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Biotools at UMassMed

David Lapointe, Ph.D. Director Scientific Computing University of Massachusetts Medical School biotools.umassmed.edu. Biotools at UMassMed. Bioinformatics has a large toolset. Bioinformatics?. Bioinformatics covers a large territory Sequence and Genome Analysis Computational Biology

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Biotools at UMassMed

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  1. David Lapointe, Ph.D. Director Scientific Computing University of Massachusetts Medical School biotools.umassmed.edu Biotools at UMassMed

  2. Bioinformatics has a large toolset

  3. Bioinformatics? • Bioinformatics covers a large territory • Sequence and Genome Analysis • Computational Biology • Databases • Visualization • Programming • Informatics applied to Biology

  4. Motivation Biotools started 2001 First as a resource for the Bioinformatics Course Later expanded access to UMass system, Worcester Colleges, and global. Last month, 12000 visits from 73 countries.

  5. Gateways to local resources Lists Wikis Tools

  6. Links to External resources

  7. Next Up Provide links to local resources Faculty developed applications Portal to data storage Develop applications for Web 3.0

  8. Web 3.0?Where is this going? The web is a great vehicle for distributing information, creating resources. The web, however, is human readable It is difficult to harvest information from websites. Resource creators are moving to semantic web along with web service models to allow machine harvest of information.

  9. Example http://www.pathguide.org

  10. So a researcher might come to me or you and ask I have 200 Entrez gene Ids. What pathways do these genes belong to? What resource would you direct them toward?

  11. There is always Google!

  12. Hmm, mostly journal articles. Let see Workflows only

  13. Ok This looks better

  14. www.myexperiment.org

  15. www.biocatalogue.org

  16. The end result is that we are approaching eScience (EU)/cyberinfrastructure(USA)‏ Genomics (NCBI, Ensembl, UCSC,GMOD)‏ meets System Biology (KEGG,BIND,GO)‏

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