Re: [SED-ML-discuss] Compute Mean/Stddev of Stochastic Traces?

[Kyle M. <me...@co...>]

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 
> <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... 
>> <mailto: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://slashdot.org>! 
>> http://sdm.link/slashdot_______________________________________________
>> SED-ML-discuss mailing list
>> SED...@li... 
>> <mailto: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