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Tuesday, September 26, 2006

Open Notebook Science

Thanks to Beth Ritter-Guth's efforts to clarify the definition of terms relating to Open Source Science, a good discussion has evolved on the Blue Obelisk mailing list. Peter Murray-Rust has made the point that this term may be confused with Open Source Software. However, as Peter notes in a follow-up post, Jamais Cascio from WorldChanging has used this definition of Open Source Science, which is fairly consistent with our use of it in UsefulChem:
...research already in progress is opened up to allow labs anywhere in the world to contribute experiments. The deeply networked nature of modern laboratories, and the brief down-time that all labs have between projects, make this concept quite feasible. Moreover, such distributed-collaborative research spreads new ideas and discoveries even faster, ultimately accelerating the scientific process.

In Open Source Software, the code is made available to anyone to modify and repurpose. What we have been trying to do with UsefulChem is to provide the analogous entity for chemical research, which is raw experimental data along with the researcher's interpretation in a format that anyone can easily re-analyze, re-interpret and re-purpose. A good example of re-purposing is using some results and observations from a failed experiment in a way that was never intended by the original researcher. This just doesn't happen regularly in science because failed experiments are almost never included in publications.

Unfortunately, in addition to the confusion with Open Source Software, others are using the term Open Source Science to mean discussions about pre-prints of regular journal articles.

To clear up confusion, I will use the term Open Notebook Science, which has not yet suffered meme mutation. By this I mean that there is a URL to a laboratory notebook (like this) that is freely available and indexed on common search engines. It does not necessarily have to look like a paper notebook but it is essential that all of the information available to the researchers to make their conclusions is equally available to the rest of the world. Basically, no insider information.

9 Comments:

  • Jean Claude
    This is really useful - I think "Open Notebook Science" captures both the description and the spirit.

    I am also exceited by the recipes you list in the example. I have spent the w/e trying to work out how to parse such text into CMLReact and feeling quite confident. It is possible that we can converge on a CMLReact representation that suits both your requirements and yours. Then we have a completely machine-readable book. So that if you feel what is on your site is the complete record I think we have real possibility. Put it in Bioclipse as a plugin and ...

    More on this in a few days.

    By Blogger Peter Murray-Rust, at 2:29 PM  

  • This is a great new term, Jean-Claude. I believe, as Peter does, that this new term "captures both the description and the spirit" of your work.

    This is precisely what I hoped would happen when I took on this project; I hoped to facilitate a useful discussion among "open chemists" about the terms used to discuss the work they share.

    By Blogger Beth Ritter-Guth, at 4:21 PM  

  • Hey this is great! So good to see scientists taking initiative to make their knowledge accessible (isn't that what science is all about?).
    The next step is to make these open notebooks as user friendly as possible. I mean this from the perspective of both the person entering the information, and the one using it.
    Hopefully the Wiki format is comfortable markup to use, was it difficult for everyone in the lab to learn? The output of the notebooks must be similarly usable, what possibilities might exist for creating live summaries and tabular data?
    Hope to see more great innovation in this area!

    By Blogger Michael, at 4:39 AM  

  • Michael

    Where applicable we are creating tables where similar experiments can be compared - see here for example

    There is also a table of contents of the experiments that gives the notebook a familiar interface to a regular paper notebook.

    By Blogger Jean-Claude Bradley, at 4:52 PM  

  • I thin this is quite a similiar idea what we want to follow with scilife.net, there researchers should also be encouraged to post protocols they would like to share. It would be interesting to compare the outcomes on such a site with the ones from open notebook.

    By Anonymous Kai, at 4:12 PM  

  • SciLife looks interesting but your link does not work it should be http://www.scilife.net

    By Blogger Jean-Claude Bradley, at 10:29 AM  

  • I also like the "Open Notebook Science" term. I think the biggest issues with it are: 1) to allow sufficient flexibility yet to have enough structure so that the notes are clear to others and are easy to manage; 2) allow to share things in a limited and easily controlled way; 3) to have open formats and a community of critical mass. At http://ipadeln.com we are trying to address all these issues. Would be interesting to get your feedback.

    By Anonymous Alexander Polonsky, at 11:37 AM  

  • Alex - good luck with the ipad project - I'll keep an eye out to see who uses it.

    By Blogger Jean-Claude Bradley, at 12:40 PM  

  • This is useful plateform to share your work and thought.
    Praveen

    By Blogger Dr Praveen Kumar Shrivastava, at 10:14 AM  

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