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Open Access Database

PathCase-SB architecture and database design

Ali Cakmak1, Xinjian Qi1, Sarp A Coskun1, Mitali Das1, En Cheng1, A Ercument Cicek1, Nicola Lai23, Gultekin Ozsoyoglu1* and Z Meral Ozsoyoglu1

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

  • † Equal contributors

Author Affiliations

1 Electrical Engineering and Computer Science Department, Case Western Reserve University, 10900 Euclid Ave., Cleveland, 44106, OH USA

2 Department of Biomedical Engineering, Case Western Reserve University, 10900 Euclid Ave., Cleveland, 44106, OH USA

3 Department of Pediatrics, Case Western Reserve University, 10900 Euclid Ave., Cleveland, 44106, OH USA

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BMC Systems Biology 2011, 5:188  doi:10.1186/1752-0509-5-188

Published: 9 November 2011

Abstract

Background

Integration of metabolic pathways resources and regulatory 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 in 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.

Description

PathCase Systems Biology (PathCase-SB) is built and released. The PathCase-SB database provides data and API for multiple user interfaces and software tools. 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 data of selected biological data sources on the web (currently, BioModels database and KEGG), and to provide more powerful and/or new capabilities via the new web-based integrative framework. This paper describes architecture and database design issues encountered in PathCase-SB's design and implementation, and presents the current design of PathCase-SB's architecture and database.

Conclusions

PathCase-SB architecture and database provide a highly extensible and scalable environment with easy and fast (real-time) access to the data in the database. PathCase-SB itself is already being used by researchers across the world.