Web 2.0 for Biologists–Are any of the current tools worth using?


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Web 2.0 for Biologists–Are any of the current tools worth using?

  1. 1. Cold Spring Harbor Laboratory
  2. 2. CSHL Press <ul><li>Founded 1933 </li></ul><ul><li>Approx. 60 staff, located at Cold Spring Harbor, Plymouth (UK), Tuebingen (Germany) and San Diego </li></ul><ul><li>Over 200 books in print, including lab manuals, monographs, textbooks, trade, and children’s books </li></ul><ul><li>Electronic media: technique videos, CDs, DVDs, electronic books, companion websites for manuals and other books </li></ul><ul><li>6 Monthly Journals: Genes & Development , Genome Research , Learning & Memory , RNA , Protein Science and CSH Protocols </li></ul><ul><li>BioSupplyNet.com: online and print directory of laboratory suppliers and products (http://www.biosupplynet.com) </li></ul><ul><li>Online catalog at http://www.cshlpress.com </li></ul>
  3. 3. Manual Publishing
  4. 4. Surely there’s a better way
  5. 5. CSH Protocols <ul><li>Approximately 1,100 protocols online </li></ul><ul><li>Protocols come from manuals, CSHL courses, newly submitted peer-reviewed articles </li></ul><ul><li>Searchable, browseable, cross-linked, updated </li></ul>
  6. 6. Write this down <ul><li>Editorial Blog </li></ul><ul><li>http://www.cshblogs.org </li></ul>
  7. 7. What is Web 2.0? <ul><li>Web as platform </li></ul><ul><li>Connecting people via social-networking technologies </li></ul><ul><li>User-generated content (blogs, wikis, folksonomies) </li></ul><ul><li>Repurposing of content (mashups, aggregators, bookmarking sites) </li></ul>Luca Cremonini Source: http://www.railsonwave.it/railsonwave/2007/1/2/web-2-0-map
  8. 8. Web 2.0 in Life Sciences Social Networking Sites Nature Network YourSci.com Scilink.com Scientificcommons.org Myexperiment.org Biomedexperts.com Swivel.com Many Eyes LinkedIn Pronetos Referral Sites Connotea CiteULike Publicationslist.org 2Collab Chemistry.org/exchange Postgenomic Scintilla Faculty of 1000 Dissectmedicine Blog sites Science Blogs Nature Network Open Wetware Video Sites JOVE Scivee.tv Wikis (expert or open) Scirus Topic Pages Google Knol Open Wetware
  9. 9. How’s it going? “ A panel of science web publishers said scientists had consistently shunned wikis, tagging, and social networks, and have even proven reticent to leave comments on web pages.” The Register, March 2007
  10. 10. What’s gone wrong <ul><li>Too much “Web 2.0 for the sake of Web 2.0” </li></ul><ul><li>Too much copycatting, not enough specific attention to the culture of science </li></ul><ul><li>Too much emphasis on social aspects, rather than timesaving aspects </li></ul>
  11. 11. Reasons for lack of adoption <ul><li>TIME (lack thereof) </li></ul><ul><li>I have yet to meet a biologist with a lot of time to spare </li></ul><ul><li>Social networking sites, blogs, wikis, etc., all demand a great deal of time from their users </li></ul><ul><li>“ I can barely keep up with the literature in my field and with what my labmates are doing. Who has time to spend reading some grad student’s blog?” </li></ul><ul><li>Anonymous Postdoc </li></ul>
  12. 12. Reasons for lack of adoption <ul><li>TIME (expediency) </li></ul><ul><li>Can you really wait around hoping someone will come to your rescue? </li></ul><ul><li>“ If I want to know why somebody used buffer x for their biochemistry experiments, or why they didn’t do control experiment xyz I email the authors, or use the phone if I know them. Why post it in the comment section of their paper, and wait for 5 weeks until they bother to check? And why does everybody else need to know about it?” </li></ul><ul><li>“ Michael” Nature Neuroscience blog commenter </li></ul>
  13. 13. Reasons for lack of adoption <ul><li>INCENTIVE </li></ul><ul><li>(lack thereof) </li></ul><ul><li>“ [It] takes too much time to comment on a scientific article properly, there’s no incentive (can’t put it in your CV) or honor to be gained (no one asked me to review this) and they are not written to be discussed.” </li></ul><ul><li>Roland Krause </li></ul><ul><li>Notes From The Biomass Blog </li></ul>
  14. 14. Reasons for lack of adoption <ul><li>If your contribution is anonymous, does that help your career? Will it help you graduate, get a job, get a grant? Where is the motivation? </li></ul>
  15. 15. Reasons for lack of adoption <ul><li>INERTIA (definition 1) </li></ul><ul><li>Sites aren’t useful until lots of people are using them. </li></ul><ul><li>“ I can't remember a specific case where the &quot;Web 2.0&quot; functions of CiteULike ever worked for me. Peeking in the bibliographies of other people can be interesting if you have some bookmarked papers in common, but the signal-to-noise ratio is very low.” </li></ul><ul><li>Michael Kuhn bioCS Blog </li></ul><ul><li>“ ME TOO” SITES </li></ul>
  16. 16. Reasons for lack of adoption <ul><li>INERTIA (definition 2) </li></ul><ul><li>If the tool is too hard to learn, too hard to use, it won’t be used </li></ul><ul><li>“ Good enough and familiar” is favored over “better and hard to learn ” </li></ul>
  17. 17. Reasons for lack of adoption <ul><li>TOOLS ARE INAPPROPRIATE </li></ul><ul><li>Scientists do not interact like teenagers chatting or rock bands reaching out to their fans. “myspace for scientists” is a poorly thought-out model for the culture of scientific research. </li></ul>
  18. 18. Tools need to be appropriate to the culture of your readers <ul><li>“ It's one thing to air your complaints in a small room at the annual meeting of the International Society of Helminthologists. It's another to post them in a place where all of your colleagues--and anyone else with an Internet connection--can read them.” </li></ul><ul><li>Carl Zimmer </li></ul><ul><li>The Loom Blog </li></ul><ul><li>Who reads papers online? Can you comment on a pdf? </li></ul>
  19. 19. The Blogosphere,March 2007 <ul><li>Nearly 60,000,000 blogs </li></ul><ul><li>175,000 new blogs daily </li></ul><ul><li>2 new blogs every second </li></ul><ul><li>From http://datamining.typepad.com/ </li></ul>
  20. 20. Should you be blogging? <ul><li>Who reads science blogs? </li></ul><ul><ul><li>Other science bloggers </li></ul></ul><ul><ul><li>Non-scientists / Non-specialists </li></ul></ul><ul><ul><li>“ Despite the proliferation of physics blogs, Carroll is not very optimistic about them taking a more prominent role in physics research. From posting papers on arXiv.org to e-mail, the current way in which physicists communicate is already efficient. Blogs, however, could serve as a place for specialists and nonspecialists to interact, chipping away at the barriers separating academia from the general public.” </li></ul></ul><ul><ul><li>Caltech :Engineering and Science:, October 2007 </li></ul></ul><ul><ul><li>Journalists </li></ul></ul><ul><ul><li>Search engines </li></ul></ul>
  21. 21. Should you be blogging? <ul><li>Is blogging good for your career? </li></ul><ul><ul><li>“ Blogs are a great way to open your notebook to the world, or just to the lab. They’re a rich medium(you can’t imbed an animation of cells exchanging mitochondria in your paper notebook), accessible from anywhere, and automatically backed up. They also make you improve your writing skills. From a social perspective, they’re the root of your identity on the web: the place where you communicate your thoughts, your CV, and where you receive communication from others. On a blog, this kind of interaction can happen 24/7 with anyone in the world. In person, you only interact with people in your lab, university, or company.” </li></ul></ul><ul><ul><ul><ul><ul><li>William Gunn http://synthesis.williamgunn.org/ </li></ul></ul></ul></ul></ul>
  22. 22. Should you be blogging? <ul><li>Is blogging good for your career? </li></ul><ul><ul><li>“ A blog raises your profile, but it raises your profile for something other than research,”Carroll said. “And even if you are extremely productive as a scholar,” he said, “some professors may view a blog as sign that you could be spending more time in the laboratory or library, engaged in traditional research.” </li></ul></ul><ul><ul><ul><ul><li>Inside Higher Ed, October 11, 2005 </li></ul></ul></ul></ul><ul><ul><li>“ In fact, conventional wisdom seems to warn that blogging may be a risky venture for those academic bloggers who have not been awarded tenure…Pretenured professors should be aware of the risks of blogging and develop strategies to avoid or mitigate the pitfalls of blogging without a tenure net.” </li></ul></ul><ul><ul><ul><li>Christine Hurt, Tung Yin, Washington University Law Review </li></ul></ul></ul>
  23. 23. Useful Tools: Social Networks <ul><li>Social Networks for scientists are about jobs, about finding jobs and about finding applicants for jobs. </li></ul>
  24. 24. Useful Tools: Wikis and Folksonomies GoPubMed: Combines text-mining with human curation
  25. 25. Useful Tools: Organization and Discovery Should you keep your reference list online? <ul><li>Benefits </li></ul><ul><li>Tags serve as a way to organize your enormous reference lists </li></ul><ul><li>Can access from anywhere, any computer </li></ul><ul><li>Easy export/import </li></ul><ul><li>Use as a discovery tool </li></ul><ul><li>Can organize any type of linked resource </li></ul>
  26. 26. Useful Tools: Connotea
  27. 27. Useful Tools: Organization and Discovery Should you keep your reference list online? <ul><li>Problems </li></ul><ul><li>Is there any real benefit to having this online? </li></ul><ul><li>Discovery aspects not that useful, more information overload? </li></ul><ul><li>Can only access with internet/subscription access </li></ul><ul><li>Have to tediously add tags </li></ul><ul><li>Online linked content only </li></ul><ul><li>Can’t search text of papers </li></ul><ul><li>Importing/exporting functions is flaky </li></ul>
  28. 28. Useful Tools: CiteULike
  29. 29. Useful Tools: 2Collab
  30. 30. Useful Tools: Organization and Discovery Should you keep your reference list locally on your computer? <ul><li>Benefits </li></ul><ul><li>Ownership, your control, if site disappears, you’ve still got something </li></ul><ul><li>Deal with all of those pdf’s you’ve already downloaded </li></ul><ul><li>Good search replaces tagging--much more efficient </li></ul><ul><li>Some programs work with multiple types of content, online and offline </li></ul>
  31. 31. Useful Tools: Papers
  32. 32. Useful Tools: Organization and Discovery Should you keep your reference list locally on your computer? <ul><li>Problems </li></ul><ul><li>Can only access on your computer </li></ul><ul><li>Works better if you tediously add folders/tags </li></ul><ul><li>Lose discovery/community aspects </li></ul><ul><li>Importing not as automatic as you’d like </li></ul><ul><li>Interaction between programs still pretty flaky, if it exists at all </li></ul>
  33. 33. Useful Tools: Zotero
  34. 34. Useful Tools: Gadgets/Widgets
  35. 35. Useful Tools: Mashups / Aggregators Epispider
  36. 36. Useful Tools: Workflows
  37. 37. Summary <ul><li>Early days--most of what’s out there now is going to fail </li></ul><ul><li>There are many promising directions, well worth investigating, if not committing time </li></ul><ul><li>Tools that show promise are “works in progress” and need more polishing </li></ul>
  38. 38. How to choose <ul><li>Look for sites that will save you time, not sites that demand time </li></ul><ul><li>Look for tools that fit your culture, not tools that demand you adapt </li></ul><ul><li>Open formats--get your work in and out easily </li></ul><ul><li>Is the tool useful if no one else adopts it? </li></ul>