Re: [SloppyCell-users] PeriodCheck

[Gutenkunst, R. N - (rgutenk) <rg...@em...>]

Hello Uriel,

This functionality was developed by Bob Kuczenski ( https://www.linkedin.com/in/bobkuczenski ) when he was a graduate student, and it hasn't been used all that much. So it may be rough around the edges.

Nevertheless: PeriodCheckResidual(key=<name for residual>, calcKey=<name of Network to get prediction from>, depVarKey=<name of variable you have period of>, indVarValue=<time at which you want to assess period>,  depVarMeasurement=<measured period>, depVarSigma=<uncertainty of period>)

If your system takes a while to settle into a periodic orbit, you can get indVarValue to be some time far into the future, when you think the transients will have damped out. Unfortunately, this isn't necessarily straightforward when optimizing, because the speed at which transients damp no doubt depends on the parameter values. So you'll need to set it far out, which is computationally costly. So you'll have to compromise, then check your results to ensure that the optimization did find a solution where the transients are indeed gone.

Best,
Ryan

On Jan 30, 2015, at 3:45 AM, José María Uriel Urquiza García <uri...@gm...> wrote:

> Dear Ryan,
> 
> I found that in sloppycell it is possible to add a period constrain in the residuals using Experiment.AddPeriodChecks. Nonetheless it is not clear for me what are the arguments clacKey and chemical. Furthermore, I have data that but i would rather set the startTime when the system is in the unforced dynamics but for which i don’t time series data. I wonder if this is possible?
> 
> Cheers and thanks for all the amazing!!! guidance so far
> 
> Uriel

--
Ryan Gutenkunst
Assistant Professor
Molecular and Cellular Biology
University of Arizona
phone: (520) 626-0569
http://gutengroup.mcb.arizona.edu