David Nickerson wrote: > 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,
It might be worth adding an editorial comment or similar to note that the metadata is where the vast majority of biological information is defined. 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. Yep, the 'signal transduction' tutorial will no longer be needed, since its main purpose is to describe the best practice for use of reaction elements to describe biochemical pathways. The question will be, do we just remove it, or do we create a new tutorial that is biochem specific, but doesn't talk about reaction elements. For example, there are two main ways to code up a biochem model: either you can use equations that describe, for example, the rate of change of conc. of species A, where species A might have a few different processes acting on it, so this equation would be a summation of the effect of these processes, OR, you can split the equation into 'fluxes,' which represent just the effect of one process on a species at a time. I think it would be worth writing a best practice guide for writing biochem models, even if it is relatively short, since there are a few things that are different from how an ephys model should be coded up. > >> 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. Perhaps we could start by formalising the actual proposal to get rid of the rxn element. Why are we doing it? How will we replace the purpose it served, using metadata for example? I realise that this has been discussed a lot in an informal manner, and was in fact decided well before my time, but I guess if we're going to do something as major as create a new spec version, we should build the foundations first. 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, It would be good to see a thorough list of pros and cons for the rxn element. If we do write a formal proposal, where should we put it? Perhaps send it out to cellml-discussion, as well as all the groups we know to be reliant on the spec for building tools, models etc. > 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, We could provide them with a new translation tool if we were so inclined, couldn't we? But I see the issue here - if SBML has reactions and we don't, then the translation process will have to be reworked and re-evaluated. of which I don't think anyone has yet > evaluated. > _______________________________________________ > cellml-discussion mailing list > [email protected] > http://www.cellml.org/mailman/listinfo/cellml-discussion _______________________________________________ cellml-discussion mailing list [email protected] http://www.cellml.org/mailman/listinfo/cellml-discussion
