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Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment
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From: Frank B. <fbergman@u.washington.edu> - 2010-04-02 17:52:23
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Hello All, sorry I have been away for the last couple of days. the motivation with the proposal for the setValue function was made so that different changes could be applied for each iteration of the nested experiment. This basically allows us to perform loop operations (such as in 'for' or 'while' loops). I'm perfectly fine with determining the target of the setValue by an XPath expression, I was just worried that really for many cases we won't have one, such as for time in the case of SBML models, that is why I think it is fine to extend it by additional keywords. So with the nested task + setValue + oneStep + steadyState the aim was to broaden the range of Simulation Experiments that can be encoded with SED-ML. This already allows for any time course simulation, (1-D, 2-D..., N-D) (steady state) parameter scans. And any kinds of pulse experiments. And that without having to define a new simulation class each time. But we don't have to stop here ... we could have a more general function like the one you are suggesting as subclass for the setValue one. I'm just not sure how you would parameterize it. ... The setValue class would take the value of the current range and through that either apply or calculate a change for a value. I'm not sure how you would parameterize your example of removing reactions ... If I were to remove a reaction I would probably do that as before by creating a changed model with the reaction removed, and then apply the nested simulation to it. But maybe I'm misunderstanding your intentions cheers Frank On Mar 30, 2010, at 7:32 AM, Richard Adams wrote: > > Frank, > I read your proposal on your blog - with the 'setValue' function, > are you thinking that is a way of manipulating the model without > constraining it to be XML based? So long as a parameter /variable is > identifiable, tools capable of accepting a model in a particular > format would still be able to manipulate it. > > I guess this would preclude sweeping structural changes applied to an > XML model that can be done with Xpath (removing a reaction, for > example) but is the increase in generality for simple cases of value > manipulation worth considering? > > Best wishes > > Richard > > > > > >> Hello Andrew: >> >>> >>> A few comments. I think that dealing with 'time' is probably one of the >>> biggest weaknesses in this approach. You wrote: >>> "We could make it convention, that if this is not defined, then the >>> models time parameter is changed". >>> Firstly, as soon as we talk about time, we lose generality; I suggest >>> 'independent variable of integration' or a similar term. I'll refer to >>> it as 'IVOI' here. >>> >> >> Given the frequent use of integration over time, I think we can >> justify having this class. But I'm open to introduce your IVOI as a >> more general case. Though I'm afraid many tools will not be able to >> handle IVOI. >> >>> Secondly, modern DAE / IDA solvers take adaptive steps in their IVOI, >>> rather than fixed steps. Your proposal seems to not allow adaptive >>> step-sizes - rather, it forces the user to specify the step size on >>> 'OneStep'. >>> >> >> Definitely, what the oneStep is meant to describe is how far you >> would like to simulate until your next output point. How many steps >> the integrator internally takes would be independent of this. >> >>> => Parameters controlling the internal stepping. For example, allowing >>> for an optional maximum step size to control errors and ensure that the >>> solver finds features like stimulation pulses. >> >> Again, the one step approach only tells you when you want your next >> output point, this can be controlled through the range element on >> the nested simulation experiment. >> >>> => Parameters controlling which data is reported. Some simulations will >>> want to report every internal step, while in others, reporting this data >>> will produce more data than is required. >> >> This will be defined through the data generators that are defined, >> just as in the current approach. >> >>> The above is implemented in CellML Simulation Metadata and the CellML >>> API and OpenCell extensions to it (this metadata focuses entirely on >>> 'time' course experiments at present, but does that one task better than >>> anything proposed for SEDML to date). >>> >> >> Great! ... so which tools can i download to experiment with it? it >> would be good to test exchange of simulation experiments that way. >> >> best >> Frank >> >>> Best wishes, >>> Andrew >>> >>>> >>>> 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 >>>> >>>> >>>> ------------------------------------------------------------------------------ >>>> Download Intel® Parallel Studio Eval >>>> Try the new software tools for yourself. Speed compiling, find bugs >>>> proactively, and fine-tune applications for parallel performance. >>>> See why Intel Parallel Studio got high marks during beta. >>>> http://p.sf.net/sfu/intel-sw-dev >>>> _______________________________________________ >>>> SED-ML-discuss mailing list >>>> SED...@li... >>>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >>> >>> >>> ------------------------------------------------------------------------------ >>> Download Intel® Parallel Studio Eval >>> Try the new software tools for yourself. Speed compiling, find bugs >>> proactively, and fine-tune applications for parallel performance. >>> See why Intel Parallel Studio got high marks during beta. >>> http://p.sf.net/sfu/intel-sw-dev >>> _______________________________________________ >>> SED-ML-discuss mailing list >>> SED...@li... >>> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Download Intel® Parallel Studio Eval >> Try the new software tools for yourself. Speed compiling, find bugs >> proactively, and fine-tune applications for parallel performance. >> See why Intel Parallel Studio got high marks during beta. >> http://p.sf.net/sfu/intel-sw-dev >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> > > > > -- > Dr Richard Adams > Software Development Team Leader, > Centre For Systems Biology Edinburgh > University of Edinburgh > Tel: 0131 650 8285 > email : ric...@ed... > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > > > ------------------------------------------------------------------------------ > Download Intel® Parallel Studio Eval > Try the new software tools for yourself. Speed compiling, find bugs > proactively, and fine-tune applications for parallel performance. > See why Intel Parallel Studio got high marks during beta. > http://p.sf.net/sfu/intel-sw-dev > _______________________________________________ > SED-ML-discuss mailing list > SED...@li... > https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss |
