{"id":24841545,"url":"https://github.com/metexplore/met4j","last_synced_at":"2025-10-13T19:17:36.976Z","repository":{"id":46732355,"uuid":"509104650","full_name":"MetExplore/met4j","owner":"MetExplore","description":"Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.","archived":false,"fork":false,"pushed_at":"2025-10-05T19:57:14.000Z","size":14192,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-10-13T19:17:35.844Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Java","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/MetExplore.png","metadata":{"files":{"readme":"README.md","changelog":"CHANGELOG.md","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,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2022-06-30T14:04:23.000Z","updated_at":"2025-08-20T06:30:33.000Z","dependencies_parsed_at":"2025-05-31T21:09:02.249Z","dependency_job_id":"d21ccacf-aca3-403c-a82e-bc3085300be4","html_url":"https://github.com/MetExplore/met4j","commit_stats":null,"previous_names":[],"tags_count":139,"template":false,"template_full_name":null,"purl":"pkg:github/MetExplore/met4j","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MetExplore%2Fmet4j","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MetExplore%2Fmet4j/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MetExplore%2Fmet4j/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MetExplore%2Fmet4j/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MetExplore","download_url":"https://codeload.github.com/MetExplore/met4j/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MetExplore%2Fmet4j/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":279016892,"owners_count":26085884,"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":"2025-10-13T02:00:06.723Z","response_time":61,"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":[],"created_at":"2025-01-31T07:18:38.328Z","updated_at":"2025-10-13T19:17:36.960Z","avatar_url":"https://github.com/MetExplore.png","language":"Java","funding_links":[],"categories":[],"sub_categories":[],"readme":"![](https://forgemia.inra.fr/uploads/-/system/project/avatar/864/met4J_logo.png?width=64)\n# Met4J : the Java library for metabolic networks\n\n[![pipeline status](https://forgemia.inra.fr/metexplore/met4j/badges/master/pipeline.svg)](https://forgemia.inra.fr/metexplore/met4j/-/commits/master)\n[![coverage report](https://forgemia.inra.fr/metexplore/met4j/badges/master/coverage.svg)](https://forgemia.inra.fr/metexplore/met4j/-/commits/master)\n[![maven](https://img.shields.io/maven-central/v/fr.inrae.toulouse.metexplore/met4j)](https://img.shields.io/maven-central/v/fr.inrae.toulouse.metexplore/met4j)\n[![version](https://img.shields.io/gitlab/v/tag/metexplore/met4j?gitlab_url=https%3A%2F%2Fforgemia.inra.fr%2F\u0026include_prereleases\u0026label=version)](https://img.shields.io/gitlab/v/tag/metexplore/met4j?gitlab_url=https%3A%2F%2Fforgemia.inra.fr%2F\u0026include_prereleases\u0026label=version)\n[![javadoc](https://javadoc.io/badge2/fr.inrae.toulouse.metexplore/met4j/javadoc.svg)](https://javadoc.io/doc/fr.inrae.toulouse.metexplore/met4j)\n[![Twitter](https://img.shields.io/twitter/url/https/twitter.com/cloudposse.svg?style=social\u0026label=Follow%20%40met4j)](https://twitter.com/met4j)\n\n**Met4J is an open-source Java library dedicated to the structural analysis of metabolic networks. It also came with a toolbox gathering CLI for several analyses relevant to metabolism-related research.**\n\n\nMet4j is composed by three main modules:\n- [met4j-core](met4j-core/README.md): it's the key module which contains all the core \nclasses for handling metabolic networks\n- [met4j-io](met4j-io/README.md): for importing/exporting metabolic networks in several \nformats (SBML, KEGG, TSV)\n- [met4j-graph](met4j-graph/README.md): for performing graph-based topological analysis of metabolic networks.  \n\nThe package [met4j-toolbox](met4j-toolbox/README.md) contains high-level apps that can be run in command line by using either jar file or Singularity or Docker containers.\n\n\n## Installation\n\n### From Maven\n\nInstall all modules :  \n```\n\u003cdependency\u003e\n\u003cgroupId\u003efr.inrae.toulouse.metexplore\u003c/groupId\u003e\n\u003cartifactId\u003emet4j-toolbox\u003c/artifactId\u003e\n\u003cversion\u003e1.4.0\u003c/version\u003e\n\u003c/dependency\u003e\n```\n\nor a specific module (example : met4j-core ):  \n```\n\u003cdependency\u003e\n\u003cgroupId\u003efr.inrae.toulouse.metexplore\u003c/groupId\u003e\n\u003cartifactId\u003emet4j-core\u003c/artifactId\u003e\n\u003cversion\u003e1.4.0\u003c/version\u003e\n\u003c/dependency\u003e\n```\n\n### From Source\n\n```\ngit clone https://forgemia.inra.fr/metexplore/met4j.git;\ncd met4j;\nmvn clean install \n```\n\nRead [met4j-toolbox](met4j-toolbox/README.md) to see how to get jar, Docker or Singularity packages containing all the met4-toolbox apps.\n\n## Usage\n\nUser documentation for the library modules can be found in each module's own README.  \nDetailed code examples can be found at [here](https://forgemia.inra.fr/metexplore/tutorialmet4j).\nJavadoc can be found at [https://javadoc.io/doc/fr.inrae.toulouse.metexplore](https://javadoc.io/doc/fr.inrae.toulouse.metexplore)\n\n## Contributing\n\nPull requests are welcome **on the gitlab repo** ([https://forgemia.inra.fr/metexplore/met4j](https://forgemia.inra.fr/metexplore/met4j)). For major changes, please open an issue first to discuss what you would like to change.  \n\nPlease make sure to update tests as appropriate.  \n\n## Issues\n\nIssues or suggestions can be posted [here](https://github.com/MetExplore/met4j/issues).\n\n## License\n\nMet4J is distributed under the open license [CeCILL-2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-en.html) (compatible GNU-GPL).  \n\n\n\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmetexplore%2Fmet4j","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmetexplore%2Fmet4j","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmetexplore%2Fmet4j/lists"}