title: Specifications of insilicoML 1.0: a multilevel biophysical model description language.
abstract: An extensible markup language format, insilicoML (ISML), version 0.1, describing multi-level biophysical models has been developed and available in the public domain. ISML is fully compatible with CellML 1.0, a model description standard developed by the IUPS Physiome Project, for enhancing knowledge integration and model sharing. This article illustrates the new specifications of ISML 1.0 that largely extend the capability of ISML 0.1. ISML 1.0 can describe various types of mathematical models, including ordinary/partial differential/difference equations representing the dynamics of physiological functions and the geometry of living organisms underlying the functions. ISML 1.0 describes a model using a set of functional elements (modules) each of which can specify mathematical expressions of the functions. Structural and logical relationships between any two modules are specified by edges, which allow modular, hierarchical, and/or network representations of the model. The role of edge-relationships is enriched by key words in order for use in constructing a physiological ontology. The ontology is further improved by the traceability of history of the model's development and by linking between different ISML models stored in the model's database using meta-information. ISML 1.0 is designed to operate with a model database and integrated environments for model development and simulations for knowledge integration and discovery.
authors.affiliation: The Center for Advanced Medical Engineering and Informatics, Osaka University, Japan.
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Asai
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Suzuki
authors.forename: Yoshiyuki
authors.initials: Y
authors.lastname: Kido
authors.forename: Hideki
authors.initials: H
authors.lastname: Oka
authors.forename: Eric
authors.initials: E
authors.lastname: Heien
authors.forename: Masao
authors.initials: M
authors.lastname: Nakanishi
authors.forename: Takahito
authors.initials: T
authors.lastname: Urai
authors.forename: Kenichi
authors.initials: K
authors.lastname: Hagihara
authors.forename: Yoshihisa
authors.initials: Y
authors.lastname: Kurachi
authors.forename: Taishin
authors.initials: T
authors.lastname: Nomura
mesh_terms: D000818:Animals; D001703:Biophysics / Q000379:methods*; D003198:Computer Simulation; D003628:Database Management Systems; D016208:Databases, Factual; D006801:Humans; D016247:Information Storage and Retrieval; D008954:Models, Biological; D011381:Programming Languages; D049490:Systems Biology; D018511:Systems Integration; D014584:User-Computer Interface