Agri-ecosystems, institutes and announcements
A major theme of last week was work in agri-ecosystems, part of an announcement by Minister of Universities and Science David Willetts of a £250M BBSRC investment of strategic support for science. The Minister also gave an excellent and more wide-ranging speech on the role of Government (and the research base) in driving growth and innovation, while George Freeman, MP for mid-Norfolk, and I both contributed to Farming Today.
I also travelled to Devon for a briefing meeting on the ANAEE (ANalysis And Experimentation on Ecosystems) programme, and then to participate in the launch of our major Farm Platform at North Wyke (part of Rothamsted Research). The automated data capture facilities of this massively impressive facility, a National Capability, will allow researchers to study in unprecedented detail the nutrient, water and energy budgets of grassland-based agriculture, making the data available to all.
Some interesting links I picked up included a page outlining the software behind Facebook, with its 570 billion page views per month,
Papers I enjoyed included one on high-bandwidth nanopore-based sensing, one on the data handling challenges of the 1000 genomes project, a review of one approach to mechanistic molecular enzymology, a forward look on cheminformatics, a heads-up about forthcoming legislation on endocrine disruptors and one on anti-infectives.
A new paper with my co-authorship has gone online, describing how to extract what in text mining are called ‘events’ (which in biochemistry – see also here – typically means interactions and transformations) from the biological literature. In contrast to the ‘bag of words’ analyses of co-occurrences of words anywhere in documents – that are very prone to false positives – this exploits the use of semantic and contextual information to act as a filter.
Many global agri-ecosystems already contain ‘genetically modified’ crops, and as pointed out by Sir John Beddington more may need to. Rational and peaceful debate around the issues of what should be regulated, how and why (e.g. as with microbes on the basis of their traits rather than how they were derived, is what is required. I am very pleased that this peaceful exchange of views was exactly what occurred during the demo at Rothamsted Research on Sunday.
- Ananiadou, S., Pyysalo, S., Tsujii, J. i. & Kell, D. B. (2010). Event extraction for systems biology by text mining the literature. Trends Biotechnol 28, 381-390.
- Clarke, L. et mult al. (2012). The 1000 Genomes Project: data management and community access. Nat Methods 9, 459-462.
- Lewis, K. (2012). Recover the lost art of drug discovery. Nature 485, 439-40.
- Miwa, M., Thompson, P., McNaught, J., Kell, D. B. & Ananiadou, S. (2012). Extracting semantically enriched events from biomedical literature. BMC Bioinformatics 13, 108. Full free text as PDF.
- Oprea, T. I., Taboureau, O. & Bologa, C. G. (2012). Of possible cheminformatics futures. J Comput Aided Mol Des 26, 107-12.
- Owen, R. & Jobling, S. (2012). The hidden costs of flexible fertility. Nature 485, 441.
- Rosenstein, J. K., Wanunu, M., Merchant, C. A., Drndic, M. & Shepard, K. L. (2012). Integrated nanopore sensing platform with sub-microsecond temporal resolution. Nat Methods 9, 487-92.
- Schramm, V. L. (2011). Enzymatic transition states, transition-state analogs, dynamics, thermodynamics, and lifetimes. Annu Rev Biochem 80, 703-32.
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