Bioinformatics Community SurveyBioGeeks, KCL 24th Feb 2011<br />William Spooner<br />whs@eaglegenomics.com<br />http://eag...
The Bioinformatics Survey<br /><ul><li>What are the key initiatives in bioinformatics?
How can these be delivered?
Do they meet operational requirements?
How could they be improved?
Results will influence development of the next generation of bioinformatics tools;
Guiding policy makers, tool designers and developers,
Published as an open-access report.</li></ul>http://eaglegenomics.com/survey<br />
Spoiler Alert<br />Bioinformaticians like to;<br /><ul><li>Develop their own solutions,
Using open-source software,
That’s stable, reliable, and published</li></ul>Bioinformaticians don’t like to;<br /><ul><li>Outsource, or use commercial...
Develop user-friendly, supported software.</li></ul>http://eaglegenomics.com/survey<br />
Company Background<br /><ul><li>Professional services company (bioinformatics);
Founded in May 2008,
To make open source/access easier for businesses.
Wide breadth of experience;
Balanced knowledge of biology and computer science,
From commercial and academic backgrounds.
We build connections and foster collaborations with academic groups.
Delivering a range of successful solutions to a global customer base. </li></li></ul><li>An Open Source Service Company<br...
Training
Support
Installation/Integration
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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

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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 &gt;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 &gt;70% respondents anticipate usingClick – there are a number of mainstream fields with 50-70% penetrationClick – and a couple of specialty areas with &lt;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
  • Bioinformatics Survey 2011 Premiminary

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