Successfully reported this slideshow.
We use your LinkedIn profile and activity data to personalize ads and to show you more relevant ads. You can change your ad preferences anytime.

Software Sustainability Institute - Fellowship Selection Day 2014 - Joe Parker

244 views

Published on

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.

Published in: Science
  • Be the first to comment

  • Be the first to like this

Software Sustainability Institute - Fellowship Selection Day 2014 - Joe Parker

  1. 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. 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. 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. 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. 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. 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

×