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A Mathematica package for biological modeling

xCellerator is a Mathematica package designed to aide biological modeling via the automated conversion of chemical reactions into ODEs and their subsequent solution via numerical integration.

This website is currently a newly maintained version of a legacy site, so some links may not work or instructions may be dated. So, please keep that in mind when using the tools and software. Enjoy and be investigative while using these powerful programs!

installation instructions for the base package are given here.

The software can be downloaded from Source Forge or Github

xCellerator is really a family of computer programs. Components include:

  • xlr8r - Reaction translation to ODE and numerical solution. The reaction syntax is backwards compatiable with Cellerator but is more general.
  • Cellzilla - Simulation of a Cellerator reaction network on a two-dimensional template.
  • SSA - Stochastic simulation usings Gillespie's stochastic simulation algorithm.
  • xSSA - extended SSA algorithm for stochastic simulation of most Cellerator reactions (not just mass action).
  • CelleratorML/CellzillaML - an XML-based text file format for saving Cellerator and Cellzilla models.
  • SBML support through xlr8r2SBML and SBML2xlr8r plugins and MathSBML.
  • py[xlr8r] - A Mathematica-free implementation of Cellerator in Python. (under development! Not all features have been implmented yet.)

In addition there are a number of other programs that are compatible with xCellerator that can be used to extend its functionality. These include:

    Sigmoid(Link currently unavailabe) - an online database of Cellerator models and a downloadable database manager, Sigmoid Model Explorer that can be used to query the database and perform simulations using xCellerator.
  • kmech - a Cellerator based enzyme mechanism language. Since xCellerator release 0.88 kMech has been fully integrated into the xCellerator distribution.
  • RedoxMech(link currently unavailable) - a Cellerator based oxidoreductase modeling framework.
  • mPower - Voronoi, Delaunay, and power diagram computation in n-dimensions via QHULL and regtet.
  • Cambium - a mathematical process language for describing developmental models; the plugin provides support for model conversion. (in development)
  • Cellerator is a similar program, that also converts reactions to odes, implemented by the same team of developers. It is not as general as xlr8r, and less efficient. Cellerator has a more restrictive use and distribution license.

For all inquiries please contact the original site author Bruce (-dot-) E (-dot-) Shapiro (-at-) csun (-dot-) edu.

Or contact emj (-at-) uci (-dot-) edu.

Creative Commons License CC-GNU GPL

The contents of this web page and its subsidiary web pages are licensed under a Creative Commons Attribution-Noncommercial-Share Alike 3.0 Unported License. Unless otherwise specified, all software posted on this and its subsidiary web pages are released under the GNU GPL version 3 or later.

Development of xCellerator was supported in part by the US National Science Foundation Frontiers in Integrative Biological Resarch Grant 0330786; and by the Beckman Institute at the California Institute of Technology. xCellerator™, Cellerator™, xlr8r™, cellzilla™, growzilla™ and arrowzilla™ are trademarks of the authors and may not be used without permission. Cellerator and Cellerator based technology is protected under United States Patent Number 7,319,945.

22 Oct 2012