Lawrence Berkeley National Laboratory

VIMSS, the Virtual Institute for Microbial Stress and Survival (http://vimss.lbl.gov), funded by the Dept. of Energy's Genomics:GTL Program, is dedicated to using integrated environmental data and functional genomic and comparative sequence data to understand mechanisms by which bacteria survive in uncertain environments while carrying out processes of interest for bioremediation and energy generation. To support this work, VIMSS developed a Web-based database and workbench for comparative functional genomics of bacteria and archaea. For some time, MicrobesOnline (http://www.microbesonline.org) has been providing a multi-species genome browser, operon and regulon predictions, a gene ontology browser, and a Bioinformatics Workbench for in-depth sequence analysis and community annotation of genomes. We recently incorporated data from Mikhail Gelfand's RegTransDB, which is a well-curated database of cis-regulatory sites and their regulators. VIMSS also is now releasing integrated functional genomic data with novel viewing and mining tools for microarray, proteomic, and phenotype microarray data on the website. The available data mostly are from the VIMSS Experiment/Information Data Repository (EIDR), which holds information and data on biomass production experiments and functional genomic data primarily on Desulfovibrio vulgaris and Shewanella oneidensis (and mutants of both organisms) exposed to stress conditions found at DOE field sites. Selecting an organism or gene of interest on MicrobesOnline will bring up links to information about and data viewers for VIMSS experiments conducted on that organism, or involving that gene or gene product. Information and data integration such as this serves, not only to provide insight into the regulation of stress responses of these microorganisms, but also to document VIMSS experiments, provide contextual access to experimental data of interest, and facilitate planning future experiments. We also are incorporating data released