{"id":22308557,"url":"https://github.com/sysbiochalmers/zebrafish-gem","last_synced_at":"2025-07-21T04:06:04.690Z","repository":{"id":39406241,"uuid":"315596574","full_name":"SysBioChalmers/Zebrafish-GEM","owner":"SysBioChalmers","description":"Genome-scale model for Danio rerio","archived":false,"fork":false,"pushed_at":"2023-12-10T15:37:11.000Z","size":20301,"stargazers_count":6,"open_issues_count":0,"forks_count":2,"subscribers_count":0,"default_branch":"main","last_synced_at":"2025-04-05T08:51:15.387Z","etag":null,"topics":["standard-gem"],"latest_commit_sha":null,"homepage":"","language":"MATLAB","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}},"created_at":"2020-11-24T10:28:09.000Z","updated_at":"2025-03-27T21:54:48.000Z","dependencies_parsed_at":"2023-12-10T16:40:52.837Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/Zebrafish-GEM","commit_stats":null,"previous_names":[],"tags_count":9,"template":false,"template_full_name":"MetabolicAtlas/standard-GEM","purl":"pkg:github/SysBioChalmers/Zebrafish-GEM","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FZebrafish-GEM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FZebrafish-GEM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FZebrafish-GEM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FZebrafish-GEM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/Zebrafish-GEM/tar.gz/refs/heads/main","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FZebrafish-GEM/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":266236669,"owners_count":23897221,"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":["standard-gem"],"created_at":"2024-12-03T20:14:22.994Z","updated_at":"2025-07-21T04:06:04.663Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n# Zebrafish-GEM: The generic genome-scale metabolic model of _Danio rerio_\n\n[![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2FZebrafish-GEM.svg)](https://badge.fury.io/gh/sysbiochalmers%2FZebrafish-GEM)\n\n\n#### Brief Model Description\n\nThis repository contains the latest version of Zebrafish-GEM, a zebrafish genome-scale metabolic model.\n\n\n#### Citation\n\n \u003e H. Wang, J. L. Robinson, P. Kocabaş, J. Gustafsson, M. Anton, P.-E. Cholley, et al. Genome-scale metabolic network reconstruction of model animals as a platform for translational research. _PNAS_ 118, e2102344118 (2021). [doi.org/10.1073/pnas.2102344118](https://doi.org/10.1073/pnas.2102344118)\n\n#### Model Keywords\n\n**Utilisation:** multi-omics integrative analysis, predictive simulation\n**Field:** metabolic-network reconstruction  \n**Type of Model:** reconstruction, curated  \n**Model source:** [Human-GEM](https://doi.org/10.1126/scisignal.aaz1482)   \n**Omic source:** genomics; metabolomics   \n**Taxonomic name:** _Danio rerio_  \n**Taxonomy ID:** [7955](https://identifiers.org/taxonomy:7955)  \n**Genome ID:** [GCA_000002035.4](https://identifiers.org/insdc.gca:GCA_000002035.4)  \n**Metabolic System:** general metabolism  \n**Tissue:**  \n**Bioreactor:**    \n**Cell type:**  \n**Cell line:**  \n**Condition:** generic metabolism\n\n\n### Model Overview\n\n|Taxonomy | Template Model | Reactions | Metabolites| Genes |\n| ------------- |:-------------:|:-------------:|:-------------:|:-----:|\n|_Danio rerio_ |   Human-GEM |  12910  | 8347 | 2714 |\n\n\n## Installation\n\n### Required Software\n* A functional MATLAB installation (MATLAB 7.3 and higher).\n* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN).\n* The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality).\n\n\n### Dependencies - Recommended Software\n* The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended).\n* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.\n\n\n### Installation Instructions\n* Clone the [main branch](https://github.com/SysBioChalmers/Zebrafish-GEM/tree/main) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Zebrafish-GEM/releases/latest).\n* Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)).\n\n\n## Usage\n\n#### Loading/saving the model\n\n`Zebrafish-GEM.mat` (Recommended if on `main` branch)\n* Load and save using the built-in MATLAB `load()` and `save()` functions.\n\n`Zebrafish-GEM.xml` (SBML format)\n* Load using the `importModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN))\n* Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN))\n\n\n## Websites\n\n- [Metabolic Atlas](https://metabolicatlas.org/) enables visualization and exploration of Zebrafish-GEM content.\n\n\n### Contributing\n\nContributions are always welcome! Please read the [contributing guidelines](.github/CONTRIBUTING.md) to get started.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fzebrafish-gem","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fzebrafish-gem","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fzebrafish-gem/lists"}