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.
| Original language | English |
|---|---|
| Article number | 188 |
| Journal | BMC Systems Biology |
| Volume | 5 |
| DOIs | |
| Publication status | Published - 9 Nov 2011 |
| Externally published | Yes |
Funding
Authors acknowledge (a) guidance and contributions of (late) Marco Cabrera for his early contributions to PathCase-SB architecture and database design, (b) PathCase-SB design and coding contributions of many graduate and undergraduate students, including Rishiraj Jadeja and others. PathCase-SB derives from PathCase, and the authors acknowledge the PathCase design and development contributions of many (more than 30) graduate students, including Mustafa Kirac (original designer and coder of the client-side code), Brendan Elliott (as the software engineer who moved PathCase from a stand-alone application into a web-based application, as well as tirelessly supervised all other students in their code developments) and many others. This research has been supported by the National Science Foundation grants DBI 0743705, DBI 0849956, CRI 0551603 and by the National Institute of Health grant GM088823.
| Funders | Funder number |
|---|---|
| National Science Foundation | DBI 0849956, DBI 0743705, CRI 0551603 |
| National Institutes of Health | |
| National Institute of General Medical Sciences | R01GM088823 |