Models and Languages for Computational Systems Biology

Review and comparison of the syntax and semantics of temporal logics LTL and CTL. Distinction between the direct observability of individual runs, and the assessment of alternative possibilities in branching-time logics like CTL. Valuation of CTL formulae on specific transition systems. Distinct expressiveness of LTL and CTL: example to show AF AG is not AFG.

Link: Slides (with CTL valuation table corrected)

Reading

Two items to read for Thursday:

• 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.

  You can get the slides from this talk here

• 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.

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