PhD Thesis Compositional Modeling of biological Systems


Molecular interactions are wired in a fascinating way resulting in complex behavior of biological systems. Theoretical modeling provides us a useful framework for understanding the dynamics and the function of such networks. The complexity of the biological systems calls for conceptual tools that manage the combinatorial explosion of the set of possible interactions. A suitable conceptual tool to attack complexity is compositionality, already successfully used in the process algebra field to model computer systems. We rely on the BlenX programming language, originated by the beta-binders process calculus, to specify and simulate high-level descriptions of biological circuits. Gillespie’s stochastic simulation algorithm applied for BlenX simulations requires the decomposition of phenomenological functions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown. The estimation/derivation of missing parameters and the challenges em

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J. Zamborszky