Pathway Commons at virtual cell: use of pathway data for mathematical modeling

Bioinformatics. 2014 Jan 15;30(2):292-4. doi: 10.1093/bioinformatics/btt660. Epub 2013 Nov 22.


Pathway Commons is a resource permitting simultaneous queries of multiple pathway databases. However, there is no standard mechanism for using these data (stored in BioPAX format) to annotate and build quantitative mathematical models. Therefore, we developed a new module within the virtual cell modeling and simulation software. It provides pathway data retrieval and visualization and enables automatic creation of executable network models directly from qualitative connections between pathway nodes.

Availability and implementation: Available at Virtual Cell ( Application runs on all major platforms and does not require registration for use on the user’s computer. Tutorials and video are available at user guide page.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Physiological Phenomena*
  • Computational Biology
  • Databases, Factual*
  • Gene Regulatory Networks*
  • Information Storage and Retrieval
  • Models, Theoretical*
  • Signal Transduction*
  • Software*