Upgrade to Pro — share decks privately, control downloads, hide ads and more …

ReproPhylo at Balti and Bioinformatics

96e8ca061c005a42d360459d366ec923?s=47 Dave Lunt
January 21, 2015

ReproPhylo at Balti and Bioinformatics

Approaches to reproducibility in phylogenomics and ReproPhylo software

96e8ca061c005a42d360459d366ec923?s=128

Dave Lunt

January 21, 2015
Tweet

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
  2. 1. Does not scale Whats wrong with phylogenomics now? 0.

    Rarely reproducible 2. Is not experimental
  3. Many reproducibility challenges are solved problems Solved problems in computer

    science, and other disciplines, do not always reach biology well, almost
  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
  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
  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
  7. ReproPhylo reproducible phylogenomics environment v1.0 http://hulluni-bioinformatics.github.io/ReproPhylo

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

    text reports
  10. Sequences, alignments & metadata pickle, git, explicit code, Docker html

    report, ms figures, tables, Methods, IPython notebook usability reproducibility
  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
  12. code output Exploratory Data Analysis

  13. Exploratory Data Analysis check this? high GC exploratory data analysis

    suggests experimental reuse with variation = reproducibility
  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
  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
  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