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
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data/pattern
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data/lattices
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data/random
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data/dev
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data/mistakes
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analysis/pattern
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analysis/lattices
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analysis/random
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analysis/dev
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analysis/mistakes
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movie_si_patt