Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment

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

Hej Frank,

I think... I need some sample code to see what you're doing :-)
Would you mind posting an example (if you have any available)?

Thanks a lot,
Dagmar


Frank Bergmann wrote:
> Hello all, 
>
> First of all thank you so much Dagmar for reviving this list. It is good to
> see the ball moving again. 
>
> I've been working with SED-ML extensively over the last months. The biggest
> concern of mine has always been the way that SED-ML is structured.
> Currently, whenever we want to exchange a new simulation experiment, we need
> to add a new class to SED-ML. (And no, the AnySimulation class will not be
> exchangeable, so it should be dropped as soon as possible). That also means
> that each time a class is added to SED-ML everyone else has to start
> implementing support for it. This is a sure way for SED-ML to fail as
> standard!
>
> Back in Waiheke last year we tried to resolve that issue by adding the Range
> classes to the existing simulation experiments like TimeCourse. And it did
> sound good back then. However, thinking on how to implement it and, perhaps
> more importantly, how to apply it to other simulation experiments, it proved
> hard to do. This concept only translates into a triple amount of work for
> the implementers of the SED-ML format. 
>
> And so here my proposal. Let us go back to the roots. By defining simple
> primitives, for a simulation step, bringing the model to steady state, and
> changing values, we can finally arrive at a truly extendable standard that
> is also easy to implement. I've placed my thoughts online: 
>
> http://precedings.nature.com/documents/4257/version/1
>
> Bergmann, Frank. A Simple Nested Simulation for SED-ML. Available from
> Nature Precedings <http://dx.doi.org/10.1038/npre.2010.4257.1> (2010)
>
>
> Let me know what you think, 
> Best
> Frank
>
>
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