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Re: [SED-ML-discuss] The 'numberOfPoints' attribute
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From: Herbert S. <uw....@gm...> - 2017-06-28 19:27:04
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There is an opportunity here to correct something that is clearly wrong, better to get it right that leave as it is. Herbert On Wed, Jun 28, 2017 at 1:10 AM, 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 > > > > > > > > ------------------------------------------------------------------------------ > > > > Check out the vibrant tech community on one of the world's most > > > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > > > SED-ML-discuss mailing list > > > > SED...@li... > > > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! > > http://sdm.link/slashdot_______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > > > > > > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! > > http://sdm.link/slashdot_______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > > > ------------------------------------------------------------------------------ > > Check out the vibrant tech community on one of the world's most > > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > > _______________________________________________ > > SED-ML-discuss mailing list > > SED...@li... > > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > > -- > > > David Nickerson > about.me/david.nickerson > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss > > > > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
