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.

Sent using BlackBerry

From: David Nickerson [mailto:david.nicker...@gmail.com]
Sent: Monday, October 29, 2012 10:36 PM
To: CellML Discussion List <cellml-discussion@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 

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 
  *   Remove the directional aspect of connections (tracker item 
  *   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 

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 

The CellML Editorial Board.
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