CellML Tools page updated

New software has been added to the CellML Tools index, including: Chaste, CellMLGUIgo, MatLab CellML tools, and CellML <-> SBML XSLT converters

The CellML Tools page has been updated with the following additions:

Chaste is a general purpose simulation package aimed at multi-scale, computationally demanding problems arising in biology and physiology. Current functionality includes tissue and cell level electrophysiology, discrete tissue modelling, and soft tissue modelling. The package is being developed by a team mainly based in the Computational Biology Group at Oxford University Computing Laboratory, and development draws on expertise from software engineering, high performance computing, mathematical modelling and scientific computing. Chaste uses CellML to specify cardiac ionic cell models, which are automatically translated into optimised C++ code using PyCml.

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.

runMatLabCellML (written by David Cumin, Auckland Bioengineering Institute) — runs a CellML model as exported from COR. To use this utility, first load a CellML model in COR and export it as MatLab.

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.

CellML to SBML - an XSLT conversion tool developed by the Biomodels Database group.

SBML to CellML - an XSLT conversion tool developed by the Biomodels Database group.

If you have a tool that uses or works with CellML, and you would like to add it to the CellML Tools listing, please contact James Lawson.