{"id":17857840,"url":"https://github.com/readdy/readdy","last_synced_at":"2025-08-09T09:19:53.094Z","repository":{"id":9046334,"uuid":"59560469","full_name":"readdy/readdy","owner":"readdy","description":"Python / C++ based particle reaction-diffusion simulator","archived":false,"fork":false,"pushed_at":"2022-07-11T14:14:21.000Z","size":7490,"stargazers_count":59,"open_issues_count":17,"forks_count":12,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-17T17:21:31.334Z","etag":null,"topics":["cplusplus","particles","python","reaction-diffusion","simulation"],"latest_commit_sha":null,"homepage":"https://readdy.github.io/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/readdy.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}},"created_at":"2016-05-24T09:41:44.000Z","updated_at":"2025-03-09T04:56:19.000Z","dependencies_parsed_at":"2022-09-07T22:20:56.488Z","dependency_job_id":null,"html_url":"https://github.com/readdy/readdy","commit_stats":null,"previous_names":[],"tags_count":16,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/readdy%2Freaddy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/readdy","download_url":"https://codeload.github.com/readdy/readdy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":244640361,"owners_count":20486026,"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":["cplusplus","particles","python","reaction-diffusion","simulation"],"created_at":"2024-10-28T04:04:07.906Z","updated_at":"2025-03-20T15:33:06.085Z","avatar_url":"https://github.com/readdy.png","language":"C++","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ![ReaDDy](https://readdy.github.io/assets/readdy_black_150px.png \"ReaDDy logo\") #\n\n[![Build Status](https://dev.azure.com/clonker/readdy/_apis/build/status/readdy.readdy?branchName=master)](https://dev.azure.com/clonker/readdy/_build/latest?definitionId=5\u0026branchName=master)\n\nReaDDy (**Rea**ction **D**iffusion **Dy**namics) is an open source particle based reaction-diffusion simulator that can be configured and run via Python.\nCurrently supported platforms are Mac and Linux.\n\n# Installation\nThe preferred way of installing the software is by using the conda package manager:\n```bash\n# optional: create environment for readdy, switch to that environment\nconda create -n readdy\nconda activate readdy\n\n# add conda-forge channel\nconda config --env --add channels conda-forge\n\n# install readdy with a specified Python version\nconda install python=3.9 readdy\n```\n\n# Documentation\nA documentation and a few examples are provided at [https://readdy.github.io/](https://readdy.github.io/).\n\n# Core features\n- particle based simulation of reaction-diffusion systems in 3D\n- particles diffuse via Brownian dynamics\n- reactions between single instances of particles (unimolecularly and bimolecularly)\n- particle interaction potentials for modeling\n  - space exclusion\n  - molecular crowding\n  - aggregation\n- particle complexes via harmonic bonds, angles, and cosine dihedrals for modeling, e.g.,\n  - domain structure\n  - polymer chains\n- spatially and temporally triggered changes in the particle complexes\n- simulation output in a compact hdf5 file\n- single-threaded and pthread-parallelized implementations available\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freaddy%2Freaddy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Freaddy%2Freaddy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Freaddy%2Freaddy/lists"}