PathCase-SB: integrating data sources and providing tools for systems biology research.
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.
Electrical Engineering and Computer Science Department, Case Western Reserve University, Cleveland, USA.
Sarp A
SA
Coskun
Xinjian
X
Qi
Ali
A
Cakmak
En
E
Cheng
A Ercument
AE
Cicek
Lei
L
Yang
Rishiraj
R
Jadeja
Ranjan K
RK
Dash
Nicola
N
Lai
Gultekin
G
Ozsoyoglu
Zehra Meral
ZM
Ozsoyoglu
D003198:Computer Simulation; D016208:Databases, Factual; D006019:Glycolysis / Q000502:physiology; D020407:Internet; D053858:Metabolic Networks and Pathways; D008954:Models, Biological; D012984:Software; D049490:Systems Biology / Q000379:methods*; D014584:User-Computer Interface