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      Rule-based modeling with Virtual Cell

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          Abstract

          Summary: 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 ( 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.

          Contact: vcell_support@ 123456uchc.edu

          Supplementary information: Supplementary data are available at Bioinformatics online.

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          Author and article information

          Journal
          Bioinformatics
          Bioinformatics
          bioinformatics
          bioinfo
          Bioinformatics
          Oxford University Press
          1367-4803
          1367-4811
          15 September 2016
          09 June 2016
          : 32
          : 18
          : 2880-2882
          Affiliations
          R. D. Berlin Center for Cell Analysis and Modeling, University of Connecticut School of Medicine, Farmington, CT 06030, USA
          Author notes
          *To whom correspondence should be addressed

          Associate Editor: Alfonso Valencia

          Article
          PMC5018377 PMC5018377 5018377 btw353
          10.1093/bioinformatics/btw353
          5018377
          27497444
          © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com
          Page count
          Pages: 3
          Categories
          Applications Notes
          Systems Biology

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