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Sciblog2008 Etchevers


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Discussion for Science Blogging 2008 (London) of uses and requirements for online laboratory notebooks from the point of view of an academic scientist at the bench.

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Sciblog2008 Etchevers

  1. 1. Laboratory notebooks online: perspective from the bench Heather Etchevers
  2. 2. What should go in a notebook <ul><li>Motivation for experiments </li></ul><ul><li>Diary – play-by-play </li></ul><ul><li>Results </li></ul><ul><ul><li>Figures </li></ul></ul><ul><ul><ul><li>Sketches, graphs, photographs, printouts </li></ul></ul></ul><ul><ul><ul><li>Tables, perhaps plots therefrom </li></ul></ul></ul><ul><li>Transmission of knowledge to later personnel </li></ul><ul><ul><li>Analysis </li></ul></ul><ul><ul><li>Periodic summary </li></ul></ul>Derived from
  3. 3. Most desired in lab notebooks <ul><li>Outsource your memory </li></ul><ul><ul><li>Preparation before experiments </li></ul></ul><ul><ul><li>Repository of results </li></ul></ul><ul><li>Archive for proof of intellectual process </li></ul><ul><ul><li>Internal (group, collaboration) </li></ul></ul><ul><ul><li>External (audits, patent contention) </li></ul></ul><ul><li>Après moi, le déluge </li></ul>
  4. 4. Typical biologists’ entries Thanks to C. Juste (chargée de recherche, INRA) for her permission to reproduce Photographs Justification Description of protocol Sketches Tabular results Graphic results
  5. 5. Multiple notebooks needed <ul><li>Lab meetings and conference notes </li></ul><ul><li>Multiple research projects </li></ul><ul><ul><li>Field notes </li></ul></ul><ul><ul><li>Correspondence with collaborators </li></ul></ul><ul><li>Large machines </li></ul><ul><li>Chronological order vs. accuracy and narrative </li></ul><ul><ul><li>Periodic summing up </li></ul></ul><ul><ul><ul><li>Hard results </li></ul></ul></ul><ul><ul><ul><li>Ideas and reflections </li></ul></ul></ul><ul><li>Protocols = cookbook – scribbles in margins </li></ul>
  6. 6. Current offerings for academics – non-exhaustive <ul><li>OpenWetWare </li></ul><ul><ul><li> </li></ul></ul><ul><li>Evernote http:// / </li></ul><ul><li>e-CAT </li></ul><ul><li>Addgene http:// / </li></ul><ul><li>Blogs cf. </li></ul><ul><ul><li>Practice writing, formulating hypotheses </li></ul></ul><ul><ul><li>Preview to lab meetings/journal clubs </li></ul></ul>
  7. 7. Advantages <ul><li>Sharing with boss/collaborators </li></ul><ul><li>Searching among your own records </li></ul><ul><li>Linking to related resources </li></ul><ul><ul><li>Protocols </li></ul></ul><ul><ul><li>Security use documents </li></ul></ul><ul><ul><li>Vector maps </li></ul></ul><ul><ul><li>PubMed entries </li></ul></ul><ul><ul><li>Tagged data elsewhere online </li></ul></ul><ul><li>Distant access </li></ul>
  8. 8. Limitations <ul><li>Organizational </li></ul><ul><li>Physical </li></ul><ul><ul><li>Tears, blood, sweat, coffee, radioactivity. “ Coomassie blue, methyl red, ethidium bromide pink, bacterial broth brown.&quot; (J. Rohn, Mind the Gap 11/4/07) </li></ul></ul><ul><ul><li>Computer memory, security, electrical vagaries… </li></ul></ul><ul><li>Legal </li></ul><ul><ul><li>Proprietary resources and non-disclosure agreements </li></ul></ul><ul><ul><li>Potential patents </li></ul></ul>
  9. 9. Options for researchers today <ul><li>Write up experiments completely before </li></ul><ul><ul><li>Things rarely go exactly as planned. </li></ul></ul><ul><li>Try to remember everything and type it up afterwards </li></ul><ul><ul><li>Errors in memory </li></ul></ul><ul><li>Write things in pen and paper, then transpose </li></ul><ul><ul><li>Errors in transposition </li></ul></ul><ul><ul><li>Double work </li></ul></ul><ul><li>B Haugen, </li></ul>
  10. 10. Other possibilities <ul><li>Optical character recognition for scanning notes </li></ul><ul><li>Pen-top computers such as Livescribe . </li></ul><ul><ul><li>date- and keyword-searchable archive </li></ul></ul><ul><ul><li>Automatic blogging structure </li></ul></ul><ul><li>One-button uploading </li></ul><ul><li>Make it easy ! </li></ul>© Peter DaSilva, The New York Times
  11. 11. How open? <ul><li>&quot;In a partially open system there is a risk for those who choose to be open. (…) Reward (…) is spread over the entire society. The sub-field I was in was highly competitive. The (personal) risk would not be worth the rewards. … Why should a grad student risk being scooped for the greater good?&quot; </li></ul><ul><li>- ponderingfool 8 Dec 2007 on The World’s Fair </li></ul>