The beginning of the week marked the move of one of my postdocs, Irena Spasić, who – based on some very nice work recorded in papers such as this and this – has secured a lectureship in Computer Science at Cardiff.
I then attended part of the programs of each of our 4 Research Committees, who were meeting near Windsor for the present grants round. It was as ever pleasing to see the high quality both of the great bulk of the applications and of the detailed discussions about the many proposals received.
I attended and spoke at the 10th anniversary meeting – FSA10 – of the Food Standards Agency (FSA). The FSA is necessarily quite a consumer-facing organisation, and the programme was purposely oriented to public interests and the public perception (and reality) of what constitutes safe food. The meeting was very effectively compered by Gavin Esler (of Newsnight and other fame). There are important interfaces with our own Food Security programme, not least on Campylobacter, that we are continuing to develop.
Industrial Biotechnology is another of our important themes, and sugar beet is a potentially important UK feedstock, both now and in the future (its wet yield in the UK last year averaged 72 t/ha!). Consequently, I enjoyed a very interesting all-day visit to British Sugar’s integrated biorefinery at Wissington (PDF). The enormous scale of the operation (18,000 tonnes per day) meant that the substrate – sugar beet roots – arrived constantly, mainly in enormous 40-tonne wagons at a rate of almost one per minute! The plant had its own combined heat and power station, carefully optimised (using pinch technology) to extract all waste heat, as well as a massive bioethanol plant for road fuel, giant chromatography columns for betaine extraction, and with the ultimate products from the sugar processes (low-grade heat and CO2) being piped to 11 ha worth of greenhouses growing a huge number of excellent tomatoes for the retail trade. (We were also given some useful gastro-advice: do not put tomatoes in the fridge as it spoils their flavour!)
As part of our public engagement activities, I gave a talk last Friday to the Darwin Society at Shrewsbury School (the School was once attended by Charles Darwin, and an excellent statue there records this fact). I was delighted and deeply impressed by the enthusiasm, as well as the levels and breadth of scientific questions, that emanated from the young audience.
I have had occasion, more than once, to publish papers bemoaning the lack of statistical rigour in many data analyses, and I was pleased to see the number of my papers achieving at least 100 citations pass 30 this week; one on computational cluster validation was the latest to achieve its century.
I have long recognised the importance of data standards for interoperability of software, not least for working with systems biology models, where the Systems Biology Markup Language (SBML) is probably the main standard. However, this covers only the model itself, and not the behaviour or results of running either a model or the data (of measured variables) from real experiments with which such a model might be compared. It is obvious that we would very much like to have such a standard. SBRML, described in the latest paper with Irena Spasić’s authorship, now provides one.
- Broadhurst D, Kell DB: Statistical strategies for avoiding false discoveries in metabolomics and related experiments. Metabolomics 2006; 2:171-196
- Dada JO, Spasić I, Paton NW, Mendes P: SBRML: a markup language for associating systems biology data with models. Bioinformatics 2010. Link to software
- Handl J, Knowles J, Kell DB: Computational cluster validation in post-genomic data analysis. Bioinformatics 2005; 21:3201-3212. Link to full, free text
- Kell DB, Sonnleitner B: GMP – Good Modelling Practice: an essential component of good manufacturing practice. Trends Biotechnol 1995; 13:481-492
- Kell DB: Metabolomics, modelling and machine learning in systems biology: towards an understanding of the languages of cells. The 2005 Theodor Bücher lecture. FEBS J 2006; 273:873-894
- Spasić I, Dunn WB, Velarde G, Tseng A, Jenkins H, Hardy NW, Oliver SG, Kell DB: MeMo: a hybrid SQL/XML approach to metabolomic data management for functional genomics. BMC Bioinformatics 2006; 7:281
- Spasić I, Simeonidis E, Messiha HL, Paton NW, Kell DB: KiPar, a tool for systematic information retrieval regarding parameters for kinetic modelling of yeast metabolic pathways. Bioinformatics 2009; 25:1404-1411. Link to software
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