{"id":13992659,"url":"https://github.com/pybel/pybel-notebooks","last_synced_at":"2025-07-22T16:31:03.490Z","repository":{"id":50662028,"uuid":"71557086","full_name":"pybel/pybel-notebooks","owner":"pybel","description":"Notebooks demonstrating the usage of PyBEL and PyBEL Tools","archived":false,"fork":false,"pushed_at":"2022-11-20T22:54:00.000Z","size":17457,"stargazers_count":8,"open_issues_count":10,"forks_count":4,"subscribers_count":4,"default_branch":"master","last_synced_at":"2024-11-29T13:39:55.588Z","etag":null,"topics":["bioinformatics","biological-expression-language","nbviewer","networks","systems-biology"],"latest_commit_sha":null,"homepage":"","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/pybel.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":"2016-10-21T10:50:15.000Z","updated_at":"2023-10-19T15:24:24.000Z","dependencies_parsed_at":"2023-01-23T13:31:13.776Z","dependency_job_id":null,"html_url":"https://github.com/pybel/pybel-notebooks","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/pybel/pybel-notebooks","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pybel%2Fpybel-notebooks","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pybel%2Fpybel-notebooks/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pybel%2Fpybel-notebooks/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pybel%2Fpybel-notebooks/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/pybel","download_url":"https://codeload.github.com/pybel/pybel-notebooks/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/pybel%2Fpybel-notebooks/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266530877,"owners_count":23944000,"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":"2025-07-22T02:00:09.085Z","response_time":66,"last_error":null,"robots_txt_status":null,"robots_txt_updated_at":null,"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":["bioinformatics","biological-expression-language","nbviewer","networks","systems-biology"],"created_at":"2024-08-09T14:02:04.857Z","updated_at":"2025-07-22T16:31:01.936Z","avatar_url":"https://github.com/pybel.png","language":"Jupyter Notebook","funding_links":[],"categories":["Jupyter Notebook"],"sub_categories":[],"readme":"# PyBEL Notebooks\n\nThis repository contains Jupyter notebooks demonstrating the [PyBEL](https://github.com/pybel/pybel) and \n[PyBEL Tools](https://github.com/pybel/pybel-tools) packages.\n\n## Cookbook\n\nThis directory contains notebooks that address small problems.\n\n## [Summary](https://github.com/pybel/pybel-notebooks/tree/master/summary)\n\nThis directory contains notebooks that analyze the contents of a BEL graph.\n\n1. Graph Summary\n2. Citation Summary\n3. Error Analysis\n\n## [Integration](https://github.com/pybel/pybel-notebooks/tree/master/integration)\n\nThis directory contains notebooks dealing with input/output and data integration.\n\n1. Parsing JGIF\n2. Resolving Protein Complexes\n\n## [Algorithms](https://github.com/pybel/pybel-notebooks/tree/master/algorithms)\n\nThis directory contains notebooks demonstrating algorithms implemented with PyBEL and NetworkX.\n\n1. Generation of Unbiased Candidate Mechanisms\n2. Subgraph Expansion\n3. Subgraph Comparison\n4. Candidate Mechanism Pertubation Amplitude\n5. Time Series Analysis with CMPA\n6. Concordance Analysis\n\n## Root Directory\n\n### Template Notebook ([source](https://github.com/pybel/pybel-notebooks/blob/master/Template.ipynb))\n\nThis notebook serves as a style guide for other notebooks in this repository.\n\n### BEL Compiler Comparison Notebook ([source](https://github.com/pybel/pybel-notebooks/blob/master/BEL%20Compiler%20Comparison.ipynb)\\) ([nbviewer](http://nbviewer.jupyter.org/github/pybel/pybel-notebooks/blob/master/BEL%20Compiler%20Comparison.ipynb)\\)\n\t\nThe speed and usability of the PyBEL compiler is compared to the two legacy options: bel.rb and the OpenBEL Framework.\n\n### test.py ([source](https://github.com/pybel/pybel-notebooks/blob/master/test.py))\n\nThis file can be run with `python3 -m nose` to check that notebooks run to completion.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpybel%2Fpybel-notebooks","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fpybel%2Fpybel-notebooks","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fpybel%2Fpybel-notebooks/lists"}