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：《数据驱动染色质模型揭示基因组组织的空间与动态特征》一文所用输入文件、力场及实验数据输入集 本仓库包含复现论文《数据驱动染色质模型揭示基因组组织的空间与动态特征》中所有分析与模拟所需的完整计算资源。所有文件均经过结构化整理，以保障研究透明度、结果可复现性与方法学清晰性。 包含资源 模拟输入文件 OpenMiChroM模拟所需的系统配置文件与参数定义 适配不同细胞类型的染色体模拟输入模板 力场文件 通过FI-Chrom优化流程得到的训练完成交互矩阵（成对λ_ij系数） 所有模拟中使用的键合与非键合参数集 可直接用于OpenMiChroM运行的能量函数配置文件 实验数据输入 用于模型训练的经过预处理的Hi-C接触矩阵 可复现性资源 用于执行能量最小化、力场训练与三维结构模拟的示例Python脚本 展示数据分析与可视化流程的Jupyter笔记本 复刻论文所述研究流程的配套教程
