Re: [SED-ML-discuss] Nested Proposal v2

[Andrew M. <ak....@au...>]

On 19/01/12 20:17, Frank T. Bergmann wrote:
> Hello,
>
> As many of you know early in 2010 I proposed a simple nested simulation
> experiment for SED-ML. Of course that was well before the SED-ML spec was
> released. Since then I listened to your feedback and made adjustments. With
> the start of the new year it is time to get the Nested Simulation Proposal
> for SED-ML ready for wide-spread adoption. I believe nested simulations are
> vital for SED-ML so that we can cover a much larger variety of simulation
> experiments.

Hi Frank and others,

I think that if a proposal like this was included in SED-ML, it would 
fundamentally change what SED-ML is, and make SED-ML into something 
which has no distinct utility over and beyond a general purpose 
programming language.

I see the place of a SED-ML document as a *description* of a simulation 
experiment, rather than merely a procedure for replicating a simulation 
experiment.

 From a description of a simulation experiment, it is possible to 
replicate the experiment, but it is also possible to do other types of 
analysis - for example, inferring the intent of the simulation 
experiment and perhaps performing automated reasoning from the result.

The nested simulations approach is getting dangerously close to simply 
describing the procedure for performing simulation experiments, rather 
than describing a simulation experiment.

Someone wanting to code a procedure, without necessarily describing 
higher level semantic information about the procedure, would be better 
off using an existing general purpose imperative programming language - 
they don't need SED-ML for that. Languages like C and Python have a 
large number of existing implementations which have already been 
thoroughly tested, build on lessons learnt from previous languages to 
give a huge amount of cumulate language design legacy, and have more 
expressive power than the nested simulations proposal. If all SED-ML is 
going to be is a general purpose way to reproduce simulation 
experiments, there is no point reinventing the wheel and competing with 
existing imperative languages.

However, SED-ML is far more useful if it is targeted at describing 
simulation experiments. This means that it does need to incorporate 
facilities for a large number of different types of simulation 
experiments. This is a significant amount of work, but it is the 
meaningful approach consistent with the current SED-ML. It means we need 
to have very streamlined processes for adding new types of simulation 
experiments to the language, and to make the language more extensible.

Best wishes,
Andrew

>
> I've taken these past weeks to fully flesh out all the details and the
> document is now available from Nature Proceedings:
>
> http://precedings.nature.com/documents/4257/version/2
>
> Unlike the last version this time there is a full description of each
> element along with examples. If you only have a couple of seconds, have a
> look at my blog where you see the examples:
>
> http://frank-fbergmann.blogspot.com/2012/01/sed-ml-nested-simulation-proposa
> l-v2.html
>
> Or try the SED-ML Web Tools, that I updated to be able to simulate the
> nested experiment:
>
> http://sysbioapps.dyndns.org/SED-ML_Web_Tools/
>
> I look forward to your feedback!
>
>
> Best
> Frank
>
>
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