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Re: [Miase-discuss] SED-ML Simulation class update
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From: Frank B. <fbergman@u.washington.edu> - 2009-07-24 15:37:50
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On Jul 24, 2009, at 4:19 AM, Dagmar Koehn wrote: > Richard Adams wrote: >> Hi Dagmar >> The system of having a supported schema and an experimental one >> seems fine, especially at this early stage, I don't think we want to >> have > 2 though, it would be too confusing. Is there any reason not >> to include the new simulation classes? >> > > Not for me, I thought you were voting for it ;-) I'm fine with the OM as it is on SF (looking at the PDF). I have not started to implement it, as I'm not sure we actually have started to discuss the new classes. The only issue i see currently is with the AnySimulation class, which has arbitrary SimulationProperty elements attached. As it is not regulated at all I'm not sure what to do with them. I'd also like to see an example of how the new Range's would be working ... And finally it might make sense for backward compatibility to keep our uniform timecourse simulation class ... but that is optional :) So far my thoughts cheers Frank > But then I got you wrong. > Sorry. > > >> Richard >> >> >> >>> Hej Richard, >>> >>> sorry for the late reply... >>> Not sure what you mean by "first MIASE paper", but >>> I agree that v0r1 is pretty outdated. >>> I would say that sed-tmp is accepted well enough to be turned into >>> v0r2. >>> But then we should include the new simulation classes as well. I am >>> reluctant on putting out a new "release" of the schema and not >>> using the >>> most current one (i.e. including the changed simulation classes). >>> >>> To my knowledge apart from you, Frank currently has an >>> implementation, >>> so I'd like to know what he thinks about updating the schema to >>> the new >>> version? Frank? >>> >>> (Maybe same question goes to Ion?! How far are you with SED-ML >>> support?) >>> >>> Best, >>> Dagmar >>> >>> >>> Richard Adams wrote: >>> >>>> Hi Dagmar, >>>> Is there any intention /need to add these changes to the Sedml >>>> schema >>>> just yet, or is it better to wait, especially if the first MIASe >>>> paper will only cover standard simulations? >>>> Also I was wondering if the 'sedml-tmp' schema is now accepted >>>> enough >>>> to become the current schema? at present we have the original >>>> version-0-release-1 which now seems rather outdated, since it >>>> does not >>>> support notes and annotations. E.g., in order for all the example >>>> models to be compliant with the version-0-release-1 schema, we >>>> need to >>>> add support for notes via SedBase extension, and also to add in >>>> 'maxOccurs=unbounded' attributes into the listOfOutputs >>>> definition. Is >>>> this worth doing, or should we just make the sedml-tmp into >>>> version-0-release-2? >>>> >>>> Cheers >>>> Richard >>>> >>>> >>>> >>>>> Dear all, >>>>> >>>>> we had some discussion on extending the SED-ML simulation class >>>>> during >>>>> the CellML combined workshop in Auckland. Frank and I tried to >>>>> come up >>>>> with a good class structure to map bifurcation analyses and >>>>> steady state >>>>> analyses. The according UML diagram can be found on sourceforge >>>>> (PDF): >>>>> http://miase.svn.sourceforge.net/viewvc/miase/sed-ml/documents/sed-om/sedom-tmp.pdf?revision=115 >>>>> >>>>> I marked the changed classes in red. >>>>> We do have three main simulation classes now, namely: >>>>> BifurcationSearch1D (a bifurcation analysis over a parameter >>>>> with a >>>>> uniform range), TimeCourse (time courses with uniform, vector or >>>>> functional range) and SteadyStateParameterScan1D (over 1 >>>>> parameter with >>>>> different ranges again). >>>>> >>>>> Questions are: >>>>> 1) Do you think this is a good way/structure of mapping steady >>>>> state and >>>>> bifurcation experiments to SED-ML? >>>>> 2) Frank suggested that the AnySimulation class should be >>>>> removed from >>>>> the diagram as (1) the use of already defined classes should be >>>>> encouraged, (2) and self-defined simulation experiment classes >>>>> cannot >>>>> be reused anyways... he also mentioned that (3) it was still >>>>> possible to >>>>> describe an experiment that is not representable in SED-ML so >>>>> far. It >>>>> could always be described inside the notes/annotation element. I >>>>> thought >>>>> however that it might be useful to have at least a structure >>>>> (even if >>>>> very general) for self-defined experiment types. But maybe it is >>>>> sufficient to state in the documentation that "not-representable >>>>> experiments should be defined in the according notes/ >>>>> annotation". Are >>>>> there any opinions on that? >>>>> >>>>> Best, >>>>> Dagmar >>>>> >>>>> ------------------------------------------------------------------------------ >>>>> Crystal Reports - New Free Runtime and 30 Day Trial >>>>> Check out the new simplified licensing option that enables >>>>> unlimited >>>>> royalty-free distribution of the report engine for externally >>>>> facing >>>>> server and web deployment. >>>>> http://p.sf.net/sfu/businessobjects >>>>> _______________________________________________ >>>>> Miase-discuss mailing list >>>>> Mia...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> >>> ------------------------------------------------------------------------------ >>> _______________________________________________ >>> Miase-discuss mailing list >>> Mia...@li... >>> https://lists.sourceforge.net/lists/listinfo/miase-discuss >>> >>> >>> >> >> >> >> > > > ------------------------------------------------------------------------------ > _______________________________________________ > Miase-discuss mailing list > Mia...@li... > https://lists.sourceforge.net/lists/listinfo/miase-discuss |
