Posted by: woodforthetrees | February 22, 2010

A tale of two wikis

The NMR spectroscopy community is near to the tipping point for Web 2.0. Image via wikimedia.

A common lament among bloggers and other enthusiastic adopters of Web 2.0 technology is the lack of mainstream uptake of these tools by active scientists. A recent report from University of California Berkeley confirmed this reluctance to embrace new forms of sharing information.

Yet two wikis focused on NMR spectroscopy between them have 5% of the magnetic resonance community as registered users – and probably many more are casual viewers. It is my belief that Web 2.0 thrives where journals don’t, and that the NMR community might be the first to reach the tipping point, where your career is harmed by not contributing.

The first, NESG wiki, became available publicly a month or so ago, and I’ve written a short news piece here and the wiki itself is here. It was developed by Northeast Structural Genomics Consortium (NESG), a centre working on high-throughput methods for solving protein structures. They provide details of their protocols, right down to buffer conditions and how to get your protein sample into the NMR tubes without losing it. It isn’t aimed at complete beginners, and certainly not at the public, but the information they have is clear, and it’s well written, and even though I have limited hands-on NMR experience I can follow it.

NESG wiki

This wiki came into existence because it met a need. NESG is composed of several groups, and the NMR side of things is made up of the labs of Gaetano Montelione, Cheryl Arrowsmith, Mark Girvin, Michael Kennedy, John Markley, Robert Powers, James Prestegard and Thomas Szyperski. These labs are spread across the United States and Canada and so a way of pooling all the information was required. For most of its life, this was a private working wiki just for these groups. Now that it is open to the public, it will be fascinating to see how this project evolves and deals with ‘outsiders’. Currently it has around 50 registered users.

The second wiki is more established: the NMR wiki. It has a wider reach and covers the whole of magnetic resonance, not just NMR. It’s an excellent place for inspiration if you are teaching NMR to postgraduates or undergraduates:  it has slides, lectures, worksheets and quizzes. In addition, you are encouraged to upload your PhD or Masters thesis and share your pulse sequences and software. Also, it advertises jobs and conferences. It has an active question and answer section. Actually, I like what they do with this Q&A section so much that I’ll write about this a bit more another day, but for now I’ll just say that one of the nice things about the way they have developed it is that you get a feel for how many people are looking at this section and you can grade the answers.

NMR wiki

The NMR wiki is a real treasure-trove of magnetic resonance science, and if I went back into the lab tomorrow, it would be my life-line. It has 430 registered users, which the Director of the BioMolecular Spectroscopy Facility at the University of California Irvine, Evgeny Fadeev, estimates to be 4% of the magnetic resonance community.

There is some overlap between the two sites, but it’s worth looking at both because they provide different information: one focuses on high-throughput; the other on more traditional lab environments. But the significant thing isn’t the medium so much as the content: most of the information being freely shared is not publishable by academic journals. Though Nature Protocols, and to a lesser extent CSH Protocols, have an interest in this general area, the important nitty-gritty details of how to perform NMR spectroscopy don’t make a compelling story. So these wikis didn’t grow because of publishers but specifically because of their absence. Equally, academic journals do not take much interest in facilitating the sharing of teaching material for this field.

Another factor worth considering is that the magnetic resonance community is relatively small, meaning that many researchers will know each other and there will be strong interconnections between groups. With some of the leading names in NMR spectroscopy now using wikis, how close are magenetic resonance researchers to the tipping point?

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Responses

  1. For the record, CSH Protocols is very interested in publishing the nitty-gritty details of how to perform techniques like NMR. We have no page charges and pay authors a royalty based on the use of their articles. More info here:
    http://cshprotocols.cshlp.org/misc/ifora.dtl

    That said, I think it’s interesting to see that the more successful Web 2.0 projects for scientists are community-driven, like those that you mention here, and those built around the use of particular model organisms (Flybase, ZFin, WormBook). There’s clearly something about the community knowing what its members and its needs that trumps an outside third party trying to build a “Facebook for Scientists”.

    • Ah, that’s good to know David – but do you not have a minimum length that you publish? Could some of these wiki-type articles – perhaps only half a page long – actually work as part of CSH Protocols?

      • We have a variety of article types:

        Protocol: most of our articles are like this, step by step instructions for a technique and they vary greatly in length.

        Topic Introduction: general background information discussing the theory and application of a technique.

        Information Panel: short sets of information important for performing a given technique.

        There are a few others, but the Information Panel is probably the most like you’re describing. They’re usually published together with protocols, but if they refer to other methods we’ve already covered, we’d welcome them. Here are a couple of examples from our free, featured articles:
        http://cshprotocols.cshlp.org/cgi/content/full/2008/5/pdb.ip49

        http://cshprotocols.cshlp.org/cgi/content/full/2008/5/pdb.ip49

  2. […] In an article (http://sbkb.org/update/2010/03/full/th_psisgkb.2010.09.html) recently posted on the Structural Biology Knowledgebase, the NESG NMR Wiki was highlighted by Maria Hodges, and the complementary nature with the ‘NMR Wiki’ project was discussed by her in a second blog article (https://woodforthetrees.wordpress.com/2010/02/22/a-tale-of-two-wikis/). […]


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