Arguments to pass for a single shoebox simulation

[ezingrebe]

An example to run a gene-cluster simulation without actin is:

python run_single_shoebox.py -b 11 -r 1 -t 10 -o gene_cluster/ -m 1 -c Control -p 3 -a 30 -x 80 -z 0 -n 0.01

where:

• a: activation rate
• x: Ser5P threshold for activation

What are the units of the following two parameters? I guess that "x" is the threshold number of Ser5P molecules in the "vicinity" of the promoter. My question is, how is the threshold radius defined, i.e. what is the minimum distance between Ser5P and promoter necessary for the conditions for activation to be fulfilled?

What is the physical meaning of the "a: activation rate" in this context, i.e. the units (must be "something over time")?

[lhilbert]

The vicinity should not be so difficult. It will be defined in the reaction network part of the simulation, in units of sigma, the size of a chromatin monomer.

Indeed, in the single shoebox simulation python code, on line 439, we have it:

pol2release_radius = 3 # For Ser5P around promoter (gene activation)

Tracing through the different scripts to find out how the activation rate was scaled is a little more tricky. In the original simulation process, I assume it was given in units of "time step delta t". Then, later, in the evaluation scripts, it should be assigned actual physical time units, but I also would need more time to take that process apart into its single parts.