A modeling tool for multilevel physiological systems


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An open platform for multilevel modeling

PhysioDesigner is an open platform that supports multilevel modeling of physiological systems in the field of integrated life sciences and systems biology, including physiology and neuroscience. Users can combine and build mathematical models of biological and physiological functions on PhysioDesigner. Users can also integrate morphometric data on a model, which is used, for example, to define a domain in which partial differential equations are solved.

The models developed by PhysioDesigner are stored in PHML (Physiological Hierarchy Markup Language) format, which is an XML-based specification, to describe a wide variety of models of biological and physiological functions with a hierarchical structure. PHML fully inherits the specifications from
insilicoML (ISML). PhysioDesigner can act as an editor and browser of the models written in PHML and ISML. It is also possible to import models written in CellML format and export models to CellML (some model expressions in PHML cannot be exported to CellML).

Another distinguishing feature of PhysioDesigner is that it provides a user function to create SBML-PHML hybrid models, which is a novel way to create multilevel physiological systems. In addition, morphological data can be integrated into the model.

Simulation of the models created by PhysioDesigner can be performed by the
Flint simulator, which is developed concurrently with PhysioDesigner. Simulations also can be run in other ways. PhysioDesigner can export C++ and JAVA source codes including numerical integration solvers. Thus, users can easily perform simulations by compiling them. Finite element simulation for partial differential equations can be done by exporting a model in FreeFem++ format and running the script on FreeFem++.

PhysioDesigner is a successor to
insilicoIDE (ISIDE), which was developed over the period from 2007 to 2011. Subsequently, all functions implemented on ISIDE were reimplemented on PhysioDesigner, and new functions were added. Details of the development history are here.