Pathway Commons at virtual cell: use of pathway data for mathematical modeling
| Autor: | Xintao Wei, Leslie M. Loew, Oliver Ruebenacker, Fei Gao, Anuradha Lakshminarayana, Ion I. Moraru, James C. Schaff, Dan Sorin Vasilescu, Michael L. Blinov, Li Ye, Frank Morgan |
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| Rok vydání: | 2013 |
| Předmět: |
Statistics and Probability
Databases Factual Computer science Gene regulatory network Computational Biology Information Storage and Retrieval Models Theoretical computer.software_genre Biochemistry Applications Notes Computer Science Applications Visualization Cell Physiological Phenomena Computational Mathematics Resource (project management) Computational Theory and Mathematics Human–computer interaction BioPAX : Biological Pathways Exchange Gene Regulatory Networks Data mining Molecular Biology computer Software Network model Signal Transduction |
| Zdroj: | Bioinformatics (Oxford, England). 30(2) |
| ISSN: | 1367-4811 |
| Popis: | 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 |
| Databáze: | OpenAIRE |
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