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*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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