Exercises in blogging at #solo11. Show me the data!

Latest stop on the GigaScience magical mystery conference tour is Science Online London, and this year they have tried to make the format more interactive by organizing several interactive workshops and breakout sessions, including one on blogging that this is posting is a product of. One of the main themes running through the meeting has of course been open science (especially in the great keynote by Michael Nielson), and open-data (particularly on the "linking with the literature" and "dealing with data" panels). Data-citation was raised on several occasions, and we did our part promoting it and the recent crowdsourcing of E. coli in the Microattribution session.

The theme of the second day has been on the better use of tools and information in the context of a the rare genetic disease SMA (Spinal Muscular Atrophy). Maryann Martony from the Neuroscience Information Network initially set the scene, discussing the state of play in Neuroscience data-sharing, and outlining the technical and cultural challenges sharing this type of data which in comparison to genomics or proteomics has a much wider and more heterogeneous set of data types. The afternoon consisted of several several workshops relevant to SMA research, and the "Beyond Scholarly Publication" workshop aimed to showcase scholarly HTML and the wordpress platform by producing blog postings on SMA research.

Due to a combination of geographic and inertia issues I’ve not written this up on wordpress, but thought I would contribute on our normal blog with some relevant issues regarding data-sharing. With it being one of the themes of the meeting, of the suggested SMA articles to discuss none of them had the raw data available in public repositories. Whilst this was mostly due to the papers being based on datatypes without well recognized repositories such as electrophysiological data, one of the papers (Wu et al., BMC Neuroscience) was based on Proteomics data, which does have the Tranche and PRIDE databases to hold raw and processed data. Heading off to the HUPO proteomics meeting tomorrow (and due to talk at the repositories session there), it’s timely to highlight the challenges this particular field still faces, and it will be very interesting to hear this week how these resources are being accepted by their communities.

Despite all of the positive words regarding datasharing at Science Online, this particular exercise has been a bit of a reality check, and its very clear that there is still an enormous of work still to do. With the meeting about to end, and the attendees all going there separate ways around the world, one positive thing to take is that they and organizations such as the NIF are at least using their combined energies to address this. Lets all hope they succeed, and #solo12 will be a nice opportunity to assess how this will progress. See you then, and don’t forget to follow the huge amounts of coverage on twitter (follow #solo11) and the soon-to-be-posted videos.


Wu CY, Whye D, Glazewski L, Choe L, Kerr D, Lee KH, et al. Proteomic
assessment of a cell model of spinal muscular atrophy. 2011;12:25+.
Available from: http://dx.doi.org/10.1186/1471-2202-12-25.

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  • Cindy Jensen

    Can nucleotide or base excision repair occur long after the damage or is there a window in which it does its action? If one wants to take supplements to enhance repair or any kind of repair enhancement, is there a time when it is too late?

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