Last week I had a useful day at The Genome Analysis Centre, discussing the scientific opportunities for the Norwich Research Park and more generally. I also participated in part of a very interesting event on scientific storytelling, and some of the celebrations attendant on this year’s Diamond Jubilee winners of the Queen’s Anniversary Prize for Higher and Further Higher Education, where a welcome number of the winners were from our BBSRC-funded community. We also had a very good meeting with Tim Wheeler and colleagues at the Department for International Development, with whom we already co-fund a number of programmes such as SARID, CIDLID and SCPRID.

Stephen Curry in his recent comments on Open Access (OA) raised some important points relating to OA and the Research Councils, quoting BBSRC as an example (in his opinion) of things not working as well as they should. Anyone who knows me will know that I am a very strong supporter of Open Access and of text and data mining. Indeed, I have blogged quite often about Open Access (and have been known to write scholarly articles such as this and this) on the subject. There is no doubt that significant aspects of my own scientific work would be made much easier if all papers were freely available, and it is straightforward to give examples in areas such as genome-based metabolic network reconstruction, text mining for systems biology, and pulling together disparate literatures and synthesising inductive knowledge in pharmacokinetics, medicine and toxicology.
Continue reading: Genomics, prizes, DFID and Open Access

This week I shall blog about a number of papers that have appeared discussing various areas of Industrial Biotechnology, a chief driver of which is the recognition that in the very-foreseeable future fossil-derived sources of organic chemical feedstocks (petrochemicals) will have run out, and that they will need to be replaced by carbohydrates derived from recent photosynthesis. Some chemical intermediates to be produced in biorefineries are of especial interest. First up is an interesting survey of the use of l(a)evulinic acid as a sugar-derived feedstock for industrial biotechnology, also discussing two others that explore the use of chemicals derived from valero-lactone. It is probable (and there are modern examples such as Botryococcus braunii) that the alkanes and alkenes found in natural oil deposits were formed biosynthetically (as opposed to via the abiotic effects of physico-chemical forces on other kinds of biomass, to form coal), and an alternative approach seeks the reactions of alkane/alkene biosynthesis themselves, an approach discussed and realized by a group from the LS9 company. One of the most important platform technologies is the use of genome-scale metabolic network reconstructions, something on which I am personally very keen (especially when they are encoded in a semantically accurate manner). A recent review highlights their utility in improving the productivity of biotechnological processes.
Continue reading: Industrial biotechnology, e-infrastructure and systems biology

One of the biggest problems confronting science right now is how we deal with the floods of data (not least genomics data), and in particular how we visualise them. En route to the Science Foo camp (SciFoo) held at the Googleplex over last weekend, I was privileged to be shown, by its curator Bonnie DeVarco and her collaborator Eileen Clegg, a wonderful exhibition of scientific visualisations (data visualisations) at MediaX at Stanford. It is also online.
Continue reading: Scientific data visualisation and #SciFoo09

One of the consequences of the flood of text and data increasingly available digitally is the need for effective means for summarising and visualising their content. One simple metric is based on the frequency of words (or indeed tags, such as those done collaboratively – a folksonomy), and a widely used visualisation device (a simple one based on tags is also used as a search device in these blog pages) is the word cloud or Wordle, in which frequency is encoded by the font size of a word. More sophisticated versions are based on text mining, and recognise phrases and terms rather than single words alone.
Continue reading: What’s in a name? A tag cloud of recent blogs

Science (whose etymological origin means ‘knowledge’) is supposed to be based on objective and verifiable facts, but as I have blogged before there can occasionally be a tendency to groupthink. This is a phenomenon in which, simply by multiple repetition of them, ‘facts’ become widely ‘known’ after a while, even when they have no or limited experimental basis (something easily amplified via the Internet). (I experienced a related issue during my D. Phil., where I traced back a series of literature references to a widely cited claim that the purportedly passive concentrative uptake ratio of a particular lipophilic cation into Escherichia coli was independent of its external concentration over a huge range.
Continue reading: Surely everyone knows this?….except that they are wrong