ebTrack: an environmental bioinformatics system built upon ArrayTrack
M. Chen1,2, S. Isukapalli2, P.G. Georgopoulos2, W. Welsh2, W. Tong1
1USFDA, 2UMDNJ-RWJMS
The ebTrack (Environmental Bioinformatics Track) system, under ongoing development through funding from the USEPA, is an integrated bioinformatics system for environmental health risk research and analysis. It addresses the issues of integration, curation, management, first level analysis and interpretation of toxicological data from diverse sources. ebTrack is built upon ArrayTrack, a microarray data management, analysis and interpretation system developed at the FDA’s National Center for Toxicology Research. It provides interfaces to R, Bioconductor, and SAM (significant analysis of microarray), and many supervised and unsupervised tools such as HCA, k-means, kNN, LDA, decision forest, SVM, etc. ebTrack extends the features of ArrayTrack by incorporating modules for the analysis of proteomic and metabonomic datasets, in addition to providing additional analysis modules for gene expression data, as well as providing a set of interfaces to other environmental health risk analysis tools as part of the DOse-Response ANalysis system (DORIAN). ebTrack is designed as a client-server system, and uses the open source database PostgreSQL as the database engine, and Java tools for user interface, analysis, visualization, and web-based deployment. ebTrack is designed to be a publicly available comprehensive bioinformatics system to support environmental toxicological and risk assessment studies. The overall design of the ebTrack, and the role it plays in understanding the environmental source-to-outcome modeling process are presented.
The viewpoints expressed in this work are solely the responsibility of the authors and do not necessarily reflect the views of USEPA or its contractors.