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FieldML: concepts and implementation.

Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ - Philos Trans A Math Phys Eng Sci (2009)

Bottom Line: It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems.It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems.It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand. r.christie@auckland.ac.nz

ABSTRACT
The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

Show MeSH
Example model hierarchies from bioengineering: (a) composite model of heart and lungs and (b) hierarchy of skeleton lower limb.
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fig3: Example model hierarchies from bioengineering: (a) composite model of heart and lungs and (b) hierarchy of skeleton lower limb.

Mentions: Modellers and modelling software may assign whatever meaning to each model object as deemed appropriate. FieldML models may correspond to parts and assemblies in computer-aided design data. In the modelling of organs and other biological systems, it may be practicable to use a single model to represent a whole organ or cell, or alternatively encapsulate distinct parts into submodels. The musculoskeletal system fits well into model hierarchies matching traditional anatomical classifications. Two examples of model hierarchies are given in figure 3.


FieldML: concepts and implementation.

Christie GR, Nielsen PM, Blackett SA, Bradley CP, Hunter PJ - Philos Trans A Math Phys Eng Sci (2009)

Example model hierarchies from bioengineering: (a) composite model of heart and lungs and (b) hierarchy of skeleton lower limb.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2665020&req=5

fig3: Example model hierarchies from bioengineering: (a) composite model of heart and lungs and (b) hierarchy of skeleton lower limb.
Mentions: Modellers and modelling software may assign whatever meaning to each model object as deemed appropriate. FieldML models may correspond to parts and assemblies in computer-aided design data. In the modelling of organs and other biological systems, it may be practicable to use a single model to represent a whole organ or cell, or alternatively encapsulate distinct parts into submodels. The musculoskeletal system fits well into model hierarchies matching traditional anatomical classifications. Two examples of model hierarchies are given in figure 3.

Bottom Line: It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems.It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems.It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

View Article: PubMed Central - PubMed

Affiliation: Auckland Bioengineering Institute, University of Auckland, Auckland 1142, New Zealand. r.christie@auckland.ac.nz

ABSTRACT
The field modelling language FieldML is being developed as a standard for modelling and interchanging field descriptions in software, suitable for a wide range of computation techniques. It comprises a rich set of operators for defining generalized fields as functions of other fields, starting with basic domain fields including sets of discrete objects and coordinate systems. It is extensible by adding new operators and by their arbitrary combination in expressions, making it well suited for describing the inherent complexity of biological materials and organ systems. This paper describes the concepts behind FieldML, including a simple example of a spatially varying finite-element field. It outlines current implementations in established, open source computation and visualization software, both drawing on decades of bioengineering modelling software development experience.

Show MeSH