Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations.
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.
Shapiro
Bruce E
BE
Jet Propulsion Laboratory, California Institute of Technology, Mail Stop 126-347, 4800 Oak Grove Drive, Pasadena, CA 91109, USA. bshapiro@jpl.nasa.gov
Levchenko
Andre
A
Meyerowitz
Elliot M
EM
Wold
Barbara J
BJ
Mjolsness
Eric D
ED
D003196:Computer Graphics; D003198:Computer Simulation; D004282:Documentation; D008954:Models, Biological; D009323:Natural Language Processing; D015398:Signal Transduction / Q000502:physiology*; D012984:Software; D009626:Terminology as Topic; D014584:User-Computer Interface