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Logo of bmcsysbioBioMed Centralsearchsubmit a manuscriptregisterthis articleBMC Systems Biology
 
BMC Syst Biol. 2012; 6: 67.
Published online Jun 14, 2012. doi:  10.1186/1752-0509-6-67
PMCID: PMC3410775
PathCase-SB: integrating data sources and providing tools for systems biology research
Reviewed by Sarp A Coskun,#1 Xinjian Qi,#1 Ali Cakmak,#1 En Cheng,#1 A Ercument Cicek,1 Lei Yang,#1 Rishiraj Jadeja,#1 Ranjan K Dash,2 Nicola Lai,#3,4 Gultekin Ozsoyoglu,corresponding author#1 and Zehra Meral Ozsoyoglu#1
1Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA
2Department of Physiology, Medical College of Wisconsin, Milwaukee, USA
3Department of Biomedical Engineering, Case Western Reserve University, Cleveland, USA
4Department of Pediatrics, Case Western Reserve University, Cleveland, USA
corresponding authorCorresponding author.
#Contributed equally.
Sarp A Coskun: sarp.coskun/at/case.edu; Xinjian Qi: xinjian.qi/at/case.edu; Ali Cakmak: ali.cakmak/at/gmail.com; En Cheng: en.cheng/at/case.edu; A Ercument Cicek: aec51/at/case.edu; Lei Yang: lei.yang/at/case.edu; Rishiraj Jadeja: rishiraj.jadeja/at/case.edu; Ranjan K Dash: rdash/at/mcw.edu; Nicola Lai: nicola.lai/at/case.edu; Gultekin Ozsoyoglu: tekin/at/case.edu; Zehra Meral Ozsoyoglu: meral/at/case.edu
Received March 29, 2011; Accepted June 14, 2012.
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.
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