Biomedical Engineering Reference
In-Depth Information
to be validated. Errors and warnings can be representational (invalid XML or ele-
ments in the wrong place) or semantic. Dimensional inconsistency on connections
is an error; dimensional or units inconsistency in equations triggers warnings. The
SED-ML processing Service (
SproS)
provides a way to access SED-ML descrip-
tions of simulation experiments (see below) from the CellML API. Currently this is
just the object model (SED-OM), but more services for fully processing SED-ML
descriptions referencing CellML models are planned.
Note that the API provides parsing of RDF for query lookup and provides ac-
cess to all RDF in a model. Planned future developments include better support for
interpreted languages (e.g. dynamic querying of interfaces supported by an object),
better SED-ML support, more language bindings and many other planned items -
see tracker.physiomeproject.org. For the current draft of the CellML metadata spec-
ification, see cellml.org/specifications/metadata/mcdraft.
8.5 OpenCell/OpenCOR
OpenCell is a software environment for working with CellML models (authoring,
visualizing, simulating). It is Open Source
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and written in C++, hosted on Source-
Forge, and uses the Mozilla XUL framework (www.opencell.org). An example of
the graphical interface is illustrated in Fig. 8.3
A new version of OpenCell is being developed based on Qt/C++ and to distin-
guish this project from the previous XUL/C++ project, the software is currently called
'OpenCOR' (opencor.ws). OpenCOR is developed, built, tested and packaged on
Windows 7, Ubuntu 11.4 (Natty Narwhal; both the 32-bit and 64-bit versions); and
Mac OS X 10.6 (Snow Leopard).
OpenCOR will be used to organise, edit, simulate and analyse CellML and, in the
future, SBML files. Some general features are:
•
available both as a command line tool and through a graphical user interface;
•
fully customisable and multi-lingual interface;
•
support for automatic updates (both for development and release versions);
•
access to the CellML Model Repository and BioModels Database through web
services;
•
support for ontologies through web services to RICORDO and support for SED-
ML;
•
two-dimensional (2D) and 3D representation of a model (using SVG and cmgui,
respectively).
Some more specific features are as follows:
Organising files
•
Access to the CellML Model Repository and BioModels Database to search, down-
load, upload, etc. a model;
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Distributed under a tri-licence MPL, GPL or LGPL.
