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<html>
<head>
<title>Links</title>
</head>
<body>
<h1>Links</h1>

<b>Stochastic Simulations.</b><br>
<ul>
  <li>
  The <a href="http://sbml.org/">SBML</a> (Systems Biology Markup Language)
  homepage has links to many software projects.
  <li> 
  <a href="http://www.me.ucsb.edu/dept_site/people/new_faculty_pages/petzold_page.html">Linda Petzold</a> and her research group at
  <a href="http://www.ucsb.edu/">UCSB</a>
  (including <a href="http://www.cs.ucsb.edu/~hongli/">Hong Li</a>,
  <a href="http://www.kevinsanft.com/">Kevin Sanft</a>,
  <a href="http://www.cse.ucsb.edu/IGERT/students/IGERT_roh.html">Min Roh</a>,
  and
  <a href="http://www.cse.ucsb.edu/IGERT/students/IGERT_drawert.html">Brian Drawert</a>)
  study stochastic simulation methods and have developed 
  <a href="http://www.engineering.ucsb.edu/~cse/StochKit/">StochKit</a>.
  <li>
  <a href="http://www.staff.ncl.ac.uk/d.j.wilkinson/">Darren Wilkinson</a>,
  provides software and test models at his web site.
  <li>
  <a href="http://dsmts.googlecode.com/">DSMTS</a>
  (Discrete Stochastic Models Test Suite) is a test suite in SBML
  format.
  <li>
  <a href="http://www.sbos.eu/">SB.OS</a> is a live DVD based on
  Ubuntu Linux that comes with a comprehensive list of Systems Biology Software.
  <li>
  <a href="http://magnet.systemsbiology.net/software/Dizzy/">Dizzy</a>
  is a chemical kinetics stochastic simulation software package written in
  Java.
  <li>
  <a href="http://www.copasi.org/">COPASI</a>
  is a software application for simulation and analysis of biochemical networks.
  <li>
  <a href="http://www.bio.ifi.lmu.de/FERN/">FERN</a>
  (Framework for Evaluation of Reaction Networks) is an extensible and
  comprehensive framework for efficient simulations and analysis of chemical
  reaction networks written in Java.
  <li>
  <a href="http://www.cellmc.org/">CellMC</a>
  is an open source program generator that compiles a mesoscopic model of a
  biochemical reaction network, expressed as SBML, into an executable program
  that realizes SSA for that model; the program can then be run for any final
  simulation time and number of realizations.
 <li>
  <a href="http://www.sysbio.pl/stocks/">STOCKS</a>
  is public domain (GNU GPL) software for stochastic simulations of
  biochemical processes. 
  <li>
  <a href="http://www.mathworks.com/products/simbiology/">SimBiology</a>
  provides graphical and programmatic tools for modeling, simulating, and
  analyzing biological systems.
</ul>

<b>Open-source software resources.</b><br>
<ul>
  <li>
  <a href="http://sourceforge.net/">SourceForge</a> hosts a wealth of
  software projects.
  <li>
  <a href="http://freshmeat.net/">freshmeat</a> maintains the Web's largest
  index of Unix and cross-platform software.
</ul>

<b>Software.</b><br>
<ul>
  <li>
  <a href="http://www.python.org/">Python</a> is a simple, powerful, and
  extensible object-oriented programming language.
  <li>
  The <a href="http://www.enthought.com/products/epd.php">
  Enthought Python Distribution</a> is a kitchen-sink-included distribution
  of Python.
  <li>
  <a href="http://www.wxpython.org/">wxPython</a> is a cross-platform GUI
  toolkit.
  <li>
  Cain uses <a href="http://matplotlib.sourceforge.net/">matplotlib</a>, a
  2D plotting library.
  <li>
  Cain uses some icons from the 
  <a href="http://tango.freedesktop.org/Tango_Desktop_Project">
  Tango Desktop Project</a>.
</ul>

</body>
</html>