Meetings & Conferences Software and Tools

An Intuitive Automated Modelling Interface for Systems Biology (BioSysBio 2009)

O Kahramanogullari et al.
Imperial College London

He works on improving the modelling and inference step. He makes use of SPiM, which is a process algebra by Microsoft. Process algebra is used to study complex reactive systems, and therefore are well-suited to modelling biological systems. They have used this technique to build a process model of Rho GTPases with GDIs (Kahramanogullari et al. 2009 Theoretical Computer Science, in press).  They also created a process model for actin polymerisation (Kahramanogullari et al. 2009, Proc of FBTC08, Elsevier). Such structures can be written in process algebra when they would be extremely difficult with differential equation techniques.

Process algebra is very difficult for anyone to use directly. So, they've developed an intuitive language interface for modelling with SPiM. The assumption in this is that biochemical species are stateful entities with connectivity interfaces to other species. Further, a species can have a number of sites through which it interacts with other species, and changes its state as a result of these interactions. So, they allow descriptions of the model in a natural-language-like narrative language. Their tool is available for download from their website: .

Wednesday Session 1

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else's. I'm happy to correct any errors you may spot – just let me know!

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