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Re: [SED-ML-discuss] Proposing a Nested Simulation Experiment
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From: Richard A. <ra...@st...> - 2010-04-02 21:43:27
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Maybe to explain better - I was recently at a talk from our Biopepa (www.biopepa.org) colleagues who have recently implemented various sorts of 'experiment' functionality to alter models in various ways and compare the results, but use a non-XML based model representation. So I was thinking that setting values based on an 'identifiable element' rather than XPath would extend the range of models whose experiments could be described in SED-ML to include all models that have identifiers (although at the expense of the complete flexibility Xpath gives you to alter a model in any way) Richard > 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 > > > ------------------------------------------------------------------------------ > 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. |
