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| <h1 data-toc-skip>Model Building</h1> | |
| <h4 data-toc-skip class="author">Jonas Förster | |
| & Jürgen Pahle</h4> | |
| <small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/vignettes/model_building.Rmd" class="external-link"><code>vignettes/model_building.Rmd</code></a></small> | |
| <div class="hidden name"><code>model_building.Rmd</code></div> | |
| </div> | |
| <div class="section level2"> | |
| <h2 id="initial-setup">Initial Setup<a class="anchor" aria-label="anchor" href="#initial-setup"></a> | |
| </h2> | |
| <div class="sourceCode" id="cb1"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://ggplot2.tidyverse.org" class="external-link">ggplot2</a></span><span class="op">)</span></span> | |
| <span><span class="kw"><a href="https://rdrr.io/r/base/library.html" class="external-link">library</a></span><span class="op">(</span><span class="va"><a href="https://github.com/jpahle/CoRC" class="external-link">CoRC</a></span><span class="op">)</span></span></code></pre></div> | |
| </div> | |
| <div class="section level2"> | |
| <h2 id="quick-model-building">Quick Model Building<a class="anchor" aria-label="anchor" href="#quick-model-building"></a> | |
| </h2> | |
| <p>Building a quick Michaelis-Menten reaction using COPASI’s | |
| automatisms. Working with reaction equations automatically creates | |
| required entities the same way the COPASI GUI does.</p> | |
| <div class="sourceCode" id="cb2"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> # A COPASI model reference:</span></span> | |
| <span><span class="co">#> Model name: "New Model"</span></span> | |
| <span><span class="co">#> Number of compartments: 0</span></span> | |
| <span><span class="co">#> Number of species: 0</span></span> | |
| <span><span class="co">#> Number of reactions: 0</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "(a = b)"</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 2 × 13</span></span></span> | |
| <span><span class="co">#> key name compa…¹ type unit initi…² initi…³ conce…⁴ number rate numbe…⁵</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> a{comp… a compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">2</span> b{comp… b compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with 2 more variables: initial_expression <chr>, expression <chr>, and</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># abbreviated variable names ¹compartment, ²initial_concentration,</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># ³initial_number, ⁴concentration, ⁵number_rate</span></span></span> | |
| <span><span class="fu"><a href="../reference/getReactions.html">getReactions</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 1 × 6</span></span></span> | |
| <span><span class="co">#> key name reaction rate_law flux numbe…¹</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> (a = b) a = b a = b FunctionDB.Functions[Reversible Michaeli… 0 0</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with abbreviated variable name ¹number_flux</span></span></span> | |
| <span><span class="fu"><a href="../reference/getParameters.html">getParameters</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 5</span></span></span> | |
| <span><span class="co">#> key name reaction value mapping</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> (a = b).Kms Kms a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">2</span> (a = b).Kmp Kmp a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">3</span> (a = b).Vf Vf a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">4</span> (a = b).Vr Vr a = b 0.1 <span style="color: #BB0000;">NA</span></span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> | |
| </div> | |
| <div class="section level2"> | |
| <h2 id="more-detail">More Detail<a class="anchor" aria-label="anchor" href="#more-detail"></a> | |
| </h2> | |
| <p>Getting more detail in can be helpful. Here we create a global | |
| quantity “substrate concentration” which applies a fixed value to | |
| species “a”. This is achieved by assigning the <code>Value</code> | |
| reference of the global quantity to species “a”.</p> | |
| <div class="sourceCode" id="cb3"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> # A COPASI model reference:</span></span> | |
| <span><span class="co">#> Model name: "New Model"</span></span> | |
| <span><span class="co">#> Number of compartments: 0</span></span> | |
| <span><span class="co">#> Number of species: 0</span></span> | |
| <span><span class="co">#> Number of reactions: 0</span></span> | |
| <span></span> | |
| <span><span class="va">subs_quant</span> <span class="op"><-</span> <span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span><span class="st">"substrate concentration"</span>, initial_value <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span> | |
| <span><span class="va">subs_value</span> <span class="op"><-</span> <span class="fu"><a href="../reference/entity_finders.html">quantity</a></span><span class="op">(</span><span class="va">subs_quant</span>, reference <span class="op">=</span> <span class="st">"Value"</span><span class="op">)</span></span> | |
| <span><span class="va">subs_value</span></span> | |
| <span><span class="co">#> [1] "{Values[substrate concentration]}"</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"assignment"</span>, expression <span class="op">=</span> <span class="va">subs_value</span><span class="op">)</span></span> | |
| <span><span class="co">#> Warning: No compartment exists. Created default compartment.</span></span> | |
| <span><span class="co">#> [1] "a{compartment}"</span></span> | |
| <span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "(a = b)"</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/getGlobalQuantities.html">getGlobalQuantities</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 1 × 9</span></span></span> | |
| <span><span class="co">#> key name type unit initi…¹ value rate initi…² expre…³</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> Values[substrate concen… subs… fixed <span style="color: #949494;">""</span> 10 <span style="color: #BB0000;">NaN</span> 0 <span style="color: #949494;">""</span> <span style="color: #949494;">""</span> </span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with abbreviated variable names ¹initial_value, ²initial_expression,</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># ³expression</span></span></span> | |
| <span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 2 × 13</span></span></span> | |
| <span><span class="co">#> key name compa…¹ type unit initi…² initi…³ conce…⁴ number rate numbe…⁵</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> a{comp… a compar… assi… mol/l 10 6.02<span style="color: #949494;">e</span>24 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">2</span> b{comp… b compar… reac… mol/l 1 6.02<span style="color: #949494;">e</span>23 <span style="color: #BB0000;">NaN</span> <span style="color: #BB0000;">NaN</span> 0 0</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with 2 more variables: initial_expression <chr>, expression <chr>, and</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># abbreviated variable names ¹compartment, ²initial_concentration,</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># ³initial_number, ⁴concentration, ⁵number_rate</span></span></span> | |
| <span><span class="fu"><a href="../reference/getReactions.html">getReactions</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 1 × 6</span></span></span> | |
| <span><span class="co">#> key name reaction rate_law flux numbe…¹</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> (a = b) a = b a = b FunctionDB.Functions[Reversible Michaeli… 0 0</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with abbreviated variable name ¹number_flux</span></span></span> | |
| <span><span class="fu"><a href="../reference/getParameters.html">getParameters</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 4 × 5</span></span></span> | |
| <span><span class="co">#> key name reaction value mapping</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><chr></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><chr></span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">1</span> (a = b).Kms Kms a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">2</span> (a = b).Kmp Kmp a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">3</span> (a = b).Vf Vf a = b 0.1 <span style="color: #BB0000;">NA</span> </span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">4</span> (a = b).Vr Vr a = b 0.1 <span style="color: #BB0000;">NA</span></span></span> | |
| <span></span> | |
| <span><span class="va">timecourse</span> <span class="op"><-</span> <span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/autoplot.copasi_ts.html">autoplot.copasi_ts</a></span><span class="op">(</span><span class="va">timecourse</span><span class="op">)</span></span></code></pre></div> | |
| <p><img src="model_building_files/figure-html/unnamed-chunk-3-1.png" width="100%"></p> | |
| <div class="sourceCode" id="cb4"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span></span> | |
| <span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> | |
| </div> | |
| <div class="section level2"> | |
| <h2 id="defining-reaction-kinetics-manually">Defining Reaction Kinetics Manually<a class="anchor" aria-label="anchor" href="#defining-reaction-kinetics-manually"></a> | |
| </h2> | |
| <p>In previous examples, we used the predefined “Reversible | |
| Michaelis-Menten” kinetic functions. In this example we create an | |
| equivalent function manually to achieve the same result.</p> | |
| <div class="sourceCode" id="cb5"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> # A COPASI model reference:</span></span> | |
| <span><span class="co">#> Model name: "New Model"</span></span> | |
| <span><span class="co">#> Number of compartments: 0</span></span> | |
| <span><span class="co">#> Number of species: 0</span></span> | |
| <span><span class="co">#> Number of reactions: 0</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/newCompartment.html">newCompartment</a></span><span class="op">(</span><span class="st">"compartment"</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "Compartments[compartment]"</span></span> | |
| <span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"fixed"</span>, initial_concentration <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "a{compartment}"</span></span> | |
| <span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"b"</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "b{compartment}"</span></span> | |
| <span><span class="fu"><a href="../reference/newKineticFunction.html">newKineticFunction</a></span><span class="op">(</span></span> | |
| <span> <span class="st">"manual MM"</span>,</span> | |
| <span> <span class="st">"((Vf * substrate) / Kms - Vr * product / Kmp) / (1 + substrate / Kms + product / Kms)"</span>,</span> | |
| <span> parameters <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span>substrate <span class="op">=</span> <span class="st">"substrate"</span>, product <span class="op">=</span> <span class="st">"product"</span><span class="op">)</span></span> | |
| <span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "FunctionDB.Functions[manual MM]"</span></span> | |
| <span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span></span> | |
| <span> <span class="st">"a = b"</span>,</span> | |
| <span> fun <span class="op">=</span> <span class="st">"manual MM"</span>,</span> | |
| <span> mapping <span class="op">=</span> <span class="fu"><a href="https://rdrr.io/r/base/list.html" class="external-link">list</a></span><span class="op">(</span></span> | |
| <span> substrate <span class="op">=</span> <span class="st">"a"</span>,</span> | |
| <span> product <span class="op">=</span> <span class="st">"b"</span>,</span> | |
| <span> Vf <span class="op">=</span> <span class="fl">0.1</span>,</span> | |
| <span> Kms <span class="op">=</span> <span class="fl">0.1</span>,</span> | |
| <span> Vr <span class="op">=</span> <span class="fl">0.1</span>,</span> | |
| <span> Kmp <span class="op">=</span> <span class="fl">0.1</span></span> | |
| <span> <span class="op">)</span></span> | |
| <span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "(a = b)"</span></span> | |
| <span></span> | |
| <span><span class="va">timecourse</span> <span class="op"><-</span> <span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/autoplot.copasi_ts.html">autoplot.copasi_ts</a></span><span class="op">(</span><span class="va">timecourse</span><span class="op">)</span></span></code></pre></div> | |
| <p><img src="model_building_files/figure-html/unnamed-chunk-4-1.png" width="100%"></p> | |
| <div class="sourceCode" id="cb6"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span></span> | |
| <span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> | |
| </div> | |
| <div class="section level2"> | |
| <h2 id="quantities-as-proxy-for-time-course-output">Quantities as Proxy for Time Course Output<a class="anchor" aria-label="anchor" href="#quantities-as-proxy-for-time-course-output"></a> | |
| </h2> | |
| <p>The <code>runTimeCourse</code> function only returns data for actual | |
| defined entities of the model. Auxiliarry information like reaction | |
| rates can be missing and needs to be added via global quantity | |
| assignments. This example creates a global quantity “reaction rate” to | |
| generate data for the main reaction’s flux.</p> | |
| <div class="sourceCode" id="cb7"><pre class="downlit sourceCode r"> | |
| <code class="sourceCode R"><span><span class="fu"><a href="../reference/newModel.html">newModel</a></span><span class="op">(</span><span class="op">)</span></span> | |
| <span><span class="co">#> # A COPASI model reference:</span></span> | |
| <span><span class="co">#> Model name: "New Model"</span></span> | |
| <span><span class="co">#> Number of compartments: 0</span></span> | |
| <span><span class="co">#> Number of species: 0</span></span> | |
| <span><span class="co">#> Number of reactions: 0</span></span> | |
| <span></span> | |
| <span><span class="va">subs_quant</span> <span class="op"><-</span> <span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span><span class="st">"substrate concentration"</span>, initial_value <span class="op">=</span> <span class="fl">10</span><span class="op">)</span></span> | |
| <span><span class="va">subs_value</span> <span class="op"><-</span> <span class="fu"><a href="../reference/entity_finders.html">quantity</a></span><span class="op">(</span><span class="va">subs_quant</span>, reference <span class="op">=</span> <span class="st">"Value"</span><span class="op">)</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/newSpecies.html">newSpecies</a></span><span class="op">(</span><span class="st">"a"</span>, type <span class="op">=</span> <span class="st">"assignment"</span>, expression <span class="op">=</span> <span class="va">subs_value</span><span class="op">)</span></span> | |
| <span><span class="co">#> Warning: No compartment exists. Created default compartment.</span></span> | |
| <span><span class="co">#> [1] "a{compartment}"</span></span> | |
| <span><span class="fu"><a href="../reference/newReaction.html">newReaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, fun <span class="op">=</span> <span class="st">"Reversible Michaelis-Menten"</span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "(a = b)"</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/runTimeCourse.html">runTC</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">$</span><span class="va">result</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 101 × 3</span></span></span> | |
| <span><span class="co">#> Time b a</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 0 1 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 10 1.75 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 20 2.40 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 30 2.97 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 40 3.48 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 50 3.94 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 60 4.35 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 70 4.72 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 80 5.06 10</span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">10</span> 90 5.37 10</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with 91 more rows</span></span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/newGlobalQuantity.html">newGlobalQuantity</a></span><span class="op">(</span></span> | |
| <span> <span class="st">"reaction rate"</span>,</span> | |
| <span> type <span class="op">=</span> <span class="st">"assignment"</span>,</span> | |
| <span> expression <span class="op">=</span> <span class="fu"><a href="../reference/entity_finders.html">reaction</a></span><span class="op">(</span><span class="st">"a = b"</span>, reference <span class="op">=</span> <span class="st">"Flux"</span><span class="op">)</span></span> | |
| <span><span class="op">)</span></span> | |
| <span><span class="co">#> [1] "Values[reaction rate]"</span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="fl">1000</span><span class="op">)</span><span class="op">$</span><span class="va">result</span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># A tibble: 101 × 4</span></span></span> | |
| <span><span class="co">#> Time b a `Values[reaction rate]`</span></span> | |
| <span><span class="co">#> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span> <span style="color: #949494; font-style: italic;"><dbl></span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 1</span> 0 1 10 0.081<span style="text-decoration: underline;">1</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 2</span> 10 1.75 10 0.069<span style="text-decoration: underline;">6</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 3</span> 20 2.40 10 0.060<span style="text-decoration: underline;">8</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 4</span> 30 2.97 10 0.053<span style="text-decoration: underline;">8</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 5</span> 40 3.48 10 0.048<span style="text-decoration: underline;">0</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 6</span> 50 3.94 10 0.043<span style="text-decoration: underline;">2</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 7</span> 60 4.35 10 0.039<span style="text-decoration: underline;">1</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 8</span> 70 4.72 10 0.035<span style="text-decoration: underline;">6</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;"> 9</span> 80 5.06 10 0.032<span style="text-decoration: underline;">6</span></span></span> | |
| <span><span class="co">#> <span style="color: #BCBCBC;">10</span> 90 5.37 10 0.029<span style="text-decoration: underline;">9</span></span></span> | |
| <span><span class="co">#> <span style="color: #949494;"># … with 91 more rows</span></span></span> | |
| <span></span> | |
| <span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div> | |
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