The input parameters that are not reported in Table 3, such as the blink acceleration threshold or the post hoc validation inputs, were set to the values that were recommended in the original articles by Nyström and Holmqvist (2010) and by Wass et al. (2013) respectively.
The sequencing depths were all set 10, and the normalized Poisson mean λ0 of untreated input was set to 10−6, unless otherwise clarified.
Thus, even though the input is set to only one source, all other sources can express changes in spectral activity, because they are interconnected.
When HGF was the stimulus (H. pylori input was set to 0 and HGF input set to 1), CNA finds only 6 knockout targets for ERK1/2 repression (HGF, c-Met, HGF/c-Met, ERK1/2, MEK, Raf1).
For example, if the activity level for an external input is set to 50% with a noise range of 5, the actual activity level, at time t, will be 50%+/-5.
For example, in a simulation consisting of 200 iterations, a user may want to see how the network behaves when an input is set to 10% ON during the first 50 iterations, 50% during iterations 51 – 100, and 100% for the remaining number of iterations.
First, the initial concentrations of all phosphorylated model species were set to zero: Furthermore, in order to resolve structural identifiability issues, the initial value of STAT5 and the scaling parameter of the input were set to one: Thereby, the forward rate constant k1 is expressed in units of the input pEpoR and the total amount of STAT5, which is conserved in this system, is set to one.
Make sure input is set to whichever auxiliary your computer is hooked into.
