First login?
Lost password?
 
 
cellml-discussion AT lists.cellml.org 
CellML Discussion List

Text archives Help


[cellml-discussion] [Tracker Item 42] New: CellML 1.1.1specification


Chronological Thread 
  • From: matt.halstead at auckland.ac.nz (Matt )
  • Subject: [cellml-discussion] [Tracker Item 42] New: CellML 1.1.1specification
  • Date: Wed, 18 Jul 2007 16:17:55 +1200
On 7/18/07, David Nickerson <david.nickerson at nus.edu.sg> wrote:
> Hi Andrew,
>
> To simply delete reaction elements from a version 1.1.1 specification
> seems the wrong approach to me. This means that while a 1.0 model is a
> valid 1.1 model it could be an invalid 1.1.1 model. So the most minor
> version change is the one that invalidates the model?!?
>
> If anything, a version 1.1.1 could mark the reaction element as
> deprecated but still valid. Although if I recall some other
> specification developments correctly (i.e., docbook), an element needs
> to be marked for deprecation a version before it is actually deprecated
> and removed from the language. Not sure what process we want to follow
> for CellML but this 1.1.1 draft specification would not be the way I
> hope we go. Otherwise how can anyone have confidence in using CellML at
> all when core elements can arbitrarily be dropped from the specification
> with no notice?

I think there does need to be some description of what the parts of a
cellml specification version number is and how it relates to the
cellml namespace(s).

My understanding is that the 1.1.1 was chosen so that this did
represent a minor step in thinking for CellML 1.1, but that the model
remains valid as a 1.1 model. i.e. A CellML 1.1 model is not
necessarily a valid 1.1.1 model and a migration step would be needed
to make it so. The namespace of a 1.1.1 model would still be
http://www.cellml.org/cellml/1.1#

I also think that this minor version should be marked in glaring red
that it is precisely a depreciation of reactions step and provide
reasons why and the tools to help people transform any models they
have with reactions into ones that don't. I think there will be some
debate around that - especially pointing to lossless transforms
between SBML and CellML and back again with existing transforms
available out there.

My assumption would be that CellML 1.2 or 2.0 namespace would be the
one where reaction elements become invalid if indeed 1.1.1 was
successful.


>
> Also, I'm wondering if we could set some ground rules for the
> development of new versions of CellML. Rather than people simply
> submitting draft specifications, I would favour an approach whereby
> people submit proposals (using whatever technology we end up using) and
> then we can discuss which version of CellML that proposal should be
> considered for. This would allow us to start developing a detailed road
> map of the features people want to include in new versions of CellML and
> the priority with which they are incorporated, as well as possible
> target dates for the various releases.
>
>
> David.
>
> cellml-tracker at cellml.org wrote:
> > http://trackerdev.cellml.org/show_bug.cgi?id=42
> >
> > Summary: CellML 1.1.1 specification
> > Product: CellML Core Specifications
> > Version: Future versions
> > Platform: PC
> > OS/Version: Linux
> > Status: NEW
> > Severity: feature
> > Priority: Moderate priority
> > Component: Reactions
> > AssignedTo: nobody at cellml.org
> > ReportedBy: ak.miller at auckland.ac.nz
> >
> >
> > I have created a proposed draft specification for CellML 1.1.1, and put
> > it up
> > at:
> > http://www.cellml.org/Members/miller/proposed_cellml_1.1.1/
> >
> > The draft is essentially the same as CellML 1.1, except that:
> > 1) The version has been increased to 1.1.1.
> > 2) The introduction is updated to make it clear that Physiome Sciences
> > Inc. is
> > no longer involved in CellML development.
> > 3) The reactions section has been deleted and all references to sections
> > after
> > it have been renumbered.
> > 4) All references to reaction have been deleted.
> > 5) An copy-and-paste error reported by Alan Garny where we incorrectly
> > used the
> > word component instead of units was fixed.
> > 6) The DTD was updated to remove reactions and so on.
> > 7) I added myself as an author.
> >
> > Still to be done (please open new tracker items on these and set them to
> > block
> > this issue you want to comment):
> > a) Update appendix D (changes since last version).
> > b) Repair figure 18, name is invalid on model (found by Alan Garny).
> > c) Fix the formula for computing new values for equations per the CellML
> > 1.1
> > errata.
> > d) Renumber figures.
> > e) Fix up some URLs which are incorrect, especially to historic data.
> >
> >
>
> --
> David Nickerson, PhD
> Research Fellow
> Division of Bioengineering
> Faculty of Engineering
> National University of Singapore
> Email: david.nickerson at nus.edu.sg
> _______________________________________________
> cellml-discussion mailing list
> cellml-discussion at cellml.org
> http://www.cellml.org/mailman/listinfo/cellml-discussion
>


Archive powered by MHonArc 2.6.18.

Top of page