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Open Access Highly Accessed Database

Web-based metabolic network visualization with a zooming user interface

Mario Latendresse* and Peter D Karp

Author Affiliations

Bioinformatics Research Group, SRI International, 333 Ravenswood Ave, Menlo Park, CA 94025

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BMC Bioinformatics 2011, 12:176  doi:10.1186/1471-2105-12-176

Published: 19 May 2011

Abstract

Background

Displaying complex metabolic-map diagrams, for Web browsers, and allowing users to interact with them for querying and overlaying expression data over them is challenging.

Description

We present a Web-based metabolic-map diagram, which can be interactively explored by the user, called the Cellular Overview. The main characteristic of this application is the zooming user interface enabling the user to focus on appropriate granularities of the network at will. Various searching commands are available to visually highlight sets of reactions, pathways, enzymes, metabolites, and so on. Expression data from single or multiple experiments can be overlaid on the diagram, which we call the Omics Viewer capability. The application provides Web services to highlight the diagram and to invoke the Omics Viewer. This application is entirely written in JavaScript for the client browsers and connect to a Pathway Tools Web server to retrieve data and diagrams. It uses the OpenLayers library to display tiled diagrams.

Conclusions

This new online tool is capable of displaying large and complex metabolic-map diagrams in a very interactive manner. This application is available as part of the Pathway Tools software that powers multiple metabolic databases including Biocyc.org: The Cellular Overview is accessible under the Tools menu.