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Murpha11

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Motivating students to Open Science using examples from computational biology.

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Murpha11

  1. 1. The Path to Open Science with Illustrations from Computational Biology  Philip E. Bourne University of California San Diego [email_address] http://www.sdsc.edu/pb Relevant Work from Us: http://www.sdsc.edu/pb/SummaryScholarComm.pdf MURPHA Sept 8, 2011
  2. 2. My Perspective … <ul><li>Background in both IT and science (chemistry, computational biology) </li></ul><ul><li>My lab. distributes for free data equivalent to ¼ the Library of Congress every month </li></ul><ul><li>I am a supporter of open access (provided there is a business model) and editor in chief of PLoS Computational Biology </li></ul><ul><li>I am Co-founder of SciVee Inc. </li></ul><ul><li>I am becoming increasingly interested in scholarly communication </li></ul>I Readily Acknowledge Each Discipline is Different
  3. 3. My Objective… <ul><li>To Excite You to the Changes that Are Taking Place and Get You Thinking on How You Might Participate </li></ul>
  4. 4. What is Open Science <ul><li>Open science is the idea that scientific data and knowledge of all kinds should be openly shared as early as is practical in the discovery process. </li></ul><ul><li>Which implies: </li></ul><ul><ul><li>Free and unrestricted access to scientific output – ideas, data, software, the process itself, the knowledge generated … </li></ul></ul>
  5. 5. Open Science Can Accelerate the Scientific Process… For some people the change may be too slow to save their life
  6. 6. Josh Sommer – A Remarkable Young Man Co-founder & Executive Director the Chordoma Foundation http://sagecongress.org/Presentations/Sommer.pdf
  7. 7. Chordoma <ul><li>A rare form of brain cancer </li></ul><ul><li>No known drugs </li></ul><ul><li>Treatment – surgical resection followed by intense radiation therapy </li></ul>http://upload.wikimedia.org/wikipedia/commons/2/2b/Chordoma.JPG
  8. 8. http://sagecongress.org/Presentations/Sommer.pdf
  9. 9. http://sagecongress.org/Presentations/Sommer.pdf
  10. 10. http://sagecongress.org/Presentations/Sommer.pdf
  11. 11. Adapted: http://sagecongress.org/Presentations/Sommer.pdf Isaac If I have seen further it is only by standing on the shoulders of giants Isaac Newton From Josh’s point of view the climb up just takes too long > 15 years and > $850M to be more precise
  12. 12. http://sagecongress.org/Presentations/Sommer.pdf
  13. 13. http://sagecongress.org/Presentations/Sommer.pdf
  14. 14. http://fora.tv/2010/04/23/Sage_Commons_Josh_Sommer_Chordoma_Foundation
  15. 15. Other Reasons for Open Science
  16. 16. We Cannot Possibly Read a Fraction of the Papers We Should Why Open Science Renear & Palmer 2009 Science 325:828-832
  17. 17. Hence We Are Scanning More Reading Less Renear & Palmer 2009 Science 325:828-832 Why Open Science
  18. 18. We Need Tools That Can Automatically Scan the Literature and Make Sense of It
  19. 19. Automatic Knowledge Discovery for Those with No Time to Read Shared Function Immunology Literature Cardiac Disease Literature
  20. 20. Open Science Does Not Just Mean the Final Publication, But the Scientific Process Itself
  21. 21. The Scientific Process Research [Grants] Journal Article Conference Paper Poster Session Reviews Blogs Community Service/Data Curation
  22. 22. The Truth About the Scientific eLaboratory <ul><li>I generate way more negative that positive data, but where is it? </li></ul><ul><li>Content management is a mess </li></ul><ul><ul><li>Slides, posters….. </li></ul></ul><ul><ul><li>Data, lab notebooks …. </li></ul></ul><ul><ul><li>Collaborations, Journal clubs … </li></ul></ul><ul><li>Software is open but where is it? </li></ul><ul><li>Farewell is for the data too </li></ul>Computational Biology Resources Lack Persistence and Usability. PLoS Comp. Biol. 4(7): e1000136
  23. 23. We Need Better Tools to Manage the Scientific Enterprise
  24. 24. Many Great Tools Out There We Need Scientist Management Tools Taverna
  25. 25. Our Own Experiment in Capturing the Scientific Process to Make it Open <ul><li>Its hard and embarrassing </li></ul><ul><li>We have a working prototype using Wings </li></ul><ul><li>I can feel the potential productivity gains </li></ul><ul><li>Its been a lot of fun and will enable us to improve our processes regardless of the workflow system itself </li></ul>
  26. 26. Yes The Workflow is Real
  27. 27. Problems with Publishing Workflows <ul><li>Workflows are not linear </li></ul><ul><li>Workflow : paper is not 1:1 </li></ul><ul><li>Confidentiality </li></ul><ul><li>Peer review </li></ul><ul><li>Infrastructure </li></ul><ul><li>Community acceptance </li></ul><ul><li>Reward system </li></ul>
  28. 28. The Problem at this Time is There is Little Reward for Such Activities
  29. 29. The Not so Hidden Truth About Science <ul><li>Scientists place more emphasis on writing and less on reading </li></ul><ul><li>We are H factor obsessed, but interested in other metrics </li></ul><ul><li>We are driven by (in order): </li></ul><ul><ul><li>Grants </li></ul></ul><ul><ul><li>Papers </li></ul></ul><ul><ul><li>Teaching </li></ul></ul><ul><ul><li>Community service </li></ul></ul>
  30. 30. Are There Killer Apps Out There That Could be A Game Changer for Improving Science as Well as the Reward Process?
  31. 31. Data – Knowledge Integration Perhaps?
  32. 32. Publishing Limitations <ul><li>A paper is an artifact of a previous era </li></ul><ul><li>It is not the logical end product of eScience, hence: </li></ul><ul><ul><li>Work is omitted </li></ul></ul><ul><ul><li>Article vs supplement is a mess </li></ul></ul><ul><ul><li>Visualization may be limited </li></ul></ul><ul><ul><li>Interaction and enquiry are non-existent </li></ul></ul><ul><ul><li>Rich media can help, but are rarely used </li></ul></ul>
  33. 33. Funding Agencies Are Imposing Data Sharing Policies <ul><li>From the NSF: </li></ul><ul><li>Investigators are expected to share with other researchers, at no more than incremental cost and within a reasonable time, the primary data, samples, physical collections and other supporting materials created or gathered in the course of work under NSF grants. Grantees are expected to encourage and facilitate such sharing. See Award & Administration Guide (AAG) Chapter VI.D.4. </li></ul>
  34. 34. Here is What I Want <ul><li>User clicks on thumbnail </li></ul><ul><li>Metadata and a webservices call provide a renderable image that can be annotated </li></ul><ul><li>Selecting a features provides a database/literature mashup </li></ul><ul><li>That leads to new papers </li></ul>1. A link brings up figures from the paper 0. Full text of PLoS papers stored in a database 2. Clicking the paper figure retrieves data from the PDB which is analyzed 3. A composite view of journal and database content results 4. The composite view has links to pertinent blocks of literature text and back to the PDB 1. 2. 3. 4. The Knowledge and Data Cycle PLoS Comp. Biol. 2005 1(3) e34
  35. 35. Interactive PDFs etc..
  36. 36. Article of the Future
  37. 37. The Embracing of Rich Media Perhaps?
  38. 38. Yes YouTube Can Increase the Rate of Discovery Unleash the full power of the Internet
  39. 39. Pubcast – Video Integrated with the Full Text of the Paper
  40. 40. Postercasts
  41. 41. The Semantic Web Perhaps?
  42. 42. Unimaginable Connections Made Automatically Through RDF Descriptions http://richard.cyganiak.de/2007/10/lod/lod-datasets_2010-09-22_colored.html
  43. 43. Living Documents
  44. 44. The Journal Has A Copy of Record that Provides a Reward
  45. 45. The App Model
  46. 47. General References <ul><li>What Do I Want from the Publisher of the Future http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000787 </li></ul><ul><li>Fourth Paradigm: Data Intensive Scientific Discovery http://research.microsoft.com/enus/ collaboration/fourthparadigm/ </li></ul>
  47. 48. What Are Your Ideas To Accelerate the Rate of Scientific Discovery?
  48. 49. References to Exemplars <ul><li>Semantic Biochemical Journal - 2010: Using Utopia </li></ul><ul><li>Article of the Future, Cell, 2009:
 </li></ul><ul><li>Prospect, Royal Society of Chemistry, 2009:
 </li></ul><ul><li>Adventures in Semantic Publishing, Oxford U, 2009: </li></ul><ul><li>The Structured Digital Abstract, Seringhaus/Gerstein, 2008
 </li></ul><ul><li>CWA Nanopublications – 2010
 
 </li></ul>
  49. 50. Questions? [email_address]

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