title: Rule-based modeling with Virtual Cell.
abstract: 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.
  
  
  
  Available as VCell (versions 6.0 and later) at the Virtual Cell web site (http://vcell.org/). 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.
  
  
  
  vcell_support@uchc.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors: R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors: James C
authors: JC
authors: Schaff
authors: R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors: Dan
authors: D
authors: Vasilescu
authors: R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors: Ion I
authors: II
authors: Moraru
authors: R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors: Leslie M
authors: LM
authors: Loew
authors: R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA.
authors: Michael L
authors: ML
authors: Blinov
mesh_terms: D002468:Cell Physiological Phenomena; D019295:Computational Biology; D003198:Computer Simulation; D053263:Gene Regulatory Networks; D008954:Models, Biological; D008962:Models, Theoretical; D011381:Programming Languages; D015398:Signal Transduction; D012984:Software