Database-Enabled Tools for Regulatory Metabolic Networks

Case Western Reserve University, Cleveland OH

Investigators

Abstract

Case Western Reserve University of Cleveland, Ohio is awarded to design and implement a database-enabled framework and tools to facilitate effective and efficient model development for multiscale mechanistic models of biological systems. The set of integrated database-enabled tools for regulatory metabolic networks, called PathCase-SB, will have enhanced functionalities to (a) link the ever expanding body of molecular information to an understanding of how intact organisms function via multiscale mechanistic models of the system, and (b) facilitate interactive model development and dynamic analysis of responses in an effective and efficient manner. PathCase-SB will provide a framework and an environment that allows for the reproducibility, verifiability, and adaptability of the maintained models. It will have four interfaces, namely, Querying Interface, Visualization Interface, Simulation Interface, and Modeler?s Interface. PathCase-SB will be designed and built, to the extent possible, as a general-purpose web-based system for regulatory metabolic network models. The system will be built, tested and enhanced while carrying out (in silico parts of) a research on multiscale computational models of oxygen transport and metabolism in skeletal muscle. PathCase-SB model database will be integrated with PathCase, an existing metabolic pathways system, to enable building ?one-shop? querying and visualization capabilities. The PathCase-SB project will provide a new and high impact visualization, querying, and simulation environment for regulatory metabolic network models. It will allow comparative analyses of results from different quantitative simulations, which will have the potential for improving the models by providing better insights on the suitability of the models. PathCase-SB will be an add-on, and complementary, to the metabolic pathways knowledge available in existing metabolic pathways data sources on the web such as Kegg, Reactome, or BioCyc. Finally, PathCase-SB will be suitable for educating students in systems biology, biology, bioinformatics, and medical sciences--to train them on the use of bioinformatics tools in terms of regulatory metabolic network models.