PathCase-SB: integrating data sources and providing tools for systems biology research
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Published:2012-06-14
Issue:1
Volume:6
Page:
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ISSN:1752-0509
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Container-title:BMC Systems Biology
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language:en
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Short-container-title:BMC Syst Biol
Author:
Coskun Sarp A,Qi Xinjian,Cakmak Ali,Cheng En,Cicek A Ercument,Yang Lei,Jadeja Rishiraj,Dash Ranjan K,Lai Nicola,Ozsoyoglu Gultekin,Ozsoyoglu Zehra Meral
Abstract
Abstract
Background
Integration of metabolic pathways resources and metabolic network models, and deploying new tools on the integrated platform can help perform more effective and more efficient systems biology research on understanding the regulation of metabolic networks. Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and intellectually challenging computational tasks.
Results
PathCase Systems Biology (PathCase-SB) is built and released. This paper describes PathCase-SB user interfaces developed to date. The current PathCase-SB system provides a database-enabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems. PathCase-SB aims to integrate systems biology models data and metabolic network data of selected biological data sources on the web (currently, BioModels Database and KEGG, respectively), and to provide more powerful and/or new capabilities via the new web-based integrative framework.
Conclusions
Each of the c urrent four PathCase-SB interfaces, namely, Browser, Visualization, Querying, and Simulation interfaces, have expanded and new capabilities as compared with the original data sources. PathCase-SB is already available on the web and being used by researchers across the globe.
Publisher
Springer Science and Business Media LLC
Subject
Applied Mathematics,Computer Science Applications,Molecular Biology,Modeling and Simulation,Structural Biology
Reference53 articles.
1. : PathCase-Systems Biology. http://nashua.case.edu/PathwaysSB/Web 2. Cakmak A, Qi X, Coskun SA, Das M, Cheng E, Cicek AE, Lai N, Ozsoyoglu ZM, Ozsoyoglu G: PathCase-SB architecture and database design. BMC Syst Biol 2011, 5: 188. 10.1186/1752-0509-5-188 3. BioModels Database—A Database of Annotated Published Models http://www.ebi.ac.uk/BioModelsDatabase-main 4. Le Novère N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M: BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res 2006,34(Database-Issue):689-691. 5. Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C: BioModels Database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4: 92. 10.1186/1752-0509-4-92
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