inputs for FI-Chrom simulations
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OpenMiChroM: Input Files, Force Fields, and Experimental Data Inputs for ‘A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization’ This repository contains the complete set of computational resources required to reproduce the analyses and simulations presented in the manuscript A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization. All files are organized to facilitate transparency, reproducibility, and methodological clarity. Included Materials Simulation Input Files System setup files and parameter definitions for OpenMiChroM simulations Input templates for chromosome simulations across cell types Force Field Files Trained interaction matrices (pairwise λ<sub>ij</sub> coefficients) obtained via the FI-Chrom optimization workflow Bonded and non-bonded parameter sets used in all simulations Energy function configuration files ready for OpenMiChroM execution Experimental Data Inputs Processed Hi-C contact matrices used for training Reproducibility Resources Example Python scripts to run energy minimization, force-field training, and 3D structural simulations Jupyter notebooks demonstrating data analysis and visualization steps Tutorials mirroring the workflow described in the manuscript
OpenMiChroM：适配《一种揭示基因组组织空间与动态特征的数据驱动染色质模型》的输入文件、力场与实验数据输入集 本开源代码仓库包含复现论文《一种揭示基因组组织空间与动态特征的数据驱动染色质模型》中所有分析与仿真实验所需的全套计算资源。所有文件均经过规范化整理，以保障研究的透明性、可复现性与方法学阐释清晰度。 收录内容 仿真输入文件 OpenMiChroM仿真所需的系统配置文件与参数定义集 适配不同细胞类型的染色体仿真输入模板 力场文件 通过FI-Chrom优化流程得到的训练完成的相互作用矩阵（成对λ<sub>ij</sub>系数） 所有仿真实验中使用的成键与非成键参数集 可直接用于OpenMiChroM运行的能量函数配置文件 实验数据输入集 用于模型训练的经预处理的Hi-C接触矩阵 可复现性配套资源 用于执行能量最小化、力场训练与三维结构仿真的示例Python脚本 用于演示数据分析与可视化流程的Jupyter Notebook 与论文所述研究流程完全匹配的教程
