An Anaconda environment can be used to easily install the required Python dependendcies. The conda_sim.sh bash script will install the required Python dependencies.
bash conda_sim.sh sim
source activate simpython sim.py [input.csv] [# of MC Error Iterations] [Polymerase Model] [Incorporation Model]A template of the input csv can be created with:
python sim.py -setupExample data set can be found in 'Example'. The example_input.csv was used with the following command in this example.
python sim.py example_input.csv 200 B DualThis reads in the rate constants and errors from the example_input.csv file and performed 200 MC error iterations using the rate constants for human polymerase epsilon.
Polymerases:
B = pol Beta
Incorporaiton Model:
Dual = Both ES1 and ES2 can be incorporated.
ES1 = Only ES1 can be incorporated.
ES2 = Only ES2 can be incorporated.