Prof. Douglas Kell, School of Chemistry, and The Manchester Interdisciplinary Biocentre, University of Manchester, 131 Princess St, MANCHESTER M1 7DN, U.K. Tel: 0161 306 4492 Fax: 0161 306 4556 [email protected] http://dbkgroup.org 31/01/2009 TO WHOM IT MAY CONCERN myExperiment Enhancement Proposal I am very pleased to know that an opportunity has risen for the continued funding of the myExperiment project. myExperiment provides an important resource by supporting new types of digital items such as workflows, and has also demonstrated to the community the value of taking a social network approach which facilitates discovery, sharing and curation rather than simply making items available in a repository. The project gives an important insight into supporting the new forms of research practice that are already being adopted by the next generation of researchers. I am pleased to be able to write in support of the myExperiment enhancement proposal. I have followed this work from the very beginning, and the idea (and utility) of sharing workflows is absolutely crucial to rolling out the ‘bioinformatics for everyone who cannot program’ agenda. I say this as an early adopter myself (see e.g. Kell, D. B. (2006). Metabolomics, modelling and machine learning in systems biology: towards an understanding of the languages of cells. The 2005 Theodor Bücher lecture. FEBS J 273, 873-894), and as someone who has hosted some of the myExperiment team in my lab so that they can see how ‘working biologists’ approach their experiments (both wet and dry). Indeed my group has contributed a considerable number of workflows to the myExperiment repositories, including some referred to in the following recent papers: Li, P., Oinn, T., Soiland, S. & Kell, D. B. (2008). Automated manipulation of systems biology models using libSBML within Taverna workflows. Bioinformatics 24, 287-289. Li, P., Castrillo, J. I., Velarde, G., Wassink, I., Soiland-Reyes, S., Owen, S., Withers, D., Oinn, T., Pocock, M. R., Goble, C. A., Oliver, S. G. & Kell, D. B. (2008). Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially expressed genes from microarray data. BMC Bioinformatics 9, 334. 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. The ability to share and reuse (and combine elements) of these workflows is an absolutely invaluable resource, and this approach is at the very forefront of the ‘new biology’. I am pleased to be able to continue to collaborate with myExperiment, including by making available many of our own tools and data as Web Services for inclusion in our carefully tested workflows (see also the ‘community consensus’ approach we have pioneered for metabolic network reconstruction Herrgård, M. J., Swainston, N., Dobson, P., Dunn, W. B., Arga, K. Y., Arvas, M., Blüthgen, N., Borger, S., Costenoble, R., Heinemann, M., Hucka, M., Le Novère, N., Li, P., Liebermeister, W., Mo, M. L., Oliveira, A. P., Petranovic, D., Pettifer, S., Simeonidis, E., Smallbone, K., Spasić, I., Weichart, D., Brent, R., Broomhead, D. S., Westerhoff, H. V., Kırdar, B., Penttilä, M., Klipp, E., Palsson, B. Ø., Sauer, U., Oliver, S. G., Mendes, P., Nielsen, J. & Kell, D. B. (2008). A consensus yeast metabolic network obtained from a community approach to systems biology. Nature Biotechnol. 26, 1155-1160). Continued funding of myExperiment will enable us to continue our collaboration (I am still working 0.2 FTE as an academic, while performing my new duties at BBSRC for 0.8 FTE). This is very timely as myExperiment has now gathered a significant momentum and this provides an opportunity to extend myExperiment’s innovations in the wider repository context. We look forward to continuing our collaboration through joint meetings and exchange of ideas, skills and expertise. It most desirable that the myExperiment program continue, and I am pleased to give the myExperiment team my full support. I wish you all success with your application. Very best, Yours ever, Douglas Kell Professor of Bioanalytical Science .