Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
Fig 5
Comparison of logarithmic (bottom row of plots) vs. linear (top row of plots) plotting of the transient response in Fig 4B, 4C and 4G, along with an excerpt of the relevant PhraSEDML code for plotting on logarithmic axes.
Fig 4G, which is a plot of String mRNA and hypothetical factor X, which degrades String mRNA, exhibits a large dynamic range. Logarithmic plotting helps visualize the dynamic range of these quantities. This is achieved in PhraSEDML by wrapping the quantities for x and y axes inside a log10 operation.