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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.

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.

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 - 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 mased enzyme mechanism language.
• 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 Bruce Shapiro at bshapiro (--at--) caltech (--dot--) edu.