Both CellML and OpenCOR are continuing to be developed. These notes will be updated to reflect new features of both. The next release of OpenCOR (0.5) will include
- the SED-ML API which means that all the variables controlling the simulation and its output can be specified in a file for that simulation
- the BioSignalML API which will allow experimental data to be read into OpenCOR in a standardised way
- colour plots, to better distinguish overlapping traces in the output windows
Priorities for later releases of OpenCOR include the incorporation of GIT into OpenCOR to enable the upload of models to PMR, graphical rendering of the model structure (using SVG), model building templates, such as templates for creating Markov models, tools for parameter estimation and tools for analysing model outputs.
The next release of CellML (1.2) will include the ability to specify a probability distribution for a parameter value. Together with SED-ML, this will allow OpenCOR to generate error bounds on the solutions, corresponding to the specified parameter uncertainty.
Link to weblab.
These notes are currently being extended to include
- a discussion of system identification and parameter estimation
- more extensive discussion of membrane protein models
- CellML modules for signal transduction pathways