Extended Data Fig. 4: COMETS simulations time benchmarking.

In order to benchmark the performance of COMETS with increasing complexity of the simulated system, we performed a 24 h batch culture run similar to that in Procedure 1, with either 1, 10 or 100 models (the E. coli model iJO1366 was used in all instances). The settings were identical to Procedure 1 in the main text. We tested three timesteps, 0.01 h (circles), 0.1 h (triangles) and 0.5 h. (squares). The x-axis shows simulated time (i.e., number of simulation steps × timeStep, in h); the y-axis shows elapsed simulation time (the time taken by the computer to run the program), in min. Simulations were performed in Python using cometspy in a personal laptop running linux (Intel Core i7-10610U CPU at 1.80 GHz × 4 cores, 15.3 GiB memory).