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

Michael L. Blinov | Zendy; James C. Schaff | Zendy; Oliver Ruebenacker | Zendy; Xintao Wei | Zendy; Dan Vasilescu | Zendy; Fei Gao | Zendy; Frank Morgan | Zendy; Ye Li | Zendy; Anuradha Lakshminarayana | Zendy; Ion I. Moraru | Zendy; Leslie M. Loew | Zendy

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

Author(s) -

Michael L. Blinov,

James C. Schaff,

Oliver Ruebenacker,

Xintao Wei,

Dan Vasilescu,

Fei Gao,

Frank Morgan,

Ye Li,

Anuradha Lakshminarayana,

Ion I. Moraru,

Leslie M. Loew

Publication year - 2013

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/btt660

Subject(s) - executable , computer science , visualization , software , resource (disambiguation) , data visualization , data mining , database , software engineering , programming language , computer network

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.

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