We had a useful meeting on the Norwich Research Park with the Directors and Directors of operations of our strategically funded Institutes, including updates on campus developments, plans for sharing facilities and much else.

We also had one of our regular meetings with the Technology Strategy Board. Although there is very frequent and considerable coworking at every level, these meetings, as for those with the Institutes, serve as effective fora to exchange thoughts and knowledge of our activities and strategies.

I have been on a couple of occasions to the Science Foo camp held at the Googleplex, and last week was able to attend an informal meeting with some UK-based folk who had too. The uniting feature is an interest in digital methods and recognition that these are going to have a massive impact on our lives, including the optimal doing of science, a view I certainly share. A couple of folk I met for the first time were Mark Hahnel from Figshare and Ben Fields from Musicmetric. The former is science-based and aimed at the open sharing of scientific results, while the latter uses time series and other computational analyses of social networks to document, visualise and understand the popularity of particular artists. There are some obvious uses for that kind of technology in analysing the scientific literature, for instance.

All of these computational methods require that data are available in the first place, and (as recognised in our data sharing policy) having them interoperable is a second prerequisite for their efficient reuse and incorporation into more refined workflows. The online availability of literature and its more convenient bibliometric analysis does, however, offer some unwelcome opportunities – that are best resisted – to game the system.

I am always on the lookout for methods, and especially computational methods, that might be used to make enzymes go faster, and thus enjoyed a new paper that used an online crowd-sourcing method to improve ~20-fold the catalytic rate constant of a ‘designed’ but sluggish Diels-Alderase. Other reading I enjoyed included a summary of open access papers in PLoS collections on genetically modified insects, including an interesting one on their appropriate regulation. Unlike one on organic reaction mechanisms to which my attention was drawn, however, it was not written in free verse.

• Alphey, L. & Beech, C. (2012). Appropriate Regulation of GM Insects. PLoS Negl Trop Dis 6, e1496. Full free text
• Bunnett, J. F. & Kearley, F. J. (1971). Comparative mobility of halogens in reactions of dihalobenzenes with potassium amide in ammonia. J Org Chem 36, 184-&
• Eiben, C. B., Siegel, J. B., Bale, J. B., Cooper, S., Khatib, F., Shen, B. W., Players, F., Stoddard, B. L., Popovic, Z. & Baker, D. (2012). Increased Diels-Alderase activity through backbone remodeling guided by Foldit players. Nature Biotechnol. (online)
• Sansone, S. A. et mult al. (2012). Toward interoperable bioscience data. Nat Genet 44, 121-6. Full free text
• Siegel, J. B. et mult al. (2010). Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329, 309-13. Full free text as manuscript
• Wilhite, A. W. & Fong, E. A. (2012). Coercive citation in academic publishing. Science 335, 542-3

Related posts (based on tags and chronology):

• Babraham, TGAC, Schrödinger and economic growth [28 November 2011]
• Elixir, Roslin and HUBS [14 November 2011]
• Beauty, truth and computation – Scifoo 2010 [05 August 2010]
• Data, dancing, development sciences and innovation [22 March 2010]
• The scientific century, global food security and data-intensive infrastructure [17 March 2010]

Horticulture is thus an important Bioindustry, and I had an interesting session at the BioIndustry Association as part of their Parliament Day, where our discussions focussed on the best ways to capture the value for the biotechnology sector from the enormous amounts of knowledge and expertise in Higher Education and Research Institutes.

Informatics and IT is an important part of our space (and of course of modern society as a whole) and a significant role in education and research has long been played by JISC. Although JISC is transitioning to a new governance and structure, I am a (co-opted) member of the present JISC Board, and we had a useful meeting. There was a particular focus on e-infrastructure, and the future provision of network infrastructure as represented by JANET. It remains the case that the growth in genomics and other biological data is quicker than exponential, and we need to be prepared for the Malthusian-type consequences of this this. While it is true that moving disks in a van can provide an effectively enormous amount of bandwidth, this is traded off against a substantial latency. Working out where we wish to make these trade-offs will be an important area of discussion for placing investments sensibly.

I occasionally have cause to give a talk at a secondary school, and last week I did one at Moreton Hall. As at a previous occasion elsewhere, I was extremely impressed by the type and quality of questions I received from my (mainly) young and (for the pupils) exclusively female audience. Regarding gender and related issues, Athene Donald’s latest blog includes some thoughtful views on the need for folk to be looking to upgrade their Athena SWAN status, a topic on which I have blogged before and to which we shall return. After the talk I took part in a quiz, and thus I now know that Macclesfield was once the hub of the UK silk industry and hence that its soccer team is known as the Silkmen.

My attention was earlier drawn to a fascinating small book with a big subtitle that sets out to explain some simple facts of economics. I have now read it and it is to be recommended.

I enjoyed a paper summarising different approaches to determining genetic networks from time series data. I also enjoyed an interesting article setting out in a new and quantitative way the question of whether a particular small molecule is or is not ‘drug-like’, although I’d comment that natural products (that for discernible reasons often make good drugs) do tend to score poorly by these criteria.

There has been some very interesting debate about the desirability or otherwise of making public the sequences of strains of H5N1 ‘avian’ influenza A viruses that are both highly pathogenic and highly transmissible. Whatever one’s intellectual position, what is clear is that the debate is being held in as sensible and transparent a fashion as possible, and this is greatly to be commended.

Finally, I have long held the view that much of Scientific Discovery involves finding a good idea for the next experiment to do in a series, whether the reasoning is inductive or deductive or otherwise. As such this then involves a search through a potentially enormous search space of possible experiments for that small subset that are good or useful experiments, and this can then be cast as a combinatorial search or optimisation problem. A paper I wrote setting this out in more detail has just been published online.

• Allen, J. D., Xie, Y., Chen, M., Girard, L. & Xiao, G. (2012). Comparing statistical methods for constructing large scale gene networks. PLoS One 7, e29348.  Full free text
• Bickerton, G. R., Paolini, G. V., Besnard, J., Muresan, S. & Hopkins, A. L. (2012). Quantifying the chemical beauty of drugs. Nat Chem 4, 90-8
• Cowen, T. (2011). The great stagnation: how America ate all the low-hanging fruit of modern history, got sick, and will (eventually) feel better. Dutton, New York
• Dobson, P. D., Patel, Y. & Kell, D. B. (2009). "Metabolite-likeness" as a criterion in the design and selection of pharmaceutical drug libraries. Drug Disc Today 14, 31-40
• Fouchier, R. A. et mult al. (2012). Pause on avian flu transmission research. Science 335, 400-1
• Kell, D. B. (2012). Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? Bioessays, in the press
• Kell, D. B. & Oliver, S. G. (2004). Here is the evidence, now what is the hypothesis? The complementary roles of inductive and hypothesis-driven science in the post-genomic era. Bioessays 26, 99-105
• Palese, P. (2012). Don’t censor life-saving science. Nature 481, 115

Related posts (based on tags and chronology):

• Networks, assessment, innovation and the semantic web [12 December 2011]
• Non-food crops, industrial biotechnology and IAH [05 December 2011]
• Athena Swan, Exploiting New Ways of Working, East Malling, and The Two Cultures [21 November 2011]
• Science, tachyons, China and e-infrastructure [26 September 2011]
• JBOS, e-infrastructure and pharmaceuticals [05 September 2011]

I then managed to attend the second half of a meeting organised in collaboration with the Food Standards Agency and the Health Protection Agency, looking at the potential impact of ‘next generation sequencing’ and related methods on the ability to detect and type potentially pathogenic strains of microbe that might be isolated from food or other matrices. Not least since the recent German E. coli outbreak, it has become pretty obvious that the most sensible – and nowadays most economic – approach to typing an organism is indeed to sequence its genome, since as well as providing a definitive typing, such data provide important information of use in epidemiology (and, by the detection of antibiotic-resistance genes, potentially in treatment). Significant investment, especially in the skills and the necessary informatics, will be necessary to realise this properly, however.

As part of our series of University visits, I enjoyed a very useful visit to Imperial College, where I gave an overview of what we are seeking to fund, and saw a variety of extremely interesting presentations on all kinds of areas in instrumentation, food security, industrial biotechnology, chemical biology (e.g. Agri-net, one of our Chemical Biology networks), synthetic biology, biomaterials and so on.

I am always on the lookout for useful papers in industrial biotechnology, especially those that exploit systems biology approaches and informatics, and I (somewhat belatedly) came upon a nice one in which in silico modelling (i.e. rational metabolic design) of L-lysine production proposed just 12 defined genome changes that took yields (0.55 g product per g glucose) and titres (120 g/L) to exceptional levels in C. glutamicum.

I was pleased to see a rather long-standing paper that I co-authored finally emerge online, looking at the control of  growth rate in baker’s yeast from a systems biology point of view.

An important part of our activities involves ensuring that we get out a whole series of messages about the importance of biology and the science, technology and skills development that we fund. Our External Relations Unit have been developing a series of practical biofuel activities for school engagement and outreach, and these are now published online. I strongly encourage all our researchers to download and disseminate them to suitable recipients. Suitable, as they say, for children of all ages.

Sometimes there can be quite a gap between a basic scientific discovery and its commercial exploitation; to this end, I noted that the just-announced awarding of a patent based on work of Sir David Baulcombe and Dr Andrew Hamilton on short interfering RNAs carries an application date of March 22nd, 2004.

Finally, my attention was drawn to an unusual take on risk on David Spiegelhalter’s blog; not something I’ll be asking our Audit Board to let me do.

• Bayer, T. S. (2010). Transforming biosynthesis into an information science. Nat Chem Biol 6, 859-61.
• Becker, J., Zelder, O. Häfner, S., Schröder, H. & Wittmann, C. (2011) From zero to hero: design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production.
• Meta bolic Engineering 13, 159–168.
• Melzer, G., Eslahpazir Esfandabadi, M., Franco-Lara, E. & Wittmann, C. (2009) Fluxdesign: in silico design of cell factories based on correlation of pathway fluxes to desired properties.
• BMCSyst.Biol.3, 120. Full free text.
• Park, J. H. & Lee, S. Y. (2008). Towards systems metabolic engineering of microorganisms for amino acid production. Curr Opin Biotechnol 19, 454-60.
• Pir, P., Gutteridge, A., Wu, J., Rash, B., Kell, D. B., Zhang, N. & Oliver, S. G. (2012). The genetic control of growth rate: a systems biology study in yeast. BMC Sys Biol. Full free text.

Related posts (based on tags and chronology):

• Appointments Board, Professors and policy evidence [19 September 2011]
• Capturing and using digital information [08 August 2011]
• ATPs, Roslin and Pharma [04 July 2011]
• Data visualisation, and the next generation of bioscientists [22 November 2010]
• A Scottish sojourn [04 October 2010]

The main visit of the week was to Harper Adams University College. Harper Adams is a major provider of agricultural education, training and knowledge transfer, as well as (largely applied) research. This was thus an exceptionally interesting visit. Without seeking to pick out specific areas, I note that Harper Adams runs the only UK degree courses in Agricultural Engineering, and I saw some very interesting work at the interface of engineering and agriculture, especially in the areas of using modern technology to plant, sense, weed, and harvest agricultural crops. The whole area of ‘precision agriculture’ is going to provide an important contribution to increasing the productivity of food and non-food crops, and we can expect it to expand significantly.

Another very interesting and important area was represented by the OpenFields project. This seeks to make available, in an accessible and structured format, the many and dispersed outputs of agricultural research (sensu lato) in a manner somewhat akin to that available for biomedical publications via UKPMC.

A lot of papers I read last week seemed to be about genomics. Thus, there was a long-heralded paper (long-heralded in that the code has been available at sourceforge for a while) on the development and very effective use of ‘coloured’ de Bruijn graphs in genome assembly, and one on the rise and benefits of analysing ‘your own’ genomics data. Another showed that what was found might be significantly affected by the platform that generated the data; this might or might not be affected by the analyses applied. Because everything is in one sense connected to everything else in biochemical networks, one might wonder whether all genes and gene-finding algorithms might have predictive value; scarily in some circumstances they might. However, the benefits of sequencing multiple cultivars of agricultural crops for finding genes underlying important traits is starting to become clear. Continuing analyses of the so-called ‘missing heritability’ lead to a reaffirmation of the importance of epistasis – a systems biology property – in the understanding of genotype-phenotype interactions.

I also note a useful report on “Understanding the UK Agricultural Research Contribution to International Development and Food Security”, and an interesting piece on the use of Search Engine Optimisation to help get one’s website messages out. A different and maybe more effective method of networking.

• Iqbal, Z., Caccamo, M., Turner, I., Flicek, P. & McVean, G. (2012). De novo assembly and genotyping of variants using colored de Bruijn graphs. Nature Genet, online; DOI:10.1038/ng.1028
• Kell DB (2002) Genotype:phenotype mapping: genes as computer programs. Trends Genet 18:555-559
• Lam, H. Y. K., Clark, M. J., Chen, R., Chen, R., Natsoulis, G., O’Huallachain, M., Dewey, F. E., Habegger, L., Ashley, E. A., Gerstein, M. B., Butte, A. J., Ji, H. P. & Snyder, M. (2012). Performance comparison of whole-genome sequencing platforms. Nature Biotechnol 30, 78-83
• Maclean, D. & Kamoun, S. (2012). Big data in small places. Nature Biotechnol 30, 33-34
• Maher, B. (2008). The case of the missing heritability. Nature 456, 18-21
• Micklos D, Lauter S, Nisselle A (2011) Lessons from a science education portal. Science 334:1657-1658
• Reumers, J., Rijk, P. D., Zhao, H., Liekens, A., Smeets, D., Cleary, J., Loo, P. V., Bossche, M. V. D., Catthoor, K., Sabbe, B., Despierre, E., Vergote, I., Hilbush, B., Lambrechts, D. & Del-Favero, J. (2012). Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing. Nature Biotechnol 30, 61-68
• Venet, D., Dumont, J. E. & Detours, V. (2011). Most random gene expression signatures are significantly associated with breast cancer outcome. PLoS Comput Biol 7, e1002240. Full free text
• Xu, X. et mult al. (2012). Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nature Biotechnol 30, 105-111
• Zuk O, Hechter E, Sunyaev SR, Lander ES: The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A 2012, online

Related posts (based on tags and chronology):

• Babraham, TGAC, Schrödinger and economic growth [28 November 2011]
• Norwich Research Park, genomics data and carbon sequestration [01 June 2011]
• Complexity, networks and reductionism [31 August 2010]
• Beauty, truth and computation – Scifoo 2010 [05 August 2010]
• Post-purdah: agriculture, biotechnology, data and soils, and grant rounds [17 May 2010]

As last year, I attended part of the Oxford Farming Conference, where I enjoyed many excellent talks, such as one from USDA Chief Economist Joe Glauber highlighting the economic benefits to be had from investment in agricultural R&D and another from the newly knighted Defra Chief Scientist Sir Bob Watson. In informal conversation I also discovered the existence (from a young OFC Scholar) of the Miscanthus Growers Group. There is no doubt that improved and sustainable agricultural productivity is very much back on the scientific and agricultural agenda.

Since the last blog, among various press releases, we also published our impact report and provided a link to a video of the recently completed interim laboratory at the Institute for Animal Health.

I co-authored a couple of papers that were published towards the back end of last year, one using the methods of synthetic biology to produce Qconcat proteins for assessing the absolute concentrations of multiple proteins in parallel, and the other describing a toolbox of modules to assist (by semi-automating) the reconstruction of metabolic networks from suitable data such as those in KEGG. One example cited a speed-up from ca 1 year of work to ~4h! I was also pleased to have a new paper accepted for publication in an area I have been thinking about for a long time, viz. the idea that much if not all of scientific discovery is best seen as a combinatorial optimisation problem.

I enjoyed a nice paper to the effect that if one has many related protein sequences, that presumably tend to fold up the same way, there are therefore (overt or hidden but) powerful constraints that effectively tell you how they do so, thus speeding the means of proceeding from protein sequence to computer-calculated structure. I also draw attention to an important speech by Minister of Universities and Science David Willetts on the role of the Research Base and other contributors for “Our hi-tech future”. Certainly part of this might include doing more with what we have, and exploiting existing data is a worthwhile activity to this end. A nice paper in Science brings out some interesting new methods that are both principled and promising. Two others on literature mining describe an interesting method for connecting different papers to make a story and one analysing the benefits of candidate drug combinations, while another describes a fascinating data-driven approach to food pairing combinations in different cultures.

I was also pleased to see the recent discussion proposal (pdf) for the means of coding distributions or uncertainty in parameters as part of SBML models. Without these it is not so easy to estimate what the true ones might be via the measurement of experimental variables.

Finally, my attention was also drawn to an amusing two-part blog to the effect that “you know you’re a biologist when…”….at least some are likely to strike a chord!

• Ahn, Y.-Y., Ahnert, S. E., Bagrow, J. P. & Barabási, A.-L. (2011). Flavor network and the principles of food pairing. Sci Rep 1, 196. Full free text
• Brownridge, P., Holman, S. W., Gaskell, S. J., Grant, C. M., Harman, V. M., Hubbard, S. J., Lanthaler, K., Lawless, C., O’Cualain, R., Sims, P., Watkins, R. & Beynon, R. J. (2011). Global absolute quantification of a proteome: Challenges in the deployment of a QconCAT strategy. Proteomics 11, 2957-70
• Carroll, K. M., Simpson, D. M., Eyers, C. E., Knight, C. G., Brownridge, P., Dunn, W., Winder, C. L., Lanthaler, K., Pir, P., Malys, N., Kell, D. B., Oliver, S. G., Gaskell, S. J. & Beynon, R. J. (2011). Absolute quantification of the glycolytic pathway in yeast: deployment of a complete QconCAT approach. Mol Cell Proteomics 10, M111 007633
• Heisey, P., Wang, S. L. & Fuglie, K. (2011). Public agricultural research spending and future U.S. agricultural productivity growth: scenarios for 2010-2050. Economic Brief No 17
• Hossain, M. S., Gresock, J., Edmonds, Y., Helm, R., Potts, M. & Ramakrishnan, N. (2012). Connecting the dots between PubMed abstracts. PLoS One 7, e29509. Full free text
• Kell, D. B. (2012). Scientific discovery as a combinatorial optimisation problem: how best to navigate the landscape of possible experiments? Bioessays, in the press
• Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R. & Sander, C. (2011). Protein 3D Structure Computed from Evolutionary Sequence Variation. PLoS One 6, e28766. Full free text
• Reshef, D. N., Reshef, Y. A., Finucane, H. K., Grossman, S. R., McVean, G., Turnbaugh, P. J., Lander, E. S., Mitzenmacher, M. & Sabeti, P. C. (2011). Detecting novel associations in large data sets. Science 334, 1518-24. Link to software
• Swainston, N., Smallbone, K., Mendes, P., Kell, D. B. & Paton, N. W. (2011). The SuBliMinaL Toolbox: automating steps in the reconstruction of metabolic networks. Integrative Bioinf 8, 186. Talk in slideshare. Full free text as pdf
• Wilkinson, S. J., Benson, N., and Kell, D. B. (2008) Proximate parameter tuning for biochemical networks with uncertain kinetic parameters. Mol Biosyst 4, 74-97
• Zhao, X.-M., Iskar, M., Zeller, G., Kuhn, M., van Noort, V. & Bork, P. (2011). Prediction of drug combinations by integrating molecular and pharmacological data. PLoS Comp Biol 7, e1002323. Full free text

Related posts (based on tags and chronology):

• Complexity, networks and reductionism [31 August 2010]
• Celebrations, talks and bioenergy [19 December 2011]
• Oxford Nanopore Technology and IBERS [17 October 2011]
• Science, tachyons, China and e-infrastructure [26 September 2011]
• Summer, cricket and Bayes [15 August 2011]

Much of the rest of the week was punctuated by celebratory events, including a trip to St James’s Palace to launch and take forward thinking on the Festival of food and farming (“Farming in the Park”) taking place in Hyde Park in September 2013. Among the speeches, including one from Caroline Spelman, Secretary of State for Environment, Food and Rural Affairs, we were honoured to be addressed by His Royal Highness Prince Philip, the Duke of Edinburgh, who spoke eloquently and without notes on the importance of British farming and food, as well as providing a witty and entertaining history of our palatial surrounding.

I was also pleased to attend a poster session and dinner at a meeting to mark the culmination of the celebrations of the Biochemical Society’s centenary. Professor Sir Tom Blundell, Chair of BBSRC Council, is also this year’s President of the Biochemical Society, whose website has links to a very nice interview with him, that led me to a very interesting paper of his on protein evolution. While much can be learned from protein (primary) sequences alone, features such as those described therein require structural knowledge.

A flurry of recent publications have pointed up the increasingly clear significance of the contribution that Biology can make to sustainable energy and chemicals, a topic that is already a significant element of our strategic plan. These publications include The Government’s Carbon Plan; Delivering our low carbon future, the UKERC’s report Energy from biomass: the size of the global resource, and the Committee on Climate Change’s Bioenergy Review.

Some drugs are designed to interact with specific molecular targets. However, an arguably better strategy is to use a function-first approach i.e. to perform chemical genomics assays at the level of the cell or organism phenotype – phenotypic screening. A recent example has led to the discovery of a very promising molecule that may be of benefit in a variety of neurodegenerative diseases.

I also enjoyed an interesting blog on science funding in hard times, and one on Open Access, as well as papers on improving algal photosynthesis and on making models reproducible. The above are all areas that I suspect we shall return to next year. Meanwhile, I wish all those who come upon this, a relaxing holiday and a stimulating and rewarding 2012.

• Chen, Q., Prior, M., Dargusch, R., Roberts, A., Riek, R., Eichmann, C., Chiruta, C., Akaishi, T., Abe, K., Maher, P. & Schubert, D. (2011). A novel neurotrophic drug for cognitive enhancement and Alzheimer’s disease. PLoSone 6, e27865. Full free text
• Stephenson, P. G., Moore, C. M., Terry, M. J., Zubkov, M. V. & Bibby, T. S. (2011). Improving photosynthesis for algal biofuels: toward a green revolution. Trends Biotechnol 29, 615-23
• Swinney, D. C. & Anthony, J. (2011). How were new medicines discovered? Nat Rev Drug Discov 10, 507-19
• Waltemath, D., Adams, R., Bergmann, F. T., Hucka, M., Kolpakov, F., Miller, A. K., Moraru, II, Nickerson, D., Sahle, S., Snoep, J. L. & Le Novere, N. (2011). Reproducible computational biology experiments with SED-ML – The Simulation Experiment Description Markup Language. BMC Syst Biol 5, 198. Full free text
• Worth, C. L. & Blundell, T. L. (2011). On the evolutionary conservation of hydrogen bonds made by buried polar amino acids: the hidden joists, braces and trusses of protein architecture. BMC Evol Biol 10, 161. Full free text

Related posts (based on tags and chronology):

• Ageing, roots and farming [19 July 2010]
• A visit to Taiwan [07 November 2011]
• Science, tachyons, China and e-infrastructure [26 September 2011]
• Cellular systems biology and organisation [01 August 2011]
• Open data, science and celebrations [13 June 2011]

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

Related posts (based on tags and chronology):

• Bioengineering and systems biology [11 January 2010]
• In touch with the Dutch [19 October 2009]
• When scientific progress means going backwards: reverse engineering of biochemical networks [20 July 2009]
• The economy is the network; non-equilibrium systems in the real world [27 April 2009]
• Beyond the magic bullet – network pharmacology meets systems biology [19 January 2009]

We had a very useful meeting of the Industrial Biotechnology Leadership Forum, including Minister for Business and Enterprise Mark Prisk. The number of examples of a move to sustainable, biologically based chemicals production is growing apace. Readers may be interested in the Forum’s autumn newsletter, as well as a paper by NESTA on Financing Industrial Biotechnology in the UK. It would seem that Finance for Industrial Biotechnology is something that is mainly likely to come not from the Venture Capital sector but more from large corporates within the relevant sectors.

On Tuesday we were delighted to hear and welcome the Chancellor’s announcement of a series of investments in BBSRC and other UK science, and in particular the £80M announced for the further development of facilities at the Institute for Animal Health at Pirbright. We were also very pleased to welcome Minister for Universities and Science David Willetts to the Institute of Animal Health for discussions, where I was also attending the relevant Institute Assessment Panel.

There was also an announcement of more detail on the £158M investment in e-infrastructure that had been previously trailed. We anticipate that details of BBSRC’s components of that should shortly be available. This investment will provide a significant encouragement to the development of e-science that will be to the great benefit of UK biology.

As part of my reading, I have been revisiting an interest in the role of fluctuations in enzyme catalysis and bioenergetics (shockingly, that paper is 25 years old!), and reading a couple of crowd-sourcing papers on social mechanisms and motivation. Full Open Access matters, although I note an unwelcome vanity subset of Open Access scholarly publishers (some of whom have certainly spammed me). By contrast, a new high-quality Open Access journal called eLife is coming. I also enjoyed Athene Donald’s accurate portrayal of the multiplicity of jobs that can come one’s way.

• Carroll MW. 2011. Why full open access matters. PLoS Biol 9:e1001210. Full, free text
• Pickard G, Pan W, Rahwan I, Cebrian M, Crane R, Madan A, Pentland A: Time-critical social mobilization. Science 2011; 334:509-512
• Welch GR, Kell DB: Not just catalysts; the bioenergetics of molecular machines. In Welch G, .R. (ed.): The Fluctuating Enzyme. New York: John Wiley, 1986:451-492
• Welch GR (ed.): The fluctuating enzyme. New York: Wiley, 1986
• Williams Woolley A, Chabris CF, Pentland A, Hashmi N, Malone TW: Evidence for a collective intelligence factor in the performance of human groups. Science 2010; 330:686-688

Related posts (based on tags and chronology):

• Animal health, Eisai, institutes and infrastructure [31 October 2011]
• Announcements, speeches and animal health [14 February 2011]
• e-infrastructure and Higher Education [06 December 2010]
• Industrial biotechnology, e-infrastructure and systems biology [12 August 2010]
• Unilever, Institutes, TSB and Foo [06 February 2012]

I had the pleasure of attending the latest Schrödinger lecture, a masterful public lecture to a very mixed audience given by Sir Paul Nurse, PRS. I also attended a meeting of the Foundation for Science and Technology on “Stimulating economic growth by increasing the contribution from research, innovation and the Higher Education sector”, where the Panel of speakers were Sir Richard Lambert (audio), Dr Graham Spittle (audio), Catherine Coates (audio), and Minister for Universities and Science David Willetts (audio). The latter told me that he had recently read The Fourth Paradigm, a survey of the move towards what it refers to as data-intensive science; some of his comments implied that it had been a very careful and appreciative read, and not just a skim!

I enjoyed a thoughtful piece on how including sustainability in the UN’s Human Development Index – that one really should be doing – changes the ranking quite considerably, and another on how best to determine the ‘right’ charges for ecosystem services. Of course often the countries of manufacture are not the countries of use, and this applies especially to information and communication technologies.

The RCUK Research Outcomes System (ROS) was launched for all BBSRC Grant holders. A user guide section has been added to Research Outcomes, focusing on the three most common tasks. Each section contains a video tutorial and a step-by-step set of instructions. By watching the video, a user is able to see exactly how to perform a task such as uploading a research output/outcome or to set up a delegated user. I encourage folk to do so.

• Hey, T., Tansley, S. & Tolle, K. (2009). The fourth paradigm: data-intensive scientific discovery. Microsoft Research; Redmond, WA
• Kinzig AP, Perrings C, Chapin FS, 3rd, Polasky S, Smith VK, Tilman D, Turner BL, 2nd: Paying for ecosystem services: promise and peril. Science 2011; 334:603-604
• Togtokh C: Time to stop celebrating the polluters. Nature 2011; 479:269
• Williams E: Environmental effects of information and communications technologies. Nature 2011; 479:354-358

Related posts (based on tags and chronology):

• Unilever, Institutes, TSB and Foo [06 February 2012]
• Elixir, Roslin and HUBS [14 November 2011]
• Surfing, surnames and sustainability [22 August 2011]
• Norwich Research Park, genomics data and carbon sequestration [01 June 2011]
• Complexity, networks and reductionism [31 August 2010]

I managed to attend the dinner discussion of the first meeting of our new Exploiting New Ways of Working Panel, and also had a first meeting since his appointment with Tim Benton, the new Global Food Security Champion.

The horticulture industry is widely (and correctly) seen as an important contributor to a healthy diet, and also to the UK economy. Scientific understanding is a major means of assisting in the improvement of both facets. To this end, I enjoyed a very useful visit to East Malling Research located by the eponymous village in Kent. I was especially interested in the huge improvements in water usage (coupled to both yields and quality) that could be effected, as well as the knowledge emerging from the apple genome sequence. Given all the positive drivers involving food security, horticulture, sustainability, perenniality, climate change and so on, as well as science drivers such as omics technologies, one can only anticipate a substantial increase in opportunities in this space.

I also enjoyed seeing an excellent play at Oxford entitled The Two Cultures, based in part on the famous 1959 Rede Lecture of that name given by CP Snow (on whose 50th anniversary I also blogged).

Other things that I read included:

• an interesting paper on the structure of nitrogenase, including a commentary stating “What the team has done would appear to be a classic case where new technology leads to new science.”
• “86 Helpful Tools for the Data Professional PLUS 45 Bonus Tools”
• an uncomfortably accurate sideways take on what the British mean by various phrases
• a blog on the likely size of the data deluge – 8 zettabytes by 2015!

I also note the Position Statement on Food Security and Safety (PDF) from the Society for General Microbiology, an interesting editorial at Nature Biotechnology on ‘Big Ideas and Grand Challenges’ (written for the US – but presumably useful for any other – Bioeconomy), and the announcement by Minister of Universities and Science David Willetts of a joint program with India in sustainable bioenergy research.

• Anon: Big ideas and grand challenges. Nat Biotechnol 2011; 29:951
• Lancaster KM, Roemelt M, Ettenhuber P, Hu Y, Ribbe MW, Neese F, Bergmann U, DeBeer S: X-ray emission spectroscopy evidences a central carbon in the nitrogenase iron-molybdenum cofactor. Science 2011; 334:974-977
• Velasco R, et mult al.: The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet 2010; 42:833-839. Link to Applegenome.org

Related posts (based on tags and chronology):

• Announcements, speeches and animal health [14 February 2011]
• That was the week that was…and the year [14 December 2009]
• Science and Technology in Society Forum 2009 [07 October 2009]
• Horticulture, fellowships and informatics [14 September 2009]
• Warwick, BioIndustry, JISC and outreach [30 January 2012]