This blog is for a past version of the course. You can also consult the current MLCSB course web pages.
This is a level 11 course in The University of Edinburgh School of Informatics, suitable for postgraduate students. The course explores a variety of methods for modelling biological pathways, and introduces formally precise languages to describe and reason about biological processes. For further details see the course descriptor.
Students taking this course may be interested in Computational Systems Biology, also in Semester 2, as well as Synthetic Biology: Modelling from Semester 1.
The course lecturer is Ian Stark. The most effective way to contact him is by personal email to Ian.Stark@ed.ac.uk from your University email address.
In this course we explore a range of modelling methods for pathways in molecular biology: whether metabolic, signalling, regulatory or transcriptional. These models draw on a rich existing theory of concurrent computational systems, with Petri nets as a unifying basic concept. Techniques range over qualitative and quantitative, discrete and continuous, differential and stochastic models. Working with these models, we look at logics for specifying and characterizing systems’ behaviour. Finally, we investigate language-based approaches to modular description and analysis of systems, studying some computationally-inspired biological process calculi.