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Hi,

I have created a proposed best current practice document, which makes
recommendations to model authors and tool developers about the form of
the top-level of a mathematical expression in a CellML model (i.e. the
child element of the MathML math element).

The document is available at
http://www.cellml.org/Members/miller/bcp-toplevel-maths/

The document attempts to do the following:
1) Provide a semantic basis for the top-level MathML operator, something
which is missing from the CellML specification.
2) Codify existing unwritten conventions about the use of mathematics in
CellML models.
3) Create a framework for the introduction of new uses of mathematics in
CellML models.
4) Introduce a way to express 'reset rules' into CellML.

The introduction of support for reset rules is motivated by the fact
that some models in the repository don't produce results which
correspond to the paper, because they are missing reset rules which are
present in the model.

For example, the Chen et. al. 2004 model "Integrative Analysis of Cell
Cycle Control in Budding Yeast" specifies the following reset conditions:
"Reset rules: When [Clb2] drops below /K/_ez , we reset [BUD] and [SPN]
to zero, and divide the mass between daughter cell and mother cell as
follows: mass -> /f/?mass for daughter, and mass -> (1 ? /f/)?mass for
mother, with /f/ = /e^?kg?D ,/ where /D/ = (1.026//k/_g ) ? 32 is the
observed daughter cell cycle time as a function of growth rate (Lord and
Wheals, 1980). When [Clb2] + [Clb5] drops below /K/_ez2 , [ORI] is reset
to 0."

These rules are important biologically (a cell splits into two, and the
model only continues to follow the mother cell, so there is a
discontinuity in state variables such as the mass). However, current
tools cannot deal with this sort of feature in models.

Please let me know if you have any comments on the document.

Best regards,
Andrew

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• [cellml-discussion] Proposal: BCP for the top-level mathematics operator, Andrew Miller, 03/22/2007

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