ReproPhylo at Balti and Bioinformatics

Approaches to reproducibility in phylogenomics and ReproPhylo software

Transcript

1. Reproducible
   Phylogenomics
   Dave Lunt, Amir Szitenberg, Max John, Mark Blaxter
   software: http://hulluni-bioinformatics.github.io/ReproPhylo
   dave.lunt@gmail.com
   ReproPhylo
   reproducible phylogenomics environment
   evohull.org
   @davelunt davelunt.net
   +davelunt
   

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2. 1. Does not scale
   Whats wrong with
   phylogenomics now?
   0. Rarely reproducible
   2. Is not experimental
   

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3. Many reproducibility
   challenges are solved
   problems
   Solved problems in computer science, and other
   disciplines, do not always reach biology
   well, almost
   

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4. Lack of
   reproducibility
   is sociological
   problem
   not a new problem
   unlikely to be solved by outlining best practice
   a problem for most areas of science and non-science
   an extensive problem
   human nature costs and benefits
   

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5. Reproducibility
   makes your life
   much easier
   ‘future you’ will reproduce your work
   reproducibility gives you new experimental powers
   we should highlight to users that
   benefits to the user- carrot not stick
   benefit
   

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6. Frictionless
   Reproducibility
   Environments
   happens in background, user
   doesn’t have to remember/care to
   behave reproducibly
   we should aim for
   “good science whether
   you like it or not”
   c/f computer backups
   ease
   

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7. ReproPhylo
   reproducible phylogenomics environment
   v1.0
   http://hulluni-bioinformatics.github.io/ReproPhylo
   

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8. ReproPhylo
   Software: http://hulluni-bioinformatics.github.io/ReproPhylo
   v1.0
   Editable User Manual: http://goo.gl/aZeRXf
   Open phylogenomics environment
   Uses standards
   Frictionless reproducibility
   Platform independent
   

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9. ReproPhylo
   Software: http://hulluni-bioinformatics.github.io/ReproPhylo
   Editable User Manual: http://goo.gl/aZeRXf
   IPython notebook
   Pickle
   text reports
   

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10. Sequences,
    alignments &
    metadata
    pickle, git, explicit
    code, Docker
    html report, ms figures,
    tables, Methods,
    IPython notebook
    usability
    reproducibility
    

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11. .zip files for Dryad and FigShare
    Docker containers
    pickled project
    git
    figures for manuscript
    tables for supp info
    Methods text
    detailed html report
    explicit python scripts
    IPython notebooks
    usability
    re-usability
    reproducibility
    likely to be used
    

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12. code
    output
    Exploratory Data Analysis
    

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13. Exploratory Data Analysis
    check this?
    high GC
    exploratory data analysis suggests experimental reuse with variation
    = reproducibility
    

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14. ReproPhylo
    reproducible phylogenomics environment
    v1.0
    Challenge is to make reproducibility the norm
    Target audience is not bioinformaticians
    successful human interaction is essential component of reuse and reproducibility
    usability
    

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15. ReproPhylo
    ReproPhylo is environment & approach
    reproducibility leads to other advantages…..
    promote experimental, exploratory &
    hypothesis-testing phylogenomics
    speed
    inherently experimental
    new ways of working? collaborative working
    

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16. Reproducible
    Phylogenomics
    Dave Lunt, Amir Szitenberg, Max John, Mark Blaxter
    software: http://hulluni-bioinformatics.github.io/ReproPhylo
    dave.lunt@gmail.com
    ReproPhylo
    reproducible phylogenomics environment
    evohull.org
    @davelunt davelunt.net
    +davelunt
    

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