From: Bruce S. <bru...@gm...> - 2014-08-13 19:18:46
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Sounds reasonable to me. Sent by an Android from another Galaxy. On Aug 13, 2014 11:36 AM, "Lucian Smith" <luc...@gm...> wrote: > Right, I am claiming that even if SBML arrays are officially static, they > can be used in non-static contexts (such as parameter scan-like functions > in tools, and in hierarchical models), and therefore should behave more > like lists than arrays. > > When they are zero-length, they would, like empty lists, be equivalent to > not including it in the model at all, except that references to it would be > allowed. > > -Lucian > > > On Wed, Aug 13, 2014 at 11:18 AM, Bruce Shapiro <bru...@gm... > > wrote: > >> I still don't understand how there would be an array parameter of zero >> length in a model. Are you saying that something might or might not exist >> in the model, and that zero length means it does not exist? >> >> >> On Wed, Aug 13, 2014 at 11:09 AM, Lucian Smith <luc...@gm... >> > wrote: >> >>> There might be the case where the SBML model is under control of some >>> other force, such as SED-ML or another simulation tool. A parameter scan, >>> for example, does not require the parameter being scanned to be >>> non-constant, but various different values are used for it over the course >>> of several experiments, in each of which the parameter in question is >>> constant. I can imagine a similar situation here, where someone is testing >>> the behavior of a model under different circumstances, the simplest of >>> which has a zero-sized array. >>> >>> Even within-SBML, one might have a hierarchical model where a submodel >>> has a zero-sized array that becomes longer when imported and changed, or >>> visa versa. >>> >>> I would say that since it doesn't seem terribly difficult to support, >>> has a clear meaning, and is potentially useful, that we allow it. >>> >>> -Lucian >>> >>> >>> On Wed, Aug 13, 2014 at 11:00 AM, Chris J. Myers <my...@ec...> >>> wrote: >>> >>>> I think in programming languages, there is often a difference between a >>>> zero-size array and a null pointer. You can use zero-size arrays as an >>>> initialization value, so you don't need to check for null all the time. >>>> However, this is with the assumption that you can later change the size of >>>> the array and add things to it. >>>> >>>> For arrays package with SBML, we made the decision that these would be >>>> static-size arrays. Therefore, a zero-size array will always be a >>>> zero-size array, and when this gets flattened to SBML core, the object is >>>> simply removed entirely. So, is such a behavior useful or simply create an >>>> unnecessary complication? >>>> >>>> Chris >>>> >>>> On Aug 13, 2014, at 11:06 AM, Bruce Shapiro <bru...@gm...> >>>> wrote: >>>> >>>> Do any computer languages allow this? Isn't there already a symbol for >>>> the empty set for this this that one would normally use instead? Nil null >>>> bupkis >>>> >>>> Sent by an Android from another Galaxy. >>>> On Aug 13, 2014 9:41 AM, "Chris J. Myers" <my...@ec...> wrote: >>>> >>>>> Hi, >>>>> >>>>> We were wondering if anyone sees a use for zero size arrays. When you >>>>> declare something as zero-szie, you are essentially declaring that it does >>>>> not exist. A zero-size species, parameter, rule, etc. would flatten to it >>>>> not being present. I suppose it is a bizarre way to delete something. You >>>>> can change its size variable to zero-size which effectively removes it. >>>>> This though likely creates validation rules as index computations may go >>>>> out-of-bounds, but this may not always be the case. >>>>> >>>>> So, my question is should we limit parameters used for size as >>>>> "non-negative" as we do now, or change it to "positive"? >>>>> >>>>> Chris >>>>> >>>>> >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> _______________________________________________ >>>>> sbml-arrays mailing list >>>>> sbm...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> _______________________________________________ >>>> sbml-arrays mailing list >>>> sbm...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>>> >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> sbml-arrays mailing list >>>> sbm...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>>> >>>> >>> >>> >>> ------------------------------------------------------------------------------ >>> >>> _______________________________________________ >>> sbml-arrays mailing list >>> sbm...@li... >>> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >>> >>> >> >> >> -- >> Bruce E. Shapiro, Ph.D. >> Department of Mathematics >> California State University, Northridge >> 18111 Nordhoff Street >> Northridge, CA 91330-8313 >> >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> sbml-arrays mailing list >> sbm...@li... >> https://lists.sourceforge.net/lists/listinfo/sbml-arrays >> >> > > > ------------------------------------------------------------------------------ > > _______________________________________________ > sbml-arrays mailing list > sbm...@li... > https://lists.sourceforge.net/lists/listinfo/sbml-arrays > > |