data/docs/reference/CoRC-package.html

<!DOCTYPE html>
<!-- Generated by pkgdown: do not edit by hand --><html lang="en"><head><meta http-equiv="Content-Type" content="text/html; charset=UTF-8"><meta charset="utf-8"><meta http-equiv="X-UA-Compatible" content="IE=edge"><meta name="viewport" content="width=device-width, initial-scale=1.0"><title>CoRC: COPASI R Connector. — CoRC-package • CoRC</title><!-- favicons --><link rel="icon" type="image/png" sizes="16x16" href="../favicon-16x16.png"><link rel="icon" type="image/png" sizes="32x32" href="../favicon-32x32.png"><link rel="apple-touch-icon" type="image/png" sizes="180x180" href="../apple-touch-icon.png"><link rel="apple-touch-icon" type="image/png" sizes="120x120" href="../apple-touch-icon-120x120.png"><link rel="apple-touch-icon" type="image/png" sizes="76x76" href="../apple-touch-icon-76x76.png"><link rel="apple-touch-icon" type="image/png" sizes="60x60" href="../apple-touch-icon-60x60.png"><!-- jquery --><script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script><!-- Bootstrap --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous"><script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script><!-- bootstrap-toc --><link rel="stylesheet" href="../bootstrap-toc.css"><script src="../bootstrap-toc.js"></script><!-- Font Awesome icons --><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous"><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous"><!-- clipboard.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script><!-- headroom.js --><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script><!-- pkgdown --><link href="../pkgdown.css" rel="stylesheet"><script src="../pkgdown.js"></script><!-- docsearch --><script src="../docsearch.js"></script><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.3/docsearch.min.css" integrity="sha256-QOSRU/ra9ActyXkIBbiIB144aDBdtvXBcNc3OTNuX/Q=" crossorigin="anonymous"><link href="../docsearch.css" rel="stylesheet"><script src="https://cdnjs.cloudflare.com/ajax/libs/mark.js/8.11.1/jquery.mark.min.js" integrity="sha256-4HLtjeVgH0eIB3aZ9mLYF6E8oU5chNdjU6p6rrXpl9U=" crossorigin="anonymous"></script><meta property="og:title" content="CoRC: COPASI R Connector. — CoRC-package"><meta property="og:description" content="CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI to R.
It provides easy access to the powerful biochemical model editing, simulation and analysis backend of COPASI.
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 or be sent to cluster or cloud facilities for more demanding calculations."><meta property="og:image" content="https://jpahle.github.io/CoRC/logo.svg"><!-- mathjax --><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/MathJax.js" integrity="sha256-nvJJv9wWKEm88qvoQl9ekL2J+k/RWIsaSScxxlsrv8k=" crossorigin="anonymous"></script><script src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.5/config/TeX-AMS-MML_HTMLorMML.js" integrity="sha256-84DKXVJXs0/F8OTMzX4UR909+jtl4G7SPypPavF+GfA=" crossorigin="anonymous"></script><!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.3/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]--></head><body data-spy="scroll" data-target="#toc">
    

    <div class="container template-reference-topic">
      <header><div class="navbar navbar-default navbar-fixed-top" role="navigation">
  <div class="container">
    <div class="navbar-header">
      <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar" aria-expanded="false">
        <span class="sr-only">Toggle navigation</span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
        <span class="icon-bar"></span>
      </button>
      <span class="navbar-brand">
        <a class="navbar-link" href="../index.html">CoRC</a>
        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="">0.12.0</span>
      </span>
    </div>

    <div id="navbar" class="navbar-collapse collapse">
      <ul class="nav navbar-nav"><li>
  <a href="../index.html">
    <span class="fa fa-home fa-lg"></span>
     
  </a>
</li>
<li>
  <a href="../articles/CoRC.html">Get Started</a>
</li>
<li class="dropdown">
  <a href="#" class="dropdown-toggle" data-toggle="dropdown" role="button" data-bs-toggle="dropdown" aria-expanded="false">
    Articles
     
    <span class="caret"></span>
  </a>
  <ul class="dropdown-menu" role="menu"><li>
      <a href="../articles/entity_management.html">Model Entity Management</a>
    </li>
    <li>
      <a href="../articles/task_management.html">Task Management</a>
    </li>
    <li>
      <a href="../articles/model_building.html">Model Building</a>
    </li>
    <li>
      <a href="../articles/issues.html">Issues</a>
    </li>
  </ul></li>
<li>
  <a href="../articles/examples.html">Examples</a>
</li>
<li>
  <a href="../reference/index.html">Reference</a>
</li>
<li>
  <a href="../news/index.html">News</a>
</li>
      </ul><ul class="nav navbar-nav navbar-right"><li>
  <a href="https://github.com/jpahle/CoRC/" class="external-link">
    <span class="fab fa-github fa-lg"></span>
     
  </a>
</li>
      </ul><form class="navbar-form navbar-right hidden-xs hidden-sm" role="search">
        <div class="form-group">
          <input type="search" class="form-control" name="search-input" id="search-input" placeholder="Search..." aria-label="Search for..." autocomplete="off"></div>
      </form>
      
    </div><!--/.nav-collapse -->
  </div><!--/.container -->
</div><!--/.navbar -->

      

      </header><div class="row">
  <div class="col-md-9 contents">
    <div class="page-header">
    <h1>CoRC: COPASI R Connector.</h1>
    <small class="dont-index">Source: <a href="https://github.com/jpahle/CoRC/blob/HEAD/R/CoRC.R" class="external-link"><code>R/CoRC.R</code></a></small>
    <div class="hidden name"><code>CoRC-package.Rd</code></div>
    </div>

    <div class="ref-description">
    <p>CoRC, the COPASI R Connector, links the Complex Pathway Simulator COPASI to R.
It provides easy access to the powerful biochemical model editing, simulation and analysis backend of COPASI.
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 or be sent to cluster or cloud facilities for more demanding calculations.</p>
    </div>


    <div id="details">
    <h2>Details</h2>
    <p>CoRC features:</p>  
<p>* high-level API for COPASI in the R language.
* Immediate access to R's data analysis capabilities and publication-ready plotting.
* Reproducible workflows from data generation to analysis and plotting (R scripts and notebooks).
* Rule-based modification of model structure to test structural variations or create large models.
* Scaling up assays, e.g. from 3 models to 3000.
* Handling of multiple models at once.
* Parallelization on multi-core machines or computing clusters.</p>
<p>It is based on a current development version of COPASI but is expected to closely follow official COPASI releases in the future.</p>
    </div>
    <div id="see-also">
    <h2>See also</h2>
    <div class="dont-index"><p>Useful links:</p><ul><li><p><a href="https://github.com/jpahle/CoRC" class="external-link">https://github.com/jpahle/CoRC</a></p></li>
<li><p>Report bugs at <a href="https://github.com/jpahle/CoRC/issues" class="external-link">https://github.com/jpahle/CoRC/issues</a></p></li>
</ul></div>
    </div>
    <div id="author">
    <h2>Author</h2>
    <p><strong>Maintainer</strong>: Jonas Förster <a href="mailto:jonasfoerster@gmail.com">jonasfoerster@gmail.com</a></p>
<p>Authors:</p><ul><li><p>Jürgen Pahle <a href="mailto:juergen.pahle@bioquant.uni-heidelberg.de">juergen.pahle@bioquant.uni-heidelberg.de</a></p></li>
</ul></div>

  </div>
  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
    <nav id="toc" data-toggle="toc" class="sticky-top"><h2 data-toc-skip>Contents</h2>
    </nav></div>
</div>


      <footer><div class="copyright">
  <p></p><p>Developed by Jonas Förster, Jürgen Pahle.</p>
</div>

<div class="pkgdown">
  <p></p><p>Site built with <a href="https://pkgdown.r-lib.org/" class="external-link">pkgdown</a> 2.0.7.</p>
</div>

      </footer></div>

  
<script src="https://cdnjs.cloudflare.com/ajax/libs/docsearch.js/2.6.1/docsearch.min.js" integrity="sha256-GKvGqXDznoRYHCwKXGnuchvKSwmx9SRMrZOTh2g4Sb0=" crossorigin="anonymous"></script><script>
  docsearch({
    
    
    apiKey: 'fcbd5b3c51a83bf9b730904eb6ce2d5a',
    indexName: 'corc',
    inputSelector: 'input#search-input.form-control',
    transformData: function(hits) {
      return hits.map(function (hit) {
        hit.url = updateHitURL(hit);
        return hit;
      });
    }
  });
</script></body></html>