{"id":16265097,"url":"https://github.com/robaina/phycogem","last_synced_at":"2026-02-21T23:04:29.924Z","repository":{"id":189476530,"uuid":"680748379","full_name":"Robaina/Phycogem","owner":"Robaina","description":"Modeling phycospheric metabolic interactions in python","archived":false,"fork":false,"pushed_at":"2024-06-27T11:20:26.000Z","size":50384,"stargazers_count":0,"open_issues_count":9,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-10-25T17:46:50.957Z","etag":null,"topics":["bioinformatics","genome-scale-metabolic-model","marine-microbial-ecology","metagenomics","phycosphere"],"latest_commit_sha":null,"homepage":"","language":"Python","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/Robaina.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}},"created_at":"2023-08-20T09:17:36.000Z","updated_at":"2024-06-27T11:20:36.000Z","dependencies_parsed_at":"2023-10-11T17:31:48.676Z","dependency_job_id":"44485372-332a-4ebd-8e36-cdafca6a5baf","html_url":"https://github.com/Robaina/Phycogem","commit_stats":{"total_commits":47,"total_committers":1,"mean_commits":47.0,"dds":0.0,"last_synced_commit":"21a18e737b27bfa08b35fddccf409f9f1457855a"},"previous_names":["robaina/phycogem"],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/Robaina/Phycogem","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FPhycogem","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FPhycogem/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FPhycogem/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FPhycogem/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/Robaina","download_url":"https://codeload.github.com/Robaina/Phycogem/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/Robaina%2FPhycogem/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29696928,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-21T18:18:25.093Z","status":"ssl_error","status_checked_at":"2026-02-21T18:18:22.435Z","response_time":107,"last_error":"SSL_read: 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","genome-scale-metabolic-model","marine-microbial-ecology","metagenomics","phycosphere"],"created_at":"2024-10-10T17:06:11.494Z","updated_at":"2026-02-21T23:04:29.890Z","avatar_url":"https://github.com/Robaina.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![logo](notebooks/images/phycogem_logo.png)\n\u003cbr\u003e\n\n# Reconstructing phycospheric metabolic networks\n\n[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)\n![license](https://img.shields.io/github/license/Robaina/Pynteny)\n![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v2.0%20adopted-ff69b4)\n![python](https://img.shields.io/badge/Python-3.11-blue)\n[![Code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)\n\n\nUpdating CarveME's universe curation pipeline in [this fork](https://github.com/Robaina/carveme_expanded_universe)\n\n\n# :bulb: About\n\nThis repo contains Python code and Jupyter Notebooks aimed at facilitating the reconstruction and analysis of community genome-scale models reconstructed from genome data.\n\n## :wrench: Installation\n\nTo install the package, first clone the repo and create the conda environment. We recomend using [mamba](https://mamba.readthedocs.io/en/latest/user_guide/mamba.html) instead of conda to speed up the process:\n\n```bash\ngit clone https://github.com/Robaina/Phycogem.git\ncd Phycogem\nmamba env create -f envs/phycogem-dev.yml\nconda activate phycogem-dev\n```\n\nThen build and install the package:\n\n```bash\npoetry build\npip install dist/phycogem*.whl\n```\n\n## :rocket: Usage\n\nTo use the package, activate the Conda environment:\n\n```bash\nconda activate phycogem-dev\n```\n\nThis environment includes a Jupyter Notebook ipykernel, so the package can be used in a notebook as well.\n\n## :notebook_with_decorative_cover: Notebooks\n\nThis repo contains several Notebooks to exemply the use of the package. They can be found within the `notebooks` folder.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fphycogem","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Frobaina%2Fphycogem","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Frobaina%2Fphycogem/lists"}