{"id":15716419,"url":"https://github.com/sysbiochalmers/gecko","last_synced_at":"2025-10-24T14:41:45.456Z","repository":{"id":38716212,"uuid":"61196838","full_name":"SysBioChalmers/GECKO","owner":"SysBioChalmers","description":"Toolbox for including enzyme constraints on a genome-scale model.","archived":false,"fork":false,"pushed_at":"2024-10-19T23:11:16.000Z","size":110283,"stargazers_count":67,"open_issues_count":13,"forks_count":50,"subscribers_count":11,"default_branch":"main","last_synced_at":"2024-10-25T04:25:01.309Z","etag":null,"topics":["data-integration","enzyme-constraints","kinetics","matlab","proteomics","systems-biology","toolbox"],"latest_commit_sha":null,"homepage":"http://sysbiochalmers.github.io/GECKO/","language":"MATLAB","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/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}},"created_at":"2016-06-15T09:48:01.000Z","updated_at":"2024-10-15T12:04:03.000Z","dependencies_parsed_at":"2023-10-11T22:45:08.332Z","dependency_job_id":"4e307677-2bcc-4ba3-bebe-ef2001cbd629","html_url":"https://github.com/SysBioChalmers/GECKO","commit_stats":{"total_commits":956,"total_committers":16,"mean_commits":59.75,"dds":0.7081589958158996,"last_synced_commit":"cb95be20329195f0e49b385fd379b2b635ec626c"},"previous_names":[],"tags_count":26,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FGECKO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FGECKO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FGECKO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FGECKO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/GECKO/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247142063,"owners_count":20890652,"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":["data-integration","enzyme-constraints","kinetics","matlab","proteomics","systems-biology","toolbox"],"created_at":"2024-10-03T21:45:35.679Z","updated_at":"2025-10-24T14:41:40.421Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"MATLAB","readme":"\u003cimg src=\"./GECKO.png\" width=\"200px\"\u003e\n\n[![Current release](https://img.shields.io/github/release/SysBioChalmers/GECKO/all.svg)](https://GitHub.com/SysBioChalmers/GECKO/releases/)\n[![GitHub Discussions](https://img.shields.io/github/discussions-search?query=repo%3Asysbiochalmers%2Fgecko\u0026label=GitHub%20Discussions)](https://github.com/SysBioChalmers/GECKO/discussions)\n[![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.7699818.svg)](https://doi.org/10.5281/zenodo.7699818)\n[![MATLAB File Exchange](https://www.mathworks.com/matlabcentral/images/matlab-file-exchange.svg)](https://se.mathworks.com/matlabcentral/fileexchange/125960-gecko-toolbox)\n\n\n## About GECKO 3\n\nThe **GECKO** toolbox enhances a **G**enome-scale model to account for **E**nzyme **C**onstraints, using **K**inetics and **O**mics. The resulting enzyme-constrained model (**ecModel**) can be used to perform simulations where enzyme allocation is either drawn from a total protein pool, or constrained by measured protein levels from proteomics data.\n\n💡 In the [`GECKO/tutorials`](https://github.com/SysBioChalmers/GECKO/tree/main/tutorials) folder there are examples of how GECKO can be applied to GEMs, in either of its _full_ or _light_ forms. Each `protocol.m` contains instructions on how to reconstruct and analyze an ecModel, demonstrating how different fuctions in GECKO can be used. These two scripts complement the [Nature Protocols](https://doi.org/10.1038/s41596-023-00931-7) paper ([**PDF**](https://drive.google.com/file/d/1_AGz6GmQPOyshfUZ6K-L2myzU43rQ6tu/view)).\n\n### Significant changes since protocol publication\n- GECKO **3.2.0**: all protein usage reactions draw from the protein pool, even if they are constrained by proteomics data. This affects **Step 58** in the protocol, changing behaviour of `constrainEnzConcs` and making `updateProtPool` obsolete, `tutorials/full_ecModel/protocol.m` is updated to reflect this change. See [#357](https://github.com/SysBioChalmers/GECKO/issues/375) for more details.  \n  \n_**Note:** Regarding code and model compatibility with earlier GECKO versions, see [Previous versions: GECKO 1 and 2](https://github.com/SysBioChalmers/GECKO/wiki/Previous-versions:-GECKO-1-and-2)_.\n\n## Cite us\n\nIf you have used GECKO in your work, please cite:\n\n\u003e Chen Y, Gustafsson J, Tafur Rangel A, Anton M, Domenzain I, Kittikunapong C, Li F, Yuan L, Nielsen J \u0026 Kerkhoven EJ. Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0. *Nature Protocols* **19**, 629-667 (2024). doi:[10.1038/s41596-023-00931-7](https://doi.org/10.1038/s41596-023-00931-7).\n\n## Documentation\n**Installation instructions** and other information is available in the **[Wiki](https://github.com/SysBioChalmers/GECKO/wiki)**. The source code documentation is also available \n[online](http://sysbiochalmers.github.io/GECKO/doc/). Use [GitHub Discussions](https://github.com/SysBioChalmers/GECKO/discussions) for support, to ask questions or leave comments.\n\n## Contributing\n\nContributions are always welcome! Please read the [contributing guidelines](https://github.com/SysBioChalmers/GECKO/blob/main/.github/CONTRIBUTING.md) to get started.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fgecko","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fgecko","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fgecko/lists"}