[Bioinformatics] Monday's Bioinformatics Seminar: Eric Mjolsness, Ph.D.
Bioinformatics IDP-Seminar Series
bioinformatics at lists.ucla.edu
Wed Jan 25 10:06:51 PST 2012
MONDAY, January 30, 2012
Eric Mjolsness, Ph.D.
Information and Computer Science, UCI
"Computational Modeling Languages for Mathematical Systems Biology"
Formally defined notations and languages can greatly assist in the process of building realistic mathematical models of complex biological systems. Starting from ordinary chemical reaction notation, we outline a series of generalizations that increase the scope and power of such languages. These extensions include rewrite rules for differential equations and labeled graphs, hence "dynamical graph grammars". Biological applications encompass: enzyme kinetics, including multiply regulated allosteric enzymes; gene regulation networks; spatial pattern formation such as reaction-diffusion models; stochastic multimolecular complex models with combinatorially large state spaces; and truly morphodynamic models that incorporate biomechanics in developmental biology. At each stage, the modeling language has a well-defined mathematical meaning specified in terms of operator algebra, which enables the derivation of special-purpose simulation and learning algorithms in terms of operator splitting and perturbation theory. Applications include central metabolism, signal transduction, and plant development.
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