Transactions on Computational Systems Biology XII: Special Issue on Modeling Methodologies

abstract action activation actual allows amount analysis annotation application approach associated assume attributed average behaviour binding Bio-PEPA biological bound branching cell changes channel chemical codon communication compartment complex components computational consider constants constraints contains corresponding cytoplasm defined definitions denotation depth described different environment evaluate example exists expressions extended first formal function gene given hairpin identifiers indices initial interaction interface language located modification module molecules mRna multiset names normal form Note objects obtained ODEs operator output parameters pathway Petri nets population possible present priorities protein reactions receiver relation represent respectively ribosome Rnap rule runs semantics signal simulation single species expressions species values steps stochastic structure syntax transcription transitions translation updated variables