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Open Access Software

PathCase-SB: integrating data sources and providing tools for systems biology research

Sarp A Coskun1, Xinjian Qi1, Ali Cakmak1, En Cheng1, A Ercument Cicek1, Lei Yang1, Rishiraj Jadeja1, Ranjan K Dash2, Nicola Lai34, Gultekin Ozsoyoglu1* and Zehra Meral Ozsoyoglu1

  • * Corresponding author: Gultekin Ozsoyoglu tekin@case.edu

  • † Equal contributors

Author Affiliations

1 Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA

2 Department of Physiology, Medical College of Wisconsin, Milwaukee, USA

3 Department of Biomedical Engineering, Case Western Reserve University, Cleveland, USA

4 Department of Pediatrics, Case Western Reserve University, Cleveland, USA

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BMC Systems Biology 2012, 6:67  doi:10.1186/1752-0509-6-67

Published: 14 June 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.