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PathCase-SB: integrating data sources and providing tools for systems biology research. BMC Syst Biol 2012 Jun 14;6(1):67

Date

06/16/2012

Pubmed ID

22697505

Pubmed Central ID

PMC3410775

DOI

10.1186/1752-0509-6-67

Scopus ID

2-s2.0-84862210684   3 Citations

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 current 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.

Author List

Coskun SA, Qi X, Cakmak A, Cheng E, Cicek AE, Yang L, Jadeja R, Dash RK, Lai N, Ozsoyoglu G, Ozsoyoglu ZM

Author

Ranjan K. Dash PhD Professor in the Biomedical Engineering department at Medical College of Wisconsin




MESH terms used to index this publication - Major topics in bold

Computer Simulation
Databases, Factual
Glycolysis
Internet
Metabolic Networks and Pathways
Models, Biological
Software
Systems Biology
User-Computer Interface
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