Description. xCellerator is a Mathematica package for signal transduction modeling. It is designed to aide biological modeling via the automated conversion of chemical reactions into ODEs. xCellerator is backwards compatible with the reaction syntax defined in Cellerator, but uses a completely different algorithm to perform the translation. Notable features include:
- Model size extensibility: faster reaction translation (as much as 100 times faster than Cellerator)
- Software extensibility: direct entry points are limited to those needed by the user to significantly reduce the possibility of global identifier collision
- Reaction extensibility: the user can define new reactions "on the fly"
- Stochastic models using Gillespie's SSA
Additional features will be documented on this site as test versions become available.
The latest alpha-test version may be obtained via the "Download" link above.
More information on specific features may be obtained via the "User's Reference" link above.
Plugin's and compatible packages:
- SSA.m Gillespie Stochastic Simulator
- MathSBML.m - SBML model manipulator
- kMech.m - Enzyme Mechanism Language
- mPower.m - Voronoi/Delaunay/Power Tesselation interfaces with Qhull and regtet (previously called mQhull).
Additional features in preparation:
- Model extensibilty: SBML input and output suppport (provided by MathSBML)
- Discrete Event Simulation
- Assignment & rate rules - ability to add additional constraints to a model as rules.
- Multicellular/mulicompartment models
To contact us, send email to: developers at xcellerator dot info
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.
The software described herein is protected by the terms of the GNU lesser public license.
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.
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