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

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

Thanks so much!

J Kyle Medley, PhD Student
Bioengineering/BPSD, Sauro Lab
University of Washington, Seattle
skype: jkylemedley

On 06/06/2017 06:23 PM, Chris Myers 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... 
>> <mailto: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 
>>> <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
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>>>
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