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 _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
