Simulation of large-scale rule-based models.

ABSTRACT:

Motivation

Interactions of molecules, such as signaling proteins, with multiple binding sites and/or multiple sites of post-translational covalent modification can be modeled using reaction rules. Rules comprehensively, but implicitly, define the individual chemical species and reactions that molecular interactions can potentially generate. Although rules can be automatically processed to define a biochemical reaction network, the network implied by a set of rules is often too large to generate completely or to simulate using conventional procedures. To address this problem, we present DYNSTOC, a general-purpose tool for simulating rule-based models.

Results

DYNSTOC implements a null-event algorithm for simulating chemical reactions in a homogenous reaction compartment. The

SUBMITTER: Colvin J 

PROVIDER: S-EPMC2660871 | biostudies-literature | 2009 Apr

REPOSITORIES: biostudies-literature