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Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
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| Department: | Control and Dynamical Systems |
| Organization: | Johns Hopkins University |
| Department: | Department of Biomedical Engineering |
| Organization: | California Institute of Biology |
| Department: | Division of Biology |
| Organization: | California Institute of Biology |
| Department: | Division of Biology |
| Organization: | University of California, Irvine |
| Department: | Department of Information and Computer Science |
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Cellerator describes single and multi-cellular signal transduction networks (STN) with a compact, optionally palette-driven, arrow-based notation to represent biochemical reactions and transcriptional activation. Multicompartment systems are represented as graphs with STNs embedded in each node. Interactions include mass-action, enzymatic, allosteric and connectionist models. Reactions are translated into differential equations and can be solved numerically to generate predictive time courses or output as systems of equations taht can be read by other programs. Cellerator simulations are fully extensible and portable to any operating system that supports Mathematica, and can be indefinitely nested within larger data structures to produce highly scaleable models.
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http://www.cellerator.org
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