Rule-based modeling with Virtual Cell.

ABSTRACT:

Unlabelled

Rule-based modeling is invaluable when the number of possible species and reactions in a model become too large to allow convenient manual specification. The popular rule-based software tools BioNetGen and NFSim provide powerful modeling and simulation capabilities at the cost of learning a complex scripting language which is used to specify these models. Here, we introduce a modeling tool that combines new graphical rule-based model specification with existing simulation engines in a seamless way within the familiar Virtual Cell (VCell) modeling environment. A mathematical model can be built integrating explicit reaction networks with reaction rules. In addition to offering a large choice of ODE and stochastic solvers, a model can be simulated using a network free appro

SUBMITTER: Schaff JC 

PROVIDER: S-EPMC5018377 | biostudies-literature | 2016 Sep

REPOSITORIES: biostudies-literature