electronic lab notebooks

[mike.t]

How do you document your bioinformatics research? When I worked at the lab bench I was meticulous in my record keeping in standard paper lab notebooks. When I started to transition to the 'bit lab' I realized that I was doing a lot of work and none of it was being written down. Then I started a system of taking notes in chronological order in an html file and storing important data files in corresponding folders. Nowadays my group is using RedMine, and we mostly use the wiki feature for keeping records, but the wiki is becoming a horrible mess. I need to develop some standards of what we need to record and how to record it but before I do that I just want to see what other labs are doing. (hopefully not nothing)

[dariober]

How do you document your bioinformatics research? When I worked at the lab bench I was meticulous in my record keeping in standard paper lab notebooks. When I started to transition to the 'bit lab' I realized that I was doing a lot of work and none of it was being written down. Then I started a system of taking notes in chronological order in an html file and storing important data files in corresponding folders. Nowadays my group is using RedMine, and we mostly use the wiki feature for keeping records, but the wiki is becoming a horrible mess. I need to develop some standards of what we need to record and how to record it but before I do that I just want to see what other labs are doing. (hopefully not nothing)

Hi- That's an interesting issue that I think is often neglected, so to prompt discussion here's my 2p... I provide bioinformatics support to our group so I handle 2-4 different projects at a time. My setup to keep track of what I do is:

- Redmine: Particularly the "projects" features and the wiki pages. This is to document what and why I do certain analyses, just like a labbook. My lab mates have access to it but I'm essentially the only user.

- svn: To maintain code and programs I can possibly re-use in the future (although an R script to produce a particular figure or a one-line bash script will probably go in a wiki page rather than here.)

- Postgresql + Python/Django: To archive samples, libraries, metadata etc. Although it has to be maintained, it is much neater and robust than using Excel spreadsheets or scattered notes on the wiki

So far I'm quite happy with this setup but I'm keen on hearing other people's opinion...

Best
Dario

[JamieHeather]

I use http://www.sparklix.com/ which covers my needs well enough (although after a year of using it I'd quite like a better way to check chronology of entries).

I probably have a 65:35 wet lab:dry lab split, so I'm not sure if for more intense usage it'd stay useful.

[shandley]

See: http://www.carlboettiger.info/2012/0...-workflow.html for an interesting use of knitr and git for maintaining a lab notebook. I would like to follow a model like this, but just haven't found the time to set it up. This might be my new weekend project!

[dsenalik]

a system of taking notes in chronological order in an html file and storing important data files in corresponding folders.

I am doing just that, it works okay, but I do feel there should be a better way.

There were some good suggestions on this earlier thread:

http://seqanswers.com/forums/showthread.php?t=19331