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

This archive contains data, code and examples associated with the manuscript "<b>Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes</b>" 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).<br><br>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.本归档文件包含与Beckwith、Brunner等人所撰论文《纳米尺度三维DNA追踪揭示有丝分裂染色体自组织机制（Nanoscale 3D DNA tracing reveals the mechanism of self-organization of mitotic chromosomes）》相关的数据、代码与示例。补充材料视频S1展示了一段100 Mb染色体进行有丝分裂压缩的动态模拟示例，更多细节请参见原文。 该ZIP归档包含以下文件： environment.yml：用于通过虚拟环境自动安装所需Python依赖包的配置文件。 LE_sim_functions.py：运行一维环挤出模拟所需的Python函数定义文件。 simulation_analysis_functions.py：用于分析模拟聚合物构象并与实验数据进行对比的Python函数定义文件。 trace_analysis_functions.py：用于分析实验聚合物构象的Python函数定义文件。 run_LE_sim.ipynb：包含一维环挤出模拟运行示例代码的Jupyter笔记本，可作为动态聚合物模拟的输入文件。 run_polychrom_LE.py：可执行Python程序，用于基于一维环挤出运行动态polychrom模拟。运行时需先进入对应环境（详见下文），执行命令为"python run_polychrom_LE --folder_path "run_LE_sim笔记本生成的文件夹路径""。注意该脚本需依赖polychrom（https://github.com/open2c/polychrom）包，推荐使用GPU运行（详见polychrom官方文档）。 simulation_analysis.ipynb：包含模拟聚合物构象示例分析代码的Jupyter笔记本。 exp_data：存储实验追踪数据的文件夹（详见文件夹内的README.txt以获取详细说明）。 如需安装所需Python依赖包，请通过conda创建对应环境： conda env create -f environment.yml conda activate mitofold_simulation_analysis 在该环境中运行本归档内的笔记本与脚本。