{"id":27943344,"url":"https://github.com/geometric-intelligence/proteo","last_synced_at":"2025-06-24T00:34:14.113Z","repository":{"id":277581817,"uuid":"765336960","full_name":"geometric-intelligence/proteo","owner":"geometric-intelligence","description":"AI Proteomics","archived":false,"fork":false,"pushed_at":"2025-06-11T23:24:12.000Z","size":333023,"stargazers_count":1,"open_issues_count":2,"forks_count":0,"subscribers_count":3,"default_branch":"main","last_synced_at":"2025-06-12T00:31:52.496Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/geometric-intelligence.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null}},"created_at":"2024-02-29T18:15:06.000Z","updated_at":"2025-03-09T01:27:33.000Z","dependencies_parsed_at":"2025-06-12T00:33:47.503Z","dependency_job_id":null,"html_url":"https://github.com/geometric-intelligence/proteo","commit_stats":null,"previous_names":["geometric-intelligence/proteo"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/geometric-intelligence/proteo","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fproteo","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fproteo/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fproteo/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fproteo/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/geometric-intelligence","download_url":"https://codeload.github.com/geometric-intelligence/proteo/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/geometric-intelligence%2Fproteo/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":261583124,"owners_count":23180639,"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","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":"2025-05-07T12:05:16.903Z","updated_at":"2025-06-24T00:34:14.106Z","avatar_url":"https://github.com/geometric-intelligence.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# AI Proteomics\n\n# Set up\n\n```shell\n$ conda create -n proteo --file conda-linux-64.lock\n$ conda activate proteo\n$ R\n$ if (!requireNamespace(\"BiocManager\", quietly = TRUE))\n$    install.packages(\"BiocManager\")\n\n$ BiocManager::install(\"WGCNA\")\n$ q()\n$ poetry install --with=dev,gpu\n$ Add \"export LD_PRELOAD=/home/lcornelis/anaconda3/envs/proteo/lib/libstdc++.so.6\" to nano ~/.bashrc file\n```\n\n# Dev\n\nOnly run if changes are made to the environment files.\n\nTo recreate the conda lock, after modifying conda.yaml:\n```shell\npip install conda-lock\nmake conda-linux-64.lock\n```\n\nTo recreate the poetry lock, after modifying pyproject.toml:\n```shell\nmake poetry.lock\n```\nNote: you need to have poetry installed for this, which means that you need to be in proteo.\n\nAnd then go back to set up step above.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeometric-intelligence%2Fproteo","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fgeometric-intelligence%2Fproteo","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fgeometric-intelligence%2Fproteo/lists"}