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

Bruce E. Shapiro | Zendy; Andre Levchenko | Zendy; Elliot M. Meyerowitz | Zendy; B Wold | Zendy; Eric Mjolsness | Zendy

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

Author(s) -

Bruce E. Shapiro,

Andre Levchenko,

Elliot M. Meyerowitz,

B Wold,

Eric Mjolsness

Publication year - 2003

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btg042

Subject(s) - computer science , arrow , notation , signal (programming language) , theoretical computer science , programming language , algebra over a field , algorithm , mathematics , pure mathematics , arithmetic

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. Multi-compartment 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 that 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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