Table 1. Catalog of all simulations run and their corresponding command-line parameters.

Initial seed (-s)	Baseline (-b)	Initial state (-f)*	Initial colony (-i)**	[Tet.] in mM (-t)	[Amp.] in mM (-a)	Run time (-r)***	Start time (-n)
Baseline glucose simulations
0	Yes	Default	-	0	0	26002	0
100
10000
Tetracycline MIC simulations
0	No	-	1	3.375E-03	0	14552	11550
100			2
10000			3
Tetracycline sensitivity simulations
0	No	-	1	1.125E-03	0	14552	11550
				2.25E-03
				4.5E-03
				9E-03
Tetracycline protein synthesis inhibition
0	No	Default	-	0	0	500	0
				5E-05
				1.08E-04
				2.32E-04
				5E-04
				1.08E-03
				2.32E-03
				5E-03
				1.08E-02
				2.32E-02
				5E-02
Ampicillin MIC simulations
0	No	-	1	0	5.72E-03	14552	11550
100			2
10000			3
Ampicillin sensitivity simulations
0	No	-	1	0	1.43E-03	14552	11550
					2.86E-03
					4.29E-03
					1.145E-02

* Default refers to the file data/wcecoli_t0.json

** Each number refers to a saved snapshot from t = 11550 s of a glucose simulation: 1 = seed 0, 2 = seed 100, 3 = seed 10000. The seed of the saved snapshot was matched to the seed of the antibiotic sim.

*** Additional 2 seconds because no data is emitted after the last 2-second timestep.