After our return from the US following the ‘big data’ mission I described last week, it was very much catching-up and preparation time in Swindon as I shall be away from the office quite a bit in the next few weeks. I did have a couple of appointments in London, the first visiting JISC, whose Board I have now joined, for a briefing about its organisational infrastructure. JISC is broadly responsible for IT infrastructure underpinning Higher Education, and (inter alia) for innovations in software and information technology that will assist the scholarly enterprise. Obviously this is going to be increasingly important given the digital and online availability of increasing amounts of text and data. JISC also looks after the JANET network that connects Higher Education Institutes.
I also acted as a judge for the postdoc research prizes at Manchester’s Faculty of Life Sciences, the winner being Qin-Jun Meng from the laboratory of Andrew Loudon, who gave a presentation based on a most interesting paper describing the contribution to the control of mammalian clock speed in mammals by casein kinas 1 (CK1). The subsequent identification of the most relevant isoforms of this protease responsible for destabilising the PER proteins that act as transcriptional repressors may allow the development of drugs to assist in jet lag and other circadian rhythm sleep disorders.
Commonly one reads abstracts of papers serially, but the modern popularity of hypertext and other ways of linking the elements of documents in a nonlinear manner (as proposed in a famous, prescient and notable essay in 1945 by Vannevar Bush) opens up other possibilities. TexFlame is one I have just come upon, that renders pubmed abstracts (as SBGN, and see paper) in the form of a graph. As yet it seems like a bit of a toy, but such approaches to enhancing digital text – when coupled to programmatic access and suitable visualisation – are going to revolutionise the way we link and analyse scientific and other information.
- Hull, D., Pettifer, S. R. & Kell, D. B. (2008). Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol 4, e1000204. doi:10.1371/journal.pcbi.1000204. Full text (PDF)
- Le Novère, N., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M., Wimalaratne, S. M., Bergman, F. T., Gauges, R., Ghazal, P., Hideya, K., Li, L., Matsuoka, Y., Villéger, A., Boyd, S. E., Calzone, L., Courtot, M., Dogrusoz, U., Freeman, T., Funahashi, A., Ghosh, S., Jouraku, A., Kim, S., Kolpakov, F., Luna, A., Sahle, S., Schmidt, E., Watterson, S., Wu, G., Goryanin, I., Kell, D. B., Sander, C., Sauro, H., Snoep, J. L., Kohn, K. & Kitano, H. (2009). The systems biology graphical notation. Nat Biotechnol 27, 735-741
- Meng, Q. J., Logunova, L., Maywood, E. S., Gallego, M., Lebiecki, J., Brown, T. M., Sladek, M., Semikhodskii, A. S., Glossop, N. R., Piggins, H. D., Chesham, J. E., Bechtold, D. A., Yoo, S. H., Takahashi, J. S., Virshup, D. M., Boot-Handford, R. P., Hastings, M. H. & Loudon, A. S. (2008). Setting clock speed in mammals: the CK1 epsilon tau mutation in mice accelerates circadian pacemakers by selectively destabilizing PERIOD proteins. Neuron 58, 78-88