Matt wrote: >> It seems there is some misunderstanding as to whether we are discussing >> a proposal to remove the reaction element from CellML or a proposed new >> specification. I thought it was the latter but you seem to be talking >> about the former... > > > Both. I think. > > So I will try another explanation. > > If we had our specification in a version control system and tagged out > releases and release candidates etc, and if we followed a protocol of > releasing at least one stable minor release that marks depreciation > only, then the following would be the result (in my mind) > > - The current trunk is the development version of cellml 1.2 (i.e. > unreleased-dev). > - This current trunk look likes CellML 1.1 and the associated > definitions in DTDs etc. > - We update this to mark out that reaction elements are going to be > depreciated, this includes comments in DTDs etc. We don't remove > reaction elements from the specification at this stage because that's > where we hang the depreciation notices. > - We tag this as 1.1.1 and release it > - We then delete reaction elements from the specification that is on trunk. > > Now, this is the kind of process I think covers the steps you have > been talking about and at the end makes available a trunk version of > 1.2-dev-unreleased that doesn't have reaction elements that people can > check out an play with (this is essentially the proposal page the > Andrew wrote up - though I think there are issues remaining now with > the absence of biology from a "Cell" ML standard.
yep - thats how I would see the specification evolving over time, subject, of course, to the various proposals being accepted and assigned to an appropriate version. I think the absence of biology from the core specification is probably a good thing, but there needs to be clear annotation of the specification describing how reactions should now be represented in a world without reactions - another best practice recommendation and examples in the model repository at the least, I would hope. > But what I am also saying is that this is still just an idea, so it > should be put forward as a proposal that has not been accepted. I.e. > that the steps I described above are purely hypothetical at the > moment, since we haven't had the chance to hear arguments from people > about it - it might turn out to be a silly proposal. definitely. Your steps describe the process for how the specification may be updated, developed, etc., but each release will be the result of a set of proposals being accepted and assigned to that particular release. this is why the proposal to remove the reaction element should have first been put forward independently of any specific future version of CellML. In this discussion forum we could then debate the merits of this proposal and, if deemed suitable, develop a schedule for the implementation of the proposal (i.e., mark reaction element for deprecation in 1.1.1 and then remove the reaction element in 1.2). Other proposals would also be similarly evaluated and possibly assigned to the same or different releases of the CellML specification. It definitely should not, at this stage, be a forgone conclusion that the reaction element should be removed in 1.2 (or some specific future version of CellML) - that is still open to discussion in my mind, especially in regard to the tools that biomodels.net are using to import/export CellML models with their repository and any other tools utilising the reaction element, of which I don't think anyone has yet evaluated. _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
