# Wiki

# D2D Software / Swameye_PNAS2003

# JAK/STAT signaling model

**Reference:** Swameye et al. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. PNAS 100(3), 1028-1033, 2003.

**Folder:** `/Examples/Swameye_PNAS2003`

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**Facts:** The model contains 46 data points, 16 free parameters and 1 experimental condition.

In this example application we demonstrate the use of cubic splines are input functions and the use of the fixed measurment noise instead of the parameterized measurement noise function.

## Cubic splines

After calling the `Setup.m`

script we see the following figure.

In this model the input `pEpoR`

is model as strictly posive splines with five knots:

pEpoR C "au" "conc." "spline_pos5(t, 0.0, sp1, 5.0, sp2, 10.0, sp3, 20.0, sp4, 60.0, sp5, 0, 0.0)"

The spline parameters `sp1-5`

are estimated together with the model dynamics and the measurement noise.

## Using fixed measurment noise

In the `Setup.m`

script we can switch the flag

useErrorModel = true; if(~useErrorModel) % do not fit error model ar.config.fiterrors = -1; % show error bars instead of error model ar.config.ploterrors = 1; % show, but not fit input data for pEpoR ar.model.data.qFit(3) = 0; % fix parameter for input and error model arSetPars('sp1',[],2); […] end

to disable the estimation of the measurement noise. The option `ar.config.fiterrors = -1`

indicates that the error model is not used but the experimentally determined measurement errors (standard deviation calculated form triplicates) given in the data sheet in the `_std`

columns. Also, the weigthed sum of squared residuals is use in the estimation instead of the full likelihood. The option `ar.config.ploterrors = 1`

indicates that the conventional error bars on the data points are plotted instead of the error model around the trajectory. The command `ar.model.data.qFit(3) = 0;`

indicates that third observable should not be used for fitten. This is because no experimentally determined measurement errors are available for this measurement. Correspindings also the spline parameters are fixed by the commands `arSetPars('sp1-5',[],2);`

.

The results in the following modified figure.

Updated