[Bioinformatics] Today's Bioinformatics Seminar: Eric Mjolsness, Ph.D.

[Bioinformatics IDP-Seminar Series]

"Computational Modeling Languages for Mathematical Systems Biology"


Eric Mjolsness, Ph.D.
Information and Computer Science, UCI

TODAY, January 30, 2012
4:00pm
Gonda 1357
Abstract:
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.

Host: Matteo Pellegrini, x50012



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