apply>
|
| 2106 |
+
<plus/>
|
| 2107 |
+
<cn type="integer"> 1 </cn>
|
| 2108 |
+
<apply>
|
| 2109 |
+
<divide/>
|
| 2110 |
+
<ci> ADP_ch </ci>
|
| 2111 |
+
<ci> stsyn_ch_Ki </ci>
|
| 2112 |
+
</apply>
|
| 2113 |
+
</apply>
|
| 2114 |
+
<apply>
|
| 2115 |
+
<plus/>
|
| 2116 |
+
<ci> ATP_ch </ci>
|
| 2117 |
+
<ci> stsyn_ch_km2 </ci>
|
| 2118 |
+
</apply>
|
| 2119 |
+
</apply>
|
| 2120 |
+
<apply>
|
| 2121 |
+
<divide/>
|
| 2122 |
+
<apply>
|
| 2123 |
+
<times/>
|
| 2124 |
+
<ci> stsyn_ch_km2 </ci>
|
| 2125 |
+
<ci> Pi_ch </ci>
|
| 2126 |
+
</apply>
|
| 2127 |
+
<apply>
|
| 2128 |
+
<times/>
|
| 2129 |
+
<ci> stsyn_ch_ka1 </ci>
|
| 2130 |
+
<ci> PGA_ch </ci>
|
| 2131 |
+
</apply>
|
| 2132 |
+
</apply>
|
| 2133 |
+
<apply>
|
| 2134 |
+
<times/>
|
| 2135 |
+
<ci> stsyn_ch_ka2 </ci>
|
| 2136 |
+
<ci> F6P_ch </ci>
|
| 2137 |
+
</apply>
|
| 2138 |
+
<apply>
|
| 2139 |
+
<times/>
|
| 2140 |
+
<ci> stsyn_ch_ka3 </ci>
|
| 2141 |
+
<ci> FBP_ch </ci>
|
| 2142 |
+
</apply>
|
| 2143 |
+
</apply>
|
| 2144 |
+
</apply>
|
| 2145 |
+
</math>
|
| 2146 |
+
<listOfParameters>
|
| 2147 |
+
<parameter id="StSyn_vm" metaid="_513878" value="40"/>
|
| 2148 |
+
<parameter id="stsyn_ch_km1" metaid="_513879" value="0.08"/>
|
| 2149 |
+
<parameter id="stsyn_ch_Ki" metaid="_513880" value="10"/>
|
| 2150 |
+
<parameter id="stsyn_ch_km2" metaid="_513882" value="0.08"/>
|
| 2151 |
+
<parameter id="stsyn_ch_ka1" metaid="_513883" value="0.1"/>
|
| 2152 |
+
<parameter id="stsyn_ch_ka2" metaid="_513884" value="0.02"/>
|
| 2153 |
+
<parameter id="stsyn_ch_ka3" metaid="_513886" value="0.02"/>
|
| 2154 |
+
</listOfParameters>
|
| 2155 |
+
</kineticLaw>
|
| 2156 |
+
</reaction>
|
| 2157 |
+
<reaction id="E17" metaid="metaid_0000047" reversible="false">
|
| 2158 |
+
<annotation>
|
| 2159 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 2160 |
+
<jd:pt x="191" y="175"/>
|
| 2161 |
+
<jd:pt x="194" y="147"/>
|
| 2162 |
+
<jd:pt x="192" y="154"/>
|
| 2163 |
+
<jd:pt x="204" y="139"/>
|
| 2164 |
+
<jd:pt x="192" y="154"/>
|
| 2165 |
+
<jd:pt x="190" y="196"/>
|
| 2166 |
+
<jd:pt x="191" y="197"/>
|
| 2167 |
+
</jd:arcSeg>
|
| 2168 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 2169 |
+
<rdf:Description rdf:about="#metaid_0000047">
|
| 2170 |
+
<bqbiol:is>
|
| 2171 |
+
<rdf:Bag>
|
| 2172 |
+
<rdf:li rdf:resource="http://identifiers.org/kegg.reaction/R02111"/>
|
| 2173 |
+
</rdf:Bag>
|
| 2174 |
+
</bqbiol:is>
|
| 2175 |
+
|
| 2176 |
+
<bqbiol:isVersionOf>
|
| 2177 |
+
<rdf:Bag>
|
| 2178 |
+
<rdf:li rdf:resource="http://identifiers.org/ec-code/2.4.1.1"/>
|
| 2179 |
+
</rdf:Bag>
|
| 2180 |
+
</bqbiol:isVersionOf>
|
| 2181 |
+
</rdf:Description>
|
| 2182 |
+
|
| 2183 |
+
|
| 2184 |
+
|
| 2185 |
+
|
| 2186 |
+
</rdf:RDF>
|
| 2187 |
+
</annotation>
|
| 2188 |
+
<listOfReactants>
|
| 2189 |
+
<speciesReference metaid="_4a841b22-e3b9-4ac6-b448-f664489dbc1a" species="x_Starch_ch"/>
|
| 2190 |
+
<speciesReference metaid="cb2fc6b8-4183-49bd-bc24-5a7b90c028c9" species="Pi_ch">
|
| 2191 |
+
<annotation>
|
| 2192 |
+
<jd:shadowRef shadowRef="___Pi_ch_1"/>
|
| 2193 |
+
</annotation>
|
| 2194 |
+
</speciesReference>
|
| 2195 |
+
</listOfReactants>
|
| 2196 |
+
<listOfProducts>
|
| 2197 |
+
<speciesReference metaid="_469df0ce-d3b6-41ed-9bdb-7c52503e7da4" species="G1P_ch"/>
|
| 2198 |
+
</listOfProducts>
|
| 2199 |
+
<kineticLaw metaid="de6955d4-d956-47d3-bb95-2cb43806acaf">
|
| 2200 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 2201 |
+
<apply>
|
| 2202 |
+
<divide/>
|
| 2203 |
+
<apply>
|
| 2204 |
+
<times/>
|
| 2205 |
+
<ci> StPase_Vm </ci>
|
| 2206 |
+
<ci> Pi_ch </ci>
|
| 2207 |
+
<ci> chloroplast </ci>
|
| 2208 |
+
</apply>
|
| 2209 |
+
<apply>
|
| 2210 |
+
<plus/>
|
| 2211 |
+
<ci> Pi_ch </ci>
|
| 2212 |
+
<apply>
|
| 2213 |
+
<times/>
|
| 2214 |
+
<ci> StPase_km </ci>
|
| 2215 |
+
<apply>
|
| 2216 |
+
<plus/>
|
| 2217 |
+
<cn type="integer"> 1 </cn>
|
| 2218 |
+
<apply>
|
| 2219 |
+
<divide/>
|
| 2220 |
+
<ci> G1P_ch </ci>
|
| 2221 |
+
<ci> StPase_kiG1P </ci>
|
| 2222 |
+
</apply>
|
| 2223 |
+
</apply>
|
| 2224 |
+
</apply>
|
| 2225 |
+
</apply>
|
| 2226 |
+
</apply>
|
| 2227 |
+
</math>
|
| 2228 |
+
<listOfParameters>
|
| 2229 |
+
<parameter id="StPase_Vm" metaid="_513888" value="40"/>
|
| 2230 |
+
<parameter id="StPase_km" metaid="_513890" value="0.1"/>
|
| 2231 |
+
<parameter id="StPase_kiG1P" metaid="_513891" value="0.05"/>
|
| 2232 |
+
</listOfParameters>
|
| 2233 |
+
</kineticLaw>
|
| 2234 |
+
</reaction>
|
| 2235 |
+
<reaction id="E18_DHAP" metaid="metaid_0000049" reversible="false">
|
| 2236 |
+
<annotation>
|
| 2237 |
+
<jd:arcSeg fillColor="6587523" lineColor="6587523" lineThickness="1" selectedLineColor="255">
|
| 2238 |
+
<jd:pt x="269" y="613"/>
|
| 2239 |
+
<jd:pt x="243" y="587"/>
|
| 2240 |
+
<jd:pt x="268" y="585"/>
|
| 2241 |
+
<jd:pt x="267" y="584"/>
|
| 2242 |
+
<jd:pt x="268" y="585"/>
|
| 2243 |
+
<jd:pt x="270" y="641"/>
|
| 2244 |
+
<jd:pt x="270" y="635"/>
|
| 2245 |
+
<jd:pt x="270" y="641"/>
|
| 2246 |
+
<jd:pt x="245" y="633"/>
|
| 2247 |
+
</jd:arcSeg>
|
| 2248 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 2249 |
+
<rdf:Description rdf:about="#metaid_0000049">
|
| 2250 |
+
<bqbiol:isVersionOf>
|
| 2251 |
+
<rdf:Bag>
|
| 2252 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051407"/>
|
| 2253 |
+
</rdf:Bag>
|
| 2254 |
+
</bqbiol:isVersionOf>
|
| 2255 |
+
</rdf:Description>
|
| 2256 |
+
|
| 2257 |
+
|
| 2258 |
+
|
| 2259 |
+
|
| 2260 |
+
</rdf:RDF>
|
| 2261 |
+
</annotation>
|
| 2262 |
+
<listOfReactants>
|
| 2263 |
+
<speciesReference metaid="_873073ad-06c3-4e49-a38c-23aa2cff0ff6" species="x_Pi_cyt">
|
| 2264 |
+
<annotation>
|
| 2265 |
+
<jd:shadowRef shadowRef="___x_Pi_cyt_0"/>
|
| 2266 |
+
</annotation>
|
| 2267 |
+
</speciesReference>
|
| 2268 |
+
<speciesReference metaid="d90a324c-34d9-46b4-913f-77a80280f507" species="DHAP_ch"/>
|
| 2269 |
+
</listOfReactants>
|
| 2270 |
+
<listOfProducts>
|
| 2271 |
+
<speciesReference metaid="_35d6e3b8-9ec0-42c9-ba72-07dcce95a246" species="x_DHAP_cyt"/>
|
| 2272 |
+
<speciesReference metaid="_37d6e9c5-3393-4792-933b-c278b5e03a84" species="Pi_ch">
|
| 2273 |
+
<annotation>
|
| 2274 |
+
<jd:shadowRef shadowRef="___Pi_ch_3"/>
|
| 2275 |
+
</annotation>
|
| 2276 |
+
</speciesReference>
|
| 2277 |
+
</listOfProducts>
|
| 2278 |
+
<listOfModifiers>
|
| 2279 |
+
<modifierSpeciesReference metaid="_00804c31-d0fd-4c8d-bf3a-f8488e50c7f2" species="PGA_ch"/>
|
| 2280 |
+
<modifierSpeciesReference metaid="_0d86dab2-f43f-4d1d-9de8-b5454dc9e23c" species="GAP_ch"/>
|
| 2281 |
+
</listOfModifiers>
|
| 2282 |
+
<kineticLaw metaid="_97b041be-1fcf-4524-b86e-f7367df3d963">
|
| 2283 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 2284 |
+
<apply>
|
| 2285 |
+
<divide/>
|
| 2286 |
+
<apply>
|
| 2287 |
+
<times/>
|
| 2288 |
+
<ci> TP_Piap_vm </ci>
|
| 2289 |
+
<ci> DHAP_ch </ci>
|
| 2290 |
+
<ci> chloroplast </ci>
|
| 2291 |
+
</apply>
|
| 2292 |
+
<apply>
|
| 2293 |
+
<times/>
|
| 2294 |
+
<ci> TP_Piap_kDHAP_ch </ci>
|
| 2295 |
+
<apply>
|
| 2296 |
+
<plus/>
|
| 2297 |
+
<cn type="integer"> 1 </cn>
|
| 2298 |
+
<apply>
|
| 2299 |
+
<times/>
|
| 2300 |
+
<apply>
|
| 2301 |
+
<plus/>
|
| 2302 |
+
<cn type="integer"> 1 </cn>
|
| 2303 |
+
<apply>
|
| 2304 |
+
<divide/>
|
| 2305 |
+
<ci> TP_Piap_kPi_cyt </ci>
|
| 2306 |
+
<ci> x_Pi_cyt </ci>
|
| 2307 |
+
</apply>
|
| 2308 |
+
</apply>
|
| 2309 |
+
<apply>
|
| 2310 |
+
<plus/>
|
| 2311 |
+
<apply>
|
| 2312 |
+
<divide/>
|
| 2313 |
+
<ci> Pi_ch </ci>
|
| 2314 |
+
<ci> TP_Piap_kPi_ch </ci>
|
| 2315 |
+
</apply>
|
| 2316 |
+
<apply>
|
| 2317 |
+
<divide/>
|
| 2318 |
+
<ci> PGA_ch </ci>
|
| 2319 |
+
<ci> TP_Piap_kPGA_ch </ci>
|
| 2320 |
+
</apply>
|
| 2321 |
+
<apply>
|
| 2322 |
+
<divide/>
|
| 2323 |
+
<ci> DHAP_ch </ci>
|
| 2324 |
+
<ci> TP_Piap_kDHAP_ch </ci>
|
| 2325 |
+
</apply>
|
| 2326 |
+
<apply>
|
| 2327 |
+
<divide/>
|
| 2328 |
+
<ci> GAP_ch </ci>
|
| 2329 |
+
<ci> TP_Piap_kGAP_ch </ci>
|
| 2330 |
+
</apply>
|
| 2331 |
+
</apply>
|
| 2332 |
+
</apply>
|
| 2333 |
+
</apply>
|
| 2334 |
+
</apply>
|
| 2335 |
+
</apply>
|
| 2336 |
+
</math>
|
| 2337 |
+
<listOfParameters>
|
| 2338 |
+
<parameter id="TP_Piap_vm" metaid="_513892" value="250"/>
|
| 2339 |
+
<parameter id="TP_Piap_kDHAP_ch" metaid="_513893" value="0.077"/>
|
| 2340 |
+
<parameter id="TP_Piap_kPi_cyt" metaid="_513894" value="0.74"/>
|
| 2341 |
+
<parameter id="TP_Piap_kPi_ch" metaid="_513895" value="0.63"/>
|
| 2342 |
+
<parameter id="TP_Piap_kPGA_ch" metaid="_513897" value="0.25"/>
|
| 2343 |
+
<parameter id="TP_Piap_kGAP_ch" metaid="_513898" value="0.075"/>
|
| 2344 |
+
</listOfParameters>
|
| 2345 |
+
</kineticLaw>
|
| 2346 |
+
</reaction>
|
| 2347 |
+
<reaction id="E18_PGA" metaid="metaid_0000039" reversible="false">
|
| 2348 |
+
<annotation>
|
| 2349 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 2350 |
+
<jd:pt x="947" y="638"/>
|
| 2351 |
+
<jd:pt x="920" y="599"/>
|
| 2352 |
+
<jd:pt x="948" y="590"/>
|
| 2353 |
+
<jd:pt x="951" y="543"/>
|
| 2354 |
+
<jd:pt x="948" y="590"/>
|
| 2355 |
+
<jd:pt x="946" y="686"/>
|
| 2356 |
+
<jd:pt x="948" y="695"/>
|
| 2357 |
+
<jd:pt x="946" y="686"/>
|
| 2358 |
+
<jd:pt x="929" y="690"/>
|
| 2359 |
+
</jd:arcSeg>
|
| 2360 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 2361 |
+
<rdf:Description rdf:about="#metaid_0000039">
|
| 2362 |
+
<bqbiol:isVersionOf>
|
| 2363 |
+
<rdf:Bag>
|
| 2364 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051408"/>
|
| 2365 |
+
</rdf:Bag>
|
| 2366 |
+
</bqbiol:isVersionOf>
|
| 2367 |
+
</rdf:Description>
|
| 2368 |
+
|
| 2369 |
+
|
| 2370 |
+
|
| 2371 |
+
|
| 2372 |
+
</rdf:RDF>
|
| 2373 |
+
</annotation>
|
| 2374 |
+
<listOfReactants>
|
| 2375 |
+
<speciesReference metaid="b45dcda5-b10a-40a9-8600-07f5329fe74b" species="x_Pi_cyt"/>
|
| 2376 |
+
<speciesReference metaid="_54ef7ab8-e0a1-41e3-a437-66dcc96973f0" species="PGA_ch"/>
|
| 2377 |
+
</listOfReactants>
|
| 2378 |
+
<listOfProducts>
|
| 2379 |
+
<speciesReference metaid="_8ed5e066-72ca-4f8b-99d6-40f5bbea616b" species="x_PGA_cyt"/>
|
| 2380 |
+
<speciesReference metaid="c2d4e7e6-d9ee-4c22-9cdf-e6c036ed4c0a" species="Pi_ch"/>
|
| 2381 |
+
</listOfProducts>
|
| 2382 |
+
<listOfModifiers>
|
| 2383 |
+
<modifierSpeciesReference metaid="fc6c710c-d712-45db-84e3-406a1c643911" species="DHAP_ch"/>
|
| 2384 |
+
<modifierSpeciesReference metaid="f0ea6fb1-34b5-4d3e-a9df-b40172308a61" species="GAP_ch"/>
|
| 2385 |
+
</listOfModifiers>
|
| 2386 |
+
<kineticLaw metaid="_8915efab-c484-4902-92c5-1c2683463639">
|
| 2387 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 2388 |
+
<apply>
|
| 2389 |
+
<divide/>
|
| 2390 |
+
<apply>
|
| 2391 |
+
<times/>
|
| 2392 |
+
<ci> PGA_xpMult </ci>
|
| 2393 |
+
<ci> TP_Piap_vm </ci>
|
| 2394 |
+
<ci> PGA_ch </ci>
|
| 2395 |
+
<ci> chloroplast </ci>
|
| 2396 |
+
</apply>
|
| 2397 |
+
<apply>
|
| 2398 |
+
<times/>
|
| 2399 |
+
<ci> TP_Piap_kPGA_ch </ci>
|
| 2400 |
+
<apply>
|
| 2401 |
+
<plus/>
|
| 2402 |
+
<cn type="integer"> 1 </cn>
|
| 2403 |
+
<apply>
|
| 2404 |
+
<times/>
|
| 2405 |
+
<apply>
|
| 2406 |
+
<plus/>
|
| 2407 |
+
<cn type="integer"> 1 </cn>
|
| 2408 |
+
<apply>
|
| 2409 |
+
<divide/>
|
| 2410 |
+
<ci> TP_Piap_kPi_cyt </ci>
|
| 2411 |
+
<ci> x_Pi_cyt </ci>
|
| 2412 |
+
</apply>
|
| 2413 |
+
</apply>
|
| 2414 |
+
<apply>
|
| 2415 |
+
<plus/>
|
| 2416 |
+
<apply>
|
| 2417 |
+
<divide/>
|
| 2418 |
+
<ci> Pi_ch </ci>
|
| 2419 |
+
<ci> TP_Piap_kPi_ch </ci>
|
| 2420 |
+
</apply>
|
| 2421 |
+
<apply>
|
| 2422 |
+
<divide/>
|
| 2423 |
+
<ci> PGA_ch </ci>
|
| 2424 |
+
<ci> TP_Piap_kPGA_ch </ci>
|
| 2425 |
+
</apply>
|
| 2426 |
+
<apply>
|
| 2427 |
+
<divide/>
|
| 2428 |
+
<ci> DHAP_ch </ci>
|
| 2429 |
+
<ci> TP_Piap_kDHAP_ch </ci>
|
| 2430 |
+
</apply>
|
| 2431 |
+
<apply>
|
| 2432 |
+
<divide/>
|
| 2433 |
+
<ci> GAP_ch </ci>
|
| 2434 |
+
<ci> TP_Piap_kGAP_ch </ci>
|
| 2435 |
+
</apply>
|
| 2436 |
+
</apply>
|
| 2437 |
+
</apply>
|
| 2438 |
+
</apply>
|
| 2439 |
+
</apply>
|
| 2440 |
+
</apply>
|
| 2441 |
+
</math>
|
| 2442 |
+
<listOfParameters>
|
| 2443 |
+
<parameter id="PGA_xpMult" metaid="_513899" value="0.75"/>
|
| 2444 |
+
<parameter id="TP_Piap_vm" metaid="_513900" value="250"/>
|
| 2445 |
+
<parameter id="TP_Piap_kPGA_ch" metaid="_513901" value="0.25"/>
|
| 2446 |
+
<parameter id="TP_Piap_kPi_cyt" metaid="_513902" value="0.74"/>
|
| 2447 |
+
<parameter id="TP_Piap_kPi_ch" metaid="_513904" value="0.63"/>
|
| 2448 |
+
<parameter id="TP_Piap_kDHAP_ch" metaid="_513905" value="0.077"/>
|
| 2449 |
+
<parameter id="TP_Piap_kGAP_ch" metaid="_513906" value="0.075"/>
|
| 2450 |
+
</listOfParameters>
|
| 2451 |
+
</kineticLaw>
|
| 2452 |
+
</reaction>
|
| 2453 |
+
<reaction id="E18_GAP" metaid="metaid_0000040" reversible="false">
|
| 2454 |
+
<annotation>
|
| 2455 |
+
<jd:arcSeg fillColor="16777215" lineColor="0" lineThickness="1" selectedLineColor="255">
|
| 2456 |
+
<jd:pt x="485" y="633"/>
|
| 2457 |
+
<jd:pt x="500" y="607"/>
|
| 2458 |
+
<jd:pt x="486" y="604"/>
|
| 2459 |
+
<jd:pt x="485" y="582"/>
|
| 2460 |
+
<jd:pt x="486" y="604"/>
|
| 2461 |
+
<jd:pt x="484" y="662"/>
|
| 2462 |
+
<jd:pt x="485" y="670"/>
|
| 2463 |
+
<jd:pt x="484" y="662"/>
|
| 2464 |
+
<jd:pt x="536" y="665"/>
|
| 2465 |
+
</jd:arcSeg>
|
| 2466 |
+
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:bqbiol="http://biomodels.net/biology-qualifiers/">
|
| 2467 |
+
<rdf:Description rdf:about="#metaid_0000040">
|
| 2468 |
+
<bqbiol:isVersionOf>
|
| 2469 |
+
<rdf:Bag>
|
| 2470 |
+
<rdf:li rdf:resource="http://identifiers.org/go/GO:0051408"/>
|
| 2471 |
+
</rdf:Bag>
|
| 2472 |
+
</bqbiol:isVersionOf>
|
| 2473 |
+
</rdf:Description>
|
| 2474 |
+
|
| 2475 |
+
|
| 2476 |
+
|
| 2477 |
+
|
| 2478 |
+
</rdf:RDF>
|
| 2479 |
+
</annotation>
|
| 2480 |
+
<listOfReactants>
|
| 2481 |
+
<speciesReference metaid="ad3603e0-9622-4f1e-af22-5782aaa6a762" species="x_Pi_cyt"/>
|
| 2482 |
+
<speciesReference metaid="_16b5b71e-ded8-4529-bc32-ec66a8d5596f" species="GAP_ch"/>
|
| 2483 |
+
</listOfReactants>
|
| 2484 |
+
<listOfProducts>
|
| 2485 |
+
<speciesReference metaid="c7bc891f-7f81-455d-9dd8-68c76fa94e66" species="x_GAP_cyt"/>
|
| 2486 |
+
<speciesReference metaid="_3f63daff-d2a8-4929-8aa4-fb4c43692743" species="Pi_ch"/>
|
| 2487 |
+
</listOfProducts>
|
| 2488 |
+
<listOfModifiers>
|
| 2489 |
+
<modifierSpeciesReference metaid="ed5ec7c0-cd89-4f9b-b0a9-6194bbedcae0" species="PGA_ch"/>
|
| 2490 |
+
<modifierSpeciesReference metaid="d53abac5-77fa-4124-87b4-b6de1526df39" species="DHAP_ch"/>
|
| 2491 |
+
</listOfModifiers>
|
| 2492 |
+
<kineticLaw metaid="_59e458ae-f636-46e2-8f41-ad165ba8d959">
|
| 2493 |
+
<math xmlns="http://www.w3.org/1998/Math/MathML">
|
| 2494 |
+
<apply>
|
| 2495 |
+
<divide/>
|
| 2496 |
+
<apply>
|
| 2497 |
+
<times/>
|
| 2498 |
+
<ci> TP_Piap_vm </ci>
|
| 2499 |
+
<ci> GAP_ch </ci>
|
| 2500 |
+
<ci> chloroplast </ci>
|
| 2501 |
+
</apply>
|
| 2502 |
+
<apply>
|
| 2503 |
+
<times/>
|
| 2504 |
+
<ci> TP_Piap_kGAP_ch </ci>
|
| 2505 |
+
<apply>
|
| 2506 |
+
<plus/>
|
| 2507 |
+
<cn type="integer"> 1 </cn>
|
| 2508 |
+
<apply>
|
| 2509 |
+
<times/>
|
| 2510 |
+
<apply>
|
| 2511 |
+
<plus/>
|
| 2512 |
+
<cn type="integer"> 1 </cn>
|
| 2513 |
+
<apply>
|
| 2514 |
+
<divide/>
|
| 2515 |
+
<ci> TP_Piap_kPi_cyt </ci>
|
| 2516 |
+
<ci> x_Pi_cyt </ci>
|
| 2517 |
+
</apply>
|
| 2518 |
+
</apply>
|
| 2519 |
+
<apply>
|
| 2520 |
+
<plus/>
|
| 2521 |
+
<apply>
|
| 2522 |
+
<divide/>
|
| 2523 |
+
<ci> Pi_ch </ci>
|
| 2524 |
+
<ci> TP_Piap_kPi_ch </ci>
|
| 2525 |
+
</apply>
|
| 2526 |
+
<apply>
|
| 2527 |
+
<divide/>
|
| 2528 |
+
<ci> PGA_ch </ci>
|
| 2529 |
+
<ci> TP_Piap_kPGA_ch </ci>
|
| 2530 |
+
</apply>
|
| 2531 |
+
<apply>
|
| 2532 |
+
<divide/>
|
| 2533 |
+
<ci> DHAP_ch </ci>
|
| 2534 |
+
<ci> TP_Piap_kDHAP_ch </ci>
|
| 2535 |
+
</apply>
|
| 2536 |
+
<apply>
|
| 2537 |
+
<divide/>
|
| 2538 |
+
<ci> GAP_ch </ci>
|
| 2539 |
+
<ci> TP_Piap_kGAP_ch </ci>
|
| 2540 |
+
</apply>
|
| 2541 |
+
</apply>
|
| 2542 |
+
</apply>
|
| 2543 |
+
</apply>
|
| 2544 |
+
</apply>
|
| 2545 |
+
</apply>
|
| 2546 |
+
</math>
|
| 2547 |
+
<listOfParameters>
|
| 2548 |
+
<parameter id="TP_Piap_vm" metaid="_513907" value="250"/>
|
| 2549 |
+
<parameter id="TP_Piap_kGAP_ch" metaid="_513908" value="0.075"/>
|
| 2550 |
+
<parameter id="TP_Piap_kPi_cyt" metaid="_513909" value="0.74"/>
|
| 2551 |
+
<parameter id="TP_Piap_kPi_ch" metaid="_513911" value="0.63"/>
|
| 2552 |
+
<parameter id="TP_Piap_kPGA_ch" metaid="_513912" value="0.25"/>
|
| 2553 |
+
<parameter id="TP_Piap_kDHAP_ch" metaid="_513913" value="0.077"/>
|
| 2554 |
+
</listOfParameters>
|
| 2555 |
+
</kineticLaw>
|
| 2556 |
+
</reaction>
|
| 2557 |
+
</listOfReactions>
|
| 2558 |
+
</model>
|
| 2559 |
+
</sbml>
|
Data/BIOMD0000000013/Poolman2004_conditions.json
ADDED
|
@@ -0,0 +1,164 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"RuBP_ch": {
|
| 3 |
+
"trajectory_type": 2,
|
| 4 |
+
"trajectory_type_name": "dec_stable",
|
| 5 |
+
"bounds": [
|
| 6 |
+
0.33644,
|
| 7 |
+
0.5562523427315322
|
| 8 |
+
],
|
| 9 |
+
"period": 0.0
|
| 10 |
+
},
|
| 11 |
+
"PGA_ch": {
|
| 12 |
+
"trajectory_type": 2,
|
| 13 |
+
"trajectory_type_name": "dec_stable",
|
| 14 |
+
"bounds": [
|
| 15 |
+
0.939828097668812,
|
| 16 |
+
3.35479
|
| 17 |
+
],
|
| 18 |
+
"period": 0.0
|
| 19 |
+
},
|
| 20 |
+
"ATP_ch": {
|
| 21 |
+
"trajectory_type": 1,
|
| 22 |
+
"trajectory_type_name": "inc_stable",
|
| 23 |
+
"bounds": [
|
| 24 |
+
0.4963069744145196,
|
| 25 |
+
0.49806
|
| 26 |
+
],
|
| 27 |
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"period": 0.0
|
| 28 |
+
},
|
| 29 |
+
"BPGA_ch": {
|
| 30 |
+
"trajectory_type": 2,
|
| 31 |
+
"trajectory_type_name": "dec_stable",
|
| 32 |
+
"bounds": [
|
| 33 |
+
0.0766184149438715,
|
| 34 |
+
0.1510892387821299
|
| 35 |
+
],
|
| 36 |
+
"period": 0.0
|
| 37 |
+
},
|
| 38 |
+
"GAP_ch": {
|
| 39 |
+
"trajectory_type": 2,
|
| 40 |
+
"trajectory_type_name": "dec_stable",
|
| 41 |
+
"bounds": [
|
| 42 |
+
0.0100405566876984,
|
| 43 |
+
0.0161191721227775
|
| 44 |
+
],
|
| 45 |
+
"period": 0.0
|
| 46 |
+
},
|
| 47 |
+
"Pi_ch": {
|
| 48 |
+
"trajectory_type": 2,
|
| 49 |
+
"trajectory_type_name": "dec_stable",
|
| 50 |
+
"bounds": [
|
| 51 |
+
0.7399966897463272,
|
| 52 |
+
1.5662
|
| 53 |
+
],
|
| 54 |
+
"period": 0.0
|
| 55 |
+
},
|
| 56 |
+
"DHAP_ch": {
|
| 57 |
+
"trajectory_type": 2,
|
| 58 |
+
"trajectory_type_name": "dec_stable",
|
| 59 |
+
"bounds": [
|
| 60 |
+
0.2208879854809188,
|
| 61 |
+
0.35461449989091
|
| 62 |
+
],
|
| 63 |
+
"period": 0.0
|
| 64 |
+
},
|
| 65 |
+
"FBP_ch": {
|
| 66 |
+
"trajectory_type": 2,
|
| 67 |
+
"trajectory_type_name": "dec_stable",
|
| 68 |
+
"bounds": [
|
| 69 |
+
0.0157463099012605,
|
| 70 |
+
0.0405834315424494
|
| 71 |
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],
|
| 72 |
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"period": 0.0
|
| 73 |
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},
|
| 74 |
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"F6P_ch": {
|
| 75 |
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"trajectory_type": 1,
|
| 76 |
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"trajectory_type_name": "inc_stable",
|
| 77 |
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"bounds": [
|
| 78 |
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1.362768797962318,
|
| 79 |
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1.9264147901777269
|
| 80 |
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],
|
| 81 |
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"period": 0.0
|
| 82 |
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},
|
| 83 |
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"E4P_ch": {
|
| 84 |
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"trajectory_type": 1,
|
| 85 |
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"trajectory_type_name": "inc_stable",
|
| 86 |
+
"bounds": [
|
| 87 |
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0.3689984581112995,
|
| 88 |
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0.7292947201796267
|
| 89 |
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],
|
| 90 |
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"period": 0.0
|
| 91 |
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},
|
| 92 |
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"X5P_ch": {
|
| 93 |
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"trajectory_type": 2,
|
| 94 |
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"trajectory_type_name": "dec_stable",
|
| 95 |
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"bounds": [
|
| 96 |
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0.0022240254195951,
|
| 97 |
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0.0049500121728123
|
| 98 |
+
],
|
| 99 |
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"period": 0.0
|
| 100 |
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},
|
| 101 |
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"SBP_ch": {
|
| 102 |
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"trajectory_type": 1,
|
| 103 |
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"trajectory_type_name": "inc_stable",
|
| 104 |
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"bounds": [
|
| 105 |
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1.56486,
|
| 106 |
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|
| 107 |
+
],
|
| 108 |
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"period": 0.0
|
| 109 |
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},
|
| 110 |
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"S7P_ch": {
|
| 111 |
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"trajectory_type": 2,
|
| 112 |
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"trajectory_type_name": "dec_stable",
|
| 113 |
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"bounds": [
|
| 114 |
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0.0009439873017859,
|
| 115 |
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0.00541
|
| 116 |
+
],
|
| 117 |
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"period": 0.0
|
| 118 |
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},
|
| 119 |
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"R5P_ch": {
|
| 120 |
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"trajectory_type": 2,
|
| 121 |
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"trajectory_type_name": "dec_stable",
|
| 122 |
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"bounds": [
|
| 123 |
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0.0037250576427227,
|
| 124 |
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0.0082909087513144
|
| 125 |
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],
|
| 126 |
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"period": 0.0
|
| 127 |
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},
|
| 128 |
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"Ru5P_ch": {
|
| 129 |
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"trajectory_type": 2,
|
| 130 |
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"trajectory_type_name": "dec_stable",
|
| 131 |
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"bounds": [
|
| 132 |
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0.0014899912685618,
|
| 133 |
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|
| 134 |
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],
|
| 135 |
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"period": 0.0
|
| 136 |
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},
|
| 137 |
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"G6P_ch": {
|
| 138 |
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"trajectory_type": 1,
|
| 139 |
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"trajectory_type_name": "inc_stable",
|
| 140 |
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"bounds": [
|
| 141 |
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3.134368350424221,
|
| 142 |
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4.430754089178524
|
| 143 |
+
],
|
| 144 |
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"period": 0.0
|
| 145 |
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},
|
| 146 |
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"ADP_ch": {
|
| 147 |
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"trajectory_type": 2,
|
| 148 |
+
"trajectory_type_name": "dec_stable",
|
| 149 |
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"bounds": [
|
| 150 |
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0.00149,
|
| 151 |
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0.00324302558548
|
| 152 |
+
],
|
| 153 |
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"period": 0.0
|
| 154 |
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},
|
| 155 |
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"G1P_ch": {
|
| 156 |
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"trajectory_type": 1,
|
| 157 |
+
"trajectory_type_name": "inc_stable",
|
| 158 |
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"bounds": [
|
| 159 |
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|
| 160 |
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0.2569837389819562
|
| 161 |
+
],
|
| 162 |
+
"period": 0.0
|
| 163 |
+
}
|
| 164 |
+
}
|
Data/BIOMD0000000013/initial_conditions.json
ADDED
|
@@ -0,0 +1,23 @@
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
{
|
| 2 |
+
"initial_time": 0.0,
|
| 3 |
+
"initial_conditions": {
|
| 4 |
+
"RuBP_ch": 0.33644,
|
| 5 |
+
"PGA_ch": 3.35479,
|
| 6 |
+
"ATP_ch": 0.49806,
|
| 7 |
+
"BPGA_ch": 0.14825,
|
| 8 |
+
"GAP_ch": 0.01334,
|
| 9 |
+
"Pi_ch": 1.5662,
|
| 10 |
+
"DHAP_ch": 0.29345,
|
| 11 |
+
"FBP_ch": 0.02776,
|
| 12 |
+
"F6P_ch": 1.36481,
|
| 13 |
+
"E4P_ch": 0.41021,
|
| 14 |
+
"X5P_ch": 0.00363,
|
| 15 |
+
"SBP_ch": 1.56486,
|
| 16 |
+
"S7P_ch": 0.00541,
|
| 17 |
+
"R5P_ch": 0.00599,
|
| 18 |
+
"Ru5P_ch": 0.00235,
|
| 19 |
+
"G6P_ch": 3.1396,
|
| 20 |
+
"ADP_ch": 0.00149,
|
| 21 |
+
"G1P_ch": 0.18206
|
| 22 |
+
}
|
| 23 |
+
}
|
Data/BIOMD0000000014/Levchenko2000.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000014/Levchenko2000.xml
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000014/Levchenko2000_conditions.json
ADDED
|
@@ -0,0 +1,776 @@
|
|
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|
|
|
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|
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Data/BIOMD0000000014/initial_conditions.json
ADDED
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@@ -0,0 +1,91 @@
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|
Data/BIOMD0000000015/Curto1998.csv
ADDED
|
The diff for this file is too large to render.
See raw diff
|
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|
Data/BIOMD0000000015/Curto1998.xml
ADDED
|
The diff for this file is too large to render.
See raw diff
|
|
|
Data/BIOMD0000000015/Curto1998_conditions.json
ADDED
|
@@ -0,0 +1,146 @@
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
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|
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|
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|
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|
|
|
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|
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|
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|
|
|
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|
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|
|
|
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|
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|
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|
|
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|
| 1 |
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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| 10 |
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| 11 |
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| 12 |
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| 14 |
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| 15 |
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| 19 |
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| 21 |
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| 22 |
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| 23 |
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| 30 |
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| 32 |
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| 33 |
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| 39 |
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| 41 |
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|
Data/BIOMD0000000015/initial_conditions.json
ADDED
|
@@ -0,0 +1,21 @@
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| 1 |
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{
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| 2 |
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| 3 |
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| 4 |
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| 5 |
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| 6 |
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|
| 7 |
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| 10 |
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| 18 |
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| 19 |
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"UA": 100.293
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| 20 |
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|
| 21 |
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|
Data/BIOMD0000000016/Goldbeter1995.csv
ADDED
|
@@ -0,0 +1,513 @@
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|
|
|
|
| 1 |
+
time,M,P0,P1,P2,Pn,Pt
|
| 2 |
+
0.0,0.1,0.25,0.25,0.25,0.25,1.0
|
| 3 |
+
0.11741682974559686,0.17251568103273465,0.235631548138436,0.23693627629007505,0.21193755893279217,0.26201639265782534,0.9465217760191287
|
| 4 |
+
0.23483365949119372,0.23907198231658902,0.22517986138889878,0.2225853552289073,0.1865087871200254,0.2659142109456091,0.9001882146834406
|
| 5 |
+
0.3522504892367906,0.30110424397411645,0.21786448232242644,0.20871513959371193,0.16846252654750338,0.2648492717417914,0.8598914202054332
|
| 6 |
+
0.46966731898238745,0.35955773784573514,0.21313997593488127,0.1961737018736983,0.1548209791014906,0.26070589493234375,0.8248405518424139
|
| 7 |
+
0.5870841487279843,0.41509062069049846,0.2106069523459157,0.18529730782822426,0.1439354420729032,0.2546393044213069,0.79447900666835
|
| 8 |
+
0.7045009784735812,0.468181426316516,0.20995934304162234,0.17615274310347923,0.1349036829238974,0.24738714638616474,0.7684029154551637
|
| 9 |
+
0.821917808219178,0.5191898183266342,0.21095323671829055,0.16867396816923266,0.12723028461795652,0.23944308296782965,0.7463005724733094
|
| 10 |
+
0.9393346379647749,0.5683939825986598,0.21338797562418327,0.1627372008002198,0.12063446387426616,0.23115403009213478,0.727913670390804
|
| 11 |
+
1.0567514677103718,0.6160140374252525,0.2170947896912731,0.15819898216988817,0.11494827760994426,0.2227726229224759,0.7130146723935815
|
| 12 |
+
1.1741682974559686,0.6622276369308626,0.2219294240415024,0.15491559683847383,0.11006170341332222,0.21448761694346102,0.7013943412367595
|
| 13 |
+
1.2915851272015655,0.7071808124134653,0.2277672013146669,0.15275212792938128,0.10589412002999679,0.2064419475280172,0.6928553968020621
|
| 14 |
+
1.4090019569471623,0.7509952511153473,0.23449969059580125,0.15158545574228954,0.10238148324889025,0.19874327404210787,0.6872099036290888
|
| 15 |
+
1.5264187866927592,0.7937740807732621,0.24203198585871014,0.15130558330711194,0.09946820657413522,0.1914722349243314,0.6842780106642887
|
| 16 |
+
1.643835616438356,0.8356054450707251,0.2502809217093252,0.15181460916973002,0.09710541470888714,0.18468710231482308,0.6838880479027655
|
| 17 |
+
1.761252446183953,0.8765653300426671,0.25917348734393847,0.15302582757120792,0.09524928892232393,0.1784280481054031,0.6858766519428735
|
| 18 |
+
1.8786692759295498,0.916720104058129,0.2686453668273179,0.15486297973941143,0.09385939264999116,0.17272111569215384,0.6900888549088743
|
| 19 |
+
1.9960861056751467,0.9561281227815042,0.2786399091692565,0.1572588609838046,0.09289896557799968,0.16758070838813016,0.6963784441191909
|
| 20 |
+
2.1135029354207435,0.9948409659317189,0.2891072126868408,0.16015424047475604,0.09233474606990408,0.16301186212404278,0.7046080613555437
|
| 21 |
+
2.23091976516634,1.0329045501793623,0.3000032744132677,0.16349695847767895,0.0921365675786091,0.1590123486889692,0.714649149158525
|
| 22 |
+
2.3483365949119372,1.0703600003697746,0.3112892707364986,0.1672410847487203,0.09227711464625515,0.15557436394732696,0.726381834078801
|
| 23 |
+
2.4657534246575343,1.1072443123684097,0.3229309536897252,0.17134618354356773,0.09273168917823577,0.15268586651642846,0.7396946929279572
|
| 24 |
+
2.583170254403131,1.1435908846940082,0.3348981280003683,0.175776634910119,0.09347804159891866,0.15033165779017207,0.7544844622995781
|
| 25 |
+
2.7005870841487276,1.1794299828817216,0.3471641776397617,0.18050102975657362,0.09449619194816929,0.14849430632564442,0.770655705670149
|
| 26 |
+
2.8180039138943247,1.2147891421941388,0.359705641094722,0.18549166093832636,0.0957682031221766,0.14715493127106372,0.7881204364262886
|
| 27 |
+
2.935420743639922,1.2496934986856165,0.3725018434989262,0.19072408938814134,0.09727795513904405,0.1462938216250428,0.8067977096511543
|
| 28 |
+
3.0528375733855184,1.2841660588066237,0.38553458037576555,0.1961767547569861,0.09901096539611777,0.14589090452469958,0.826613205053569
|
| 29 |
+
3.170254403131115,1.3182279291214167,0.39878783877305984,0.20183062467717938,0.10095424146057236,0.1459261083379433,0.8474988132487549
|
| 30 |
+
3.287671232876712,1.351898518705154,0.41224754691078663,0.20766888992738292,0.10309613578708517,0.14637965435670758,0.8693922269819623
|
| 31 |
+
3.4050880626223092,1.3851957154510441,0.42590135164302195,0.21367670311386575,0.1054262009419828,0.14723228411436384,0.8922365398132344
|
| 32 |
+
3.522504892367906,1.4181360363359523,0.4397384238029702,0.2198409494174344,0.10793506243700264,0.1484654231143452,0.9159798587717525
|
| 33 |
+
3.6399217221135025,1.4507347538361743,0.45374928993039204,0.22615004489438598,0.11061431511745123,0.15006128771564925,0.9405749376578785
|
| 34 |
+
3.7573385518590996,1.4830060082848209,0.46792568012584534,0.23259375593078477,0.11345642832431321,0.152002961677793,0.9659788260587364
|
| 35 |
+
3.8747553816046967,1.5149629050872313,0.4822603946751559,0.23916304602471583,0.11645465741364619,0.1542744426814905,0.9921525407950084
|
| 36 |
+
3.9921722113502933,1.5466176250627313,0.49674715548220744,0.24584990125873604,0.11960294805646032,0.15686071839009288,1.0190607231874966
|
| 37 |
+
4.10958904109589,1.577981459113719,0.5113805474162892,0.2526472690757492,0.12289589297512052,0.15974768581071414,1.046671395277873
|
| 38 |
+
4.227005870841487,1.6090649015024343,0.5261558900784032,0.25954891357478416,0.12632865460077025,0.16292219644476744,1.0749556546987251
|
| 39 |
+
4.344422700587084,1.6398776994964397,0.541069161883899,0.26654933035754824,0.12989691076100088,0.16637201646488978,1.1038874194673378
|
| 40 |
+
4.46183953033268,1.6704288832768657,0.556116949437081,0.27364368775235975,0.13359681512437072,0.17008577777449344,1.133443230088305
|
| 41 |
+
4.579256360078277,1.7007268294142242,0.5712963541098167,0.2808277247925126,0.1374249392918448,0.17405297742057102,1.1636019956147452
|
| 42 |
+
4.6966731898238745,1.7307792954579029,0.5866049347819855,0.2880976876026726,0.14137823179173406,0.17826393240831265,1.1943447865847048
|
| 43 |
+
4.814090019569472,1.7605934463391244,0.6020406585930849,0.29545028076846414,0.145453988822415,0.18270974034156384,1.2256546685255278
|
| 44 |
+
4.931506849315069,1.790175881882586,0.6176018512826429,0.3028826134404798,0.14964981955020953,0.18738223400079476,1.257516518274127
|
| 45 |
+
5.048923679060665,1.8195326651749433,0.6332871457182199,0.3103921456635657,0.15396361263080424,0.19227394333006398,1.2899168473426537
|
| 46 |
+
5.166340508806262,1.8486693251528852,0.6490954598309643,0.31797666772382455,0.15839351950209016,0.19737804002706216,1.3228436870839413
|
| 47 |
+
5.283757338551859,1.877590867528137,0.66502595872037,0.32563426257518224,0.1629379289249447,0.20268831186142927,1.3562864620819262
|
| 48 |
+
5.401174168297455,1.9063018156444533,0.6810779957579913,0.3333632423164293,0.16759542840870037,0.20819910365979633,1.3902357701429173
|
| 49 |
+
5.518590998043052,1.9348061738130249,0.6972511179092508,0.3411621629705487,0.17236480819447425,0.2139052996429497,1.4246833887172232
|
| 50 |
+
5.636007827788649,1.9631074672594877,0.71354500661746,0.3490297604663601,0.17724502162317332,0.21980227074144362,1.459622059448437
|
| 51 |
+
5.7534246575342465,1.9912087427406944,0.7299594506417483,0.35696492566340565,0.18223516867517012,0.22588583667668974,1.495045381657014
|
| 52 |
+
5.870841487279844,2.019112497948004,0.7464943781938385,0.364966752203106,0.18733452079377344,0.2321522591623615,1.5309479103530794
|
| 53 |
+
5.98825831702544,2.046820802431525,0.7631497297402857,0.3730343908605959,0.19254243209730584,0.23859815943707954,1.5673247121352671
|
| 54 |
+
6.105675146771037,2.0743351270821773,0.7799255534427095,0.3811671865880859,0.1978584150895364,0.2452205550052541,1.604171710125586
|
| 55 |
+
6.223091976516634,2.1016564964529736,0.7968218780700995,0.3893645157255264,0.2032820454744043,0.2520167559099427,1.6414851951799727
|
| 56 |
+
6.34050880626223,2.1287853158331713,0.8138387801820595,0.3976258931155943,0.20881302501395527,0.2589844135940484,1.6792621119056574
|
| 57 |
+
6.457925636007827,2.1557214828869338,0.8309763027208245,0.40595087412776515,0.21445111611759649,0.2661214284111944,1.7174997213773804
|
| 58 |
+
6.575342465753424,2.1824642874623543,0.848234458600217,0.4143390798303694,0.2201961600249569,0.27342597251084927,1.7561956709663924
|
| 59 |
+
6.692759295499021,2.2090124170233074,0.8656132053261507,0.42279017372121774,0.22604805952082357,0.28089644970856104,1.795347888276753
|
| 60 |
+
6.8101761252446185,2.23536394236799,0.8831124204012185,0.4313038467527796,0.23200676596373362,0.28853146562186893,1.8349544987396007
|
| 61 |
+
6.927592954990215,2.261516249554132,0.9007318765625926,0.4398798155555178,0.23807227738508033,0.29632983429895365,1.8750138038021444
|
| 62 |
+
7.045009784735812,2.287466072671065,0.9184712263043479,0.4485177945731967,0.24424462068383418,0.30429052101212906,1.915524162573508
|
| 63 |
+
7.162426614481409,2.313209368345475,0.9363299756240784,0.45721751778750563,0.25052386216476863,0.31241266889020736,1.95648402446656
|
| 64 |
+
7.279843444227005,2.338741387720503,0.9543074623539135,0.4659786906798635,0.25691007646513403,0.32069553532153106,1.9978917648204422
|
| 65 |
+
7.397260273972602,2.3640565229540775,0.9724028294954138,0.47480101610999653,0.263403367431638,0.32913852170225205,2.0397457347393004
|
| 66 |
+
7.514677103718199,2.389148364758058,0.9906150081482243,0.48368416137919246,0.27000383898729635,0.33774111947939833,2.0820441279941115
|
| 67 |
+
7.632093933463796,2.4140095940090105,1.0089426786776141,0.49262775866214736,0.2767116005600194,0.3465029221699321,2.124784960069713
|
| 68 |
+
7.749510763209393,2.438631955741608,1.0273842505070336,0.5016313944379522,0.28352675867012694,0.35542360392319655,2.1679660075383094
|
| 69 |
+
7.86692759295499,2.4630062192173674,1.0459378283909395,0.5106945979624246,0.29044940580531764,0.36450290314881756,2.211584735307499
|
| 70 |
+
7.984344422700587,2.4871220897386737,1.064601160943643,0.5198168315939315,0.29747961429910397,0.3737406266390974,2.255638233475776
|
| 71 |
+
8.101761252446183,2.5109682596631613,1.0833716810543093,0.5289974847431631,0.3046174357728704,0.3831365978668325,2.3001231994371754
|
| 72 |
+
8.21917808219178,2.5345323024788686,1.102246432000945,0.5382358621651789,0.31186288996908623,0.39269066733384644,2.345035851469057
|
| 73 |
+
8.336594911937377,2.557800449726735,1.1212218795594049,0.5475311773041174,0.3192159539904658,0.4024027679625782,2.3903717788165664
|
| 74 |
+
8.454011741682974,2.5807579138812855,1.1402942074505942,0.5568825391236918,0.32667656581943055,0.4122727585665184,2.436126070960235
|
| 75 |
+
8.571428571428571,2.6033886001821855,1.1594590741066586,0.5662889454178432,0.33424461108496717,0.42230050460342383,2.4822931352128927
|
| 76 |
+
8.688845401174168,2.6256749937760606,1.1787114433617605,0.5757492907872077,0.34191992454432474,0.43248590810422877,2.5288665667975216
|
| 77 |
+
8.806262230919765,2.6475982331164216,1.1980457324345994,0.5852623412616212,0.3497022778562644,0.4428288325144891,2.5758391840669743
|
| 78 |
+
8.92367906066536,2.6691381145319295,1.2174558561614488,0.5948267184803894,0.35759137076043435,0.4533290634808709,2.6232030088831437
|
| 79 |
+
9.041095890410958,2.690272974423682,1.236934999093601,0.604440887495445,0.36558682848923263,0.46398636743048777,2.6709490825087663
|
| 80 |
+
9.158512720156555,2.7109797621659286,1.2564755380701476,0.6141030972107019,0.37368819001917286,0.4748005034973885,2.7190673287974105
|
| 81 |
+
9.275929549902152,2.7312337722762408,1.2760692511539335,0.623811490098062,0.3818949115687755,0.4857711042261621,2.767546757046933
|
| 82 |
+
9.393346379647749,2.751008770749035,1.2957070930437857,0.6335640005009489,0.39020635266537296,0.4968977475949912,2.816375193805099
|
| 83 |
+
9.510763209393346,2.770277512441553,1.315379019414059,0.643358365426658,0.39862177546185074,0.5081799454809978,2.8655391057835655
|
| 84 |
+
9.628180039138943,2.7890107420113153,1.3350742419122104,0.6531921164462084,0.40714033222877644,0.5196171021129795,2.915023792700175
|
| 85 |
+
9.74559686888454,2.8071776811318028,1.354781027722211,0.6630625676808787,0.4157610623098217,0.5312085209681575,2.9648131786810685
|
| 86 |
+
9.863013698630137,2.8247465491376094,1.3744866504260267,0.6729668353672283,0.42448287304976534,0.5429533900589972,3.0148897489020174
|
| 87 |
+
9.980430528375733,2.8416844305868443,1.394177360100869,0.6829018236832195,0.4333045347492238,0.5548507713510491,3.065234489884361
|
| 88 |
+
10.09784735812133,2.8579562269514174,1.4138383673834856,0.6928641607093925,0.44222469659804575,0.56689959780204,3.115826822492964
|
| 89 |
+
10.215264187866927,2.8735258657055303,1.433453796456317,0.7028502422930744,0.45124185405984707,0.5790986548420461,3.1666445476512846
|
| 90 |
+
10.332681017612524,2.8883577247669505,1.4530068640582565,0.7128562014026263,0.46035431755148803,0.591446558804993,3.2176639418173636
|
| 91 |
+
10.450097847358121,2.9024132375337324,1.4724794085991584,0.7228779123694891,0.46956026623429054,0.6039417734706128,3.268859360673551
|
| 92 |
+
10.567514677103718,2.9156533611566924,1.491852157185879,0.7329109722197472,0.47885769689413527,0.6165825806019664,3.3202034069017277
|
| 93 |
+
10.684931506849315,2.928039875138979,1.5111049939336418,0.7429506546790848,0.48824446104881236,0.6293670740971872,3.3716671837587264
|
| 94 |
+
10.80234833659491,2.9395332777882417,1.530216477652475,0.7529919467356367,0.4977182167929315,0.6422931494863041,3.423219790667347
|
| 95 |
+
10.919765166340508,2.9500930712561373,1.5491638531506124,0.7630295344113402,0.5072764253744422,0.6553584934506274,3.474828306387023
|
| 96 |
+
11.037181996086105,2.959679587068153,1.5679234514279137,0.7730577924062028,0.5169163825189881,0.6685605829268244,3.5264582092799293
|
| 97 |
+
11.154598825831702,2.9682548673664892,1.586470916701767,0.7830708052339812,0.5266352339080882,0.681896687183579,3.5780736430274156
|
| 98 |
+
11.272015655577299,2.9757791146960573,1.604780119556166,0.7930622758624027,0.5364298743783162,0.6953638158462317,3.629636085643117
|
| 99 |
+
11.389432485322896,2.9822138538125342,1.6228240175605573,0.8030255826364958,0.5462970196804419,0.7089587430147991,3.681105362892294
|
| 100 |
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| 509 |
+
59.53033268101761,2.896247876661439,1.624660223189052,0.825167914348951,0.5826972043597538,0.7671919172526507,3.7997172591504076
|
| 510 |
+
59.647749510763205,2.8968617919657116,1.6394606854409772,0.8341179779801714,0.5920364393198062,0.7801357388136044,3.845750841554559
|
| 511 |
+
59.765166340508806,2.896302220486467,1.6538458568201015,0.8429990044297866,0.6014229095108301,0.7931845634664472,3.891452334227165
|
| 512 |
+
59.8825831702544,2.8945491503936935,1.6677887182355382,0.8518031606305889,0.610851763472432,0.8063328460718593,3.936776488410418
|
| 513 |
+
60.0,2.891583783110335,1.6812601864729855,0.8605220714099827,0.6203178264464977,0.8195746834134829,3.9816747677429487
|