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Galaxy a Genome Analysis Platform and more

September 2012 • Björn Grüning

  • An analysis and data integration tool

  • Open source, community driven software that makes integrating our own tools simple

  • Part of GMOD

http://galaxyproject.org

"Enable accessible, reproducible, and transparent computational research."
accessible - Webinterface
"Enable accessible, reproducible, and transparent computational research."
reproducible - Reload experiments
reproducible - Reload experiments
reproducible - Workflows
"Enable accessible, reproducible, and transparent computational research."
transparent - sharing everything
share
transparent for other researchers
transparent
tools
  • Text Manipulation
  • Format Converters
  • Filtering and Sorting
  • Join, Subtract, Group
  • Sequence Tools
  • Multi-species Alignment Tools
  • Genomic Interval Operations
  • Summary Statistics
  • Graphing / Plotting
  • Regional Variation
  • EMBOSS
  • Evolution / Phylogeny
  • RNA-seq
  • ChIP-seq
  • GATK
  • RGenetics
  • CADDSuite
  • ...and more

    Integrating your own tools in Galaxy

    basic example
    transparent
    community is key
    • ~1000 additional tools

    • ~415 publications, 250 in 2012

    • 24 known public instances

    • 3000 registered users (galaxy-users)

    • 600 registered developers (galaxy-dev)

    • 400 mails per month

    • annual international community conference

    centralized - Galaxy main
    • ~500 new users per month

    • ~100 TB of user data

    • ~140,000 analysis jobs per month


    Centralized solution cannot scale to meet data analysis demands

    http://usegalaxy.org

    local Galaxy instances
    • completely self-contained

    • easy to deploy

    • run jobs on existing compute clusters


    http://galaxy.pharmaceutical-bioinformatics.org

    downsides
    • investment in training users

    • missing tools

    • reproducibility and transparentness is storage intensive


    RNA-seq tutorial
    What else?
    The vision - Join forces!
    • share tools, workflows, knowledge
    • regular training session (Bern/Freiburg)
    • enter the cluster?

    http://galaxy.bfg.uni-freiburg.de

    Questions?

    Thank You!

    Björn Grüning

    bjoern@gruenings.eu

    http://www.pharmaceutical-bioinformatics.org