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Re: [sbml-arrays] [whole-cell] [wholle-cell] Questions
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From: Chris J. M. <my...@ec...> - 2015-09-24 20:03:51
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I agree to not complicate things. Libsbml support is pretty easy since only affects validation and it does not validate arrays as far as I'm aware. Chris Sent from my iPhone > On Sep 24, 2015, at 1:00 PM, Lucian Smith <luc...@gm...> wrote: > > I hesitate only because we couldn't get an implementation in place for libsbml in time for COMBINE, and people aren't exactly chomping at the bit to have those capabilities at the moment anyway. Maybe post-COMBINE, if people there still seem to want it? > > -Lucian > >> On Thu, Sep 24, 2015 at 11:55 AM, Chris J. Myers <my...@ec...> wrote: >> Thanks. Are you going to add the strict option? >> >> Chris >> >> Sent from my iPhone >> >>> On Sep 24, 2015, at 12:52 PM, Lucian Smith <luc...@gm...> wrote: >>> >>> I was looking through them myself, and basically came to the same conclusions! For now, I went with 'non-negative', and adjusted some wording in the other places. >>> >>> The only thing I remember you wanting to revert at one point was the id's on the examples, but I think we eventually agreed that removing them was sufficiently helpful that it was OK that iBioSim didn't produce exactly that. >>> >>> At any rate, I've updated and checked in the new version. >>> >>> -Lucian >>> >>>> On Thu, Sep 24, 2015 at 11:18 AM, Chris J. Myers <my...@ec...> wrote: >>>> Here are the comments I found: >>>> >>>> Lucian: Check to see if ’non-zero’ is a requirement. It also might still be worth having a discussion about the ’defined initial value’. >>>> >>>> Text says above “positive non-zero integer”, but this is redundant, since positive does mean non-zero. We have gone back and forth about allowing zero or not. Personally, I think 0 is strange since it basically means it does not exist, but it is a quick way to “delete” something I guess. Anyway, I think the text should either read, “positive integer” or “non-negative integer” depending on our decision about 0. I can go either way on this. >>>> >>>> Leandro: how is JSBML currently implemented? >>>> >>>> As for “defined initial value”, you are correct that we agreed to add a flag that effectively disable the validation rules that required static arrays. This would mean crazy things could happen like dynamic array out-of-bounds problems, but we decided at Harmony to give people the option to do this, if they like. If you have time to add to the specification before COMBINE, that would be great. Hopefully we can convince you to implement in Antimony and Ilya in BioUML, and we can finally ratify this thing :-). >>>> >>>> Lucian: I removed the IDs of X and Y’s Dimension becuase they made this example more confusing than it needed to be. >>>> >>>> This is okay. My only reservation is this means the XML has been edited now after what came out of iBioSim. It introduces a slight risk of invalid SBML. >>>> Lucian: This bit will have to change after we finally get the ’MathML packages’ up and running, but we might as well leave it for now. >>>> >>>> Agreed. >>>> >>>> Lucian: I don’t know what you mean here by ’invalid to have a value of type vector’. In fact, it seems to me that things >>>> >>>> 3 could be a ton simpler if you allowed simple vector assignment, a la: 4 >>>> >>>> Lucian: Is there a reason you don’t want this? This (or something similar) will also be necessary in the case of distrib, >>>> >>>> 26 where it needs vector input and output. 27 >>>> >>>> >>>> I agree that this would be simpler XML, but it makes validation and flattening harder. Since it is software and not humans that generate the XML, I do not think we should add this type of assignment for now. This, in my opinion, violates our design decision of no implicit arrays. >>>> >>>> Finally, I also looked through all your text modifications and they look good to me. Do you think any new validation rules are implied by these changes? >>>> >>>> I could not find the change that I remember thinking you made was wrong. Maybe I’m misremembering. Leandro: do you have any recollection of this? >>>> >>>> Cheers, >>>> >>>> Chris >>>> >>>>> On Sep 24, 2015, at 11:59 AM, Lucian Smith <luc...@gm...> wrote: >>>>> >>>>> Oh, right--we had discussed making a new 'strict' flag or something that we would use for things like 'defined/fixed boundaries', etc. Should I write that into this proposal? >>>>> >>>>> -Lucian >>>>> >>>>>> On Thu, Sep 24, 2015 at 10:47 AM, Chris J. Myers <my...@ec...> wrote: >>>>>> This version still has some notes in there that you put in. I think we discussed them all in Germany. Can you remove or update based on this? Also, I seem to remember you made some changes that we said needed to be unwound, but I cannot remember what these were. Do you remember? >>>>>> >>>>>> Chris >>>>>> >>>>>> >>>>>>> On Sep 24, 2015, at 11:45 AM, Lucian Smith <luc...@gm...> wrote: >>>>>>> >>>>>>> I went ahead and updated the version in SVN to be version 0.3 alpha, compiled it, and updated the arrays page to point to the new version. Let me know if anything else needs to be updated. >>>>>>> >>>>>>> -Lucian >>>>>>> >>>>>>>> On Thu, Sep 24, 2015 at 10:22 AM, Ilya Kiselev <ax...@de...> wrote: >>>>>>>> Hi. >>>>>>>> >>>>>>>> Well this version certainly looks more elaborate. I will read it and get back to you. >>>>>>>> >>>>>>>> Thanks! >>>>>>>> >>>>>>>> Best regards, Ilya >>>>>>>> >>>>>>>> 2015-09-24 22:55 GMT+06:00 Chris J. Myers <my...@ec...>: >>>>>>>>> Hi, >>>>>>>>> >>>>>>>>> The latest version is attached. We really need to update the one online which is very old. I see your confusion now. >>>>>>>>> >>>>>>>>> Indices are actually on attributes of SBML elements. For example, the compartment attribute of a species can have an index. >>>>>>>>> >>>>>>>>> Leandro: maybe you can send your COMBINE 2014 slides as well, which I think might be easier to digest. >>>>>>>>> >>>>>>>>> Chris >>>>>>>>> >>>>>>>>> >>>>>>>>> >>>>>>>>>> On Sep 24, 2015, at 10:01 AM, Ilya Kiselev <ax...@de...> wrote: >>>>>>>>>> >>>>>>>>>> Thanks for your answers and explanations! >>>>>>>>>> >>>>>>>>>> But it made me wonder if specification I have read is actually up to date because I have no Idea how you can set compartment of arbitrarty index to species like that (unless it is done implicitly by setting S[n] in C[m], where n = 2m, but you said nothing is done implicitly): >>>>>>>>>> >>>>>>>>>> >Another example with n != m, consider: >>>>>>>>>> >parameter n=8 >>>>>>>>>> >parameter m=4 >>>>>>>>>> >compartment C[m] >>>>>>>>>> >species S[n] with compartment C[floor(d0/2)] where d0 is the dimension id for dimension 0 of S >>>>>>>>>> >>>>>>>>>> Species can not have Index and even if ithey had - Index can not be applyed to attributes.... >>>>>>>>>> >>>>>>>>>> I took specification from here http://sbml.org/Documents/Specifications/SBML_Level_3/Packages/arrays. I have also attached it to this email. >>>>>>>>>> >>>>>>>>>>> >>>>>>>>>>> If you read the parts of the specification about flattening and the validation rules, it should help. >>>>>>>>>> >>>>>>>>>> Specification which I have read does not contain such parts. >>>>>>>>>> >>>>>>>>>>>> 5.One thing that bothers me a bit is that multiple rules for the same variable are allowed (for different components of the vector but still). Hence if stripped from the extension, this file would not be valid SBML document. >>>>>>>>>>> >>>>>>>>>>> That is not correct. We do not allow multiple rules for the same variable. It still must be valid when stripped. >>>>>>>>>> >>>>>>>>>> Specification that I have read has examples for that. Its in the paragraph 4.2., Array of Rate Rules >>>>>>>>>> >>>>>>>>>> <listOfRules> >>>>>>>>>> <!-- Create rate rules dx(i)/dt = y for i = 1,2,3,4,5 --> >>>>>>>>>> <rateRule variable="x"> >>>>>>>>>> <arrays:orderedListOfDimensions> >>>>>>>>>> <arrays:dimension id="i" size="m"/> >>>>>>>>>> </arrays:orderedListOfDimensions> >>>>>>>>>> <arrays:orderedListOfIndices> >>>>>>>>>> ... >>>>>>>>>> </rateRule> >>>>>>>>>> <!-- Create rate rules dx(i)/dt = 2*y for i = 6,7,8 --> >>>>>>>>>> <rateRule variable="x"> >>>>>>>>>> <arrays:orderedListOfDimensions> >>>>>>>>>> <arrays:dimension id="i" size="o"/> >>>>>>>>>> </arrays:orderedListOfDimensions> >>>>>>>>>> <arrays:orderedListOfIndices> >>>>>>>>>> ... >>>>>>>>>> </rateRule> >>>>>>>>>> </listOfRules> >>>>>>>>>> >>>>>>>>>> -- >>>>>>>>>> >>>>>>>>>> <arrays proposal.pdf> >>>>>>>> >>>>>>>> ------------------------------------------------------------------------------ >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> >>>> _______________________________________________ >>>> 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 |