title: Pathway Commons at virtual cell: use of pathway data for mathematical modeling.
abstract: 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.
  
  
  METHODS
  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.
authors.affiliation: Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, CT 06030, USA.
authors.forename: Michael L
authors.initials: ML
authors.lastname: Blinov
authors.forename: James C
authors.initials: JC
authors.lastname: Schaff
authors.forename: Oliver
authors.initials: O
authors.lastname: Ruebenacker
authors.forename: Xintao
authors.initials: X
authors.lastname: Wei
authors.forename: Dan
authors.initials: D
authors.lastname: Vasilescu
authors.forename: Fei
authors.initials: F
authors.lastname: Gao
authors.forename: Frank
authors.initials: F
authors.lastname: Morgan
authors.forename: Li
authors.initials: L
authors.lastname: Ye
authors.forename: Anuradha
authors.initials: A
authors.lastname: Lakshminarayana
authors.forename: Ion I
authors.initials: II
authors.lastname: Moraru
authors.forename: Leslie M
authors.initials: LM
authors.lastname: Loew
mesh_terms: D002468:Cell Physiological Phenomena; D019295:Computational Biology; D016208:Databases, Factual; D053263:Gene Regulatory Networks; D016247:Information Storage and Retrieval; D008962:Models, Theoretical; D015398:Signal Transduction; D012984:Software