README.md

Modelling protein translocation

Environment setup

1. Make sure Python is installed (preferably a version > 3.9)
2. Create a virtual environment like this: python3 -m venv preferred-venv-location
3. Activate the environment you just created by running source path-to-your-venv/bin/activate
4. Install all necessary dependencies by running: pip3 install -r requirements.txt

Running simulations

1. The parameter values for the model can be set in the parameters.py file. Whether all are used, depends on the rate functions defined in model.py.
2. Define your rate functions (Linear, Exponential, Gaussian-like, etc.)
3. Run model.py (output plots will be locally written to ./output/volume_file_used/)