Re: [cellml-discussion] embedded stimulus currents in CellML models

2007-07-18 Thread James Lawson
Alan Garny wrote: Shouldn't we therefore offer at least two different sets of CellML 1.0 files? One that only contains the model itself and another that also includes some simulation specific information? I actually replied to this somewhere else - I'll repeat it... We just talked about this

Re: [cellml-discussion] embedded stimulus currents in CellML models

2007-07-18 Thread James Lawson
Alan Garny wrote: Depending on the end-user, it could be a, b and/or c, as well as the fact that apart from PCEnv, no other CellML-capable software that I am aware of can deal with CellML 1.1 models. This emphasises my view that we have to make the CellML API easy to use and provide several

Re: [cellml-discussion] embedded stimulus currents in CellML models

2007-07-18 Thread David Nickerson
Of course. And in the same sense you could simply delete the stimulus protocol component if you didn't want it. I think the issue is in fact a curation issue - we are specifying one of our curation 'levels' as model is the same as is described in the paper. If there is a stimulus protocol

Re: [cellml-discussion] [TrackerItem 42]New: CellML1.1.1specification

2007-07-18 Thread David Nickerson
From what I gather, publicity. We need some way to direct people's attention to our intention to deprecate reaction elements. sure - but its still not clear to me if 1.1.1 is making clear our intention to deprecate reaction elements or if it is making reaction elements invalid in a 1.1.1

Re: [cellml-discussion] [TrackerItem 42]New: CellML1.1.1specification

2007-07-18 Thread David Nickerson
Andrew Miller wrote: David Nickerson wrote: From what I gather, publicity. We need some way to direct people's attention to our intention to deprecate reaction elements. sure - but its still not clear to me if 1.1.1 is making clear our intention to deprecate reaction elements or if it

[cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread Andrew Miller
David Nickerson wrote: Andrew Miller wrote: David Nickerson wrote: From what I gather, publicity. We need some way to direct people's attention to our intention to deprecate reaction elements. sure - but its still not clear to me if 1.1.1 is making clear our

Re: [cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread David Nickerson
Correct me if I am wrong, but I believe that nothing in the text of the CellML 1.1 specification says that reactions will or will not be deprecated in any future version of CellML, and therefore there is no need for an erratum to CellML 1.1 (and indeed, such an erratum would be

Re: [cellml-discussion] CellML 1.1.1 specification

2007-07-18 Thread Andrew Miller
David Nickerson wrote: Correct me if I am wrong, but I believe that nothing in the text of the CellML 1.1 specification says that reactions will or will not be deprecated in any future version of CellML, and therefore there is no need for an erratum to CellML 1.1 (and indeed, such an

[cellml-discussion] CellML version interoperability strategy

2007-07-18 Thread Andrew Miller
David Nickerson wrote: I think that we disagree about how the specification process should work and what it aims to address. I see a given version of a CellML specification as being a 'protocol' which both tools and model authors speak, therefore allowing them to interwork. All I'm