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

[Richard A. <ra...@st...>]

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?
    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 I agree that v0r1 is pretty outdated.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 version-0-release-1 which now seems rather outdated, since it does not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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-- 
Dr Richard Adams
Senior Software Developer,
Computational Systems Biology Group,
University of Edinburgh
Tel: 0131 650 8285
email : ric...@ed...

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