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2025
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| Online Access: | https://doi.org/10.5281/zenodo.18088647 |
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| author | Oliveira Junior, Antonio Bento |
| author_facet | Oliveira Junior, Antonio Bento |
| contents | <p><strong>OpenMiChroM: Input Files, Force Fields, and Experimental Data Inputs for ‘A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization’</strong></p> <p>This repository contains the complete set of computational resources required to reproduce the analyses and simulations presented in the manuscript <em>A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization</em>. All files are organized to facilitate transparency, reproducibility, and methodological clarity.</p> <h3><strong>Included Materials</strong></h3> <ul> <li> <p><strong>Simulation Input Files</strong></p> <ul> <li> <p>System setup files and parameter definitions for OpenMiChroM simulations</p> </li> <li> <p>Input templates for chromosome simulations across cell types</p> </li> </ul> <p> </p> </li> <li> <p><strong>Force Field Files</strong></p> <ul> <li> <p>Trained interaction matrices (pairwise λ<sub>ij</sub> coefficients) obtained via the FI-Chrom optimization workflow</p> </li> <li> <p>Bonded and non-bonded parameter sets used in all simulations</p> </li> <li> <p>Energy function configuration files ready for OpenMiChroM execution</p> </li> </ul> </li> <li> <p><strong>Experimental Data Inputs</strong></p> <ul> <li> <p>Processed Hi-C contact matrices used for training<br><br></p> </li> </ul> </li> <li> <p><strong>Reproducibility Resources</strong></p> <ul> <li> <p>Example Python scripts to run energy minimization, force-field training, and 3D structural simulations</p> </li> <li> <p>Jupyter notebooks demonstrating data analysis and visualization steps</p> </li> <li> <p>Tutorials mirroring the workflow described in the manuscript</p> </li> </ul> </li> </ul> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_18088647 |
| institution | Zenodo |
| language | |
| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | inputs for FI-Chrom simulations Oliveira Junior, Antonio Bento <p><strong>OpenMiChroM: Input Files, Force Fields, and Experimental Data Inputs for ‘A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization’</strong></p> <p>This repository contains the complete set of computational resources required to reproduce the analyses and simulations presented in the manuscript <em>A Data-Driven Chromatin Model Reveals Spatial and Dynamic Features of Genome Organization</em>. All files are organized to facilitate transparency, reproducibility, and methodological clarity.</p> <h3><strong>Included Materials</strong></h3> <ul> <li> <p><strong>Simulation Input Files</strong></p> <ul> <li> <p>System setup files and parameter definitions for OpenMiChroM simulations</p> </li> <li> <p>Input templates for chromosome simulations across cell types</p> </li> </ul> <p> </p> </li> <li> <p><strong>Force Field Files</strong></p> <ul> <li> <p>Trained interaction matrices (pairwise λ<sub>ij</sub> coefficients) obtained via the FI-Chrom optimization workflow</p> </li> <li> <p>Bonded and non-bonded parameter sets used in all simulations</p> </li> <li> <p>Energy function configuration files ready for OpenMiChroM execution</p> </li> </ul> </li> <li> <p><strong>Experimental Data Inputs</strong></p> <ul> <li> <p>Processed Hi-C contact matrices used for training<br><br></p> </li> </ul> </li> <li> <p><strong>Reproducibility Resources</strong></p> <ul> <li> <p>Example Python scripts to run energy minimization, force-field training, and 3D structural simulations</p> </li> <li> <p>Jupyter notebooks demonstrating data analysis and visualization steps</p> </li> <li> <p>Tutorials mirroring the workflow described in the manuscript</p> </li> </ul> </li> </ul> |
| title | inputs for FI-Chrom simulations |
| url | https://doi.org/10.5281/zenodo.18088647 |