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Hi Andre,

Support for models with parameter uncertainty is pretty urgent in relation to
grants but I'm in your hands re optimal strategy for getting there.

Cheers,
Peter
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Sent using BlackBerry


From: David Nickerson [mailto:david.nickerson at gmail.com]
Sent: Monday, October 29, 2012 10:36 PM
To: CellML Discussion List <cellml-discussion at cellml.org>
Subject: [cellml-discussion] Solicitation of feedback on CellML 1.2

Dear all,

At the 5th International CellML
Workshop<http://www.cellml.org/community/events/workshop/2011/>, we discussed
the main list of features that were desirable to have in CellML 1.2. The
CellML Editorial Board has been discussing the implementation of these
features in regard to the next version of the CellML standard. Early on, we
decided that the entire list of features arising from the workshop was too
broad and far reaching to accommodate an easy transition from CellML 1.1 to
CellML 1.2 in a timely manner. We have therefore selected a subset of these
features which we feel address immediate shortcomings in the CellML 1.1
specification and introduce a minimal set of often requested new features.

Tracker item
55<https://tracker.physiomeproject.org/showdependencytree.cgi?id=55> shows a
detailed overview of our current plans. This is by no means meant to be the
final composition of CellML 1.2, but it reflects the current view of the
editorial board as to the types of models users wish to encode in CellML and
what is possible to implement in both the specification and software tools.

Jonathan Cooper presented our thoughts on CellML 1.2 at the recent COMBINE
2012 meeting<http://co.mbine.org/events/COMBINE_2012/agenda>. Please see the
slides and video of the presentation to get a more consumable view of the
proposed changes.

This email is to solicit specific feedback from the community regarding the
subset of changes that we have selected for inclusion in CellML 1.2. The
CellML 1.2 specification will mark a significant change in the way the CellML
standard is specified, and we hope that this change will enable a more rapid
process for standardising new features that modellers require in order to
encode and share their models using CellML.

From tracker item 55<https://tracker.physiomeproject.org/show_bug.cgi?id=55>,
we would like to highlight the following main changes that we think should be
in CellML 1.2:


* Remove reaction element (tracker item
49<https://tracker.physiomeproject.org/show_bug.cgi?id=49>);
* Remove the directional aspect of connections (tracker item
337<https://tracker.physiomeproject.org/show_bug.cgi?id=337>);
* Replace grouping with a simplified encapsulation-only mechanism
(tracker item 356<https://tracker.physiomeproject.org/show_bug.cgi?id=356>);
* Delayed variables (introduction of the evaluatedAt operator with
reduced functionality to allow infinitesimal delays and initial values)
(tracker item 70<https://tracker.physiomeproject.org/show_bug.cgi?id=70>).

In addition, we specifically ask for feedback on the issue of moving to
MathML 3.0 (tracker item
67<https://tracker.physiomeproject.org/show_bug.cgi?id=67>) and the inclusion
of stochastic variation in models (tracker item
2809<https://tracker.physiomeproject.org/show_bug.cgi?id=2809>). The editors
generally agree that switching to MathML 3.0 at this time provides too little
benefit (mathematical clarity) for the cost involved in making the change
(tool support, interoperability with other exchange formats). While the
proposal for stochastic variation is fairly mature, we feel that it requires
further work to meet the requirements for inclusion in the CellML standard.
We also think that given sufficient impetus from the community this could be
one of the first proposals to pass through the new development process for
CellML.

The editorial board will shortly be releasing our proposed guidelines for the
development of the CellML standard. As mentioned above, we hope this new
process will allow new features (such as for stochastic variation in models)
to move more quickly from feature requests through to changes in the standard
specifications.

Thanks,
The CellML Editorial Board.
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• [cellml-discussion] Solicitation of feedback on CellML 1.2, David Nickerson, 10/29/2012
  • [cellml-discussion] Solicitation of feedback on CellML 1.2, Peter Hunter, 10/30/2012
  • [cellml-discussion] Solicitation of feedback on CellML 1.2, Andrew Miller, 10/30/2012

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