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

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

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version-0-release-1 which now seems rather outdated, since it does not  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

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