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Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations

Bruce E Shapiro
Organization: Caltech
Department: Control and Dynamical Systems
Andre Levchenko
Organization: Johns Hopkins University
Department: Department of Biomedical Engineering
Elliot Meyerowitz
Organization: California Institute of Biology
Department: Division of Biology
Barbara Wold
Organization: California Institute of Biology
Department: Division of Biology
Eric Mjolsness
Organization: University of California, Irvine
Department: Department of Information and Computer Science
Journal / Anthology

Year: 2003
Volume: 19
Issue: 5
Page range: 677-678

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.

*Science > Bioinformatics