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<center><h1>SloppyCell</h1></center>


<p>SloppyCell is a software environment for simulation and analysis of biomolecular networks developed by the groups of <a href="http://www.lassp.cornell.edu/sethna/">Jim Sethna</a> and <a href="http://www.tc.cornell.edu/~myers/">Chris Myers</a> at <a href="http://www.cornell.edu">Cornell University</a>.</p>

<p>Examples of models developed in SloppyCell can be found at <a href="http://www.lassp.cornell.edu/sethna/GeneDynamics/">Jim Sethna's Gene Dynamics page</a>.</p>

<h2>Features</h2>
<ul>
<li>support for much of the <a href="http://sbml.org">Systems Biology Markup Language (SBML)</a> level 2 version 3</li>
<li>deterministic and stochastic dynamical simulations</li>
<li>sensitivity analysis without finite-difference derviatives</li>
<li>optimization methods to fit parameters to experimental data</li>
<li>simulation of multiple related networks sharing common parameters</li>
<li>stochastic Bayesian analysis of parameter space to estimate error bars
associated with optimal fits</li>
</ul>

<h2>News</h2>
<blockquote>October 10th, 2007: <strong>New documentation</strong>
<blockquote>
<p>As part of his thesis, Ryan Gutenkunst has written both user and developer documenation for SloppyCell. They are linked below.</p> 
</blockquote>
</blockquote>

<blockquote>July 21st, 2007: <strong>SloppyCell 0.81 released</strong>
<blockquote>
<p>Additions include support for scale factor priors, a new Monte Carlo
algorithm that recalculates the sampling matrix each step, and numerous
bug fixes.</p> 

<p>See our <a href="http://sourceforge.net/project/showfiles.php?group_id=140498">download page</a>.</p>
</blockquote>
</blockquote>

<blockquote>May 9th, 2007: <strong>SloppyCell 0.8 released!</strong>
<blockquote>
<p>SloppyCell continues to evolve rapidly.</p>

<p>This release sees very signficant speed increases.
We've added support for automatically building C versions of all the
integration functions. In testing on various networks, this yields a
speed up of between a factor of 5 and 20 depending on the application.
Additionally, network compilation and sensitivity integration are faster.</p>

<p>Finally, algebraic rules are now fully supported, and we have moved
completely to using DASKR as our integrator.</p>

<p>See our <a href="http://sourceforge.net/project/showfiles.php?group_id=140498">download page</a>.</p>
</blockquote>
</blockquote>

<blockquote>January 23rd, 2007: <strong>SloppyCell 0.6 released!</strong>
<blockquote>
<p>Lots of work over the past few months. The parallel processing code has
been completely rewritten. Preliminary support for algebraic rules is also
in. (Many thanks to Jordan Atlas for his help.)</p>

<p>Grab it from our <a href="http://sourceforge.net/project/showfiles.php?group_id=140498">download page</a>.</p>
</blockquote>
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<h2>Documentation</h2>
<ul>
<li><a href="user.pdf">User documentation</a> (pdf)</li>
<li><a href="devel.pdf">Developer documentation</a> (pdf)</li>
<li><a href="api/SloppyCell.ReactionNetworks-module.html">API documentation</a> generated API_DOC_GEN_DATE</li>
<li><a href="http://lists.sourceforge.net/lists/listinfo/sloppycell-users">Mailing list</a></li>
</ul>

<h2>Miscellaneous</h2>
<ul>
<li>Sourceforge <a href="http://www.sourceforge.net/projects/sloppycell/">project page</a></li>
<li>Browse the <a href="http://sloppycell.cvs.sourceforge.net/sloppycell/SloppyCell/">CVS repository</a></li>
<li>CVS snapshot (<a href="SloppyCell-CVS.tar.gz">.tar.gz</a>, <a href="SloppyCell-CVS.zip">.zip</a>) generated Wed Jun  3 10:14:54 2009</li>
<li><strong>Reference:</strong><br>
Ryan N. Gutenkunst, Jordan C. Atlas, Fergal P. Casey, Robert S. Kuczenski, Joshua J. Waterfall, Chris R. Myers, and James P. Sethna.<br>
SloppyCell. <a href="http://sloppycell.sourceforge.net/">http://sloppycell.sourceforge.net/</a> (2007)</li>
</ul>

<p>$Date: 2007/10/02 01:38:39 $</p>
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