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Scifoo Lives On session: Open notebook science case studies

25 September 2007 7 Comments

Yesterday afternoon the Open Notebook Science case studies session was held as part of the Scifoo lives on sessions at Nature Island, Second Life. Jean-Claude Bradley organised, moderated and spoke first followed by me and Jeremiah Faith. We all spoke about experiences and implementation of different approaches to open notebook science.

Jean-Claude has put the transcript up here.

There was an active discussion about the need for more fun in science and the way in which science has become secretive has taken a lot of the fun out of it. CW Underwood talked about being sick of the ‘Secret Squirrel’ nature of science. One thing that was very encouraging was that Jeremiah said that in his search for his next post he had raised the issue as to whether the possible PI objected to him keeping his notebook open. So far he had had no objections.

Other issues that came up:

Open notebook science takes work and discipline.

It does involve some effort to get set up and to keep systems running as well as to maintain the observation that makes sure that things are running properly. CW pointed out that his PI would regard this as a waste of time. I can see this perspective being quite a strong one and a slow one to counter. Arguably the benefits of putting the effort in are not yet tangible enough to be convincing to people who are happy with the way their science works as it is.

What is the best system for holding the notebook?

Three different systems were presented. The UsefulChem Wiki by Jean-Claude using publically available hosted services. Our Blog based notebook which is a custom built and somewhat closed system. And Jeremiah uses Tex to generate a PDF of the whole thing. Jeremiah’s presentation included the comment that he had shown several people both a Wiki and the Tex based system and they had all preferred the Tex based one. This is the opposite of my experience where people seem to prefer whatever is closest to Word. This may be different communities or maybe just different people we have had contact with.

My feeling is that the three groups have evolved different systems because of three main things. Firstly a different initial aim, my initial aim for instance was not really an open notebook but an effective means of capturing data and procedures. Secondly differences in the procedures being carried out and the culture we work within. I am still slowly working my way through putting up Exp098 from UsefulChem in our blog system and this is certainly showing up some differences but I’m not sure I know what they mean yet.

Finally I think we have a different view of what the lab book is and what the ‘ideal’ lab book would look like. Jeremiah’s point was that he, and others, wanted it to ‘look like a lab book’, which is fair enough. I think my group is somewhere in the middle and Jean-Claude has pushed the idea of what a lab book is one step further. The finished product is a summary of the experiment – not precisely a point by point record of everything that happened along the way, that is all in the history tab – but the visual product is a clear description of the experiment that is immediately accessible to an outsider as to how to repeat the experiment and what the data and conclusions were. The point is,within the wiki framework, there is no need to worry about editing the page because the history is all still there. This means that it can be taken from the record as it goes – which is still kept – right through to ‘finished’ in a form that can go straight into a thesis or paper. I’m still not entirely comfortable with this, but I’m not entirely sure that this is particularly logical.

In any case in the end I think it will depend on what you want and why you want to go down the ONS route. There’s still a lot of work to be done.

Limits to openness

There was a discussion on where the boundaries should lie as to what can be open or not. I will handle this in another post because I think this is something I want to think about quite hard.

Postscript

On my way into work on Thursday last week I bumped into one of my RAL colleagues who, among other things, works on our communications and public relations. He thought that the ‘talk’ in SL made a nice little story and went to our central STFC comms people to see whether he might place it somewhere (website, newsletter, etc). Apparently the answer came back that they wouldn’t issue a press release (which would have been rather over the top in any case) because we didn’t have an institutional policy on Open Access.

Postscript 2

Jean-Claude has also reviewed the session at the UsefulChem Blog.


  • Cameron,
    I really enjoyed your presentation and your analysis of the session – the transcript is available here.

  • Cameron,
    I really enjoyed your presentation and your analysis of the session – the transcript is available here.

  • Nice summary of the session.

    I agree with your point that everyone wants something that is most similar to Word. I think that the Latex solution is more similar to Word, because what you get is a document, rather than an interconnected Wiki-thing. Though the process to get to the document in latex is pretty unfriendly to non-programmer folks. As you mentioned it is very community based. Since I’m a bioinformatics student, most of the people around me can program, so that writing their wet-lab experiments up in latex doesn’t require learning anything particularly complicated to them. I do think that wikis are quite nice in the case where you have multiple folks editing the same document together though. I’m just not sure you want your entire lab editing the same thing. Maybe the entire lab should have a wiki or a blog for press-release and big-idea/direction type stuff, but then individuals have their own individual word document, latex document or blog.

    The problem with using the wiki history is that it can be pretty challenging to recreate how you got from A to B by digging through the history. In a publication, we throw away the process of how we got from A to B, and we tell the story of how we should’ve gotten from A to B if we had known how to do it already. I think we should try and leave the sloppy, windy real-process of scientific discovery unadulterated in our lab notebooks.

  • Nice summary of the session.

    I agree with your point that everyone wants something that is most similar to Word. I think that the Latex solution is more similar to Word, because what you get is a document, rather than an interconnected Wiki-thing. Though the process to get to the document in latex is pretty unfriendly to non-programmer folks. As you mentioned it is very community based. Since I’m a bioinformatics student, most of the people around me can program, so that writing their wet-lab experiments up in latex doesn’t require learning anything particularly complicated to them. I do think that wikis are quite nice in the case where you have multiple folks editing the same document together though. I’m just not sure you want your entire lab editing the same thing. Maybe the entire lab should have a wiki or a blog for press-release and big-idea/direction type stuff, but then individuals have their own individual word document, latex document or blog.

    The problem with using the wiki history is that it can be pretty challenging to recreate how you got from A to B by digging through the history. In a publication, we throw away the process of how we got from A to B, and we tell the story of how we should’ve gotten from A to B if we had known how to do it already. I think we should try and leave the sloppy, windy real-process of scientific discovery unadulterated in our lab notebooks.

  • I agree, Jeremiah, with the idea of some sort of ‘push publishing’ from the notebook which records the raw events as they happen to a more organised and coherent description of the experiments that can be more easily replicated by others.

    We are trying to think about how this might be done because it links in with the whole issue of how we present the information. In principle if our blog format is more ‘machine readable’ then we should be able to process it automatically to produce a nice easy to read version. We haven’t got that far yet though. I think the first step will be to try and extract the relevant data from the blog for a specific paper so it can be submitted as supplementary information.

  • I agree, Jeremiah, with the idea of some sort of ‘push publishing’ from the notebook which records the raw events as they happen to a more organised and coherent description of the experiments that can be more easily replicated by others.

    We are trying to think about how this might be done because it links in with the whole issue of how we present the information. In principle if our blog format is more ‘machine readable’ then we should be able to process it automatically to produce a nice easy to read version. We haven’t got that far yet though. I think the first step will be to try and extract the relevant data from the blog for a specific paper so it can be submitted as supplementary information.

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