CellML 2.0.pptx (3.39 MB)
CellML 2.0
presentation
posted on 2020-10-04, 22:38 authored by David NickersonDavid Nickerson, Michael ClerxMichael Clerx, Michael T. Cooling, Jonathan CooperJonathan Cooper, Alan GarnyAlan Garny, Keri MoyleKeri Moyle, Poul NielsenPoul Nielsen, Hugh SorbyHugh SorbyPresentation delivered at COMBINE 2020 on CellML 2.0
The CellML format is based on the extensible markup language (XML), and is intended to enable the representation and dissemination of reproducible and reusable mathematical models of biology. The changes were motivated by community feedback on the 1.0 and 1.1 specifications, as well as a desire to separate the normative and informative aspects of the CellML specification.
Included are the introduction of a reset element which allows discontinuities to be modelled without ambiguity; the restriction of allowed MathML elements; the removal of comments and annotations; and the removal of the reaction element and its children.
The reset element is designed to allow discontinuities and discrete changes in variables based on conditional statements. This was possible in earlier versions using piecewise expressions, but the use of an order attribute within the resets means that the behaviour of conflicting switches can now be resolved uniquely. Possible applications include modelling a cell dividing as its size exceeds a threshold; the discrete switching of electrical stimuli; and re-initialising conditions during a simulation.
The normative specification is available on the CellML website at https://www.cellml.org/specifications/cellml_2.0, with an informative specification with a discussion of examples, explanations, and common mistakes also provided.
Abstract: CellML 2.0 was released on April 17, 2020, and contains significant changes since the previous 1.1 version. Here, we will present a summary of the CellML format and the changes introduced in CellML 2.0.
The CellML format is based on the extensible markup language (XML), and is intended to enable the representation and dissemination of reproducible and reusable mathematical models of biology. The changes were motivated by community feedback on the 1.0 and 1.1 specifications, as well as a desire to separate the normative and informative aspects of the CellML specification.
Included are the introduction of a reset element which allows discontinuities to be modelled without ambiguity; the restriction of allowed MathML elements; the removal of comments and annotations; and the removal of the reaction element and its children.
The reset element is designed to allow discontinuities and discrete changes in variables based on conditional statements. This was possible in earlier versions using piecewise expressions, but the use of an order attribute within the resets means that the behaviour of conflicting switches can now be resolved uniquely. Possible applications include modelling a cell dividing as its size exceeds a threshold; the discrete switching of electrical stimuli; and re-initialising conditions during a simulation.
The normative specification is available on the CellML website at https://www.cellml.org/specifications/cellml_2.0, with an informative specification with a discussion of examples, explanations, and common mistakes also provided.
