E. Coli ALE simulator using keras mutation rate schedulers. Install requirements.txt.
Example run with 8M cells (~100µL @ OD0.1) for three days. The run begins at growth rate 1.0 with a target of 2.0:
Vertical dotted lines indicate the time taken for any cell to reach 95% of the target growth rate with the given mutation rate scheduler. In this example, stepwise scheduling is 36% faster than a constant mutation rate.
The program takes three commandline arguments: maximum growth rate (starts at 1.0), number of cells to simulate (remains constant), and number of hours to run the simulation. Passages are currently fixed at 10% of the population every hour.
python pyalesim.py 2.0 8000000 72