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

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

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

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 Justification Description of protocol Sketches Tabular results Graphic results

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

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

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

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

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/

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 ! © Peter DaSilva, The New York Times

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 !

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

"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