Rule-Based Modelling and Model Perturbation

摘要: Rule-based modelling has already proved to be successful for taming the combinatorial complexity, typical of cellular signalling networks, caused by combination physical protein-protein interactions and modifications that generate astronomical numbers distinct molecular species. However, traditional rule-based approaches, based on an unstructured space agents rules, remain susceptible other explosions mutated and/or splice variant agents, share most but not all their rules with wild-type counterparts; drugs, which must clearly distinguished from physiological ligands. In this paper, we define a syntactic extension Kappa, established platform, enables expression structured allows us express variants, families related proteins ligand/drug interventions uniformly. This also mode model construction where, starting current consensus model, attempt reproduce in numero mutational--and more generally perturbational--analyses were used process inferring those pathways first place.