- Download and compile Nupack 3 and set the NUPACKHOME environment variable to the nupack root directory
- Install python requirements via
pip install -r requirements.txt
You can make a set of plots for a single sequence by running
python plot_conc_space.py [SEQUENCE] R105_states.txt -o output.png -t [TITLE]
The R105_states.txt specifies the input and reporter sequences as well as which complexes to include in the calculation.