Here you'll find the code for generating and analyzing Notch-Delta mediated pattern formation. Our results can be found in "Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway"

Please cite the publication if you use this code.

Galbraith, M., Bocci, F. & Onuchic, J. N. Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway. PLOS Computational Biology (2022) doi:10.1371/journal.pcbi.1010306.

https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1010306

Files to generate the data include:

• seedsForSims.txt
• generate_data.py

Files to analyze the data:

• analyze_data.py
• aux_functions.py

Files to generate figures in the manuscript:

• aux_functions.py
• plot_script_functions.py
• produce_data_for_figures.py
• FiguresForMain.ipynb

Files to generate figures in the SI:

• pseudocount.py
• get_data_for_si.py
• get_psuedo_change.py
• figures_for_SI.ipynb

Files to generate movies for the SI:

• SI_pattSim_rand_nucl.py

Files to generate and analyze one cell gillespie simulation:

• gill_oneCell_2020.py
• analyze_oneCell.py

Will need to create the directories

• data/pattern

• data/lattices

• data/random

• data/dev

• data/mistakes

• analysis/pattern

• analysis/lattices

• analysis/random

• analysis/dev

• analysis/mistakes

• movie_si_patt