Figure 2 of the reference publication has been reproduced here. Green plots are obtained with the initial conditions used in the model. However, in the paper the plots are obtained starting from the steady state conditions. In the paper, this is done as follows using Copasi.

First set the model initial time as -3600s (=1h), then suppress output before -30s, and run the simulation for 3720s (=3600+120).

 

SBMLsimulator 1.0 was used to run the simulation starting from initial condition (reference) and steady state condition. To obtain the plots from steady state conditions, the species' steady state values were set as initial condition. The plot data was obtained from SBMLsimulator and the plots were generated using gnuplot.