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Computer Algebra Support for Biological Modeling

Eric Mjolsness
Organization: University of California, Irvine
Department: Department of Information and Computer Science
Alexey Vorobyov
Guy Yosiphon
Bruce E Shapiro
Organization: Caltech
Department: Control and Dynamical Systems

2005 Wolfram Technology Conference
Conference location

Champaign IL

Several projects in computational biology at the Scientific Inference Systems Laboratory at the University of California, Irvine depend heavily on the use of computer algebra representations and processing. One of these is Cellerator, a large Mathematica package that functions as a generator for models of cellular and developmental dynamics. Systems modeled include signal transduction pathways and metabolic networks in single cells of yeast and bacteria, respectively, as well as developmental dynamics for the shoot of the plant Arabidopsis thaliana. Cellerator has been applied in many laboratories and is the engine for a web-accessible model simulation and databasing environment called “Sigmoid”. It is also being used in a K–12 outreach program for modeling biological growth. Another example is a prototype implementation of a finite element code for 3D biological models. And a third example is a prototype interpreter for “stochastic parameterized grammars”, which potentially constitute a very general mathematical modeling language, particularly amenable to multiscale models of complex systems. Using these examples, we will describe the rationale, implementation, and prospects for computer algebra representations in building models of biological processes.

*Science > Biology

5755.zip (4.5 MB) - ZIP archive