Abstraction in physiological modelling languages

Conference item

In this paper we discuss two projects looking at applying advanced abstraction mechanisms from software engineering to the field of physiological modelling. We focus on two abstraction mechanisms commonly found in modern object-oriented programming languages: generics and inheritance. Generics allows classes to take other classes as parameters, allowing common behaviour to be described with particularities abstracted away. We demonstrate this technique on an example from heart modelling. Inheritance allows one to reuse code and to establish a subtype of an existing object. We focus on the benefits reaped from inheritance where this property enables run-time substitutability. This technique is demonstrated within the context of multi-scale tumour modelling. Finally, we look at how combining both techniques enables greater modularity and the construction of a model driven framework for the rapid creation and extension of families of biological models.

Authors: McKeever, S; Gill, M; Connor, A; Johnson, D

• Publication status: Published
• Peer review status: Peer reviewed
• Publisher: Curran Associates, Inc.
• Host title: Simulation Series
• Volume: 45
• Issue: 4
• Pages: 76-83
• Publication date: 2013-01-01
• ISSN: 0735-9276
• ISBN: 9781627480321
• Keywords: inheritance; biological modelling; domain specific languages; mathematical modelling; generics