Spatial rule-based modeling: a method and its application to the human mitotic kinetochore.

ABSTRACT: A common problem in the analysis of biological systems is the combinatorial explosion that emerges from the complexity of multi-protein assemblies. Conventional formalisms, like differential equations, Boolean networks and Bayesian networks, are unsuitable for dealing with the combinatorial explosion, because they are designed for a restricted state space with fixed dimensionality. To overcome this problem, the rule-based modeling language, BioNetGen, and the spatial extension, SRSim, have been developed. Here, we describe how to apply rule-based modeling to integrate experimental data from different sources into a single spatial simulation model and how to analyze the output of that model. The starting point for this approach can be a combination of molecular interaction data, reaction ne

SUBMITTER: Ibrahim B 

PROVIDER: S-EPMC3972674 | biostudies-literature | 2013 Jul

REPOSITORIES: biostudies-literature