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Virginia Tech News / Articles / 2007 / 07 

Virginia Bioinformatics Institute hosts new bioinformatic resource center web site

July 13, 2007

PATRIC, the PathoSystems Resource Integration Center project, has a new-look website hosted at Virginia Tech's Virginia Bioinformatics Institute (VBI).

PATRIC is a multi-resource bioinformatic portal that serves as a gateway to diverse genomic and associated information as well as tools for important viral and bacterial pathogens. The PATRIC project is funded by the National Institute of Allergy and Infectious Diseases (NIAID).

The website has been significantly re-engineered by the PATRIC team and the Department of Computer Science in the College of Engineering at Virginia Tech to improve usability based on an extensive survey of user needs.

In addition to new tools, the new site also has a completely new visual identity developed in collaboration with New City Media of Blacksburg, Va.

“The way in which PATRIC’s new website has been put together is a perfect example of transdisciplinary product development happening at our institute and Virginia Tech,” said Bruno Sobral, VBI’s executive and scientific director. “This project brought together the Department of Computer Science’s user interface design expertise, New City Media’s design skills and VBI’s extensive domain knowledge to create a user-friendly, easily accessible and informative resource. Web sites are a key component of work at VBI and we are continually striving to improve not only the range of products and services that we offer but also the quality of the user experience at the other end of the transaction.”

The new site incorporates tools identified by PATRIC users as capabilities that would make the site more user-friendly. New organization and navigation make it easier to move among website areas, while specific search, comparison, and collection functions have been expanded and upgraded. Beyond the new navigation, organization and user interface, the PATRIC site now provides additional support for comparative genomics, a suite of new searches and filtering options, as well as enhanced features for collecting related gene and protein sequences of interest.

Users can now perform a multiple sequence alignment across members of an ortholog group and arrange members onscreen based on phylogeny. A full list of the search capabilities, including the new additions, is available online.

Collecting related sequences of interest is made easier with an improved feature cart that allows you to collect items of interest as you browse. This feature will be intuitive to users who shop at online stores. Large sets of features from organism feature tables, ortholog group pages, search result tables, and individual feature tables can be collected with this powerful tool and then exported as FASTA DNA or FASTA protein sequences.

The new features and re-alignment of the PATRIC web site will serve the significant growth in user requirements anticipated in the years ahead.

In June 2004, Bruno Sobral (principal investigator) and João Setubal (co-principal investigator) from VBI were awarded a five-year $10.3 million contract from the National Institute of Allergy and Infectious Diseases (NIAID) to establish a multi-organism relational database for infectious disease research that focuses on biodefense and emerging infectious diseases. The PathoSystems Resource Integration Center (PATRIC), under development in Dr. Sobral’s Cyberinfrastructure Group, is a comprehensive web-based resource for genomic and associated information on important viral and bacterial pathogens.

PATRIC is one of eight Bioinformatics Resource Centers (BRC) in the United States established with the support of the NIAID. The BRCs were created to facilitate a research community that would collect and share information vital to the development of new diagnostics, drugs, and vaccines. PATRIC is funded through NIAID contract HHSN266200400035C.