What is PhysioDesigner?
An open platform for multilevel modeling
PhysioDesigner is an open platform for supporting multilevel modeling of physiological systems in the field of integrated life-science and systems biology, including physiology, neuroscience and so on. 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 is stored in PHML(Physiological Hierarchy Markup Language) format which is an XML-based specification, to describe wide variety of models of biological and physiological functions with hierarchical structure. PHML fully inherits the specification from insilicoML (ISML). PhysioDesigner can act as an editor and browser of the models written in PHML and ISML. Besides that, PhysioDesigner can import models written in CellML format and export into it (some of model expressions in ISML cannot be exported into CellML).
One of distinguished feature of PhysioDesigner, it provides a function for users to create SBML-PHML hybrid models, which is a novel way to create multi-level physiological systems. Besides, it is possible to integrate morphological data in a model.
Simulations of the models created by PhysioDesigner can be performed by a simulator called Flint, which is bundled in the PhysioDesigner package. There are other ways to run simulations. PhysioDesigner can export C++ and JAVA source codes including numerical integration solvers. Thus users can perform simulations easily by compiling them. Finite element simulation for partial differential equations can be done by exporting PHML into FreeFem++ script. Users can perform finite element simulation by running the script on FreeFem++.
PhysioDesigner is a successor of insilicoIDE (ISIDE) which has been developed since 2007 till 2011. After that, all functions implemented on ISIDE were re-implemented on PhysioDesigner, and new functions were added. Details of development history is here.