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Re: [SED-ML-discuss] Using data with SED-ML at Combine
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From: Frank B. <fbe...@ca...> - 2015-09-17 14:03:28
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Hello Ally, the reason is basically, that there was a community vote many years back, where the decision to use NUML rather than any other format. The primary reason is that this way the mapping could be done once, that people implementing support would have to implement. Internally tools could support as many other formats as required / useful for them. best Frank > On Sep 17, 2015, at 3:09 PM, Ally Hume <a....@ed...> wrote: > > Hi David, everyone, > > Thanks for pointing me to these documents (they don't seem to be linked to from the sed-ml.org which is why I only read L1V2 initially). > > While I'm can understand that it's a drag when new voices come along querying old decisions I'm going to do that anyway! I apologise if this is derailing so please bat me away if this as ready been endlessly discussed. > > Essentially my question is why do we need NuML? Would HDF5 not provide all (and more) of the functionality? Domain specific references to ontology terms could be added to the HDF5 metadata and then it looks like it would provide everything in NuML. HDF5 has widespread adoption, many tools and APIs, and is a far more compact and efficient format for multidimensional data than NuML which looks to be extremely verbose. > > It would seem to me to be far simpler to adopt HDF5 and simply add any domain specific metadata we decide is required. Clearly there is an challenge in getting the required implementations for any specifications so where possibly we should be adopting existing standard already accepted and implemented elsewhere. > > Regards, > > Ally > > > Ally Hume > Researcher, SynthSys, The University of Edinburgh > Software and Data Architect, EPCC, The University of Edinburgh > > > > On 17 Sep 2015, at 00:56, David Nickerson <dav...@gm...> wrote: > >> Hi Ally, Herb, everyone, >> >> We don't have a specific agendas set for any of the SED-ML breakout >> sessions at the COMBINE meeting and the current session titles reflect >> topics that we believe to be useful topics to at least kick off the >> sessions. >> >> Just over a year ago, the SED-ML editors released a draft for the next >> version of SED-ML which is available here: >> http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1. >> The main change in this specification is the addition of data to >> SED-ML and being able to use data to control the simulation >> experiment, model variables, etc. The additions to the specification >> represented the consensus achieved during much discussion over the >> preceding HARMONY and COMBINE meetings (and various google docs, etc). >> As far as I am aware, there is currently only one implementation that >> supports the L1V3 draft (Frank Bergmann's .NET framework) and while >> some of us hoped to get our own implementations up and running at the >> HARMONY meeting earlier this year, a second implementation has yet to >> appear. And thus the L1V3 draft is still a draft :) >> >> For the COMBINE breakout on data with SED-ML, it would be good to >> discuss both the potential implementation of the L1V3 specification in >> code as well as producing some examples or use-cases (to also help >> address the issue of examples that Lucian has raised on this list >> recently). So yes - the topics you mentioned Ally would be ideal to >> discuss. The main background reading would be the L1V3 draft spec >> (http://co.mbine.org/specifications/sed-ml.level-1.version-3-draft-1) >> which would also lead you to the NuML specification: >> https://github.com/NuML/NuML/blob/master/numl-spec-l1v1.pdf. Since the >> use of data in SED-ML is dependent on NuML, we will also likely be >> discussing the state of NuML and where that project is heading. >> >> >> Cheers, >> David. >> >> >> >> On Thu, Sep 17, 2015 at 4:39 AM, Herbert Sauro <hs...@gm...> wrote: >>> We'd be looking for the same things. >>> >>> Herbert >>> >>> On Wed, Sep 16, 2015 at 7:05 AM, Ally Hume <a....@ed...> wrote: >>>> >>>> Hi, >>>> >>>> I notice that there will be a session at Combine entitled "Using data with >>>> SED-ML". I was wondering if somebody could tell me a more detailed >>>> description of what may be discussed here? I've looked in the archives for >>>> recent posts to this list but nothing seems to cover this topic. >>>> >>>> I've recently been looking at adding external time course data to SBML >>>> models. In our use case this is temperature data but it could obviously be >>>> many other measurements as well. I've written code to add external data to >>>> SBML models as a parameter with an associated assignment rule that defines >>>> the data using a piecewise function [1]. This works for our purposes but >>>> does not seem like the cleanest way to do things. >>>> >>>> SED-ML looks like a place where this could be done a lot better. >>>> >>>> Adopting similar strategies to those already used in SED-ML it would be >>>> nice to include: >>>> - references to datasets (similar to references to models) >>>> - link between entities in these datasets and parameters in a model >>>> - specification of an interpolation algorithm (ontology-based like >>>> simulation algorithms) >>>> >>>> This would be a considerable improvement over my current approach of >>>> writing this into SBML where the interpolation algorithm and original >>>> dataset are effectively lost (although I could add annotations to document >>>> such details). >>>> >>>> There could also be an argument made for some basic data pre-processing >>>> possibly similar to the post-processing of result data already in SED-ML. >>>> >>>> I'm sure there will be alternative ideas but I just wondering if this is >>>> the type of thing that will be in the session. I will be attending Combine >>>> but I don't want to wait for the session and discover it's actually on >>>> something totally different, or discover there is actually a lot of >>>> background documentation that I could have read in advance. >>>> >>>> Thank you, >>>> >>>> Ally >>>> >>>> [1] https://github.com/allyhume/SBMLDataTools >>>> >>>> >>>> Ally Hume >>>> Researcher, SynthSys, The University of Edinburgh >>>> Software and Data Architect, EPCC, The University of Edinburgh >>>> >>>> >>>> -- >>>> The University of Edinburgh is a charitable body, registered in >>>> Scotland, with registration number SC005336. >>>> >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog! >>>> Get real-time metrics from all of your servers, apps and tools >>>> in one place. >>>> SourceForge users - Click here to start your Free Trial of Datadog now! >>>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> >>> ------------------------------------------------------------------------------ >>> Monitor Your Dynamic Infrastructure at Any Scale With Datadog! >>> Get real-time metrics from all of your servers, apps and tools >>> in one place. >>> SourceForge users - Click here to start your Free Trial of Datadog now! >>> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >> >> >> >> -- >> >> >> David Nickerson >> about.me/david.nickerson >> >> ------------------------------------------------------------------------------ >> Monitor Your Dynamic Infrastructure at Any Scale With Datadog! >> Get real-time metrics from all of your servers, apps and tools >> in one place. >> SourceForge users - Click here to start your Free Trial of Datadog now! >> http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > ------------------------------------------------------------------------------ > Monitor Your Dynamic Infrastructure at Any Scale With Datadog! > Get real-time metrics from all of your servers, apps and tools > in one place. > SourceForge users - Click here to start your Free Trial of Datadog now! > http://pubads.g.doubleclick.net/gampad/clk?id=241902991&iu=/4140 > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
