Systems biology Advance Access publication November 22, 2013 Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling

Summary: Pathway Commons is a resource permitting simultan-eous 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 simula-tion 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 Cel