sciblog2008 etchevers
DESCRIPTION
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.TRANSCRIPT
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Laboratory notebooks online: perspective from the bench
Heather Etchevers
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What should go in a notebook
Motivation for experiments Diary – play-by-play Results
– Figures Sketches, graphs, photographs, printouts Tables, perhaps plots therefrom
Transmission of knowledge to later personnel– Analysis– Periodic summary
Derived from http://www.physics.hmc.edu/howto/labnotebook.html
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Most desired in lab notebooks
Outsource your memory– Preparation before experiments – Repository of results
Archive for proof of intellectual process– Internal (group, collaboration)– External (audits, patent contention)
Après moi, le déluge
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Typical biologists’ entries
Thanks to C. Juste (chargée de recherche, INRA) for her permission to reproduce
Photographs
JustificationDescription of protocol
SketchesTabularresults
Graphicresults
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Multiple notebooks needed
Lab meetings and conference notes Multiple research projects
– Field notes– Correspondence with collaborators
Large machines Chronological order vs. accuracy and narrative
– Periodic summing up Hard results Ideas and reflections
Protocols = cookbook – scribbles in margins
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Current offerings for academics – non-exhaustive
OpenWetWare– http://www.openwetware.org/wiki/Etchevers:Main
Evernote http://evernote.com/
e-CAT Addgene http://www.addgenelabs.org/
Blogs cf. http://rrresearch.blogspot.com/
– Practice writing, formulating hypotheses– Preview to lab meetings/journal clubs
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Advantages
Sharing with boss/collaborators Searching among your own records Linking to related resources
– Protocols– Security use documents– Vector maps– PubMed entries– Tagged data elsewhere online
Distant access
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Limitations
Organizational Physical
– Tears, blood, sweat, coffee, radioactivity. “Coomassie blue, methyl red, ethidium bromide pink, bacterial broth brown." (J. Rohn, Mind the Gap 11/4/07)
– Computer memory, security, electrical vagaries…
Legal– Proprietary resources and non-disclosure agreements– Potential patents
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Options for researchers today
Write up experiments completely before– Things rarely go exactly as planned.
Try to remember everything and type it up afterwards
– Errors in memory
Write things in pen and paper, then transpose– Errors in transposition– Double work
B Haugen, http://connectedbases.com/2007/07/19/
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Other possibilities
Optical character recognition for scanning notes
Pen-top computers such as Livescribe. – date- and keyword-searchable archive – Automatic blogging structure
One-button uploading Make it easy!
© P
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How open?
"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?"
- ponderingfool 8 Dec 2007 on The World’s Fair