{"id":31542619,"url":"https://github.com/sysbiochalmers/ecoli-gem","last_synced_at":"2026-02-15T00:30:59.789Z","repository":{"id":312720412,"uuid":"928232580","full_name":"SysBioChalmers/Ecoli-GEM","owner":"SysBioChalmers","description":"Genome-scale metabolic model for Escherichia coli","archived":false,"fork":false,"pushed_at":"2025-09-01T14:46:15.000Z","size":9381,"stargazers_count":0,"open_issues_count":3,"forks_count":0,"subscribers_count":1,"default_branch":"main","last_synced_at":"2025-09-01T16:37:03.215Z","etag":null,"topics":["genome-scale-models","standard-gem","systems-biology"],"latest_commit_sha":null,"homepage":"https://sysbiochalmers.github.io/Ecoli-GEM/","language":"HTML","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"cc-by-4.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/SysBioChalmers.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":".github/CONTRIBUTING.md","funding":null,"license":"LICENSE.md","code_of_conduct":".github/CODE_OF_CONDUCT.md","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":"2025-02-06T09:40:53.000Z","updated_at":"2025-09-01T14:31:28.000Z","dependencies_parsed_at":"2025-09-01T16:47:18.764Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/Ecoli-GEM","commit_stats":null,"previous_names":["sysbiochalmers/ecoli-gem"],"tags_count":3,"template":false,"template_full_name":"MetabolicAtlas/standard-GEM","purl":"pkg:github/SysBioChalmers/Ecoli-GEM","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEcoli-GEM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEcoli-GEM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEcoli-GEM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEcoli-GEM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/Ecoli-GEM/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEcoli-GEM/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278308618,"owners_count":25965654,"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":"2025-10-04T02:00:05.491Z","response_time":63,"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":["genome-scale-models","standard-gem","systems-biology"],"created_at":"2025-10-04T11:59:37.647Z","updated_at":"2025-10-04T11:59:44.846Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Ecoli-GEM: Genome-scale metabolic model for Escherichia coli\n\n[![Version](https://badge.fury.io/gh/SysBioChalmers/Ecoli-GEM.svg)](https://badge.fury.io/gh/sysbiochalmers/Ecoli-GEM)  \n[![Zenodo](https://zenodo.org/badge/{{Zenodo ID}}.svg)](https://zenodo.org/badge/latestdoi/{{Zenodo ID}})  \n[![Gitter chat](https://badges.gitter.im/SysBioChalmers/Ecoli-GEM.svg)](https://gitter.im/SysBioChalmers)\n\n\n#### Description\n\nThis repository contains the latest version the Ecoli-GEM, a genome scale metabolic model of _Escherichia coli str. K-12 substr. MG1655_. \n\n\n#### Citation\n\nThe latest version of the E. coli GEM, iML1515, was taken from BiGG Models with the following publication:\n  \u003e Monk, J.M., Lloyd, C.J., Brunk, E. et al (2017). iML1515, a knowledgebase that computes Escherichia coli traits. Nat Biotechnol 35, 904–908 [doi:10.1038/nbt.3956](https://doi.org/10.1038/nbt.3956)\n\n#### Keywords\n\n**Utilisation:** experimental data reconstruction; multi-omics integrative analysis; _in silico_ strain design; model template  \n**Field:** metabolic-network reconstruction  \n**Type of model:** reconstruction; curated  \n**Model source:** [EscherichiaColi](https://doi.org/10.1038/nbt.3956)   \n**Omic source:** {{ genomics; metabolomics }}  \n**Taxonomic name:** _Escherichia coli str. K-12 substr. MG1655_   \n**Taxonomy ID:** [taxonomy:511145](https://identifiers.org/taxonomy:511145)   \n**Genome ID:** [insdc.gca:GCA_000005845.2](https://identifiers.org/insdc.gca:GCA_000005845.2)   \n**Metabolic system:** {{ general metabolism }}  \n**Cell type:** Prokaryotic \n**Strain:** MG1655  \n**Condition:** {{ aerobic; glucose-limited; defined media }}  \n\n\n### Installation\n\n{{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }}\n\n\n### Usage\n\n{{ Describe how to load and save the model. }}\n\n\n### Contributing\n\nContributions are always welcome! Please read the [contributing guideline](.github/CONTRIBUTING.md) to get started.\n\n\n### Contributors\n\nCode contributors are reported automatically by GitHub under [Contributors](https://github.com/SysBioChalmers/Ecoli-GEM/graphs/contributors), while other contributions come in as [Issues](https://github.com/SysBioChalmers/Ecoli-GEM/issues).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fecoli-gem","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fecoli-gem","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fecoli-gem/lists"}