Sssc retreat.bioinfo resources.20110411

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Ten minute talk to the Staff Scientist and Staff Clinicians from NCI regarding bioinformatics resources.

Ten minute talk to the Staff Scientist and Staff Clinicians from NCI regarding bioinformatics resources.

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Transcript

  • 1. Bioinformatics Resources
    An Incomplete List
    April 11, 2011, SS/SC Retreat
    Sean Davis, M.D., Ph.D.
    Genetics Branch, Center for Cancer Research
    National Cancer Institute
    National Institutes of Health
  • 2. Normal Karyotype
    TumorKaryotype
  • 3. The Central Dogma
  • 4. Patient and Population Characteristics
    Gene Expression
    Gene Copy Number
    Transcriptional Regulation
    phenotype
    DNA Methylation
    Chromatin Structure and Function
    Sequence Variation
  • 5. Overview
    Hardware
    Software
    Online databases
    Training and Education
    Getting Answers
  • 6. Hardware
    Computers
    Current desktops quite capable
    High-performance resources
    Helix/Biowulf (CIT)
    Advanced Biomedical Computing Center (ABCC)
    Amazon EC2
    Storage
    Local storage
    Helix/Biowulf
    NCI group drives
  • 7. Software
    Commercial
    Open Source
  • 8. Software
  • 9. Software
    Bioconductor
    Bio-[Python, Java, Ruby, Perl]
    BRB ArrayTools
    GenePattern
    And the list goes on….
  • 10. Software
  • 11. Online Databases
  • 12. Online Databases
  • 13. Training and Education
    Google
    CIT/Helix training
    http://training.cit.nih.gov
    NIH Library
    http://nihlibrary.nih.gov/ResearchTools/Pages/Bioinformatics.aspx
    Cold Spring Harbor, AACR, OpenHelix, BioConductor, ….
  • 14. Getting Answers
    Google
    http://seqanswers.com/
    http://biostar.stackexchange.com/
    http://bioinformatics.nci.nih.gov/
    CCR Bioinformatics Core
    http://ccrifx.cancer.gov/
  • 15. Contact and Acknowledgements