This blog is for a past version of the course. You can also consult the current MLCSB course web pages.
These first entries provide basic material for the course. The remainder of the references are divided into different specific areas, mostly focusing on applications to Systems Biology. I shall be adding material as the course proceeds — feel free to add your own recommendations in the comments.
- Darren Wilkinson, Stochastic Modelling for Systems Biology. Chapman & Hall/CRC, April 2006.
- Michael Huth and Mark Ryan. Logic in Computer Science: Modelling and Reasoning about Systems. CUP, 2004.
Chapter 3 covers LTL, CTL and model checking.
- Formal Methods for Computational Systems Biology. Advanced Lectures from SFM 2008, the 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, Bertinoro, Italy, June 2–7, 2008. Lecture Notes in Computer Science 5016, Springer-Verlag, 2008.
This summer school covered a range of topics relevant to MLCSB.
- Monika Heiner, David Gilbert, and Robin Donaldson. Petri Nets for Systems and Synthetic Biology. In Formal Methods for Computational Systems Biology, Lecture Notes in Computer Science 5016. Springer-Verlag, 2008.
- H. de Jong. Qualitative modeling and simulation of bacterial regulatory networks. In Computational Methods in Systems Biology: Proceedings of the 6th International Conference CMSB 2008, Lecture Notes in Bioinformatics 5307, p. 1. Springer-Verlag, 2008.
- P. T. Monteiro, D. Ropers, R. Mateescu, A. T. Freitas, and H. de Jong. Temporal logic patterns for querying dynamic models of cellular interaction networks. Bioinformatics, 24(16):227–233, 2008.
The first of these is an invited conference talk, giving an overview of some work on applying model-checking to problems in systems biology. The second is a more detailed article on the material.