[cellml-discussion] Solicitation of feedback on CellML 1.2

2012-10-29 Thread David Nickerson
*Dear all,

At the 5th International CellML
Workshophttp://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 
55https://tracker.physiomeproject.org/showdependencytree.cgi?id=55shows
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 55https://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
49https://tracker.physiomeproject.org/show_bug.cgi?id=49
   );
   - Remove the directional aspect of connections (tracker item
337https://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
67https://tracker.physiomeproject.org/show_bug.cgi?id=67)
and the inclusion of stochastic variation in models (tracker item
2809https://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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Re: [cellml-discussion] Solicitation of feedback on CellML 1.2

2012-10-29 Thread Peter Hunter
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
--
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 
Workshophttp://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 
55https://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 
meetinghttp://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 55https://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 
49https://tracker.physiomeproject.org/show_bug.cgi?id=49);
  *   Remove the directional aspect of connections (tracker item 
337https://tracker.physiomeproject.org/show_bug.cgi?id=337);
  *   Replace grouping with a simplified encapsulation-only mechanism (tracker 
item 356https://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 
70https://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 67https://tracker.physiomeproject.org/show_bug.cgi?id=67) 
and the inclusion of stochastic variation in models (tracker item 
2809https://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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Re: [cellml-discussion] Solicitation of feedback on CellML 1.2

2012-10-29 Thread Andrew Miller

On 29/10/12 22:36, David Nickerson wrote:

*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=55shows
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);


+1


  * Remove the directional aspect of connections (tracker item 337
https://tracker.physiomeproject.org/show_bug.cgi?id=337);


+1


  * Replace grouping with a simplified encapsulation-only mechanism
(tracker item 356


+1


https://tracker.physiomeproject.org/show_bug.cgi?id=356);
  * Delayed variables (introduction of the evaluatedAtoperator with
reduced functionality to allow infinitesimal delays and initial
values) (tracker item 70
https://tracker.physiomeproject.org/show_bug.cgi?id=70).


+1




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).


I think that it would be worth including MathML 3.0 in CellML 1.2 because:
  1. It makes implementation easier by providing clear rules about the 
mathematical interpretation of models.
  2. It is more cleanly extensible through the use of OpenMath content 
dictionaries.
  3. It is mostly forwards and backwards compatible with MathML 2.0 - 
nearly every MathML 2.0 expression is valid MathML 3.0, and you can 
write MathML 3.0 so it is valid MathML 3.0.
  4. The only implementation of the CellML 1.2 proposals so far has 
already been coded to use MathML 3.0 - so the cost in terms of tool 
support so far would actually be higher to change that implementation to 
support MathML 2.0.



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.


I'm not sure there even is a stochastic variation proposal (unless it is 
private to the editorial board). I put together a proposal for parameter 
uncertainty (which is different from stochastic variation - a system is 
stochastic if the relationship between the initial and a later state is 
not deterministic, while it has parameter uncertainty if the true 
initial state is not known).


I don't think there needs to be 'one CellML' that every tool implements 
exactly - parameter uncertainty is probably most appropriate as an 
officially endorsed secondary specification that adds to core CellML.


Best wishes,
Andrew

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