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

[David N. <dav...@gm...>]

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
>
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-- 


David Nickerson
about.me/david.nickerson