PathCase-MAW

Abstract

Metabolic networks have become one of the centers of attention in life sciences research with the advancements in the metabolomics field. A vast array of studies analyzes metabolites and their interrelations to seek explanations for various biological questions, and numerous genome-scale metabolic networks have been assembled to serve for this purpose. The increasing focus on this topic comes with the need for software systems that store, query, browse, analyze, and visualize metabolic networks. PathCase Metabolomics Analysis Workbench (PathCase MAW ) is built, released, and running on a manually created generic mammalian metabolic network. The PathCase MAW system provides a database-enabled framework and web-based computational tools for browsing, querying, analyzing, and visualizing stored metabolic networks. PathCase MAW editor, with its user-friendly interface, can be used to create a new metabolic network and/or update an existing metabolic network. The network can also be created from an existing genome-scale reconstructed network using the PathCase MAW SBML parser. The metabolic network can be accessed through a web interface or an iPad application. For metabolomics analysis, Steady-State Metabolic Network Dynamics Analysis (SMDA) algorithm is implemented and integrated with the system. SMDA tool is accessible through both the web-based interface and the iPad application for metabolomics analysis based on a metabolic profile. PathCase MAW is a comprehensive system with various data input and data access sub-systems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes.