Menu
▾
▴
Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?
|
From: Chris M. <my...@ec...> - 2017-06-06 23:14:29
|
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 <http://bioportal.bioontology.org/ontologies/KISAO?p=classes&conceptid=http://www.biomodels.net/kisao/KISAO#KISAO_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 <http://sysbioapps.dyndns.org/SED-ML_Web_Tools/Home/SimulateUrl?url=http%3A%2F%2Fsvn.code.sf.net%2Fp%2Flibsedml%2Fcode%2Ftrunk%2FSamples%2Fsedx-archives%2Fnestedv3%2Fv3-example3-repeated-stochastic-runs.sedx> 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 |
