Modeling environments

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.

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.