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Bioinformatics in the ZBSA

Galaxy, one solution for data intensive biology for everyone?

March 2013 • Björn Grüning

The problems ...

Sboner et al. Genome Biology 2011 12:125 "The real cost of sequencing: higher than you think!"

What is needed?
  • reproducible pipelines to reduce the raw-data

  • easy access to tools and protocols

    (not to forget the annoying file format problems)

  • data visualisation

  • central data storage and backups

  • 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
Galaxy Main View
accessible - get your data
UCSC Data integration
"Enable accessible, reproducible, and transparent computational research."
reproducible - Reload experiments
History panel
reproducible - Reload experiments
History panel
    
reloaded tool
reproducible - Workflows
reloaded tool
"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
  • Unix Tools
  • Alignment Tools
  • Genomic Interval Operations
  • Summary Statistics
  • Plotting
  • Mapping
  • EMBOSS
  • Evolution / Phylogeny
  • RNA-seq
  • ChIP-seq
  • GATK
  • RGenetics
  • NCBI Blast+
  • ...and many more (1000+)
    Proteomics/Metabolomics
        
    • OMSSA
    • MassSpecAccess
    • X!TANDEM
    • Protk
    • Trans Proteomic Pipeline
    • PeptideShaker
    • Scaffold (commercial)
  • OpenMS
  • MSConvert
  • ProteinPilot
    • Mascot
    • MSGF+
    • ms2preproc
  • digestdb
  • MTSiP
  • NCBO's BioPortal
  • Blast2GO
  • Onto-toolkit
  • Mothur
  • ChemicalToolBoX
  • Integrating your own tools - basic example
    transparent
    transparent
    Visualisation - Scatterplot
    Scatterplot
    Visualisation - Trackster
    Trackster
    Visualisation - Sweepster
    Sweepster
    What else?
    Teaching and documentation - Pages
    community is key
    • ~1000 additional tools

    • ~800 publications since 2010, 91 in 2013

    • 29 known public instances

    • ~4000 registered users (galaxy-users Mailinglist)

    • ~600 registered developers (galaxy-dev Mailinglist)

    • 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

    personal Galaxy instances
    • completely self-contained

    • easy to deploy

    • run jobs on existing compute clusters

    • cloud computing (Amazon's EC2 ...)


    http://galaxy.pharmaceutical-bioinformatics.org

    downsides
    • investment in training/teaching

    • cluster and galaxy administration

    • missing tools

    • reproducibility and transparentness
      is storage intensive


    The vision - Join forces!
    • standardise workflows and protocols
    • share tools, workflows, knowledge
    • enable reproducible research
    • regular training session (Bern/Freiburg)
    • Galaxy instances in FR, TÜ, HD, Bern, Basel ...

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

    Genome Annotation

    Genome Annotation

    Prof. Bechthold
    Prof. Müller
    (Pharmacy)

    Whole‐Genome Bisulfite-Seq

    Methylation

    Prof. Hein
    (Pharmacology, SFB 992)

    Galaxy training and administration

    Methylation

    Prof Backofen (Bioinformatics, SFB 992)
    Dr. Manke (MPI, SFB 992)

    Cheminformatics

    Methylation

    Jun. Prof. Günther
    (Pharmaceutical Bioinformatics)

    Thank You!

    Björn Grüning

    bjoern@gruenings.eu

    http://www.pharmaceutical-bioinformatics.org

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

    http://wiki.galaxyproject.org/Learn

    Toolshed - the Research Appstore
    Toolshed