My first and very interesting appointment of last week was to attend and speak at a wonderful symposium – Visions of a (Semantic) Molecular Future – held in Cambridge to celebrate the visionary activities of Peter Murray-Rust. Peter long ago recognized the power of computers in helping us to attack complex biochemical problems in drug discovery, and therefore started developing e-science long before it became known as such. The symposium was streamed and will be available online in due time, though since it was tweeted pretty effectively, it is easy to get a feel for events by following the hashtag #pmrsymp. Inspection of the programme suggests that this is probably the first occasion in which both the Chair and Chief Executive of BBSRC have given scientific talks at the same symposium! My own talk focused on the use of semantic technologies to describe biochemical networks in a principled manner, and how such knowledge could assist our understanding of how pharmaceutical drugs get into cells and how this can explain the very clear drug-metabolite similarities that exist.
The pdf file has become the de facto standard for exchanging scientific papers in a manner that makes them look identical to their published form. It is, however, a less than ideal medium for maximizing the ease of linking scientific content and data to manuscripts. Several of the speakers from Cambridge then went on to a meeting entitled ‘Beyond the pdf’ that seeks to do something about this.
As well as a great many internal meetings, I also met Iain Gordon, the new Chief Executive of the James Hutton Institute, a new Institute formed from the merger of the Scottish Crops Research Institute and the Macaulay Land Use Research Institute. Clearly this merger provides some terrific opportunities to bring together the simultaneous optimization of both crop improvement and land use.
The availability of genomics resources continues apace, and while work on forest tree genomics has somewhat lagged that of model and edible crop plants, a recent review provides a useful overview of progress.
- 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
- Attwood TK, Kell DB, McDermott P, Marsh J, Pettifer S, Thorne D: Utopia Documents: linking scholarly literature with research data. Bioinformatics 2010; 26:i568-574. Full free text
- Dobson PD, Kell DB: Carrier-mediated cellular uptake of pharmaceutical drugs: an exception or the rule? Nat Rev Drug Discov 2008; 7:205-220
- Dobson PD, Patel Y, Kell DB: “Metabolite-likeness” as a criterion in the design and selection of pharmaceutical drug libraries. Drug Disc Today 2009; 14:31-40
- Herrgård MJ, et mult al.: A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol 2008; 26:1155-1160
- Neale DB, Kremer A: Forest tree genomics: growing resources and applications. Nat Rev Genet 2011; 12:111-122
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