Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling

M. L. Blinov, J. C. Schaff, O. Ruebenacker, X. Wei, D. Vasilescu, F. Gao, F. Morgan, L. Ye, A. Lakshminarayana, I. I. Moraru, L. M. Loew
2013 Bioinformatics  
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
more » ... des. Availability and implementation: Available at Virtual Cell (http:// vcell.org/). 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.
doi:10.1093/bioinformatics/btt660 pmid:24273241 pmcid:PMC3892693 fatcat:4pqgu6tbvfeu7hnv4kt3btrivm