Compartmental and Spatial Rule-Based Modeling with Virtual Cell.

ABSTRACT: In rule-based modeling, molecular interactions are systematically specified in the form of reaction rules that serve as generators of reactions. This provides a way to account for all the potential molecular complexes and interactions among multivalent or multistate molecules. Recently, we introduced rule-based modeling into the Virtual Cell (VCell) modeling framework, permitting graphical specification of rules and merger of networks generated automatically (using the BioNetGen modeling engine) with hand-specified reaction networks. VCell provides a number of ordinary differential equation and stochastic numerical solvers for single-compartment simulations of the kinetic systems derived from these networks, and agent-based network-free simulation of the rules. In this work, compartmental

SUBMITTER: Blinov ML 

PROVIDER: S-EPMC5627391 | biostudies-literature | 2017 Oct

REPOSITORIES: biostudies-literature