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Dear all,



Quick Summary:



The current CellML Repository uses incorrect MathML for e-notation. This
will be repaired across the entire repository when the models are migrated
over to PMR2 (the new version of the repository) by the end of May. CellML
software tool developers may, therefore, need to modify their software to
handle the correct notation.



Details:



At our latest CellML meeting (of which the minutes can be found at
http://www.cellml.org/meeting_minutes/abi-meeting-minutes-2009-04-22/), we
discussed an issue that we believe should be of direct interest to you,
developers of CellML tools (http://www.cellml.org/tools/).



The issue is related to the MathML e-notation, which none of the models in
the CellML repository (http://www.cellml.org/models/) currently represent
correctly. Indeed, say that you have a model that uses 1.23e45 as a
constant. At the moment, this constant will be represented as follows:



<cn cellml:units="some_unit">1.23e45</cn>



However, according to the MathML specifications
(http://www.w3.org/TR/MathML2/chapter4.html#contm.typeattrib), this is plain
wrong and should, instead, be represented as:



<cn type="e-notation" cellml:units=" some_unit ">1.23<sep/>45</cn>



This is clearly an oversight on our end and we do apologise for it. This
must, however, be fixed and we do intend to do it as part of the staging of
PMR2 (the next version of the CellML model repository - it will support
CellML 1.1, version control, etc.; for more information, please see the
presentation given by Tommy Yu at the recent CellML SBGN SBO BioPAX MIASE
Workshop:
http://www.cellml.org/workshop/workshop2009/presentations/yu_pmr2.pdf and
http://www.cellml.org/workshop/workshop2009/audio-files/2009-04-06-tommy.mp3
for the audio).



So, this message should be taken as an advance warning that by the end of
May 2009, i.e. the time by which PMR2 will be up and running, all of the
models in PMR2 will use the correct MathML e-notation formulation. In this
context, we would like to suggest that you update and release an updated
version of your respective CellML tool(s), and this prior to the staging of
PMR2.



Sorry again for the inconvenience, but we believe that this should,
hopefully, not require too much work on your side.



Best regards, Alan.



PS: sorry if you have received this more than once, but I wanted to make
sure that I didn't miss anyone.




Dr Alan Garny

University of Oxford, Department of Physiology, Anatomy & Genetics

Sherrington Building, Parks Road, Oxford, OX1 3PT, England

http://noble.physiol.ox.ac.uk/people/agarny/

http://cor.physiol.ox.ac.uk/




Note: I am currently in New Zealand and will be back in Oxford on 27 April
2009



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• [cellml-discussion] CellML - MathML e-notation issue, Alan Garny, 04/24/2009

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