Biomedical Engineering Reference
In-Depth Information
in the case of the FieldML model repository; OpenCMISS or OpenCell/OpenCOR
in the case of the CellML model repository. Population data is stored in a separate
atlas database along with the medical images (in DICOM format). Another XML
standard called SED-ML is being developed to specify the numerical simulation
itself, including the choice of numerical algorithm. Time varying signal data en-
coded in the BioSignalML format is stored in a separate database that can also be
accessed from the computational software environments (OpenCMISS and Open-
Cell/OpenCOR) via an API. Finally, genomic and proteomic bioinformatic data is
accessed from a number of databases via a separate API. Details on these standards,
tools and databases are presented in the following sections (Hunter and Viceconti,
2009).
8.3 Syntax and semantics of VPH/Physiome models
Key steps that have been taken in the last 10 years to help improve the robustness
and reproducibility of published models are the development of specifications for
the “minimum information” needed for a model, and the development of model en-
coding standards so that a model can be checked and implemented in a completely
automated fashion.
Minimum information specifications exist for experimental measurements in spe-
cific areas and a web site at mibbi.org has been established to provide a portal for
these and for model annotation. Note that MIBBI is an acronym for “Minimum In-
formation about a Biomedical or Biological Investigation”. Examples of minimum
information standards for biological modelling are MIAME (“Minimum Informa-
tion about a Microarray Experiment”), MIRIAM (“Minimal Information Required
In the Annotation of biochemical Models” - see also biomodels.net/miriam) and
MIASE (“Minimum Information About a Simulation Experiment” - see biomod-
els.net/miase).
Several standards for encoding models have been developed over the past ten
years. They typically use the eXtensible Markup Language (XML) standard devel-
oped by the WorldWide Web consortium (www.w3c.org), as well as a variety of
other XML-based standards, such as MathML for encoding mathematics.
Two XML-based model encoding standards are currently being developed un-
der the VPH/Physiome Project (Hunter and Borg, 2003; Hunter and Nielsen, 2005):
CellML (www.cellml.org) is designed to encode lumped parameter biophysically
based systems of ordinary differential equations (ODEs) and both linear and non-
linear algebraic equations - together called differential algebraic or DAE systems
(Cuellar et al., 2003). FieldML (www.fieldml.org) is designed to encode spatially
and temporally varying field information such as anatomical structure, the spatial
distribution of protein density or computed fields such as the electrical potential or
oxygen concentration throughout a tissue (Christie et al., 2009). A third markup
language called the 'Systems Biology Markup Language' or SBML (sbml.org) has
been developed by the systems biology community. This has similar expressiveness
