BBSRC Systems Biology Grantholder Workshop, University of Nottingham, 15 December 2008.
This is the third BBSRC grantholders' workshop for systems biology. The participants include grantholders and their staff; people connected with the activities of the 6 SB centres; guests from BBSRC-sponsored institutes; guests from outside of these institutes; and finally, members of the BBSRC peer-review panels. Why is this workshop happening? It's an opportunity for sponsors and participants to discover and say how things are going; also interested in everyone sharing experiences with colleagues; and, of course, to talk about new ways to solve biological problems. I'll be providing my notes on most of the talks that are given over the next few days.
Now for my notes on the updates from the directors of the six Centres for Integrated Systems Biology (CISBs).
CISBAN (Tom Kirkwood): Why and how do we age? Limited investment in cell maintenance (the disposable soma theory). Ageing is caused primarily by damage, and longevity is regulated by resistance and repair. There are multiple mechanisms: it is a highly complex system which is inherently stochastic. There are a number of interesting questions that revolve around optimality, plasticity, and trade-offs. Now involved as an academic partner in the EU network of excellence, LifeSpan. One area of major research within CISBAN is that of telomere length homeostasis. Work includes high-throughput (HT) yeast robot experiments, which has led to the identification of a large number of genes that affect telomere maintenance. CISBAN also studies the intrinsic ageing of mammalian cells, where there is considerable cell-to-cell heterogeneity. Research has shown that it is much more than just telomere erosion: there is significant crosstalk between telomere and, for example, mitochondrial dysfunction. He also gave an overview of BASIS, a web application that allows the researcher to upload SBML models and run simulations on the BASIS server. There is a large amount of research going on within CISBAN that has a statistical focus, and there is also work going on with respect to data integration.
CISBIC (Brian Robertson): CISBIC focuses on host-pathogen interactions, and contains 3 exemplar sub-projects. They have core facilities in glycoproteomics, metabolomics, transcriptomics and cell imaging. They are interested in combating disease in both plants and animals. They use infection as a perturbation to study host biology, mainly focusing on the interaction between the microbe and the innate immune response. They have tried very hard to create a community of systems biologists, and also have collaborations with people outside the centre. Top questions from experimental biologists: "How do I start in SB?", "How do I start modelling?", "Which modelling approach should I take?". They're considering starting a summer school to train people.
CPIB (Charlie Hodgman): Began with a nice screencast/automated slideshow of pictures and work going on at CPIB. Main research works on plant roots, and how they respond to external stimuli. The research program is split into 4 strands: root cell elongation, root apical meristem, lateral root development, and an integrated root model. Models they are developing include: static and dynamic network modelling, biomechanical modelling, tissue-scale computational modelling, and more. Technological developments include vertical-stage confocal imaging, automated focusing time-lapse microscopy. Outreach work includes: advanced hormone-transport workshop in May 2008, and had their first plant modelling summer school in September 2008. In December 2007 there had a Maths and Plant Sciences Study Group.
CSBE (Igor Goryanin): This centre is focused on dynamic biological systems rather than on any particular biological project. They are concentrating on cell-to-cell interactions, and their main aim is to streamline the modelling process. Mentioned the Bio-PEPA Eclipse Plug-in, which can run simulations within Eclipse.
MCISB (Hans Westerhoff): Focus on one project, using S. cerevisiae: they want to make SB work, in a complete sense. This means from the individual sequences right up to modelling a complete cell.
OCISB (Judy Armitage): Their remit is to build upon the strengths of groups within Oxford to provide a focus for the catalytic development of a wide range of systems approaches. They were trying to understand, predic ad control physiological behaviour by integrating knowledge of interactions at the molecular, cellular and population levels. Their initial core testbeds are: bacterial chemotaxis and sensory transduction, cell cycle, hypoxia and the Trypanosome flagellum. New projects include: plant metabolomics and signalling, extracellular matrix, t-cell signalling, diversity of host responses in malarial infection, meiosis, biofilm development and synthetic signaling networks. They're also doing more work in outreach, including open seminar series and one-day workshops.
I really liked how each of the directors thought it was important to point out the outreach – it is an opinion I share. Additionally, what was interesting is that every director made a specific point of how their Centre was quite unusual in the amount of interchange and multidisciplinary research they do. This type of collaboration has traditionally been very rare, and the Centres were originally quite unusual in that regard. However, what is gratifying is that, in order to be successful in SB, outreach and collaboration have become a necessity, and I am hearing them talked about much more these days. Perhaps those directors can now all remove the word "unusual" from the next versions of those presentations. Wouldn't that be nice? 🙂
These are just my notes and are not guaranteed to be correct. Please feel free to let me know about any errors, which are all my fault and not the fault of the speaker. 🙂
the mind wobbles 