Simulation and analysis code for the paper "Smc5/6 association with microtubules controls dynamic pericentromeric chromatin folding"

This folder contains the code to reproduce simulations and plots in the paper "Smc5/6 association with microtubules controls dynamic pericentromeric chromatin folding". Code to install dependencies The code relies heavily on the the GPU-capable simulation framework openmm and the polymer-simulation specific wrapper polychrom. To run the code in this folder these, and other dependencies, must be installed. A minimal conda environment can be created using the following commands:conda create -n testenvconda install -c omnia openmmpip install -U git+https://github.com/mirnylab/polychrompip install h5py ipython ipykernel matplotlib numpy tqdm multiprocess joblib noctiluca Code to run simulations The repository contains the following scripts to generate simulation data: 1_Time_calibration_and_WT.py 2_softer_microtubule_sim.py 3_larger_persistence_length.py 4_larger_persistence_length_with_softer_microtubule.py To run these scripts, the folder starting_conformation_diploid_fullyequill and the file Currently_used_Yeast_params.py must be in the same directory as the script (and unzipped if folder). Having performed the above-listed installations of dependencies, the scripts may be run from a GPU-capable computer with a command like:python 2_softer_microtubule_sim.py 0 3 where the first index specifies the GPU to use (should always be 0 if there is only one on the computer) and the second index specifies which replicate this is. The only effect of the second index is in naming the output files (see examples in the data folder). The output from this example call would be the folder 2_softer_microtubule_sim_3 within which the polymer configurations during the simulation are stored along with some metadata.Each of the scripts above were run in 7 replicates to generate the results in the data folder. Code to generate analysis plots The simulation results were analyzed in the three jupyter notebooks Analyze_1_Time_calibration_and_WT.ipynb This notebook analyzes the results of the "wild type" simulation (1_Time_calibration_and_WT.py) and generates the plot used for Figure 4a as well as the time calibration. Analyze_2_larger_persistence_length.ipynb This notebook analyzes the results of the simulation 2_larger_persistence_length.py and generates the plots for Figure 4c and Figure S7. Analyze_3_larger_persistence_length_with_softer_microtubule.ipynb This notebook analyzes the results of simulations 2_softer_microtubule_sim.py 3_larger_persistence_length_with_softer_microtubule.py and generates the plots for Figure 4b and 4d and Figure S6 and Figure S8. All notebooks require that the data folder be unzipped prior to running.