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Mik Black bioinformatics symposium
 

Mik Black bioinformatics symposium

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Mik Black bioinformatics symposium

Mik Black bioinformatics symposium

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    Mik Black bioinformatics symposium Mik Black bioinformatics symposium Presentation Transcript

    • How to make bioinformatics accessible to normal people!  Mik Black Department of Biochemistry University of Otago
    • Some musings… •  Accessibility - two aspects: 1.  Methodology development & distribution (can you get it?) 2.  Methodology uptake (can you use it?) •  “Normal people”: 1.  Who are they? 2.  What do they want? What do they need? Is there a happy medium?
    • My background •  Statistical design and analysis of microarray experiments: –  Methodology development –  Applying existing bioinformatics techniques –  Adapting “standard” statistical methods –  “Forensic” analysis •  Technologies: –  Microarrays (mRNA, SNPs, CNV/CGH) –  Second generation sequencing (SNP/CNV)
    • http://www.r-project.org/
    • The joys of the command line… •  Large amounts of statistical genomics methodology available via R –  Accessible? –  Uptake? –  Who are the end users? •  Can’t we just teach EVERYONE to use R?
    • http://www.broad.mit.edu/cancer/software/genepattern/ Reich et al. (2006) GenePattern 2.0., Nature Genetics, 38, 500-501. •  GenePattern provides a web-based method for analysing microarray (and other) data. •  Provides a simple interface to tools developed in Java, R, Matlab and other languages. •  Analysis performed on server: –  no compute resources required by users. –  Facilitates sharing of results.
    • Using GenePattern •  User friendly –  Third year bioinformatics course at Otago. –  Workshop for lab personnel at TGen. •  Guided analysis –  Facilitates use of standard analysis methods. –  Pipeline creation and “versioned” analysis. •  End users? –  At Otago: 3rd & 4th year Biochemistry students –  At TGen: lab techs, iterns, bench scientists, PIs
    • Common analysis tasks •  Basic data analysis/exploration: –  Heatmap creation –  Hierarchical clustering –  Identifying differentially expressed genes –  Gene set analysis –  Survival analysis •  GenePattern provides these tools in a modular format.
    • GenePattern interface
    • Simple analysis pipeline
    • Power calculations Δ P
    • Network analysis
    • BeSTGRID: Broadband-enabled Science and Technology GRID http://www.bestgrid.org
    • GenePattern on BeSTGRID •  Services: –  GenePattern server –  Development environment (server and SVN) •  GenePattern training (coming soon): –  Basic usage –  Module development (uptake path for bioinformatics tool developers)
    • Next steps… •  Full GenePattern deployment: –  Transfer of development modules to public server –  Documentation and training –  Use of ROCKS cluster for job submission •  Modules for Second Gen Sequencing data: –  DNAseq, RNAseq, ChIPseq –  R/Bioconductor (e.g., ShortRead, Biostrings, RSamTools, GenomeGraphs…) –  Analysis, visualization and quality assurance
    • Community effort •  Some current examples: –  VISG/MapNet: statisticians & geneticists –  BeSTGRID: middleware development & deployment through to end users –  CTCR: cancer researchers & clinicians •  Each group has the goal of placing powerful (and useful, and usable) tools into the hands of end users.
    • Bioinformatics community •  NZGL provides opportunity for community-based effort. –  National infrastructure for genomics research –  Includes strong bioinformatics component •  Key issue: engagement with end users –  Methodology development and distribution –  Uptake, interaction and training
    • Bioinformatics community •  NZGL provides opportunity for community-based effort. –  National infrastructure for genomics research –  Includes strong bioinformatics component •  Key issue: engagement with end users –  Methodology development and distribution –  Uptake and interaction LETS GO FIND US SOME “NORMAL” PEOPLE!
    • Acknowledgements University of Otago The University of Auckland Marcus Davy Nick Jones Tim Molteno Mark Gahegan Thomas Allen Yuriy Halytskyy Sarah Song Cristin Print Chris Brown Daniel Hurley Anthony Reeve Christoff Knapp Tony Merriman University of Canterbury Vladimir Mencl