9 thoughts on “Experiments and structured data

  1. I thought you were just pointing to Cameron’s posts :).

    But seriously, this one and Cameron’s posts are very very good. Can’t wait to spend some time taking them in.

    In my day job we face these challenges all the time from data being generating by the gigabytes of all types. By and large things are structured and usually process driven, but their is a lot of variation, leading to all kinds of challenges in software design.

  2. A bit of a sidenote, but the New Yorker recently had a fascinating artilce titled The Checklist which describes how hospitals have slowly structured their thousands of steps for the hundreds of routine procedures that must occur for even the simplest medical condition into pragmatic checklists of tasks. By codifying this seemingly trivial activity, enormous operational improvements were obtained. Draw lessons about structured steps in experiments if you will, but be glad that someone will not be dying if you make a mistake.

  3. Pingback: Unilever Centre for Molecular Informatics, Cambridge - petermr’s blog » Blog Archive » Structured Experiments and OR08

  4. I don’t see the point of eletronic lab notebooks either and I am a computer scientist. My bench is miles away from my computer and while pipetting I need to look at my notes. It’s easier to work with a pipette in one hand and a pen in the other hand than with a whole big keyboard / screen around my bench, where there really isn’t enough space for all of this anyways.

  5. @max – I thought you were a computer scientist; what are you doing with a pipette? ;)

    I take your point – practically, it’s much easier to record at the bench in a paper notebook. Have a look at Cameron’s blog for some ideas about how in the future, a lot of this recording could be done by the machines in the lab.

    A lot of this discussion is based on open notebook science, or at least shared notebook science. If you’re interested in sharing raw experimental data: with the group, colleagues or the outside world, electronic is the only option.

  6. Pingback: A data model for life-science experiments; FuGE « peanutbutter

  7. Pingback: Science in the open » Data models for capturing and describing experiments - the discussion continues

  8. True, but it’s much easier to define a model after you have all the data/have finished the experiment (which is the point at which it’s getting passed to the bioinformatician, or you’re repeating the experiment several times). To define all the fields beforehand is really difficult.

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