Biomedical Engineering Reference
In-Depth Information
Fig. 8.3. A screen-shot of the Open Source software OpenCell. This is one of a number of soft-
ware programs that read and write CellML files and run simulations (www.cellml.org/tools). The
particular model displayed here is the human cardiac electrophysiology model [49] - see www.
cellml.org/models/tentusscher noble noble panfilov 2004 version05. (Reproduced with permis-
sion from [49])
access to a local file browser;
access to a file organiser to virtually arrange files (e.g. a virtual folder that contains
a symbolic link to all the CellML files used in a given modelling study).
Editing files
Editing of a CellML file is possible using one of several views:
-
a raw XML view and a COR-like view (i.e. a compact format, see cor.physiol.
ox.ac.uk);
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an improved COR-like view (i.e. a COR-like view without CellML-specific
concepts such as public/private interfaces, encapsulation hierarchy and con-
nections);
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a tree-like view (with the ability to show/hide various CellML features);
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a graphical view (using SVG or cmgui, and based on the metadata/ontology
information present in a CellML file).
Graphical rendering of unit/variable definitions, mathematical equations, etc.
CellML validation (list of warnings/errors highlighting a particular problem).
Basic metadata support (i.e. model authors/description/curators, etc.).
Advanced metadata support so that, using domain-specific ontologies (through
RICORDO), models can be comprehensively annotated.
Visual difference of two CellML files (only for text-based views).
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