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

被引：81

作者：

Shapiro, BE

Levchenko, A

Meyerowitz, EM

Wold, BJ

Mjolsness, ED

机构：

[1] CALTECH, Jet Prop Lab, Pasadena, CA 91109 USA

[2] Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD 21218 USA

[3] CALTECH, Div Biol, Pasadena, CA 91125 USA

[4] Univ Calif Irvine, Dept Informat & Comp Sci, Irvine, CA 92647 USA

来源：

BIOINFORMATICS | 2003年 / 19卷 / 05期

基金：

美国国家航空航天局;

关键词：

D O I：

10.1093/bioinformatics/btg042

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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 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.

引用

页码：677 / 678

页数：2