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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<title>PySCeS: The Python Simulator for Cellular Systems</title>
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<nav class="navbar navbar-expand-lg navbar-dark bg-dark">
<a class="navbar-brand" href="https://pysces.github.io/">PySCeS</a>
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<img src="images/pysces_header.gif" alt="PySCeS" width="1200" height="400" class="img-fluid">
<h3 class="text-center"> </h3>
<h3 class="text-center">A flexible, user friendly tool for the analysis of cellular systems<br/><br/></h3>
<h5 class="text-center">Computer modelling has become an integral tool in the analysis and understanding of the reaction networks that underlie cellular processes. PySCeS, first released in 2003, is extremely flexible, user-extendible, open source, software actively used and developed by a community of researchers and developers.<br/><br/></h5>
<h4 class="text-center">The latest PySCeS release is version 1.2.2
(August 2024).</h4>
<p> </p>
</div>
</div>
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<div class="container">
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<div class="col-lg-3 col-lg-6 col-12">
<h2>User friendly</h2>
<ul>
<li>Define models with human readable, <strong>Model Description Language</strong>. </li>
<li>Use the full power of Python available to <strong>test, build and share</strong> your modelling experiments. </li>
<li>User friendly methods for generating and 1, 2 and n-dimension <strong>parameter scans</strong>.</li>
<li><strong>Visualise</strong> results of simulations with flexible Matplotlib and Gnuplot interfaces.</li>
<li>PySCeS supports <strong>open community standards</strong> for model exchange (SBML) and archiving (SEDML, OMEX).</li>
</ul>
</div>
<div class="col-lg-3 col-lg-6 col-12">
<h2>Modelling features</h2>
<ul>
<li><strong>Simulate</strong> your time courses with solvers like LSODA. </li>
<li>Efficiently determine <strong>steady states</strong> using a selection of non-linear, root-finding algorithms (e.g. HYBRD, NLEQ2). </li>
<li>Use <strong>Metabolic Control Analysis</strong> (MCA) to investigate control and regulation of cellular systems (elasticities, flux control and response coefficients).</li>
<li>Perform <strong>structural analysis</strong> and determine nullspaces and reduced stoichiometric and MCA matrices</li>
<li>Investigate systems which exhibit multiple (stable and unstable) steady-state solutions using PITCON based <strong>bifurcation analysis</strong> module.</li>
</ul>
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<div class="card">
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<h3 class="card-title">Installing PySCeS </h3>
<p class="card-text">PySCeS is available for all major operating systems. The easiest way to install PySCeS is to use a Python package manager.</p>
<div class="text-center">
<a class="btn btn-danger btn-lg" href="https://pypi.org/project/pysces/#files" role="button">PyPi</a>
<a class="btn btn-lg btn-info" href="https://github.com/PySCeS/pysces" role="button">GitHub</a>
<a class="btn btn-warning btn-lg" href="https://anaconda.org/pysces/pysces" role="button">Anaconda</a>
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<ul>
<li>PyPI<br/><code>pip install pysces</code></li>
<li>Conda<br/><code>conda install -c conda-forge -c pysces pysces</code></li>
<li>Latest source (GitHub see <a href="https://github.com/PySCeS/pysces/blob/master/INSTALL.md">install.md</a> for instructions)<br/>
<code>git clone https://github.com/PySCeS/pysces.git</code></li>
</ul>
<p>The <em>main</em> branch contains the latest release code, for the latest development code, checkout the <em>development</em> branch. I you would like to contribute to PySCeS please do so using pull requests against <em>development</em>.</p>
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<div class="card">
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<div class="card-body">
<h3 class="card-title">Contact us </h3>
<ul>
<li>Chat to a developer or user community? Try the <a href="https://groups.google.com/g/pysces">PySCeS Google group</a>.</li>
<li>Report a specific code issue or discuss existing or new functionality? <a href="https://github.com/PySCeS/pysces/issues">Create an issue</a> on the PySCeS GitHub repository.</li>
</ul>
</div>
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</div>
<div class="col-sm-6">
<div class="card">
<div class="card-body">
<h3 class="card-title">Live demo </h3>
<p class="card-text">Click the button below to try PySCeS in a JupyterLab environment; an example notebook and models are provided. Note that this runs in a web-assembly environment and any changes are saved to your local browser storage, which is <strong>not persistent</strong>. When the browser cache or site data are cleared, any modifications will be lost.
</p>
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<a class="btn btn-warning btn-lg" target="_blank" href="./try" role="button">Try PySCeS</a>
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<h3 class="card-title">Documentation</h3>
<p class="card-text">For more information on using and citing PySCeS try the documentation or 2005 Bioinformatics publication.</p>
<div class="text-center">
<a class="btn btn-info btn-lg" href="https://pyscesdocs.readthedocs.io/" role="button">Documentation</a>
<a class="btn btn-warning btn-lg" href="https://doi.org/10.1093/bioinformatics/bti046" role="button">Publication</a>
</div>
<p class="card-text"> </p>
<p class="card-text">PySCeS source code, issue tracker and wiki available on <a href="https://github.com/PySCeS/pysces">GitHub</a> and see who is citing PySCeS on <a href="https://scholar.google.nl/scholar?hl=en&as_sdt=2005&cites=17307229048471592416&scipsc=&q=&scisbd=1">Google Scholar</a>.</p>
<p class="card-text">PySCeS releases are archived on <a href="https://zenodo.org/">Zenodo </a>and can be referred to as DOI: <a href="https://doi.org/10.5281/zenodo.2600905">10.5281/zenodo.2600905</a><br>
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