{"id":20100765,"url":"https://github.com/mattbit/active-network-er","last_synced_at":"2026-06-09T17:31:31.403Z","repository":{"id":79842418,"uuid":"261190024","full_name":"mattbit/active-network-er","owner":"mattbit","description":"The ER simulation framework provides tools to simulate and analyze motion on network structures which resemble the endoplasmic reticulum.","archived":false,"fork":false,"pushed_at":"2023-11-09T22:25:25.000Z","size":6289,"stargazers_count":0,"open_issues_count":3,"forks_count":1,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-02T16:49:34.365Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/mattbit.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}},"created_at":"2020-05-04T13:43:01.000Z","updated_at":"2022-07-12T16:25:02.000Z","dependencies_parsed_at":null,"dependency_job_id":"db3b4628-c246-4f11-ad02-d4e78d95b4d4","html_url":"https://github.com/mattbit/active-network-er","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/mattbit/active-network-er","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mattbit%2Factive-network-er","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mattbit%2Factive-network-er/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mattbit%2Factive-network-er/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mattbit%2Factive-network-er/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mattbit","download_url":"https://codeload.github.com/mattbit/active-network-er/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mattbit%2Factive-network-er/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":34118751,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-05-26T15:22:16.424Z","status":"online","status_checked_at":"2026-06-09T02:00:06.510Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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":[],"created_at":"2024-11-13T17:17:02.580Z","updated_at":"2026-06-09T17:31:31.386Z","avatar_url":"https://github.com/mattbit.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ER active flow network simulations\n\n[![Build Status](https://travis-ci.com/mattbit/active-network-er.svg?token=zKpBnjBx4d1NEMb7zFbd\u0026branch=master)](https://travis-ci.com/mattbit/active-network-er)\n[![GPLv3 license](https://img.shields.io/badge/License-GPLv3-blue.svg)](http://perso.crans.org/besson/LICENSE.html)\n[![DOI](https://zenodo.org/badge/261190024.svg)](https://zenodo.org/badge/latestdoi/261190024)\n\nThe code provides a framework to implement simulations of particle motion on networks. Different models can be used for the network and the particle behaviour. In particular, the code provides an implementation of the active-flow network model to describe motion on the endoplasmic reticulum.\n\nSome examples of network structures are provided in graphml format in `resources/graphs`.\n\nThe code has been tested on Python 3.10.\n\n#### Active-flow network generates molecular transport by packets\n\nThe code to reproduce the figures of “Active flow network generates molecular transport by packets” (Proceedings of the Royal Society B, 2020) by Matteo Dora \u0026 David Holcman is provided in the `scripts_prsb` subfolder.\nEach script will run the required simulations and produce the corresponding figures (it can take some time!). Simulation data and figures will be saved in the locations specified in `config.py`.\n\nThe published article can be found [here](https://royalsocietypublishing.org/doi/10.1098/rspb.2020.0493).\n\n### [Documentation](https://mattbit.github.io/active-network-er/)\n\nDocumentation can be found [here](https://mattbit.github.io/active-network-er/) or it can be generated with sphinx (look in `docsrc`).\n\nIf you have troubles running the code, you have doubts or need any help, don't hesitate to reach out with any question at matteo.dora@ieee.org!\n\n### Development\n\nDevelopment is done using `poetry` to manage dependencies. Tests can be run with python's `unittest` (`$ python -m unittest discover test`) or with `pytest`.\n\n### Authors\n\nThe code was written by Matteo Dora (matteo.dora@ieee.org) at the Biology Department of the École Normale Supérieure in Paris as part of his PhD thesis at [David Holcman's lab](https://github.com/holcman-lab).\n\n### License\n\nThe code is released under the GPLv3 license (see `LICENSE`).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmattbit%2Factive-network-er","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmattbit%2Factive-network-er","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmattbit%2Factive-network-er/lists"}