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Bioinformatics Survey 2011 Premiminary

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William Spooner's talk at Kings College London on 25th Feb 2011 - BioGeeks series. Presents preliminary results from Eagle's 2011 Bioinformatics Community Survey http://eaglegenomics.com/survey

William Spooner's talk at Kings College London on 25th Feb 2011 - BioGeeks series. Presents preliminary results from Eagle's 2011 Bioinformatics Community Survey http://eaglegenomics.com/survey

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  • The survey was originally intended as an internal marketintellegence exercise. When we were preparing the survey, Cass called and asked if I wanted to give a BioGeeks talk. I thought, Why not put the survey up on surveymonkey get a few responses and give a talk on that. Others must be interested.We launched the survey on Valentine’s day, and had over 50 responses within a week. Took a snapshot 2 days ago, and have been looking through the data since. This talk presents what we’ve found so far. Caveats:I’m not a survey specialist. This was never designed ‘properly’Even with 60 responses, the survey is underpowered, probably.Think of this as a ‘Eagle and friends’ focus group, and we should be OK.
  • So here’s what we found. Bioinformaticians like to write elegant code that works and can be published. Getting bioinformaticians to accept ousourcing is like getting turkeys to vote for Christmas.
  • About 50% of our responses came from the UK, and 25% from ‘known’ locationsClick – 11 responses came from London. There’s more people that that here. Some of you did not do the survey!
  • So – other than location, where did our respondents come from? 50% from University 50% from departments with >10 bioinformaticians 75% with more than 5 years experience 50% without management experience, SO – A bunch of university postdoc looking for a fellowship.
  • So where are people workingClick – there are 2 ‘blockbuster’ areas, gene expression and variation analysis, that >70% respondents anticipate usingClick – there are a number of mainstream fields with 50-70% penetrationClick – and a couple of specialty areas with <50% penetration
  • Data integration = #1 bioinformatics technology priority.
  • The Genome-CMS concept is not new, there is a wide variety of existing platforms that fall under the umbrella. Ensembl and SRS, for instance, are both over 10 years old. Platforms can, to some extent be classified into those which are workflow (i.e. data creation) oriented, and those which are database (i.e. data management) oriented. Another key differentiator is the license under which the software are offered; open source or proprietary. At Eagle we specialise in open source
  • Transcript

    • 1. Bioinformatics Community SurveyBioGeeks, KCL 24th Feb 2011
      William Spooner
      whs@eaglegenomics.com
      http://eaglegenomics.com/survey
    • 2. The Bioinformatics Survey
      • What are the key initiatives in bioinformatics?
      • 3. How can these be delivered?
      • 4. Do they meet operational requirements?
      • 5. How could they be improved?
      • 6. Results will influence development of the next generation of bioinformatics tools;
      • 7. Guiding policy makers, tool designers and developers,
      • 8. Published as an open-access report.
      http://eaglegenomics.com/survey
    • 9. Spoiler Alert
      Bioinformaticians like to;
      • Develop their own solutions,
      • 10. Using open-source software,
      • 11. That’s stable, reliable, and published
      Bioinformaticians don’t like to;
      • Outsource, or use commercial software,
      • 12. Develop user-friendly, supported software.
      http://eaglegenomics.com/survey
    • 13. Company Background
      • Professional services company (bioinformatics);
      • 14. Founded in May 2008,
      • 15. To make open source/access easier for businesses.
      • 16. Wide breadth of experience;
      • 17. Balanced knowledge of biology and computer science,
      • 18. From commercial and academic backgrounds.
      • 19. We build connections and foster collaborations with academic groups.
      • 20. Delivering a range of successful solutions to a global customer base.
    • An Open Source Service Company
      Collaboration
      Service
      Business
      Open Community(e.g. Academia)
      Service Company
    • Eagle’s Collaborations with Academia
      • For Eagle;
      • 26. Credibility
      • 27. Ongoing knowledge transfer
      • 28. For the academic group;
      • 29. Increased user base (e.g. SMEs)
      • 30. Tangible economic impact
      • 31. important for funding agencies
      • 32. Collaborative development
      • 33. contribution of code and documentation
      • 34. Financial rewards
    • Over 50 responses in a week
      Biogeeks? Max 11
    • 35. Demographic
      University ~ 50%
      >10 people ~ 50%
      None~ 50%
      >5 years ~ 75%
    • 36. Bioinformatics Areas
      The big two
      Blockbuster
      >70%
      Mainstream
      50-70%
      %
      Specialty
      <50%
      Specialty
    • 37. Areas, Public V. Private
      Mature
      Emerging
      Commercialised
      %
    • 38. Technologies
      Integration
      wins!
      NGS
      NGS
      NGS
      NGS
      NGS
      GWAS old news already?
      %
      Bad Omission
    • 39. The Sequencing Cliff
    • 40. Bioinformatics Crash Landing?
      What needs to change?
      The following must increase:
      Hardware scalability,
      In-house bioinformaticians, and/or bioinformatics outsourcing
      Software quality.
    • 41. Delivery of Bioinformatics
      In-house vs. outsourced
      2. In-house vs. outsourced
      3. Software
      quality
      1. Hardware
      scalability
      %
    • 42. Different attitudes to delivery?
      In-house vs. outsourced
      2. In-house vs. outsourced
      3. Software
      quality
      1. Hardware
      scalability
      %
    • 43. 1. Hardware scalability
      Yes
      No
      Yes
      No
    • 44. 2. In-house Vs. Outsourcing
      In-house wins overall
      Outsource wins in scalability
      %
    • 45. 3. Software Quality
      Technical attributes win
      Technical attributes win
      Technical attributes win
      Usability attributes lose
      Usability attributes lose
      Usability attributes lose
      %
    • 46. 3. Software Quality
      Technical attributes win
      Technical attributes win
      Technical attributes win
      Usability attributes lose
      Usability attributes lose
      Usability attributes lose
      %
    • 47. BUT…can this Approach scale?
      Bioinformaticians like to;
      • Develop their own solutions,
      • 48. Using open-source software,
      • 49. That’s stable, reliable, and published
      Bioinformaticians don’t like to;
      • Outsource, or use commercial software,
      • 50. Develop user-friendly, supported software.
    • Is this the Answer?
      “Genome Content Management is the set of processes and technologies that support the creating, managing, and reporting of genomic data.”
      Create
      TIMELINE: 100% Bespoke…..…Common Schemas/APIs…..…Content Management Systems
      Create
      Reuse
      Extend
      Manage
      Manage
      Report
      Share
      Report
    • 51. Genome Content Management Systems (G-CMS)
      Open Source
      Proprietary
      Workflow Oriented
      Database Oriented
    • 52. And Finally
      • The survey closes at the end of march,
      • 53. Those that participated, thanks!
      • 54. Those that did not, please participate!
      • 55. Tell your friends! Tell your enemies!
      • 56. We will run it again next year; suggestions?
      http://eaglegenomics.com/survey

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