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Yun Zhang J. Craig Venter Institute San Diego, CA, USA August 4, 2012

Integrated Bioinformatics Data and Analysis Tools for Herpesviridae Viruses in the Virus Pathogen Resource ( ViPR ). Yun Zhang J. Craig Venter Institute San Diego, CA, USA August 4, 2012. Introduction to Virus Pathogen Resource ( ViPR ).

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Yun Zhang J. Craig Venter Institute San Diego, CA, USA August 4, 2012

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  1. Integrated Bioinformatics Data and Analysis Tools for Herpesviridae Viruses in the Virus Pathogen Resource (ViPR) Yun Zhang J. Craig Venter Institute San Diego, CA, USA August 4, 2012

  2. Introduction to Virus Pathogen Resource (ViPR) • NIH/NIAID-funded free bioinformatics database online • Bioinformatics Resource Centers (BRC) contract • Fourteen human virus families including Herpesviridae • Integrated data from various sources • Suite of data analysis and visualization tools

  3. www.viprbrc.org

  4. Integrated Data from Many Sources

  5. Sequence Search Options

  6. Analysis and Visualization Tools

  7. GBrowse for Genome Viewing

  8. Comparative Analysis Tools Multiple Sequence Alignment Phylogenetic Tree Metadata-driven Comparative Analysis Tool (Meta-CATS)

  9. 3D Protein Structure Visualization

  10. Host Factor Data • Lynn Enquist / MoriahSzpara, Princeton University • Obtain and assemble deep sequencing data of HSV-1 isolates • Differentially expressed genes in human neuronal cells during a time course of infection

  11. Summary • Free and open access with no use restrictions • Developed by a team of research scientists, bioinformaticians and professional software developers • Comprehensive collection of public data • Novel derived data, novel analytical tools, unique functions • New tools and new data driven by user requests • Training and support • www.viprbrc.org/

  12. Acknowledgements J. Craig Venter Institute • Richard H. Scheuermann, Ph.D., Principal Investigator • Brett Pickett, Ph.D. • Lucy Stewart, MBA • Yun Zhang, M.Sc. Northrop Grumman Health IT • Mike Atassi, Program Manager • Ed Klem, Ph.D., Project Manager • Patty Berger • ZhipingGu, Ph.D. • Sherry He • WenjieHua • Wei Jen • Sanjeev Kumar • Xiaomei Li, Ph.D. • Jason Lucas • Bruce Quesenberry • Barbara Rotchford • Prabhu Shankar • Tom Smith, Ph.D. • Hongbo Su, Ph.D. • Bryan Walters • Sam Zaremba, Ph.D. • Hongtao Zhao, Ph.D. • Liwei Zhou, Ph.D. Vecna Technologies • Chris Larsen, Ph.D. • Al Ramsey, Ph.D. • Guangyu Sun, Ph.D. Co-PI’s • Michael Gale, Ph.D. (University of Washington) • Jingming Ma, Ph.D. (University of Rochester Medical Center) Scientific Working Group • Richard Kuhn ( Purdue University) • Raul Andino ( University of California, San Francisco) • Slobodan Paessler ( University of Texas Medical Branch at Galveston) • X.J. Meng ( Virginia Polytechnic Institute and State University) • Colin Parrish ( Cornell University) • Elliot Lefkowitz ( University of Alabama, Birmingham) • Carla Kuiken ( Los Alamos National Laboratory) • David Knipe ( Harvard University) • Matthew Henn ( Broad Institute) • Richard Whitley ( University of Alabama, Birmingham) • John Young ( Salk Institute for Biological Studies) NIAID / DMID • Alison Yao, Ph.D., Program Officer, Microbial Genomics & Advanced Technologies N01AI2008038

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