Rule-Based Models for Signal Transduction, the HOG MAPK Pathway - a Case Study
The PhD project is on modeling signaling pathways in cells in a rule-based manner (Kappa). Defined as a graph-rewriting language, rule-based models allow a compact description of protein-protein interactions in spite of combinatorial number of protein complexes interacting in the cellular system. The overall project goals include developing formal frameworks for different computational semantics of rule-based programs. In particular, the focus is on the stochastic semantics, with the following two goals: (1) establishing formal theoretical grounds for (i) exact, as well as (ii) approximate automatic model reductions, and (2) applying the methods on a case study; The case study of particular interest is the osmotic stress pathway in budding yeast.
Keywords: Formal Methods, Signaling Pathways, Rule-based Models, Stochasticityback