The understanding of biochemical and other networks is an important part of systems biology, and I enjoyed attending an interesting seminar on “network-based drug design” by Péter Csermely of Semmelweiss University, where I was alerted to a number of his papers such as this one, and even a book, that had passed me by. Not for the first time, one is led to lament the difficulty of keeping up with the voluminous literature.
We had a meeting of the Chairs of the Institute Assessment Panels. Council also met.
I attended the launch by Minister of Universities and Science David Willetts of the Innovation and Research Strategy for Growth paper (pdf), which set down a number of important initiatives for the research base.
The only realistic means of dealing properly with the scientific literature (as well as other Web-available documents) is to have computers do a lot of the analysis. This involves imbuing the relevant text (and for that matter biochemical models for systems biology) with meaning, seen as the domain of the semantic web and semantic computing. To this end, I gave a plenary lecture at the Semantic Web for Life Sciences Workshop, on Semantic Approaches in Biotechnology and Biological Sciences. While there is an enormous way to go, some of the tools available are helping us make great progress, albeit that comparatively few are really usable by most working biologists. One of the challenges will be to make available such tools, and the funds for producing them, that might be.
I enjoyed reading articles on perennial crops, and a well-argued blog on the merits of Open Access. With just a fortnight to go, and likely just one more blog, I have downloaded for Christmas e-reading a nice little summary of the origins of well-known phrases.
- Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer SR, Thorne D: Calling International Rescue: knowledge lost in literature and data landslide! Biochem J 2009; 424:317-333. Full free text. Link to free software
- Courtot, M. et mult al. (2011). Controlled vocabularies and semantics in Systems Biology. Mol Syst Biol 7, 543. Full free text
- Cryer, M. (2011) Who said that first? Summersdale Publishers, Chichester
- Csermely, P. (2008). Creative elements: network-based predictions of active centres in proteins and cellular and social networks. Trends Biochem Sci 33, 569-76
- Csermely, P. (2009). Weak links. Springer, Heidelberg
- Hull D, Pettifer SR, Kell DB: Defrosting the digital library: bibliographic tools for the next generation web. PLoS Comput Biol 2008; 4:e1000204. Full free text
- Kell, D. B. (2009). Iron behaving badly: inappropriate iron chelation as a major contributor to the aetiology of vascular and other progressive inflammatory and degenerative diseases. BMC Medical Genomics 2, 2. Full free text
- Kell DB, Mendes P: The markup is the model: reasoning about systems biology models in the Semantic Web era. J Theoret Biol 2008; 252:538-543
- Mims, C. (2011). Crops that don’t need replanting. Sci Amer 305, 48
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