Modeling environments
Native CellML environments
These tools use CellML natively. They are capable of model creation, editing, simulation, validation, and visualisation.
OpenCOR
OpenCOR is a cross-platform modelling environment, which is aimed at organising, editing, simulating and analysing CellML files on Windows, Linux and macOS. It is an open source environment (released under the Apache v2.0 license) being developed at the Auckland Bioengineering Institute. The latest available release is OpenCOR 0.5.
OpenCell (deprecated in favour of OpenCOR)
OpenCell is an open source environment that was developed at the Auckland Bioengineering Institute. It makes use of the CellML API. It is built on top of the Mozilla platform. The last available release is OpenCell 0.8.
Cellular Open Resource (COR) (deprecated in favour of OpenCOR)
COR is a Windows environment for cellular modelling that is built around CellML. It was developed by Alan Garny, from whom you can still get a copy of the software.
Other modelling environments
The following modelling environments differ from full CellML environments in that they are not based entirely on CellML but rather offer various levels of support for utilising CellML. These environments provide tools for the support of general mathematical modelling as well as interfaces specific to certain areas of biological modelling.
JSim
JSim is a Java-based simulation system for building quantitative numeric models and analyzing them with respect to experimental reference data. JSim's primary focus is in physiology and biomedicine, however its computational engine is quite general and applicable to a wide range of scientific domains. JSim models may intermix ODEs, PDEs, implicit equations, integrals, summations, discrete events and procedural code as appropriate. JSim's model compiler can automatically insert conversion factors for compatible physical units as well as detect and reject unit unbalanced equations. JSim also imports the SBML and CellML model archival formats.
JSim is developed by the National Simulation Resource for Transport, Metabolism and Reaction at the University of Washington.
Virtual Cell
The Virtual Cell is developed at the National Resource for Cell Analysis and Modeling (NRCAM) located at the University of Connecticut Health Center. It is a tool to build models and run simulations of cellular processes, including the modelling of reactions, diffusion, membrane transport, flow, electrical potential and currents. VCell has the facilities for compartmental and spatial simulations (1-, 2-, and 3-dimensional) on analytical or image-based geometries. It provides a collaborative working environment via a shared database, and interoperability through the use of various data formats (including CellML and SBML).
insilicoIDE
The insilicoIDE is developed at the Center for Advanced Medical Engineering and Informatics at Osaka University. It is a tool to browse, build and run simulation models of physiological dynamics. It can import models in CellML format. It is used for exploring the hierarchical structure of models, editing, modifying, and networking models, and for simulating dynamics of models.
Myokit :: The Maastricht Myocyte Toolkit
The Maastricht Myocyte Toolkit, myokit for short, is a software package designed to simplify the use of numerical models in the analysis of cardiac myocytes. Specifically, models that can be formulated as an ODE. Myokit allows partial CellML model definitions to be imported, with particular focus on the types of models and expressions common in the electrophysiological models in the model repository.
CellMLGUIgo
CellMLGUIgo is a graphical editor for CellML 1.0 models written by David Cumin. This application will open a CellML file and display each component as a rectangle, with variables shown within; public interface:in variables on the left, public interface:out on the right, and others in the middle. Connected variables are linked with lines. Users can create components and variables within them, connect variables, and edit the math parts of the component (although this functionality is still under development). The colour of the represented components and variables can also be changed. When a CellML file is saved, XML attributes describing the visual representation of the CellML file within CellMLGUIgo are added. This application is written in Java and can be run using the Java Runtime Environment.
Miscellaneous modeling tools
fitMatLabCellML (written by David Cumin, Auckland Bioengineering Institute) — performs parameter estimation on a CellML model as exported from COR. To use this utility, first load a CellML model in COR and export it as MatLab.
