{"id":15977857,"url":"https://github.com/srom/archaea-vs-bacteria","last_synced_at":"2026-01-22T10:34:35.563Z","repository":{"id":252943057,"uuid":"841978838","full_name":"srom/archaea-vs-bacteria","owner":"srom","description":"Code from paper \"Archaea produce peptidoglycan hydrolases that kill bacteria\"","archived":false,"fork":false,"pushed_at":"2025-05-28T09:55:25.000Z","size":62016,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-05-28T10:53:23.237Z","etag":null,"topics":["antimicrobial","archaea","bacteria","microbiology","phylogenetics"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1101/2024.09.18.613068","language":"Jupyter Notebook","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/srom.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,"zenodo":null}},"created_at":"2024-08-13T12:31:09.000Z","updated_at":"2025-05-28T09:54:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"3d64b3be-15fd-40a5-95e0-74d7ab26e4d5","html_url":"https://github.com/srom/archaea-vs-bacteria","commit_stats":{"total_commits":51,"total_committers":2,"mean_commits":25.5,"dds":"0.039215686274509776","last_synced_commit":"a0a270c469a676d621fb29b41c3ccc13b100aacf"},"previous_names":["srom/archaea-vs-bacteria"],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/srom/archaea-vs-bacteria","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Farchaea-vs-bacteria","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Farchaea-vs-bacteria/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Farchaea-vs-bacteria/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Farchaea-vs-bacteria/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/srom","download_url":"https://codeload.github.com/srom/archaea-vs-bacteria/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/srom%2Farchaea-vs-bacteria/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28661874,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-22T01:17:37.254Z","status":"online","status_checked_at":"2026-01-22T02:00:07.137Z","response_time":144,"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":["antimicrobial","archaea","bacteria","microbiology","phylogenetics"],"created_at":"2024-10-07T23:02:25.320Z","updated_at":"2026-01-22T10:34:35.558Z","avatar_url":"https://github.com/srom.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Archaea vs Bacteria\n\nCode from paper: \n\n\u003e Archaea produce peptidoglycan hydrolases that kill bacteria\n\u003e\n\u003e Romain Strock, Valerie WC Soo, Pauline Misson, Georgia Roumelioti, Pavel V Shliaha, Antoine Hocher, Tobias Warnecke\u003cbr\u003e\n\u003e PLOS Biology 23(8): e3003235; doi: https://doi.org/10.1371/journal.pbio.3003235\n\n## Content\n\n- `notebook/`: python notebooks to reproduce all the figures.\n- `src/`: scripts to produce all the data used in the paper. Scripts are referenced in notebooks.\n- `figures/`: all unassembled figures as produced by the relevant notebooks.\n- `data/`: input data and data produced by the scripts and notebooks in this repo.\n  - includes supplementary data such as tree alignments or the result of homology search.\n\n## Install\n\n```sh\ngit clone https://github.com/srom/archaea-vs-bacteria.git\ngit lfs pull origin main  # optional - see below\ncd archaea-vs-bacteria\nconda env create -f environment.yml\nconda activate AvB\n```\n\nNote: some of the larger files in `data/` are tracked with [Git Large File Storage](https://git-lfs.com/). They won't get  downloaded with `git pull` or through GitHub's UI. To download these files, install `git-lfs` and use `git lfs pull`.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsrom%2Farchaea-vs-bacteria","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsrom%2Farchaea-vs-bacteria","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsrom%2Farchaea-vs-bacteria/lists"}