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

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Stochastic-Notch-Patterns

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

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

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