{"id":44938389,"url":"https://github.com/markziemann/5pillars","last_synced_at":"2026-02-18T07:34:59.533Z","repository":{"id":169578491,"uuid":"645577204","full_name":"markziemann/5pillars","owner":"markziemann","description":"Five pillars of computational reproducibility","archived":false,"fork":false,"pushed_at":"2024-02-06T23:49:19.000Z","size":738,"stargazers_count":6,"open_issues_count":4,"forks_count":2,"subscribers_count":3,"default_branch":"main","last_synced_at":"2024-05-09T21:13:42.183Z","etag":null,"topics":["bioinformatics","computational-biology","data-science","journal-article","reproducible-research"],"latest_commit_sha":null,"homepage":"https://ziemann-lab.net/public/5pillars/5pillars.html","language":"TeX","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/markziemann.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}},"created_at":"2023-05-26T01:10:03.000Z","updated_at":"2024-03-13T05:39:51.000Z","dependencies_parsed_at":"2023-09-27T04:29:04.321Z","dependency_job_id":null,"html_url":"https://github.com/markziemann/5pillars","commit_stats":null,"previous_names":["markziemann/5pillars"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/markziemann/5pillars","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markziemann%2F5pillars","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markziemann%2F5pillars/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markziemann%2F5pillars/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markziemann%2F5pillars/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/markziemann","download_url":"https://codeload.github.com/markziemann/5pillars/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/markziemann%2F5pillars/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29572507,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-18T06:19:27.422Z","status":"ssl_error","status_checked_at":"2026-02-18T06:18:44.348Z","response_time":162,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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","computational-biology","data-science","journal-article","reproducible-research"],"created_at":"2026-02-18T07:34:59.436Z","updated_at":"2026-02-18T07:34:59.520Z","avatar_url":"https://github.com/markziemann.png","language":"TeX","funding_links":[],"categories":[],"sub_categories":[],"readme":"# 5pillars\n\nThis repo contains the manuscript entitled *Five pillars of computational reproducibility*.\nThis is an effort to solidify some previously proposed best-practices into a simple infographic.\nIt highlights the importance of these five concepts to reproducibility:\n\n* Code version control and persistent sharing.\n\n* Compute environment control.\n\n* Literate programming.\n\n* Documentation.\n\n* Persistent data sharing.\n\nA live version of the manuscript is available at the Ziemann lab website [here](https://ziemann-lab.net/public/5pillars/5pillars.html).\n\n## Contents\n\nThere are three folders:\n\n* `manuscript`: the source document and bibliography.\n\n* `img`: images.\n\n* `LICENCE`: MIT Licence.\n\n* `README.md`: This helpful document.\n\n* `main.sh`: Master script. Execute this to reproduce the manuscript HTML. Requries Docker.\n\n* `helper.sh`: This is a helper script required by the main.sh script.\n\n## Recipe\n\nThis is an executable manuscript, follow the recipe to reproduce it on your system.\n\n**REQUIREMENTS:** Ubuntu 22 (or similar Unix system) with 1 CPU thread and 4GB RAM.\nDocker must be installed.\nTo install it on Ubuntu, run the following in a terminal:\n\n```\n\nsudo apt update \u0026\u0026 sudo apt install docker.io #skip this if you have docker already installed\n\n```\n\nTo generate the manuscript run the following in a terminal.\nIt will take 2-3 minutes.\n\n```\n\nbash main.sh\n\n```\n\nIf the process completed, the HTML document was copied from the container to the host.\nIt can be visualised with firefox or your favourite web browser.\n\n```\n\nfirefox 5pillars.html\n\n```\n\n## How to contribute\n\nRaise an issue on GitHub to report problems with the article or give your suggestions.\n\n## Funding\n\nNo external funding was required.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkziemann%2F5pillars","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmarkziemann%2F5pillars","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmarkziemann%2F5pillars/lists"}