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How online networks (mostly) kept a lone
bioinformatician from going insane
Neil Saunders
DIGITAL PRODUCTIVITY
www.csiro.au
Social Networking: Slide 2 of 29
obligatory advertising slide
Transformational Bioinformatics Team
Australian eHealth Rese...
Social Networking: Slide 3 of 29
a quick introduction to me
for the purpose of this talk
Social Networking: Slide 4 of 29
back in the year 2000
sequencing microbial genomes
one Windows machine, several thousand ...
Social Networking: Slide 5 of 29
online support back then came in one form
the mailing list
Social Networking: Slide 6 of 29
what I learned from mailing lists
“community norms” :-)
Neil,
I’ve never written a “RTFM”...
Social Networking: Slide 7 of 29
the mailing list is not (quite) dead
Social Networking: Slide 8 of 29
experiments in more “personal” community
the Nodalpoint portal
Social Networking: Slide 9 of 29
what we learned from Nodalpoint
if you build it, they might come
Social Networking: Slide 10 of 29
the rise of the bioinformatics blog
2004 - 2008
Social Networking: Slide 11 of 29
blogs as community
bio::blogs
Social Networking: Slide 12 of 29
what we learned from blogs
want to express an opinion? be prepared to engage
https://xkc...
Social Networking: Slide 13 of 29
structural bioinformatics Brisbane 2006 - 2009
predicting protein-protein interactions (...
Social Networking: Slide 14 of 29
an unlikely science community
the life scientists group at FriendFeed
Social Networking: Slide 15 of 29
rewards & recognition via online networks
Social Networking: Slide 16 of 29
why was FriendFeed important?
because it was not one of these - “facebook for scientists...
Social Networking: Slide 17 of 29
health “omics” CSIRO 2009 - present
this is very much the age of Twitter
but what can yo...
Social Networking: Slide 18 of 29
post links to interesting articles
possibly your own
Social Networking: Slide 19 of 29
provide status updates
services, software
Social Networking: Slide 20 of 29
advertise jobs
also meetings, events
Social Networking: Slide 21 of 29
advertise your other online content
Social Networking: Slide 22 of 29
ask/answer questions
Social Networking: Slide 23 of 29
discuss topical issues
Social Networking: Slide 24 of 29
and so back to forums...
forums have evolved and are still valuable
Social Networking: Slide 25 of 29
thoughts on online community 1/n
four ages of online interaction (at least since c. 2000...
Social Networking: Slide 26 of 29
thoughts on online community 2/n
online communities
No matter who you are, most of the s...
Social Networking: Slide 27 of 29
thoughts on online community 3/n
don’t be a lone bioinformatician
https://biomickwatson....
Social Networking: Slide 28 of 29
thoughts on online community 4/n
local versus online
is online community “enough communi...
DIGITAL PRODUCTIVITY
www.csiro.au
CSIRO Digital Productivity
Neil Saunders
t
e
w website
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How online networks (mostly) kept a lone bioinformatician from going insane

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Talk for Westmead Millennium Institute Bioinformatics SIG June 4 2015.

In April 2000 I was shown a desktop folder full of ABI sequence chromatograms from a microbial genome, told to do some bioinformatics and left to get on with it. I turned to the Web for help, where I discovered my first online support network - the Bioperl mailing list.

In the 15 years since, I've worked on a variety of bioinformatics-based projects with 3 different organisations. In that time I've witnessed several shifts in the types of online communication tools used by the bioinformatics community: from mailing lists, through blogs to Twitter.

In this talk I'd like to examine how online networks have helped me do bioinformatics over the years, how they've changed and developed and to what extent they provide a sense of community for the "lone bioinformatician".

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How online networks (mostly) kept a lone bioinformatician from going insane

  1. 1. How online networks (mostly) kept a lone bioinformatician from going insane Neil Saunders DIGITAL PRODUCTIVITY www.csiro.au
  2. 2. Social Networking: Slide 2 of 29 obligatory advertising slide Transformational Bioinformatics Team Australian eHealth Research Centre, CSIRO http://aehrc.com/research/biomedical-imaging Goal: develop advanced computational and statistical methodologies and apply them to large datasets in the health/life sciences space Bill Wilson Denis Bauer Firoz Anwar James Doecke Neil Saunders Sam Burnham Aidan O’Brien Type Detail Value People Software NGSANE: Lightweight Production Informatics Framework for High Throughput Data Analysis Collaborators: MQ, Garvan, ANU Denis Contract Colo Vantage modeling CRC interventions Janssen (J&J Pharma) $100,000 $125,000/yr for 2 years Rob Sam Publication A blood based predictor for neocortical Aβ burden in Alzheimer's disease: results from the Australian Imaging, Biomarkers and lifestyle study of ageing Burnham et al. Molecular Psychiatry. IF=15 Sam, James, Bill Grant MND Research Institute $100,000 Denis, Bill
  3. 3. Social Networking: Slide 3 of 29 a quick introduction to me for the purpose of this talk
  4. 4. Social Networking: Slide 4 of 29 back in the year 2000 sequencing microbial genomes one Windows machine, several thousand chromatograms
  5. 5. Social Networking: Slide 5 of 29 online support back then came in one form the mailing list
  6. 6. Social Networking: Slide 6 of 29 what I learned from mailing lists “community norms” :-) Neil, I’ve never written a “RTFM” post in my life...
  7. 7. Social Networking: Slide 7 of 29 the mailing list is not (quite) dead
  8. 8. Social Networking: Slide 8 of 29 experiments in more “personal” community the Nodalpoint portal
  9. 9. Social Networking: Slide 9 of 29 what we learned from Nodalpoint if you build it, they might come
  10. 10. Social Networking: Slide 10 of 29 the rise of the bioinformatics blog 2004 - 2008
  11. 11. Social Networking: Slide 11 of 29 blogs as community bio::blogs
  12. 12. Social Networking: Slide 12 of 29 what we learned from blogs want to express an opinion? be prepared to engage https://xkcd.com/386/
  13. 13. Social Networking: Slide 13 of 29 structural bioinformatics Brisbane 2006 - 2009 predicting protein-protein interactions (Predikin) something else happened in 2006 (more on that later)
  14. 14. Social Networking: Slide 14 of 29 an unlikely science community the life scientists group at FriendFeed
  15. 15. Social Networking: Slide 15 of 29 rewards & recognition via online networks
  16. 16. Social Networking: Slide 16 of 29 why was FriendFeed important? because it was not one of these - “facebook for scientists” a.k.a. fb4sci social networks for scientists N. Saunders (SMMS, UQ) Science networks November 26, 2008 8 / 29
  17. 17. Social Networking: Slide 17 of 29 health “omics” CSIRO 2009 - present this is very much the age of Twitter but what can you do with a real-time stream of 140-character messages?
  18. 18. Social Networking: Slide 18 of 29 post links to interesting articles possibly your own
  19. 19. Social Networking: Slide 19 of 29 provide status updates services, software
  20. 20. Social Networking: Slide 20 of 29 advertise jobs also meetings, events
  21. 21. Social Networking: Slide 21 of 29 advertise your other online content
  22. 22. Social Networking: Slide 22 of 29 ask/answer questions
  23. 23. Social Networking: Slide 23 of 29 discuss topical issues
  24. 24. Social Networking: Slide 24 of 29 and so back to forums... forums have evolved and are still valuable
  25. 25. Social Networking: Slide 25 of 29 thoughts on online community 1/n four ages of online interaction (at least since c. 2000) the age of forums/mailing lists and portals the age of blogs the age of “facebook for scientists” the age of Twitter
  26. 26. Social Networking: Slide 26 of 29 thoughts on online community 2/n online communities No matter who you are, most of the smartest people work for someone else - Bill Joy It’s not information overload. It’s filter failure. - Clay Shirky clearly they are A Good Thing they’ve provided me with advice, support and comfort for 15+ years
  27. 27. Social Networking: Slide 27 of 29 thoughts on online community 3/n don’t be a lone bioinformatician https://biomickwatson.wordpress.com/2013/04/23/a-guide-for-the-lonely-bioinformatician/
  28. 28. Social Networking: Slide 28 of 29 thoughts on online community 4/n local versus online is online community “enough community”? what about local communities? what about bioinformatics in Sydney?
  29. 29. DIGITAL PRODUCTIVITY www.csiro.au CSIRO Digital Productivity Neil Saunders t e w website

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