Biomedical Engineering Reference
In-Depth Information
The general strategy for developing the modelling standards is as follows:
•
develop markup languages (MLs) for encoding models, including metadata, and
data;
•
develop application programming interfaces (APIs) for interacting with the MLs;
•
develop libraries of open source tools that can read and write ML-encoded files;
•
develop data and model repositories based on the MLs;
•
develop reference descriptions to demonstrate model reproducibility;
•
develop services/libraries for a variety of tasks including access to automated
scripts to run the models and compare results against experimental data, optimize
parameter values for new experimental data and provide sensitivity analyses for
changes in model parameters.
Fig. 8.1 provides an overview of how the standards, tools and databases work to-
gether. Models at the cell, tissue or organ level are encoded in the CellML, SBML
or FieldML standards (using Open Source tools) and deposited in model reposito-
ries. These models are curated (to ensure consistency of units and other checks on the
validity of the models) and annotated (to provide controlled vocabulary annotations
for the variables and parameters in the model). A model can then be loaded from
a database into the simulation environment: e.g. cmgui, GIMIAS or OpenCMISS
Fig. 8.1.
The overall framework for the use of the software tools, together with the model and data
repositories based on the VPH/Physiome standards
