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!

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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