CellML and CESE
 PDF version |
The current version of CESE contains a preliminary support for models described using the CellML (http://www.cellml.org) format. CellML describes model equations and variables using extensive markup language (derived from the content MathML specification). It also provides support for describing model structure (i.e. how model components, such as currents and ionic storages, in case of electrophysiological models) relate to one another, and how they are interacting.
CESE provides means to extract model equations and variables and to convert CellML code into the Java source files, conforming to the JavaBeans specification.
This source code can afterwards be verified, compiled, and packaged similar to the regular CESE model.
Usage
CellML to CESE model transformation remains extremely experimental at this stage. It is targeted to CESE developers who want to to try the conversion routine and improve it. Only partial support for CellML 1.0 is available.
If you want to try the code, download some example CellML models from the CellML repository at http://www.cellml.org.
Copy the downloaded XML files to $CESE_HOME/bin/cellml.
Run a transformation script located in the $CESE_HOME/ directory, using model's name as a parameter (do not specify the full path), for example:
sm:~/sources/cese> ./cellml.sh beeler_reuter_model_1977.xml Converting: beeler_reuter_model_1977.xml Source: /home/smissan/sources/cese/bin/cellml/beeler_reuter_model_1977.xml Destination: /home/smissan/sources/cese/bin/cellml/beeler_reuter_model_1977.java
The model Java source code is now located in the $CESE_HOME/bin/cellml directory. Verify the code, and send reports about problems and inconsistencies to support@simulogic.com.
Status
CellML to CESE model transformation uses heavily-modified and updated XSL stylesheet developed by Mathml-X project. It scans the CellML source code and extracts all variables, wrapping them in getters and setters according to the JavaBeans specification.
The equations are converted from MathML to Java notation, and placed in the correspondent methods. The support for the content MathML is extensive, but still incomplete.
Initial variable values are extracted and properly assigned.
Some basic metadata is extracted and placed in the source code as Java comments.
CellML denotes the hierarchical structure of the model components. Currently, cellml2Java stylesheet extracts components as a flat list.
CellML units are not supported.
CellML reactions are not supported.
Compatibility
Certain key parameters in CellML models have different names compared to CESE models. These include V, time, dtime (all in CellML notation).
Future work
Beta version of the CellML transformer is included in the current version of CESE. BeanInfo creation and packaging is still manual at this stage.