A computational framework to describe and solve temporo-spatial biological models

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Copyright: Chang, Chan-Wei David
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Abstract
With the ever-increasing volume and complexity of mathematical biological models and experimental datasets becoming available, there is a strong need for a set of representation languages which can describe and represent these models and data in standard forms and store them in publically available repositories for universal dissemination. To help address this issue, the Modelling Markup Language (MML) computational framework was developed in this project. It consists of representation languages and application toolsets that can represent, store and solve biological temporo-spatial models. The representation languages are comprised of ModelML, responsible for maintaining relational information between different external models, along with the Field Markup Language (FML), responsible for maintaining geometric field information such as anatomical data. The MML framework also utilises the existing CellML specification to represent biological systems models. With these three representation languages, a temporo-spatial model can be created, re-used, interchanged and shared. In addition, specially-developed application toolsets provide utilities which aid in the creation and processing of the MML models. To demonstrate the capability of the MML framework, a series of simulations of cardiac electrical activity are presented, including simulations of the cardiac pacemaker (sinoatrial node) and atrial tissue activation. In the sinoatrial node simulations, tissue electrical conductivity was adjusted to observe its effect on sinoatrial node entrainment and inhibition by the atria, using several 1D, 2D, and 3D tissue geometry layouts and cellular mathematical models. Additional simulations were performed by modifying the magnitude of the hyperpolarisation-activated membrane current (if) of the underlying cellular models, to observe its effect on pacemaker activation and impulse propagation into the atria. The use of the MML framework allowed these models to be constructed rapidly through its ability to efficiently reuse and modify underlying geometric and mathematical components.
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Author(s)
Chang, Chan-Wei David
Supervisor(s)
Dokos, Socrates
Lovell, Nigel
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Publication Year
2010
Resource Type
Thesis
Degree Type
PhD Doctorate
UNSW Faculty
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