A platform for in silico modeling of physiological systems II. CellML compatibility and other extended capabilities

The number of biological models published in peer reviewed journals and complexity of each of those models are rapidly increasing, making it difficult to reproduce simulation results of the published models and to reuse the models by third persons. This paper is a continuation of our previous report on a software platform development as a solution to such difficulties. We describe progresses of our development. Those include improvement in functional capabilities to import and simulate published models in the CellML model repository, to browse and edit CellML models and then to export them as new models either with the CellML format or with a XML format defined for our platform (ISML), and to newly construct large scale models by connecting CellML/ISML models. Several advantages to use ISML in parallel with CellML are; 1) ISML can deal with geometry (morphology) of a model, enabling the user to perform geometry dependent modeling and simulations. 2) ISML can deal with time series data, both simulated and experimentally acquired data, for visualization of dynamics.