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This article is part of the supplement: Proceedings of the First International Conference on Toxicogenomics Integrated with Environmental Sciences (TIES-2007)

Open Access Proceedings

ebTrack: an environmental bioinformatics system built upon ArrayTrack™

Minjun Chen12, Jackson Martin3, Hong Fang3, Sastry Isukapalli1, Panos G Georgopoulos1, William J Welsh2 and Weida Tong3*

Author Affiliations

1 Department of Environmental and Occupational Medicine, UMDNJ-RWJMS, 675 Hoes Lane, Piscataway, NJ 08854, USA

2 Department of Pharmacology, UMDNJ-RWJMS, 675 Hoes Lane, Piscataway, NJ 08854, USA

3 Z-Tech Corporation, an ICF International Company at National Center for Toxicological Research (NCTR), US Food and Drug Administration, 3900 NCTR Road, HFT 230, Jefferson, AR 72079, USA

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BMC Proceedings 2009, 3(Suppl 2):S5  doi:10.1186/1753-6561-3-S2-S5

Published: 10 March 2009

Abstract

ebTrack is being developed as an integrated bioinformatics system for environmental research and analysis by addressing the issues of integration, curation, management, first level analysis and interpretation of environmental and toxicological data from diverse sources. It is based on enhancements to the US FDA developed ArrayTrack™ system through additional analysis modules for gene expression data as well as through incorporation and linkages to modules for analysis of proteomic and metabonomic datasets that include tandem mass spectra. ebTrack uses a client-server architecture with the free and open source PostgreSQL as its database engine, and java tools for user interface, analysis, visualization, and web-based deployment. Several predictive tools that are critical for environmental health research are currently supported in ebTrack, including Significance Analysis of Microarray (SAM). Furthermore, new tools are under continuous integration, and interfaces to environmental health risk analysis tools are being developed in order to make ebTrack widely usable. These health risk analysis tools include the Modeling ENvironment for TOtal Risk studies (MENTOR) for source-to-dose exposure modeling and the DOse Response Information ANalysis system (DORIAN) for health outcome modeling. The design of ebTrack is presented in detail and steps involved in its application are summarized through an illustrative application.