Talk at "Genome Informatics Alliance 2012" meeting

Talk at "Genome Informatics Alliance 2012" meeting

A talk on distributed collaborations and data platforms

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Deepak Singh

March 29, 2012
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Transcript

  1. Most of the smartest people work for someone else D

    e e p a k S i n g h P r i n c i p a l P r o d u c t M a n a g e r , A m a z o n E C 2
  2. None
  3. “No matter who you are, most of the smartest people

    work for someone else”
  4. ?

  5. None
  6. 3

  7. “crowdsourcing”

  8. ad hoc collaboration

  9. small things loosely coupled

  10. ... one more thing

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  12. open data

  13. ... but I’ve been collaborating since I was in grad

    school
  14. not your adviser’s collaboration

  15. The Wisdom of Crowds

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  17. None
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  21. None
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  23. None
  24. The Polymath Project

  25. Tim Gowers

  26. None
  27. Fields Medallist

  28. http://gowers.wordpress.com/2009/01/27/is-massively-collaborative-mathematics-possible/

  29. social experiment

  30. ideas/progress on his blog

  31. comment section

  32. None
  33. time to solve problem #1?

  34. 37 days

  35. 27 people

  36. None
  37. Nucl. Acids Res. (2010) 38 (suppl 1): D633-D639

  38. I'd also be remiss if I didn't also note the

    critical role online collaboration played in this effort. Of the seven coauthors on this paper, two I've met only once in real life, and two I've never met in person. We are spread over four cities, five organizations, and nine time zones. Initiating and executing this collaboration happened virtually entirely online, aided by the FriendFeed Life Scientists room and Molecular and Cellular Biology WikiProject at Wikipedia. It was an eye-opener in terms of how effective online collaboration can be done.
  39. http://en.wikipedia.org/wiki/Portal:Gene_Wiki

  40. None
  41. Image: Yael Fitzpatrick (AAAS)

  42. extend Image: Bethan

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  44. 40 TB

  45. MapReduce

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  48. None
  49. http://www.1000genomes.org/using-1000-genomes-data-amazon-web-service-cloud

  50. Community http://cloudbiolinux.org/ http://sourceforge.net/projects/seqware http://wiki.g2.bx.psu.edu/Admin/Cloud

  51. Community http://bowtie-bio.sourceforge.net/myrna/index.shtml http://bowtie-bio.sourceforge.net/crossbow/index.shtml

  52. Community http://sagebase.org/research/Synapse1.php http://www.genomespace.org/

  53. Full case study at http://aws.amazon.com/swf/testimonials/swfsagebio/

  54. http://bcbio.wordpress.com

  55. a request

  56. OK ... 2 requests

  57. put APIs in front of your data

  58. https://postgres.heroku.com/dataclips/psywmdixgtrxkorpzcueiohkwona

  59. use github

  60. None
  61. to conclude

  62. people produce data

  63. the consumers are everywhere

  64. “No matter who you are, most of the smartest people

    work for someone else”
  65. lets help them succeed

  66. deesingh@amazon.com Twitter:@mndoci http://speakerdeck.com/u/mndoci http://deepaksingh.net Inspiration and ideas from Matt Wood,

    Michael Nielsen & Larry Lessig Credit” Oberazzi under a CC-BY-NC-SA license