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Re: [SED-ML-discuss] The 'numberOfPoints' attribute
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From: Cooper, J. <j.p...@uc...> - 2017-06-28 09:40:11
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I don’t like the idea of removing an attribute in a version increment – I think removing constructs should only happen when the level increases really. So I’d like to keep the existing numberOfPoints with its existing meaning (albeit perhaps clarified in the spec – but I think the spec was already pretty clear on this).
However, I agree that it’s a confusing attribute! So I think I would like to see the addition of ‘numberOfSteps’ and users encouraged to use this instead.
With regards to the outputTimeInterval, we could have that as well as an option if we want. Am I correct in thinking that the current spec allows points to be unevenly distributed, thus supporting adaptive integrators without needing to interpolate?
Best wishes,
Jonathan
On 28/06/2017, 09:10, "Alan Garny" <ala...@in...> wrote:
I am also in favour of option 1. Once agreed, the meaning of an attribute shouldn’t change. If anything, a new one should be created.
While on the topic of ‘numberOfPoints’, I must confess that I don’t like having to specify a number of points. This ‘forces me’ to recompute that number whenever ‘outputStartTime’ and/or ‘outputEndTime’ change/s.
I did ask about this before (on this mailing list), but what about something like ‘outputTimeInterval’? The idea is that if ‘outputStartTime’ is set to 0 and ‘outputEndTime’ to 1000, then I could specify an ‘outputTimeInterval’ of, say, 1.3, which would mean outputting at 0, 1.3, 2.6, …, 998.4, 999.7 and 1000 (yes, the last interval would be smaller, but that’s because I used a rather unusual value for ‘outputTimeInterval’). The rationale for this is that it matches what people do on the experimental side of things.
In summary, I would personally go for option 1 and add a new attribute: ‘outputTimeInterval’.
Alan
On 28/06/2017, 06:15, "David Nickerson" <dav...@gm...> wrote:
My preference is also option 1.
Cheers,
David.
On 27 June 2017 at 14:58, Bergmann, Frank T. <fbe...@ca...> wrote:
> I’d prefer option 1.
>
> Cheers
> Frank
>
>
> On Jun 27, 2017, at 2:03 PM, Kyle Medley <me...@co...> wrote:
>
> I was under the mistaken in impression that this change was going to impact
> SED-ML L1V2 retroactively, but it's actually slated for L1V3 and won't
> affect libsedml's ability to read older versions, so I also agree with
> Herbert (i.e. option 2).
>
> J Kyle Medley, PhD Candidate
> Bioengineering/BPSD, Sauro Lab
> University of Washington, Seattle
> skype: jkylemedley
>
> On 6/27/17 1:47 PM, Moraru,Ion wrote:
>
> I agree with Herbert.
> Ion
>
> From: Herbert Sauro [mailto:uw....@gm...]
> Sent: Tuesday, June 27, 2017 4:21 PM
> To: sed...@li...
> Subject: Re: [SED-ML-discuss] The 'numberOfPoints' attribute
>
> Given that the sedml community is still very small, it would be better to
> get it right at this early stage, hence I prefer option
>
> 2) change the name to set thing else, e.g. numberOfSteps
>
> For those clinging to earlier versions they can check the version of the
> sedml and interpret numberofpoints in the old way. In that sense I don't
> think it affects backward compatibility.
>
> Herbett
>
>
> On Tue, Jun 27, 2017 at 1:08 PM Kyle Medley <me...@co...> wrote:
>
> It seems to me that breaking backwards compatibility defeats one of the
> major advantages of having a standard encoding, so I would prefer option 1.
> If people are not happy with that, I have a different suggestion:
>
> 4) Allow 'numberOfPoints', and do not change its meaning, but also create a
> new attribute 'numberOfSteps' with the same semantics. 'numberOfPoints'
> would not be deprecated.
>
> Cheers,
>
> Kyle
>
> J Kyle Medley, PhD Candidate
>
> Bioengineering/BPSD, Sauro Lab
>
> University of Washington, Seattle
>
> skype: jkylemedley
>
> On 6/27/17 12:46 PM, Lucian Smith wrote:
>
> At HARMONY, the issue was brought up that the 'numberOfPoints' attribute is
> confusing, because the literal number of expected points in the output file
> is one more than that: the initial conditions, and the number of *computed*
> points.
>
> It was proposed that we fix this for SED-ML Level 1 Version 3. There are a
> few options:
>
> 1) No change: simply make it more clear in the spec that 'numberOfPoints'
> means 'number of computed points' aka 'number of steps'.
>
> 2) Change the name of the attribute to 'numberOfSteps' or possibly
> 'numberOfComputedPoints'.
>
> 3) Deprecate but allow 'numberOfPoints', and make a new 'numberOfSteps'
> attribute that people are encouraged to use instead.
>
> Any opinions? It seems like the advantage is preventing future confusion,
> and the cost is having a non-backwards-compatible spec, and the cost of
> implementation changes for the groups that currently support SED-ML.
>
> -Lucian
>
>
>
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--
David Nickerson
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