Archive of data and code associated with the publication "Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes" by Beckwith, Brunner, et.al.

This archive contains data, code and examples associated with the manuscript "Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes" by Beckwith, Brunner, et.al.Supplementary Movie S1 shows an example of a dynamic simulation of a 100 Mb chromosome undergoing mitotic compaction, see manuscript for more details.The zip archive contains the following files:environment.yml: File used to automatically install needed python packages into a virtual environment.LE_sim_functions.py: Python function specifications required to run 1D loop extrusion simulationssimulation_analysis_functions.py: Python function specifications for functions required to analyse simulated polymer conformations and compare to experimental data.trace_analysis_functions.py: Python function specifications for functions required to analyse experimental polymer conformations.run_LE_sim.ipynb: Jupyter notebook containing code examples to run 1D loop extrusion simulations to be used as input for dynamic polymer simulations.run_polychrom_LE.py: Executable python program to run dynamic polychrom simulations based on the 1D loop extrusions. Run by using in the appropriate environment (see below) "python run_polychrom_LE ----folder_path "Path to folder created by run_LE_sim notebook" ". Note this script requires the polychrom (https://github.com/open2c/polychrom) package to run, at is recommended to run on a GPU (see polychrom documentation).simulation_analysis.ipynb: Jupyter notebook containing example analysis of simulated polymer conformations.exp_data: Folder with experimental tracing data (see README.txt inside folder for a detailed description).To install the necessary Python packages create the associated environment using conda:conda env create -f environment.ymlconda activate mitofold_simulation_analysisRun the notebooks and scripts in this environment.