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Plot of the behaviors of an alternative regulatory function and Mathematica code for reproducing Figure 8B.
For example, Novak's 1997 cell cycle model can be run with at least two different setups, either reproducing Figure 2a or b of Novak and Tyson (55).
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R scripts reproducing figures 2, 3, 4, 5, 6, 7, 8 are included with SBMLR as an illustrative example of package use.
Reproduced figure with permission from Tibély, G. et al., Phys Rev E 83 5):056120112011.
If we change the water level and high-cut frequency, the structure is almost reproduced (Figure 3b,c).
Andrea Bair is thanked for providing original digital files to reproduce figure 1.
The authors thank C. Viboud for permission to reproduce Figure 2.
We then repeated the mapping procedure, using these random sets of positions instead of the SDRs, and reproduced figure 1 for each random set of residues (Figure S1).
This reproduces Figure 2B from (Bushdid et al., 2014 ), and can be subsequently used to reproduce Figure 3A and ultimately Figure 3C from (Bushdid et al., 2014 ).
The resulting autocatalytic network reproduces Figure one from [ 28] in our notation.
The R code files import the data files and exactly reproduce Figure 9.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com