For more information about this meeting, contact Tim Reluga, Andrew Belmonte, Mari Royer.
| Title: | Network-free Simulation Method for Rule-Based Models of Biochemical Systems |
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| Seminar: | The Pritchard Lab Seminar |
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| Speaker: | James Faeder, Dept of Computational Biology, University of Pittsburgh |
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| Abstract: |
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| Signalling with cells generally involves protein-protein interactions,
which can produce myriad protein complexes. Such protein-protein interactions
can be represented compactly and precisely using graphical reaction rules,
which can be processed automatically to obtain a chemical reaction network.
However, reaction networks implied by typical sets of rules are often too large
for conventional simulation procedures to handle. To address this challenge,
we have developed a kinetic Monte Carlo method that can take advantage of a
rule-based model specification. Rules are used directly to advance a
simulation, thus avoiding the computationally expensive step of generating the
underlying chemical reaction network implied by the rules. Unlike previously
proposed methods that adaptively generate species and reactions in response to
network activity, the method is not overwhelmed when the likelihood of
encountering new species each time a reaction fires becomes high. The method
is illustrated by using it to characterize the interaction of a trivalent
ligand with a bivalent cell-surface receptor. The results of the simulations
suggest formation of extremely large receptor aggregates under typical
experimental conditions. |
Room Reservation Information
| Room Number: | MB216 |
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| Date: | 03 / 16 / 2009 |
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| Time: | 02:30pm - 03:30pm |
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