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Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?
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From: Kyle M. <me...@co...> - 2017-06-07 04:53:36
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Thanks David! J Kyle Medley, PhD Student Bioengineering/BPSD, Sauro Lab University of Washington, Seattle skype: jkylemedley On 6/6/17 7:24 PM, David Nickerson wrote: > Hi Kyle, > > I use the C++ libSEDML and you can see a couple of maybe useful > examples of using custom annotations here > https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L606 > and https://github.com/nickerso/get-simulator/blob/OutputTypes/src/sedml.cpp#L1131. > > Cheers, > David. > > > On 7 June 2017 at 13:23, Chris Myers <my...@ec...> wrote: >> I’m using jlibSEDML. Some of the code is here: >> >> https://github.com/MyersResearchGroup/iBioSim/blob/master/analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/util/SEDMLutilities.java >> >> and more here: >> >> https://github.com/MyersResearchGroup/iBioSim/blob/master/gui/src/main/java/edu/utah/ece/async/ibiosim/gui/analysisView/AnalysisView.java >> >> Chris >> >> On Jun 6, 2017, at 6:24 PM, Kyle Medley <me...@co...> wrote: >> >> Thanks for your help Chris! Out of curiosity, are you using libSEDML (C++ or >> C#?) or are you writing the XML yourself? I was just curious because it >> would be helpful to have an example of how to work with custom annotations >> in libSEDML. >> >> J Kyle Medley, PhD Student >> Bioengineering/BPSD, Sauro Lab >> University of Washington, Seattle >> skype: jkylemedley >> >> On 06/06/2017 04:14 PM, Chris Myers wrote: >> >> I believe that we agreed at COMBINE that using repeated task for this was >> overkill. Instead, you should be able to specify the number of runs, then >> be able to select in your graph which run or statistic to plot. We use this >> KISAO term: >> >> http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http%3A%2F%2Fwww.biomodels.net%2Fkisao%2FKISAO%23KISAO_0000326 >> >> to specify number of runs for a stochastic simulation. We have currently >> added a custom annotation to the dataGenerator to indicate which data set to >> generate data from. For example, this can be a run number or a statistic >> like mean, using custom annotation for now. See attached example. >> >> Chris >> >> >> >> >> On Jun 6, 2017, at 2:06 PM, Kyle Medley <me...@co...> wrote: >> >> Hi All, >> >> I was just wondering if it is possible to compute the mean and standard >> deviations of stochastic simulations in SED-ML. Frank has a great demo of >> running multiple stochastic traces, but I'm not sure how to extend it to >> allow computing the first two moments. My understanding is that a repeated >> task generates data with one more dimension than the input, so Frank's >> example is essentially flattening the data before plotting it. I'm not sure >> if it's possible to manipulate these higher dimensions in a dataGenerator or >> use some clever MathML to sum along one axis. Any ideas? >> >> Thanks, >> Kyle >> >> -- >> J Kyle Medley, PhD Student >> Bioengineering/BPSD, Sauro Lab >> University of Washington, Seattle >> skype: jkylemedley >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot_______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> >> >> >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! >> http://sdm.link/slashdot_______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> >> >> >> ------------------------------------------------------------------------------ >> Check out the vibrant tech community on one of the world's most >> engaging tech sites, Slashdot.org! http://sdm.link/slashdot >> _______________________________________________ >> SED-ML-discuss mailing list >> SED...@li... >> https://lists.sourceforge.net/lists/listinfo/sed-ml-discuss >> > > |
