par-protein-transport-model

This repository contains code for our PAR protein transport paper: https://doi.org/10.1101/2021.06.28.450200

Authors

• Cole Zmurchok https://zmurchok.github.io
• William R. Holmes https://holmeslab.home.blog/

Requirements

• We used Python 3.8.7 available from https://www.python.org/
• A list of required packages is available in 'reqs.txt'

Contents

• README and LICENSE
• reqs.txt: contains a list of Python packages and versions
• Jupyter notebooks for all figures in the paper:
  • FigX.ipynb produces (all or part of) Figure X in the paper
  • ABM_Validation.ipynb makes Supplemental Figure 1
  • Fig2.ipynb also makes Supplemental Figures 2--5
  • DiffusionEstimation.ipynb makes Supplemental Figure 6
  • Model_ParamSweep.ipynb makes Supplemental Figures 7--10
  • Fig3-4.ipynb also makes Supplemental Figure 11

Running

Some notebooks require directories '/data' and '/figures' to be placed in main working directory. After running these notebooks, data and parameter sets will be saved in these folders in a pickle format (.pkl). This allows for easy plotting adjustments since the stochastic simulations will not be re-run if the data exists.