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<h1 data-toc-skip>CoRC Introduction</h1>
<h4 data-toc-skip class="author">Jonas Förster
&amp; Jürgen Pahle</h4>
<small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/vignettes/CoRC.Rmd" class="external-link"><code>vignettes/CoRC.Rmd</code></a></small>
<div class="hidden name"><code>CoRC.Rmd</code></div>
</div>
<div class="section level2">
<h2 id="getting-started">Getting started<a class="anchor" aria-label="anchor" href="#getting-started"></a>
</h2>
<div class="section level3">
<h3 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h3>
<p>Install the CoRC package directly from GitHub:</p>
<div class="sourceCode" id="cb1"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"remotes"</span><span class="op">)</span></span>
<span><span class="fu">remotes</span><span class="fu">::</span><span class="fu"><a href="https://remotes.r-lib.org/reference/install_github.html" class="external-link">install_github</a></span><span class="op">(</span><span class="st">"jpahle/CoRC"</span><span class="op">)</span></span></code></pre></div>
<p>The installation may take a few minutes.</p>
<p>CoRC runs it’s own version of the COPASI backend which it will
download for your platform during installation.</p>
<p>In case there is no internet connection, the package can be
downloaded from the (<a href="https://github.com/jpahle/CoRC/releases" class="external-link">github releases</a>).
Both the package and the correct platform-specific libraries need to be
downloaded. In most cases it’s easiest to just specify the location of
the libraries prior to installation by setting the
<code>COPASI_LIB_PATH</code> environment variable. E.g. for CoRC Version
0.10.0 on windows:</p>
<div class="sourceCode" id="cb2"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/base/Sys.setenv.html" class="external-link">Sys.setenv</a></span><span class="op">(</span>COPASI_LIB_PATH <span class="op">=</span> <span class="st">"C:/Users/jonas/Downloads/COPASI_windows_x86_64.dll"</span><span class="op">)</span></span>
<span><span class="fu"><a href="https://rdrr.io/r/utils/install.packages.html" class="external-link">install.packages</a></span><span class="op">(</span><span class="st">"C:/Users/jonas/Downloads/CoRC_0.10.0.tar.gz"</span>, repos <span class="op">=</span> <span class="cn">NULL</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="startup">Startup<a class="anchor" aria-label="anchor" href="#startup"></a>
</h3>
<p>To start, load the library.</p>
<div class="sourceCode" id="cb3"><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://github.com/jpahle/CoRC" class="external-link">CoRC</a></span><span class="op">)</span></span></code></pre></div>
<p>From this point on, CoRC keeps an instance of COPASI running in the
background. This instance can load up as many models as desired.</p>
</div>
<div class="section level3">
<h3 id="loading-a-model">Loading a model<a class="anchor" aria-label="anchor" href="#loading-a-model"></a>
</h3>
<p>Initially, no model is loaded.</p>
<div class="sourceCode" id="cb4"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="co">#&gt; Error: No model currently in use.</span></span></code></pre></div>
<p>You can load a model by using one of the model management
commands.</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="fu"><a href="../reference/loadModel.html">loadModel</a></span><span class="op">(</span><span class="va">path</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadModelFromString.html">loadModelFromString</a></span><span class="op">(</span><span class="va">model_string</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadSBML.html">loadSBML</a></span><span class="op">(</span><span class="va">path</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadSBMLFromString.html">loadSBMLFromString</a></span><span class="op">(</span><span class="va">sbml_string</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/loadExamples.html">loadExamples</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>When loading a model, the returned object is a reference to the model
that will give basic information when printed.</p>
<div class="sourceCode" id="cb6"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">model</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/loadSBML.html">loadSBML</a></span><span class="op">(</span><span class="st">"https://www.ebi.ac.uk/biomodels/model/download/BIOMD0000000329.2?filename=BIOMD0000000329_url.xml"</span><span class="op">)</span></span>
<span><span class="va">model</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "Kummer2000 - Oscillations in Calcium Signalling"</span></span>
<span><span class="co">#&gt; Number of compartments: 1</span></span>
<span><span class="co">#&gt; Number of species: 3</span></span>
<span><span class="co">#&gt; Number of reactions: 8</span></span></code></pre></div>
<p>This reference can be used with most functions using the
<code>model</code> argument but can also be safely ignored when working
with a single model.</p>
</div>
<div class="section level3">
<h3 id="workflow">Workflow<a class="anchor" aria-label="anchor" href="#workflow"></a>
</h3>
<p>CoRC contains a plethora of functions for working with COPASI models.
The most basic ones required for common workflows are used for
manipulation of model entities and running tasks.</p>
<div class="sourceCode" id="cb7"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="https://rdrr.io/r/utils/str.html" class="external-link">str</a></span><span class="op">(</span><span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="op">)</span><span class="op">)</span></span>
<span><span class="co">#&gt; tibble [3 × 13] (S3: tbl_df/tbl/data.frame)</span></span>
<span><span class="co">#&gt; $ key : chr [1:3] "G-alpha{compartment}" "activePLC{compartment}" "Calcium{compartment}"</span></span>
<span><span class="co">#&gt; $ name : chr [1:3] "G-alpha" "activePLC" "Calcium"</span></span>
<span><span class="co">#&gt; $ compartment : chr [1:3] "compartment" "compartment" "compartment"</span></span>
<span><span class="co">#&gt; $ type : chr [1:3] "reactions" "reactions" "reactions"</span></span>
<span><span class="co">#&gt; $ unit : chr [1:3] "nmol/l" "nmol/l" "nmol/l"</span></span>
<span><span class="co">#&gt; $ initial_concentration: num [1:3] 0.01 0.01 0.01</span></span>
<span><span class="co">#&gt; $ initial_number : num [1:3] 0.602 0.602 0.602</span></span>
<span><span class="co">#&gt; $ concentration : num [1:3] NaN NaN NaN</span></span>
<span><span class="co">#&gt; $ number : num [1:3] NaN NaN NaN</span></span>
<span><span class="co">#&gt; $ rate : num [1:3] 0 0 0</span></span>
<span><span class="co">#&gt; $ number_rate : num [1:3] 0 0 0</span></span>
<span><span class="co">#&gt; $ initial_expression : chr [1:3] "" "" ""</span></span>
<span><span class="co">#&gt; $ expression : chr [1:3] "" "" ""</span></span></code></pre></div>
<div class="sourceCode" id="cb8"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/setSpecies.html">setSpecies</a></span><span class="op">(</span><span class="st">"G-alpha"</span>, initial_concentration <span class="op">=</span> <span class="fl">0.02</span><span class="op">)</span></span>
<span><span class="va">timecourse</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span>duration <span class="op">=</span> <span class="fl">100</span>, intervals <span class="op">=</span> <span class="fl">10000</span><span class="op">)</span></span></code></pre></div>
<p>This enables quick definition of loops, for example to scan through
various concentration values of a species.</p>
<div class="sourceCode" id="cb9"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">ga_concentrations</span> <span class="op">&lt;-</span> <span class="fl">1</span><span class="op">:</span><span class="fl">5</span></span>
<span></span>
<span><span class="kw">for</span> <span class="op">(</span><span class="va">ga_conc</span> <span class="kw">in</span> <span class="va">ga_concentrations</span><span class="op">)</span> <span class="op">{</span></span>
<span> <span class="fu"><a href="../reference/setSpecies.html">setSpecies</a></span><span class="op">(</span><span class="st">"G-alpha"</span>, initial_concentration <span class="op">=</span> <span class="va">ga_conc</span><span class="op">)</span></span>
<span> </span>
<span> <span class="va">ga_state</span> <span class="op">&lt;-</span> <span class="fu"><a href="../reference/getSpecies.html">getSpecies</a></span><span class="op">(</span><span class="st">"G-alpha"</span><span class="op">)</span></span>
<span> </span>
<span> <span class="fu"><a href="https://rdrr.io/r/base/print.html" class="external-link">print</a></span><span class="op">(</span><span class="fu"><a href="https://rdrr.io/r/base/paste.html" class="external-link">paste</a></span><span class="op">(</span></span>
<span> <span class="st">"Current concentration:"</span>, <span class="va">ga_state</span><span class="op">$</span><span class="va">initial_concentration</span>, <span class="va">ga_state</span><span class="op">$</span><span class="va">unit</span></span>
<span> <span class="op">)</span><span class="op">)</span></span>
<span> </span>
<span> <span class="co"># further commands e.g.:</span></span>
<span> <span class="co"># runTimecourse()</span></span>
<span> <span class="co"># saveModel(paste0("ga", ga_value, ".cps"))</span></span>
<span><span class="op">}</span></span>
<span><span class="co">#&gt; [1] "Current concentration: 1 nmol/l"</span></span>
<span><span class="co">#&gt; [1] "Current concentration: 2 nmol/l"</span></span>
<span><span class="co">#&gt; [1] "Current concentration: 3 nmol/l"</span></span>
<span><span class="co">#&gt; [1] "Current concentration: 4 nmol/l"</span></span>
<span><span class="co">#&gt; [1] "Current concentration: 5 nmol/l"</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="corc-data">CoRC data<a class="anchor" aria-label="anchor" href="#corc-data"></a>
</h3>
<p>Data generated by CoRC is returned as common R structures such as
lists, data frames and matrices. Data frames are wrapped in an
equivalent structure called a <a href="https://cran.r-project.org/web/packages/tibble/README.html" class="external-link"><code>tibble</code></a>
which behaves identical in most circumstances but gives a reasonable
overview when printing.</p>
<div class="sourceCode" id="cb10"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="va">timecourse</span><span class="op">$</span><span class="va">result</span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># A tibble: 10,001 × 4</span></span></span>
<span><span class="co">#&gt; Time `G-alpha` activePLC Calcium</span></span>
<span><span class="co">#&gt; <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span> <span style="color: #949494; font-style: italic;">&lt;dbl&gt;</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 1</span> 0 0.02 0.01 0.01 </span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 2</span> 0.01 0.022<span style="text-decoration: underline;">7</span> 0.010<span style="text-decoration: underline;">2</span> 0.000<span style="text-decoration: underline;">320</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 3</span> 0.02 0.025<span style="text-decoration: underline;">5</span> 0.010<span style="text-decoration: underline;">3</span> 0.000<span style="text-decoration: underline;">359</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 4</span> 0.03 0.028<span style="text-decoration: underline;">4</span> 0.010<span style="text-decoration: underline;">6</span> 0.000<span style="text-decoration: underline;">400</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 5</span> 0.04 0.031<span style="text-decoration: underline;">4</span> 0.010<span style="text-decoration: underline;">8</span> 0.000<span style="text-decoration: underline;">442</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 6</span> 0.05 0.034<span style="text-decoration: underline;">4</span> 0.011<span style="text-decoration: underline;">1</span> 0.000<span style="text-decoration: underline;">486</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 7</span> 0.06 0.037<span style="text-decoration: underline;">6</span> 0.011<span style="text-decoration: underline;">4</span> 0.000<span style="text-decoration: underline;">530</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 8</span> 0.07 0.040<span style="text-decoration: underline;">8</span> 0.011<span style="text-decoration: underline;">8</span> 0.000<span style="text-decoration: underline;">576</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;"> 9</span> 0.08 0.044<span style="text-decoration: underline;">1</span> 0.012<span style="text-decoration: underline;">2</span> 0.000<span style="text-decoration: underline;">624</span></span></span>
<span><span class="co">#&gt; <span style="color: #BCBCBC;">10</span> 0.09 0.047<span style="text-decoration: underline;">5</span> 0.012<span style="text-decoration: underline;">6</span> 0.000<span style="text-decoration: underline;">672</span></span></span>
<span><span class="co">#&gt; <span style="color: #949494;"># … with 9,991 more rows</span></span></span></code></pre></div>
<p>It is encouraged to use the <a href="https://cran.r-project.org/web/packages/ggplot2/index.html" class="external-link">ggplot2
package</a> for generating publication-ready plots from CoRC data. The
helper function <code>autoplot.copasi_ts</code> can be used to quickly
print timecourse data.</p>
<div class="sourceCode" id="cb11"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="co"># library(ggplot2)</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="CoRC_files/figure-html/unnamed-chunk-11-1.png" width="100%"></p>
</div>
<div class="section level3">
<h3 id="final-steps">Final steps<a class="anchor" aria-label="anchor" href="#final-steps"></a>
</h3>
<p>Finally, a model can be saved via several model management
commands.</p>
<div class="sourceCode" id="cb12"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/saveModel.html">saveModel</a></span><span class="op">(</span><span class="va">filename</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/saveModelToString.html">saveModelToString</a></span><span class="op">(</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/saveSBML.html">saveSBML</a></span><span class="op">(</span><span class="va">path</span>, level <span class="op">=</span> <span class="fl">3</span>, version <span class="op">=</span> <span class="fl">1</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/saveSBMLToString.html">saveSBMLToString</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
<p>To free up memory, unload any loaded models or restart R.</p>
<div class="sourceCode" id="cb13"><pre class="downlit sourceCode r">
<code class="sourceCode R"><span><span class="fu"><a href="../reference/unloadModel.html">unloadModel</a></span><span class="op">(</span><span class="va">model</span><span class="op">)</span></span>
<span><span class="fu"><a href="../reference/unloadAllModels.html">unloadAllModels</a></span><span class="op">(</span><span class="op">)</span></span></code></pre></div>
</div>
<div class="section level3">
<h3 id="examples">Examples<a class="anchor" aria-label="anchor" href="#examples"></a>
</h3>
<p>Information regarding different aspects of CoRC and simple examples
can be found in the articles on <a href="https://jpahle.github.io/CoRC/articles/entity_management.html">model
entity management</a>, <a href="https://jpahle.github.io/CoRC/articles/task_management.html">task
management</a> and <a href="https://jpahle.github.io/CoRC/articles/model_building.html">model
building</a> on the CoRC website. More sophisticated examples and
case-studies illustrating further benefits of using CoRC can be found in
the <a href="https://jpahle.github.io/CoRC/articles/examples.html">examples
article</a>.</p>
</div>
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