Tuesday, 13 July 2010

Electronic laboratory notebooks

I was recently in conversation with some geneticists about this and it's an interesting problem.

Lab notebooks are much more than a statement of what was done when, but in fact can be a statement of record as part of commercially focused research, especially in the biomedical sciences.

Equally human factors come into play and it is unrealistic to expect researchers to enter data at the end of the day and associate metadata with it, which is why the old hardback notebook is still with us. Paper is extremely versatile as recording medium, and unlike hi tech devices, can usually survive close contact with reagents.

One could imagine a thought design for an electronic solution however:
  1. Provide a custom application running on a device such as an ipad - it's on, it's on the bench, data can be entered as the day goes on. On startup each day the application asks the researcher to confirm name, date, and project code. The device needs to be simple to use, versatile, relatively stateless and disposable. Labs are messy places and things go wrong. A web based application is probably better than a locally running application. A netbook could be equally suitable.
  2. Researcher enters notes sequentially throughout the day. The notes are stored in a buffer on the server and retrievable in the event of a crash, network, or end node device failure.
  3. At end of day, researcher hits 'commit'. Posts are nicely formatted and posted to a Wordpress blog. Grant code and researcher id are encoded in post header. Blog is a private blog only viewable by members of the research group for review etc
  4. The RSS feed from the blog is monitored by a second application. This takes the blog post, generates appropriate metadata based on lookup of researcher and grant id's, generates a pdf and ingests it into a dark repository, perhaps a private instance of dspace, as a statement of record.
Now this isn't just for genetics and other bench sciences - one could imaging such a sloution being usable for anthropological field notes, in the behavioural sciences, and even as a research diary in paleography, in fact any discipline where there is a degree of repeated work and observation.

Anyway, after the discussion, I was sure that there would be a solution out there. And a number of people have tried this, mostly using wiki software but as yet there seems to be no killer solution.

However it does appear to be a live problem. I've put together a page of links on this topic which I'll maintain as my understanding of the requirements develops. Comments and suggestions for additional links are welcome.

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