Bioinformatics Vol. 19 no. 5 2003
Pages 677-678
© 2003 Oxford University Press
Applications Note |
Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
1 Jet Propulsion Laboratory, California
Institute of Technology, Mail Stop 126-347, 4800 Oak Grove
Drive, Pasadena, CA 91109, USA
2 Department of Biomedical Engineering, Johns
Hopkins University, Baltimore, MD 21218, USA
3 Division of Biology, California Institute of Biology, Pasadena, CA
91125, USA
4 Department of Information and Computer
Science, University of California, Irvine 92647, USA
Received on May 30, 2002
; revised on September 26, 2002
; accepted on November 4, 2002
Summary: 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.
Availability: Cellerator can be licensed free of charge to noncommercial academic, U.S. government, and nonprofit users. Details and sample notebooks are available at http://www-aig.jpl.nasa.gov/public/mls/cellerator.
Contact: bshapiro{at}jpl.nasa.gov
* To whom correspondence should be addressed.
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