Pathway Commons at Virtual Cell
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General Information
DescriptionUse of pathway data for mathematical modeling
Homepagehttp://vcell.org/
Publications
Pathway Commons at Virtual Cell: use of pathway data for mathematical modeling
Michael L. Blinov; James C. Schaff; Oliver Ruebenacker; Xintao Wei; Dan Vasilescu; Fei Gao; Frank Morgan; Li Ye; Anuradha Lakshminarayana; Ion I. Moraru; Leslie M. Loew
Summary: 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 (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.
Contact: vcell_support@uchc.edu
DOI: https://doi.org/10.1093/bioinformatics/btt660
Metrics:
3
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