Rule-based modeling with Virtual Cell

Bioinformatics. 2016 Sep 15;32(18):2880-2. doi: 10.1093/bioinformatics/btw353. Epub 2016 Jun 9.


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 approach through the NFSim simulation engine.

Availability and implementation: Available as VCell (versions 6.0 and later) at the Virtual Cell web site ( The application installs and runs on all major platforms and does not require registration for use on the user's computer. Tutorials are available at the Virtual Cell website and Help is provided within the software. Source code is available at Sourceforge.


Supplementary information: Supplementary data are available at Bioinformatics online.

MeSH terms

  • Cell Physiological Phenomena*
  • Computational Biology
  • Computer Simulation*
  • Gene Regulatory Networks
  • Models, Biological*
  • Models, Theoretical*
  • Programming Languages
  • Signal Transduction
  • Software*