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.