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When is open notebook science not?

3 September 2007 12 Comments

Well when it’s not open obviously.

There are many ways to provide all the information imagineable while still keeping things hidden. Or at least difficult to figure out or to find. The slogan ‘No insider information’ is useful because it provides a good benchmark to work towards. It is perhaps an ideal to attain rather than a practical target but thinking about what we know but is not clear from the blog notebook has a number of useful results. Clearly it helps us to see how open we are being but also it is helpful in identifying what it is that the notebook is not successfully capturing.

I have put up a series of posts recently in the ‘Sortase Cloning‘ blog notebook. The experiments I did on 29th August worked reasonably well. However this is not clear from the blog. Indeed I suspect our hypothetical ‘outsider’ would have a hard time figuring out what the point of the experiment is. Certainly the what is reasonably obvious, although it may be hidden in the detail, but the why is not. So the question is how to capture this effectively. We need a way of noting that an experiment works and that the results are interesting. In this case we have used Sortase to do two things that I don’t believe have yet been reported, fluorescently label a protein, and ligate a protein to a piece of DNA. This therefore represents the first report of this type of ligation using Sortase.

Perhaps more importantly, how do we then provide the keys that let interested people find the notebook? UsefulChem does this by providing InChi and smiles codes that identify specific molecules. Searching on the code by Google will usually bring UsefulChem up in the top few searches if the compound has been used. Searching on ‘Sortase’ the enzyme we are doing our conjugation with brings up our blog at number 14 or so. So not bad but not near the top and on the second page not the first. For other proteins with a wider community actively interested the blog would probably be much further down. Good tags and visibility on appropriate search engines (whatever they may turn out to be) is fairly critical to making this work.


  • You’ve got some good points here but setting a broken link to your keywords (Sortase Cloning link) won’t make the SE bots help you out much more. ;-)

    I agree that there has to be a proper exposition of the info contained in the notebook. The information contained within should be structured and ready to be followed by such “outsiders” at any given point. There should also be small background notes as to what and why the protocol or research results exist for.

  • You’ve got some good points here but setting a broken link to your keywords (Sortase Cloning link) won’t make the SE bots help you out much more. ;-)

    I agree that there has to be a proper exposition of the info contained in the notebook. The information contained within should be structured and ready to be followed by such “outsiders” at any given point. There should also be small background notes as to what and why the protocol or research results exist for.

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  • Ricardo, thanks for that. Should be working now. I think an interesting question is whether it is better to have the exposition within the notebook or whether it is better to have it somehow separate. UsefulChem uses a separate blog and notebook which has benefits but it also creates a separation. On the flip side if there are notes within the notebook there is still a risk of them getting lost. One thing we need to work on is how to provide different types of views of the blog for people with different needs (users, supervisor, outsiders)

  • Ricardo, thanks for that. Should be working now. I think an interesting question is whether it is better to have the exposition within the notebook or whether it is better to have it somehow separate. UsefulChem uses a separate blog and notebook which has benefits but it also creates a separation. On the flip side if there are notes within the notebook there is still a risk of them getting lost. One thing we need to work on is how to provide different types of views of the blog for people with different needs (users, supervisor, outsiders)

  • Yes, it is difficult for an outsider who falls onto one of your blog pages to get the context. As you mention we try to do that in UsefulChem with higher level posts that speak to progress of the larger project while linking to experiment pages in the wiki. We also have an “objective” section in each experiment page that should link to these higher level posts. (This is the case in many experiments but we need to do a better job overall to get this part done in a timely fashion).

    Would it be possible to do something like that in your blog? You can use me as a tester to see if I can figure out what you are doing in any given post based on the information and links you provide.

    It will be really interesting to see how your system evolves to address these requirements.

  • Yes, it is difficult for an outsider who falls onto one of your blog pages to get the context. As you mention we try to do that in UsefulChem with higher level posts that speak to progress of the larger project while linking to experiment pages in the wiki. We also have an “objective” section in each experiment page that should link to these higher level posts. (This is the case in many experiments but we need to do a better job overall to get this part done in a timely fashion).

    Would it be possible to do something like that in your blog? You can use me as a tester to see if I can figure out what you are doing in any given post based on the information and links you provide.

    It will be really interesting to see how your system evolves to address these requirements.

  • I think that a mix of good category usage and also somehow setting up an “intro” text for each category could get this done.

    You click on a certain category, you are presented with an intro text and then the post(s) related.

  • I think that a mix of good category usage and also somehow setting up an “intro” text for each category could get this done.

    You click on a certain category, you are presented with an intro text and then the post(s) related.

  • One of the quite good features we have is at the bottom of each post you get a list of ‘what links here’ (from within the blog). If an intro or summary page has a sensible title then that would provide a reasonably obvious route to the exposition. Our aim is to also ultimately provide user configurable ‘views’ as well as to try and understand what sort of views are appropriate for which reader.

    These would be based on the ‘sections’. So for instance the default view you get on entering the blog (in the ‘expected’ way) doesn’t show any product posts as these complicate the view quite a lot.

    Another effective way to organise looking at the blog is through graphical interfaces. We have a ‘timeline view’ (e.g. http://chemtools.chem.soton.ac.uk/projects/timeline/blogs.php?id=13) which can provide a much more natural view of what is going on. We would like to expand this to a ‘network’ view but this is proving a little more challenging at the moment.

  • One of the quite good features we have is at the bottom of each post you get a list of ‘what links here’ (from within the blog). If an intro or summary page has a sensible title then that would provide a reasonably obvious route to the exposition. Our aim is to also ultimately provide user configurable ‘views’ as well as to try and understand what sort of views are appropriate for which reader.

    These would be based on the ‘sections’. So for instance the default view you get on entering the blog (in the ‘expected’ way) doesn’t show any product posts as these complicate the view quite a lot.

    Another effective way to organise looking at the blog is through graphical interfaces. We have a ‘timeline view’ (e.g. http://chemtools.chem.soton.ac.uk/projects/timeline/blogs.php?id=13) which can provide a much more natural view of what is going on. We would like to expand this to a ‘network’ view but this is proving a little more challenging at the moment.

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