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<div class="section level1">
<div class="page-header"><h1 id="id_--the-copasi-r-connector">
<img src="reference/figures/logo.png" alt="CoRC logo" width="200"> — the <b>CO</b>PASI <b>R</b> <b>C</b>onnector<a class="anchor" aria-label="anchor" href="#id_--the-copasi-r-connector"></a>
</h1></div>
<div class="section level2">
<h2 id="overview">Overview<a class="anchor" aria-label="anchor" href="#overview"></a>
</h2>
<p>Development Stage: <strong>Beta</strong></p>
<p>CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI (<a href="http://copasi.org" class="external-link">copasi.org</a>) and the (statistical) programming environment R (<a href="http://r-project.org" class="external-link">r-project.org</a>). It provides easy access to the powerful biochemical model editing, simulation and analysis backend of COPASI from the convenient R command line interface. This allows the user to develop elaborate scripts and workflows for analyses that would require a great deal of tedious manual work otherwise. These scripts can then be run interactively from the R command line interface or be sent to cluster or cloud facilities for more demanding calculations.</p>
<p>CoRC features:</p>
<ul>
<li>high-level API for COPASI in the R language.</li>
<li>Immediate access to R’s data analysis capabilities and publication-ready plotting.</li>
<li>Reproducible workflows from data generation to analysis and plotting (R scripts and notebooks).</li>
<li>Rule-based modification of model structure to test structural variations or create large models.</li>
<li>Scaling up assays, e.g. from 3 models to 3000.</li>
<li>Handling of multiple models at once.</li>
<li>Parallelization on multi-core machines or computing clusters.</li>
</ul>
<p>It is currently based on COPASI version 4.39 Build (272) and aims to closely follow COPASI releases in the future.</p>
<p>CoRC comes with the Artistic License 2.0. By using CoRC you agree to this license.</p>
</div>
<div class="section level2">
<h2 id="installation">Installation<a class="anchor" aria-label="anchor" href="#installation"></a>
</h2>
<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>
</div>
<div class="section level2">
<h2 id="usage">Usage<a class="anchor" aria-label="anchor" href="#usage"></a>
</h2>
<div class="sourceCode" id="cb2"><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>
<span><span class="fu"><a href="reference/loadExamples.html">loadExamples</a></span><span class="op">(</span><span class="fl">1</span><span class="op">)</span></span>
<span><span class="co">#&gt; [[1]]</span></span>
<span><span class="co">#&gt; # A COPASI model reference:</span></span>
<span><span class="co">#&gt; Model name: "The Brusselator"</span></span>
<span><span class="co">#&gt; Number of compartments: 1</span></span>
<span><span class="co">#&gt; Number of species: 6</span></span>
<span><span class="co">#&gt; Number of reactions: 4</span></span>
<span></span>
<span><span class="fu"><a href="reference/runTimeCourse.html">runTimeCourse</a></span><span class="op">(</span><span class="op">)</span><span class="op">$</span><span class="va">result</span></span>
<span><span class="co">#&gt; # A tibble: 201 × 3</span></span>
<span><span class="co">#&gt; Time X Y</span></span>
<span><span class="co">#&gt; &lt;dbl&gt; &lt;dbl&gt; &lt;dbl&gt;</span></span>
<span><span class="co">#&gt; 1 0 3 3 </span></span>
<span><span class="co">#&gt; 2 0.5 3.41 0.817</span></span>
<span><span class="co">#&gt; 3 1 1.90 1.28 </span></span>
<span><span class="co">#&gt; 4 1.5 0.876 1.87 </span></span>
<span><span class="co">#&gt; 5 2 0.346 2.37 </span></span>
<span><span class="co">#&gt; 6 2.5 0.183 2.66 </span></span>
<span><span class="co">#&gt; 7 3 0.147 2.86 </span></span>
<span><span class="co">#&gt; 8 3.5 0.141 3.05 </span></span>
<span><span class="co">#&gt; 9 4 0.141 3.23 </span></span>
<span><span class="co">#&gt; 10 4.5 0.142 3.41 </span></span>
<span><span class="co">#&gt; # … with 191 more rows</span></span></code></pre></div>
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<h2 data-toc-skip>Links</h2>
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<li><a href="https://github.com/jpahle/CoRC/" class="external-link">Browse source code</a></li>
<li><a href="https://github.com/jpahle/CoRC/issues" class="external-link">Report a bug</a></li>
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<h2 data-toc-skip>License</h2>
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<li>
<a href="https://www.r-project.org/Licenses/Artistic-2.0" class="external-link">Artistic-2.0</a> | file <a href="LICENSE-text.html">LICENSE</a>
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<h2 data-toc-skip>Citation</h2>
<ul class="list-unstyled">
<li><a href="authors.html#citation">Citing CoRC</a></li>
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<div class="developers">
<h2 data-toc-skip>Developers</h2>
<ul class="list-unstyled">
<li>Jonas Förster <br><small class="roles"> Author, maintainer </small> </li>
<li>Jürgen Pahle <br><small class="roles"> Author </small> </li>
</ul>
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