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

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 mod...

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Bibliographic Details
Published in:Bioinformatics 2014-01, Vol.30 (2), p.292-294
Main Authors: Blinov, Michael L, Schaff, James C, Ruebenacker, Oliver, Wei, Xintao, Vasilescu, Dan, Gao, Fei, Morgan, Frank, Ye, Li, Lakshminarayana, Anuradha, Moraru, Ion I, Loew, Leslie M
Format: Article
Language:English
Subjects:
Applications Notes
Cell Physiological Phenomena
Computational Biology
Computer programs
Computer simulation
Data retrieval
Databases, Factual
Format
Gene Regulatory Networks
Information Storage and Retrieval
Mathematical models
Models, Theoretical
Networks
Pathways
Signal Transduction
Software
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Description
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. 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.
ISSN:1367-4803
1367-4811
1460-2059
DOI:10.1093/bioinformatics/btt660