title: A generic representation format of physiological experimental protocols for computer simulation using ontology.
abstract: For computer simulations of physiological experiments using physiological models, a machine-readable format of experimental protocols is effective. Here, we propose an XML-based language, PEPML (Physiological Experimental Protocol Markup Language). In the PEPML, conditions and procedures of an experimental protocol are procedurally described as a list of events, each of which consists of a condition for execution and an action to be executed. Since variables used in a protocol can be specified using an ontology, the protocol can be applied to various models without editing tasks. The PEPML allows both application of multiple protocols to a single model and application of a single protocol to multiple models. This feature facilitates the efficient simulation for verifications, comparisons and utilizations of physiological models.
authors.affiliation: ASTEM Research Insutitute of Kyoto, Kyoto, 600-8813, Japan. simayosi@astem.or.jp
authors.forename: Takao
authors.initials: T
authors.lastname: Shimayoshi
authors.forename: Akira
authors.initials: A
authors.lastname: Amano
authors.forename: Tetsuya
authors.initials: T
authors.lastname: Matsuda
mesh_terms: D002468:Cell Physiological Phenomena; D003198:Computer Simulation; D019146:Hypermedia; D008954:Models, Biological; D010827:Physiology / Q000379:methods*