BioNetGen at Virtual Cell: Features

BioNetGen@VCell is a software tool for automatically generating a biochemical reaction network from user-specified rules for biomolecular interactions on the level of protein domains. A BioNetGen@VCell service is callable from the Virtual Cell and runs within the Virtual Cell framework on a client computer. The first release of BioNetGen@VCell

1. Ready to be used with the Virtual Cell account: no installation and registration required.
2. Implements the latest version of BioNetGen 2, in which connectivity of proteins in the complex can be explicitly specified.
3. Creates a Virtual Cell BioModel from the BioNetGen-generated reaction network.
4. Includes
   • - iterative network generation of the reaction network from a given set of seed species according to user-specified reaction rules;
   • - Time courses simulation using ODE-based deterministic simulation of a pre-generated network, SSA-based stochastic simulation of a pre-generated network, or on-the-fly network simulation and generation;
   • - Visualization of simulation results and different data export options.
5. Provides a capability to pre-equilibrate a network and to restart time courses simulation from any time point with modified parameter values.
6. Provides compatibility with other modeling and simulation tools (SBW etc) via export of the biochemical reaction network in SBML L2 format.