Re: [Miase-discuss] SED-ML Simulation class update

[Dagmar K. <dag...@un...>]

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 ;-)
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 I agree that v0r1 is pretty outdated.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 version-0-release-1 which now seems rather outdated, since it does not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
>>>>
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>>>>
>>>>         
>>>
>>>
>>>       
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