{"id":27645923,"url":"https://github.com/open2c/polychrom","last_synced_at":"2025-04-24T01:13:56.012Z","repository":{"id":41348916,"uuid":"178608195","full_name":"open2c/polychrom","owner":"open2c","description":"Chromosome polymer simulations and in silico capture experiments","archived":false,"fork":false,"pushed_at":"2025-04-16T23:30:31.000Z","size":20626,"stargazers_count":48,"open_issues_count":9,"forks_count":16,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-04-24T01:13:50.180Z","etag":null,"topics":["chromatin","chromosomes","hi-c","loop-extrusion","polymer","simulation"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/open2c.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2019-03-30T20:30:23.000Z","updated_at":"2025-04-16T22:38:37.000Z","dependencies_parsed_at":"2025-04-16T23:44:58.591Z","dependency_job_id":"42bbba89-25e4-4070-bdb3-2e86c8e553b0","html_url":"https://github.com/open2c/polychrom","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/open2c%2Fpolychrom","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/open2c%2Fpolychrom/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/open2c%2Fpolychrom/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/open2c%2Fpolychrom/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/open2c","download_url":"https://codeload.github.com/open2c/polychrom/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250540916,"owners_count":21447427,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["chromatin","chromosomes","hi-c","loop-extrusion","polymer","simulation"],"created_at":"2025-04-24T01:13:55.364Z","updated_at":"2025-04-24T01:13:56.004Z","avatar_url":"https://github.com/open2c.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# polychrom\n\n[![DOI](https://zenodo.org/badge/178608195.svg)](https://zenodo.org/badge/latestdoi/178608195)\n\n## Open2C polymer simulation library\n\nThis library is designed to easily set up polymer simulations of chromosomes subject to a set of forces or constraints. \nPolychrom is designed to build mechanistic models - i.e. models that simulates a biological process. \nWe then compare results of the simulation to Hi-C maps or microscopy, and to other sources of data. \n\nPolychrom is not designed to make a simulation based on a Hi-C map alone, without a hypothesis in mind. \nFor distinction between mechanistic and data-driven models see https://pubmed.ncbi.nlm.nih.gov/26364723/ \n\nPolychrom documentation is hosted on readthedocs. \nhttps://polychrom.readthedocs.io/en/latest/\n\nOne of the main uses of polychrom now is to simulate loop extrusion. An example loop extrusion simulation is presented here.\nhttps://github.com/mirnylab/polychrom/tree/master/examples/loopExtrusion . It is a good starting point for loop extrusion simulations. \n\nSimplest example simulation that does nothing, which is a good starting point for novel simulations or polymer physics projects.  \nhttps://github.com/mirnylab/polychrom/blob/master/examples/example/example.py\n\n### Transitioning from openmm-polymer (\"openmmlib\")\nCompared to openmm-polymer, it has a new storage format described here: https://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/hdf5_reporter.ipynb\nFor backwards compatibility with analysis routines, we have legacy reporter that saves into openmmlib format \nhttps://github.com/mirnylab/polychrom/blob/master/examples/storage_formats/legacy_reporter.ipynb\n\npolychrom.polymerutils.load function  is backwards compatible with both new and old style \nformat. https://github.com/mirnylab/polychrom/blob/master/polychrom/polymerutils.py#L22\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fpolychrom","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopen2c%2Fpolychrom","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopen2c%2Fpolychrom/lists"}