Abstract

Molecular interactions are wired in a fascinating way resulting in complex behavior of bio-logical 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 interac-tions. A suitable conceptual tool to attack complexity is compositionality, already success-fully 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 si-mulate high-level descriptions of biological circuits. Gillespie’s stochastic simulation algo-rithm applied for BlenX simulations requires the decomposition of phenomenological func-tions into basic elementary reactions. Systematic unpacking of complex reaction mechanisms into BlenX templates is shown. The estimation/derivation of missing parameters and the challenges emerging from compositional model building in stochastic process algebras are discussed. A biological example on circadian clock is presented as a case study of modeling.