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Reproducible Phylogenomics Dave Lunt, Amir Szitenberg, Max John, Mark Blaxter software: http://hulluni-bioinformatics.github.io/ReproPhylo [email protected] ReproPhylo reproducible phylogenomics environment evohull.org @davelunt davelunt.net +davelunt

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

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

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

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

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.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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code output Exploratory Data Analysis

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

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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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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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Reproducible Phylogenomics Dave Lunt, Amir Szitenberg, Max John, Mark Blaxter software: http://hulluni-bioinformatics.github.io/ReproPhylo [email protected] ReproPhylo reproducible phylogenomics environment evohull.org @davelunt davelunt.net +davelunt