{"id":29838064,"url":"https://github.com/pauleve/updating-modes-notebooks","last_synced_at":"2025-07-29T13:18:40.447Z","repository":{"id":53775747,"uuid":"379225399","full_name":"pauleve/updating-modes-notebooks","owner":"pauleve","description":"Notebooks demonstrating colomoto.minibn for computing dynamics of Boolean networks with various update modes","archived":false,"fork":false,"pushed_at":"2022-08-05T11:28:27.000Z","size":185,"stargazers_count":1,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-05-01T22:14:36.663Z","etag":null,"topics":["boolean-networks","notebooks"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pauleve.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2021-06-22T10:11:46.000Z","updated_at":"2024-05-01T22:14:36.664Z","dependencies_parsed_at":"2022-09-10T00:11:37.389Z","dependency_job_id":null,"html_url":"https://github.com/pauleve/updating-modes-notebooks","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/pauleve/updating-modes-notebooks","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pauleve%2Fupdating-modes-notebooks","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pauleve%2Fupdating-modes-notebooks/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pauleve%2Fupdating-modes-notebooks/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pauleve%2Fupdating-modes-notebooks/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pauleve","download_url":"https://codeload.github.com/pauleve/updating-modes-notebooks/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pauleve%2Fupdating-modes-notebooks/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":267694097,"owners_count":24129140,"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","status":"online","status_checked_at":"2025-07-29T02:00:12.549Z","response_time":2574,"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":["boolean-networks","notebooks"],"created_at":"2025-07-29T13:18:39.824Z","updated_at":"2025-07-29T13:18:40.437Z","avatar_url":"https://github.com/pauleve.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"\nSupplementary material to the chapter 6 \"**Boolean networks and their dynamics: the impact of updates**\" by [Loïc Paulevé](https://loicpauleve.name) and [Sylvain Sené](https://pageperso.lis-lab.fr/~sylvain.sene/) of the book \"*Systems Biology Modelling and Analysis: Formal Bioinformatics Methods and Tools*\" (First Edition), edited by Elisabetta De Maria (Wiley, 2023).\n\nThese notebooks demonstate how to use the Python module\n[`colomoto.minibn`](https://github.com/colomoto/colomoto-jupyter) for computing\ndynamics of Boolean networks with various updating modes.\n\nThey can be visualized online at https://nbviewer.jupyter.org/github/pauleve/updating-modes-notebooks/\n\nThey can be executed and modified online at https://mybinder.org/v2/gh/pauleve/updating-modes-notebooks/main\n\n## Local installation\n\nThe module can be installed with a recent Python (≥3.7) distribution, using\n`pip` or `conda`.\n\n### Using pip (Python)\n\nIn a terminal/powershell\n```sh\npip install -U colomoto-jupyter\n```\n\n### Using conda\n\n```sh\nconda install -c conda-forge -c colomoto colomoto-jupyter\n```\n\n### Using the CoLoMoTo Docker image\n\nThese notebooks can be executed within the [CoLoMoTo Docker distribution](https://colomoto.org/notebook) version `2022-07-01`:\n1. download the notebooks from  https://github.com/pauleve/updating-modes-notebooks/archive/main.zip and extract the zip file\n2. execute the following commands, where ``notebooks`` is the folder in which you extracted the notebooks\n```sh\nsudo pip install -U colomoto-docker # you may have to use pip3 instead of pip\ncolomoto-docker -V 2022-07-01 --bind notebooks\n```\n\n## Related documentation\n\nOther tutorials regarding the `minibn` module can be found at\n    https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/minibn/\nas well as other tools related to boolean networks at\n    https://nbviewer.jupyter.org/github/colomoto/colomoto-docker/tree/master/tutorials/\n\nSee http://colomoto.org/notebook for more information.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpauleve%2Fupdating-modes-notebooks","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpauleve%2Fupdating-modes-notebooks","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpauleve%2Fupdating-modes-notebooks/lists"}