File size: 12,283 Bytes
9d54b72 |
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 |
<?xml version="1.0" encoding="UTF-8"?>
<!--This biomodel was generated in VCML Version Alpha_Version_7.4.0_build_85-->
<vcml xmlns="http://sourceforge.net/projects/vcell/vcml" Version="Alpha_Version_7.4.0_build_85">
<BioModel Name="BioModel2">
<Model Name="model">
<Compound Name="s0"/>
<Compound Name="s1"/>
<Feature Name="c0"/>
<LocalizedCompound Name="s0" CompoundRef="s0" Structure="c0" OverrideName="true"/>
<LocalizedCompound Name="s1" CompoundRef="s1" Structure="c0" OverrideName="true"/>
<SimpleReaction Structure="c0" Name="r0" Reversible="true" FluxOption="MolecularOnly">
<Reactant LocalizedCompoundRef="s0" Stoichiometry="1"/>
<Product LocalizedCompoundRef="s1" Stoichiometry="1"/>
<Kinetics KineticsType="MassAction">
<Parameter Name="J" Role="reaction rate" Unit="uM.s-1">((Kf * s0) - (Kr * s1))</Parameter>
<Parameter Name="Kf" Role="forward rate constant" Unit="s-1">1.0</Parameter>
<Parameter Name="Kr" Role="reverse rate constant" Unit="s-1">2.0</Parameter>
</Kinetics>
</SimpleReaction>
<Diagram Name="c0" Structure="c0">
<SimpleReactionShape NodeReferenceModeAttrTag="molecule" SimpleReactionRef="r0" LocationX="252"
LocationY="102"/>
<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s0" LocationX="144"
LocationY="86"/>
<LocalizedCompoundShape NodeReferenceModeAttrTag="molecule" LocalizedCompoundRef="s1" LocationX="361"
LocationY="118"/>
</Diagram>
<ModelUnitSystem VolumeSubstanceUnit="uM.um3" MembraneSubstanceUnit="molecules"
LumpedReactionSubstanceUnit="molecules" VolumeUnit="um3" AreaUnit="um2" LengthUnit="um"
TimeUnit="s"/>
</Model>
<SimulationSpec Name="Application0" Stochastic="false" UseConcentration="true" RuleBased="false"
MassConservationModelReduction="false" InsufficientIterations="false"
InsufficientMaxMolecules="false">
<NetworkConstraints RbmMaxIteration="1" RbmMaxMoleculesPerSpecies="10" RbmSpeciesLimit="800"
RbmReactionsLimit="2500"/>
<Annotation></Annotation>
<Geometry Name="non-spatial" Dimension="0">
<Extent X="10.0" Y="10.0" Z="10.0"/>
<Origin X="0.0" Y="0.0" Z="0.0"/>
<SubVolume Name="Compartment" Handle="0" Type="Compartmental"/>
</Geometry>
<GeometryContext>
<FeatureMapping Feature="c0" GeometryClass="Compartment" SubVolume="Compartment" Size="50000.0">
<BoundariesTypes Xm="Flux" Xp="Flux" Ym="Flux" Yp="Flux" Zm="Flux" Zp="Flux"/>
</FeatureMapping>
</GeometryContext>
<ReactionContext>
<LocalizedCompoundSpec LocalizedCompoundRef="s0" ForceConstant="false" WellMixed="false"
ForceContinuous="false">
<InitialConcentration>5.0</InitialConcentration>
<Diffusion>0.0</Diffusion>
</LocalizedCompoundSpec>
<LocalizedCompoundSpec LocalizedCompoundRef="s1" ForceConstant="false" WellMixed="false"
ForceContinuous="false">
<InitialConcentration>4.0</InitialConcentration>
<Diffusion>0.0</Diffusion>
</LocalizedCompoundSpec>
<ReactionSpec ReactionStepRef="r0" ReactionMapping="included"/>
</ReactionContext>
<MathDescription Name="Application0_generated">
<Constant Name="_F_">96485.3321</Constant>
<Constant Name="_F_nmol_">9.64853321E-5</Constant>
<Constant Name="_K_GHK_">1.0E-9</Constant>
<Constant Name="_N_pmol_">6.02214179E11</Constant>
<Constant Name="_PI_">3.141592653589793</Constant>
<Constant Name="_R_">8314.46261815</Constant>
<Constant Name="_T_">300.0</Constant>
<Constant Name="K_millivolts_per_volt">1000.0</Constant>
<Constant Name="Kf">1.0</Constant>
<Constant Name="KMOLE">0.001660538783162726</Constant>
<Constant Name="Kr">2.0</Constant>
<Constant Name="s0_init_uM">5.0</Constant>
<Constant Name="s1_init_uM">4.0</Constant>
<Constant Name="Size_c0">50000.0</Constant>
<VolumeVariable Name="s0" Domain="Compartment"/>
<VolumeVariable Name="s1" Domain="Compartment"/>
<Function Name="J_r0" Domain="Compartment">((Kf * s0) - (Kr * s1))</Function>
<CompartmentSubDomain Name="Compartment">
<BoundaryType Boundary="Xm" Type="Value"/>
<BoundaryType Boundary="Xp" Type="Value"/>
<BoundaryType Boundary="Ym" Type="Value"/>
<BoundaryType Boundary="Yp" Type="Value"/>
<BoundaryType Boundary="Zm" Type="Value"/>
<BoundaryType Boundary="Zp" Type="Value"/>
<OdeEquation Name="s0" SolutionType="Unknown">
<Rate>- J_r0</Rate>
<Initial>s0_init_uM</Initial>
</OdeEquation>
<OdeEquation Name="s1" SolutionType="Unknown">
<Rate>J_r0</Rate>
<Initial>s1_init_uM</Initial>
</OdeEquation>
</CompartmentSubDomain>
</MathDescription>
<Simulation Name="Simulation0">
<SolverTaskDescription TaskType="Unsteady" UseSymbolicJacobian="false"
Solver="Combined Stiff Solver (IDA/CVODE)">
<TimeBound StartTime="0.0" EndTime="1.0"/>
<TimeStep DefaultTime="0.1" MinTime="1.0E-8" MaxTime="1.0"/>
<ErrorTolerance Absolut="1.0E-9" Relative="1.0E-9"/>
<OutputOptions KeepEvery="1" KeepAtMost="1000"/>
<NumberProcessors>1</NumberProcessors>
</SolverTaskDescription>
<MathOverrides/>
<Version Name="temp simulation" KeyValue="487586140" BranchId="1" Archived="1"
Date="30-Nov-2022 12:21:03" FromVersionable="false">
<Owner Name="temp" Identifier="123"/>
<GroupAccess Type="1"/>
</Version>
</Simulation>
<AnalysisTaskList>
<ParameterEstimationTask Name="DefaultTask">
<parameterMappingSpecList>
<parameterMappingSpec parameterReferenceAttribute="model.r0.Kf" lowLimit="0.1" highLimit="10.0"
currentValue="0.2" selected="true"/>
<parameterMappingSpec parameterReferenceAttribute="model.r0.Kr" lowLimit="0.2" highLimit="20.0"
currentValue="0.3" selected="true"/>
<parameterMappingSpec parameterReferenceAttribute="Application0.s0_scs.initConc" lowLimit="0.0"
highLimit="20.0" currentValue="2.0" selected="true"/>
<parameterMappingSpec parameterReferenceAttribute="Application0.s1_scs.initConc" lowLimit="0.0"
highLimit="0.0" currentValue="0.0" selected="false"/>
<parameterMappingSpec parameterReferenceAttribute="Application0.c0_mapping.Size"
lowLimit="5000.0" highLimit="500000.0" currentValue="50000.0"
selected="false"/>
</parameterMappingSpecList>
<referenceData numRows="22" numColumns="2">
<dataColumnList>
<dataColumn Name="t" weight="1.0"/>
<dataColumn Name="s1" weight="1.0"/>
</dataColumnList>
<dataRowList>
<dataRow>0.0 4.0</dataRow>
<dataRow>1.295720285971286E-4 3.999611366663021</dataRow>
<dataRow>4.924083761030788E-4 3.998523873442699</dataRow>
<dataRow>0.003065662851935472 3.990845173277069</dataRow>
<dataRow>0.0076815973758065205 3.9772186929899127</dataRow>
<dataRow>0.014574181044930384 3.957219491908877</dataRow>
<dataRow>0.02497272803898938 3.92781938129364</dataRow>
<dataRow>0.040662945860187746 3.8851582405505694</dataRow>
<dataRow>0.07469412103283095 3.799249276503241</dataRow>
<dataRow>0.10735857823648513 3.724643285643995</dataRow>
<dataRow>0.15042425159162362 3.636817112208214</dataRow>
<dataRow>0.2109351969932674 3.531099655992511</dataRow>
<dataRow>0.29257831007997415 3.4157235027261508</dataRow>
<dataRow>0.37422142316668094 3.325411678114914</dataRow>
<dataRow>0.45586453625338774 3.2547192053620813</dataRow>
<dataRow>0.5375076493400945 3.1993839741215537</dataRow>
<dataRow>0.6191507624268013 3.156069775277858</dataRow>
<dataRow>0.7007938755135081 3.1221651582678236</dataRow>
<dataRow>0.7824369886002149 3.0956259843893053</dataRow>
<dataRow>0.8640801016869217 3.0748521838801746</dataRow>
<dataRow>0.9457232147736285 3.058591286326842</dataRow>
<dataRow>1.0 3.049787087039816</dataRow>
</dataRowList>
</referenceData>
<referenceDataMappingSpecList>
<referenceDataMappingSpec referenceDataColumnName="t" referenceDataModelSymbol="t"/>
<referenceDataMappingSpec referenceDataColumnName="s1" referenceDataModelSymbol="s1"/>
</referenceDataMappingSpecList>
<optimizationSolverSpec optimizationSolverType="Evolutionary Programming" NumOfRuns="1">
<ListOfParameters>
<Parameter Name="Number of Generations" Value="200.0"/>
<Parameter Name="Population Size" Value="20.0"/>
<Parameter Name="Random Number Generator" Value="1.0"/>
<Parameter Name="Seed" Value="0.0"/>
</ListOfParameters>
</optimizationSolverSpec>
</ParameterEstimationTask>
</AnalysisTaskList>
<MicroscopeMeasurement Name="fluor">
<ConvolutionKernel Type="ProjectionZKernel"/>
</MicroscopeMeasurement>
</SimulationSpec>
<pathwayModel>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" version="3.0"/>
</pathwayModel>
<relationshipModel>
<RMNS version="3.0"/>
</relationshipModel>
<vcmetadata>
<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"/>
<nonrdfAnnotationList/>
<uriBindingList/>
</vcmetadata>
</BioModel>
</vcml>
|