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Tutorial: Rule-based modeling of biochemical systems with BioNetGen
From Q-bio
James R. Faeder (University of Pittsburgh School of Medicine)
Assistants: G. Matthew Fricke, William S. Hlavacek, Bin Hu, Michael I. Monine and Ambarish Nag
- Abstract
- Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects. The approach allows one to systematically incorporate site-specific details about protein-protein interactions into a model for the dynamics of a signal-transduction system, but the method has other applications as well, such as following the fates of individual carbon atoms in metabolic reactions. The consequences of protein-protein interactions are difficult to specify and track with a conventional modeling approach because of the large number of protein phosphoforms and protein complexes that these interactions potentially generate. Here, we focus on how a rule-based model is specified in the BioNetGen language (BNGL) and how a model specification is analyzed using the BioNetGen software tool. We also discuss new developments in rule-based modeling that should enable the construction and analyses of comprehensive models for signal transduction pathways and similarly large-scale models for other biochemical systems.
- References
- Faeder JR, Blinov ML, Hlavacek WS (in press) Rule-based modeling of biochemical systems with BioNetGen. Methods Mol. Biol. (pdf) The tutorial will largely be based on this article, a copy of which will be provided to participants at the tutorial.
- Hlavacek WS et al. (2006) Rules for modeling signal-transduction systems. Sci. STKE 2006, re6 (click here for toll-free access)
- BioNetGen web site
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