Jean-Claude Bradley and coworkers has pioneered the concept of Open Science in chemistry – and it goes beyond that. On UsefulChem he writes:
The fact that Alicia’s masters thesis “Synthesis of Diketopiperazines, Possible Malaria Enoyl Reducatase Inhibitors Using Open Source Science” is being written on a wiki was noted by Pharyngula, A Blog around the Clock and Pimm – Partial Immortalization.
I am particularly happy that Attila from Pimm has obtained permission from his supervisor to write at least part of his thesis on his blog. Outside of the sciences, I recall Mark Wagner doing something similar for his thesis on educational gaming. Also see Laura Blankenship‘s thesis on blogging in the classroom.
Yes – there has been a lot of interest in this innovative approach and I’m delighted to echo it. Since they wish this to be an open process here are my comments directly for Alicia to use if she wishes:
- I didn’t see any license on the thesis. I’m hoping it is Creative Commons sharealike (like J-C’s blog) but it’s not explicit. If that is confirmed I can highlight the thesis at Uppsala next week
- Do all the molecules have machine-readable connection tables? I noticed some that link through to SMILES – but do they all? And it would be useful to have InChIs so we could search the thesis.
- Much of the data is rendered as bitmaps of rather low quality. Could we have the reaction schemes and particularly the spectra in greater clarity. (Obviously I’d prefer CML or SVG or JCAMP… )
My immediate technical goal would be the creation of a datument (everything in XML) for the thesis – I’m not going to do all that myself. But I would be keen to see the reaction sequences in animated SVG…
The same goes, of course, for anyone else writing Open theses.
Peter – answers to your questions:
1) The license is at the bottom of every page: Contributions to http://usefulchem.wikispaces.com are licensed under a Creative Commons Attribution Share-Alike 2.5 License. One of the reasons I use Wikispaces is that this is automatic for all content on the free accounts.
2) Alicia isn’t quite done with cleaning up the wiki – at the bottom of every page will be the list of InChI’s under a Tag section, similar to how we do for all experiment pages.
3) Almost all of the spectral data (except for early experiments) are available in JCAMP format via JSpecView in the originial experiment pages. The wiki pages of the thesis represent what gets converted into a pdf -yes, I can hear you cringing 🙂 – as required for deposition by our university and thus use static images. In order to gain interactive access to the data you must click on the links to the lab notebook pages. If that wasn’t clear then the whole point of what we are doing was missed – how can we make that clearer? Feel free to comment in italics and bold directly in the thesis to make your points. If you need an account to UsefulChem just request it at the top left of the wiki.
Thanks for the feedback!
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Sorry about missing this. It went into SPAM and I now get ca. 300 a day on the blog
3) Almost all of the spectral data (except for early experiments) are available in JCAMP format via JSpecView in the originial experiment pages. The wiki pages of the thesis represent what gets converted into a pdf -yes, I can hear you cringing 🙂 – as required for deposition by our university and thus use static images. In order to gain interactive access to the data you must click on the links to the lab notebook pages. If that wasn’t clear then the whole point of what we are doing was missed – how can we make that clearer? Feel free to comment in italics and bold directly in the thesis to make your points. If you need an account to UsefulChem just request it at the top left of the wiki.
PMR: I found the molecules – but read fairly quickly and probably missed the spectra. I’ll look more carefully.
I don’t mind a PDF as long as the raw data are also available. I shall now have some time to think and see how XML and RDF might be involved. More later.
From a mining standpoint of view it would be useful, if all data could be downloaded in one file. Could this be added to the Blue obelisk data repository
http://sourceforge.net/projects/bodr
And maybe the repository should provide different directories, like
structures/small_molecules
structures/proteins
spectras
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I completely agree. Wikis and HTML are not the best ways of managing data-rich projects – it needs XML and/or RDF to manage the structure. On the other hand XML is harder for communal projects than HTML/Wikis. Is there a way of dumping the particular Wiki as XML?
Is there any way the data should be kept in a structured form that is downloadable.
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