Notification: Representation of e-notation in CellML Repository models will be changing

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.cds.caltech.edu/%7Emhucka/meeting/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.