WEBNG - WE sampling of BNGL models¶
BioNetgen (BNG) is a modelling language for rule-based modelling of complex biological systems. WESTPA is a python package that implements the weighted ensemble sampling scheme which focuses compuational power to sample rare events in stochastic simulations. Models written with BioNetGen langauge (BNGL) can be simulated as ODEs or can be simulated stochastically using stochastic simulation algorightm (SSA). This can lead to rare events which are hard to sample and WESTPA can help sample these events.
WEBNG is a command line tool designed to simplify the installation of BNG and WESTPA while also providing a simplepipeline to get a WESTPA simulation setup of a model written in BNGL. The tool also includes some sample analyses that are specifically tailored for BNGL models.
Please see Quick Start page to learn how to use webng.
This documentation is still a work in progress and is incomplete.