An online system for metabolic network analysis.

A E Cicek,S Alshalwi,G Ozsoyoglu,Z M Ozsoyoglu,S R Johnson,A Cakmak,X Qi,X Han

doi:10.1093/database/bau091

A E Cicek, S Alshalwi + Show 6 more

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https://doi.org/10.1093/database/bau091

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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 (PathCaseMAW) is built, released and runs on a manually created generic mammalian metabolic network. The PathCaseMAW system provides a database-enabled framework and Web-based computational tools for browsing, querying, analyzing and visualizing stored metabolic networks. PathCaseMAW 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 PathCaseMAW 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. PathCaseMAW is a comprehensive system with various data input and data access subsystems. It is easy to work with by design, and is a promising tool for metabolomics research and for educational purposes.Database URL: http://nashua.case.edu/PathwaysMAW/Web

Highlights

Metabolomics is a relatively new ‘omics’ platform in life sciences research
The network can be created from an existing genome-scale reconstructed network using the PathCaseMAW SBML parser
state metabolic network dynamics analysis (SMDA) tool is accessible through both the Web-based interface and the iPad application for metabolomics analysis based on a metabolic profile

Summary

Introduction

Metabolomics is a relatively new ‘omics’ platform in life sciences research. The advancements in analytical methodology and high-throughput rates have led to the collection of large metabolic data sets. Metabolic profiles and genome-scale metabolic networks [1] are used in various contexts, such as (i) predicting flux distribution for the metabolic activity over the network [metabolic control analysis (MCA) [2], flux balance analysis (FBA) [3] and constraint-based methods] and (ii) drug discovery and disease research [4,5,6,7]. The increase in the number and importance of metabolic networks has come with the need for carefully designed databases to store/organize metabolic networks, and efficient online tools to browse/ analyze/visualize metabolic data. The goal of PathCaseMAW (Metabolic Analysis Workbench) is to provide a metabolic network database and a Web- or tablet-based system that enables users to interact with the underlying metabolic network. PathCaseMAW provides the following functionalities: 1. A metabolic network database that captures the metabolic network with a compartment hierarchy and metabolic regulation relationships

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