[Show abstract][Hide abstract] ABSTRACT: Physiome and systems biology have been recognized as emerging and important research areas that can integrate quantitatively growing knowledge about biological structure and physiological functions at multiple scales of time and space. For the integration, it is important to build physiologically plausible and sharable mathematical models that can be used for dynamic simulations of functions at multi-scale and multi-level. Here we describe new features of our open platform insilicoML (ISML) and insilicoIDE (ISIDE) that have been presented previously. The platform can support reuse existing mathematical models of physiological functions in the model databases, to construct brand new models, and to simulate models. The major new features of the platform include improvement of the capabilities to incorporate experimentally obtained data such as time-series and morphological data with dynamic simulation of models that may be driven by the data, and extension of variety of model types that can be described by ISML and simulated on ISIDE, such as multi agent systems and models described by partial differential equations that are solved by the finite element method.
Full-text · Article · Jan 2009 · Conference proceedings: ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference
[Show abstract][Hide abstract] 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.
Full-text · Article · Dec 2008 · The Journal of Physiological Sciences