On the Modeling of Signaling Networkswith Petri Nets

[摘要] The whole-cell behavior arises from the interplay among signaling, metabolic,and regulatory processes. Proper modeling of the overall function requires accurateinterpretations of each component. The highly concurrent nature of the inner-cellinteractions motivates the use of Petri nets as a framework for the whole-cell modeling.Petri nets have been successfully used in modeling of metabolic pathways, asit allows for a straightforward mapping from its stoichiometric matrix to the Petrinet structure. The Boolean interpretation and modeling of transcription regulationnetworks also lends itself easily to Petri net modeling. However, Petri net modeling ofsignal transduction networks has been largely lacking, with the exception of simple adhoc applications to specific signaling pathways. In this thesis, I investigate the applicabilityof Petri nets to modeling of signaling networks, by systematically analyzinginitial token assignments, firing strategies, and robustness to errors and abstractionsin the estimates of molecule concentrations and reaction rates.

[发布机构] Rice University

[效力级别] science