Software Sustainability Institute - Fellowship Selection Day 2014 - Joe Parker
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Five-minute presentation for the SSI Fellowship selection day at Manchester University, 10th November 2014. I present and overview of the current state of genome-scale evolutionary analyses ('phylogenomics') and highlight some technical and cultural problems in the field which I hope to address using funding from the SSI to run a series of phylogenetic software curation hackathons.
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Software Sustainability Institute - Fellowship Selection Day 2014 - Joe Parker
- 1. Massively parallel phylogenomics Joe Parker Queen Mary University of London Phylogenomics matters flickr/ste phe njjo hnso n Illumina. co m spe ctrum. ie e e . o rg • Interface of genetics, evolution, statistics, computation • Disease, adaptation, climate change, medicine • Distributed, parallel & high-performance computation
- 2. Challenges • Size of data sets • Heterogeneous architecture • Use of non-standard workflows • Limited testing • Time-limited projects • Versioning / legacy • Collaboration / silos • Compatibility Distribution Source / binaries Plugins, Git / SVN Commercial Open Languages Python Perl C/C++ Java Javascript Ruby R Matlab
- 3. Objective Portal for phylo tools (e.g. wiki / blog / searchable metdata feed / stack exchange) “ What are we all doing? ” “ Surely this has been done before? ” Solutions Projects Binaries Source Discovery Tag clouds / wiki Metadata Catalogue Inputs / outputs Versioning Architecture “ How do you do that? ”
- 4. Approach Six Hackspace / networking events “ Live stack e xchang e fo r phylo g e ne tics” Portal Share Hack Learn Discovery Existing tools Best practice Problems Community Build network Develop consensus Engage • Build awareness / community, develop consensus on best-practice, share hacks and develop phlyo tools portal. • Research software engineers from academia, industry (including SMEs and startups) and hackers. • London’s Silicon Roundabout; space hire, refreshments and dissemination. (L-R): Joe Parker; GeorgiaTsagkogeorga; Kalina Davies; Steve Rossiter; Xiuguang Mao; Seb Bailey
- 5. Outputs Live-blog & documentation Live stack e xchang e fo r phylo g e ne tics, disseminate Resource for tools metadata Community-spe cifie d, de ve lo pe d and maintaine d Supporting SSI Aims Sustainability through community Re pe atability, communicatio n and co ntinuity Legacy of best-practice Pe e r-base d disseminatio n o f skills, pro blems, so lutio ns
- 6. Outputs Live-blog & documentation Live stack e xchang e fo r phylo g e ne tics, disseminate Resource for tools metadata Community-spe cifie d, de ve lo pe d and maintaine d Supporting SSI Aims Sustainability through community Re pe atability, communicatio n and co ntinuity Legacy of best-practice Pe e r-base d disseminatio n o f skills, pro blems, so lutio ns
Notas del editor
- Lots of existing tools - not pralleleised for batch ‘cloud, db, network cartoons + phylogeny’
- binaries from author plugins repos vendor
- Repository for bio tools Input Output Process Binaries / test harnesses Turn these into a network diag
- Identify areas for collaboration / enhancements Awareness of other developers / groups Document best practices, hacks, common pitfalls Live stack exchange for phylogenetics Use ‘SSI Aims - action - outcome’
- Identify areas for collaboration / enhancements Awareness of other developers / groups Document best practices, hacks, common pitfalls Live stack exchange for phylogenetics Use ‘SSI Aims - action - outcome’