Sciblog2008 Etchevers
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Transcript of Sciblog2008 Etchevers
Laboratory notebooks online: perspective from the bench
Heather Etchevers
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
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
Typical biologists’ entries
Thanks to C. Juste (chargée de recherche, INRA) for her permission to reproduce
Photographs
JustificationDescription of protocol
SketchesTabularresults
Graphicresults
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
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
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
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
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/
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