{"id":22308573,"url":"https://github.com/sysbiochalmers/panyeast-gem","last_synced_at":"2026-03-19T22:22:55.455Z","repository":{"id":39406581,"uuid":"140536161","full_name":"SysBioChalmers/panYeast-GEM","owner":"SysBioChalmers","description":"Reconstruction of a pan-genome metabolic model for S. cerevisiae - the pan model and scripts to make strain-specific models.","archived":false,"fork":false,"pushed_at":"2022-05-27T10:51:50.000Z","size":6765,"stargazers_count":0,"open_issues_count":8,"forks_count":1,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-01-30T22:51:18.880Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":null,"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":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2018-07-11T07:12:11.000Z","updated_at":"2022-05-27T10:51:52.000Z","dependencies_parsed_at":"2022-09-08T13:22:54.404Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/panYeast-GEM","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FpanYeast-GEM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FpanYeast-GEM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FpanYeast-GEM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FpanYeast-GEM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/panYeast-GEM/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245571109,"owners_count":20637280,"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":[],"created_at":"2024-12-03T20:14:26.109Z","updated_at":"2025-10-25T05:11:14.960Z","avatar_url":"https://github.com/SysBioChalmers.png","language":null,"funding_links":[],"categories":[],"sub_categories":[],"readme":"# 1,011 strain-specific models\n\nThe 1,011 strain-specific models matching [Lu et al. (2019)](https://www.nature.com/articles/s41467-019-11581-3) are available from [Zenodo](https://doi.org/10.5281/zenodo.6585439).\n\n# panYeast-GEM: The pan-genome metabolic model of _Saccharomyces cerevisiae_\n\n[![GitHub version](https://badge.fury.io/gh/sysbiochalmers%2FpanYeast-gem.svg)](https://badge.fury.io/gh/sysbiochalmers%2FpanYeast-gem) [![Join the chat at https://gitter.im/SysBioChalmers/panYeast-GEM](https://badges.gitter.im/SysBioChalmers/panYeast-GEM.svg)](https://gitter.im/SysBioChalmers/panYeast-GEM?utm_source=badge\u0026utm_medium=badge\u0026utm_campaign=pr-badge\u0026utm_content=badge)\n\n* Brief Model Description:\n\nThis repository contains the pan-genome metabolic model of _Saccharomyces cerevisiae_. **This README.md is mostly copied from `yeast-GEM`.**\n\n* Model KeyWords:\n**redefine**\n**GEM Category:** Species; **Utilisation:** predictive simulation, multi-omics integrative analysis, _in silico_ strain design, model template; **Field:** metabolic-network reconstruction; **Type of Model:** curated, reconstruction; **Model Source:** [Yeast 7.6](https://sourceforge.net/projects/yeast/); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; **Condition:** aerobic, glucose-limited, defined media, maximization of growth.\n\n* Last update: 2018-06-28\n\n* Main Model Descriptors:\n\n|Taxonomy | Template Model | Reactions | Metabolites| Genes |\n|:-------:|:--------------:|:---------:|:----------:|:-----:|\n|_Saccharomyces cerevisiae_|[yeast-GEM](https://github.com/SysBioChalmers/yeast-GEM)|x|x|x|\n\nThis repository is administered by xx ([@xx](https://github.com/xx)), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.\n\n## Installation\n\n### Required Software - User:\n** Copied from yeast-GEM **\n* Matlab user:\n  * A functional Matlab installation (MATLAB 7.3 or higher).\n  * The [COBRA toolbox for MATLAB](https://github.com/opencobra/cobratoolbox).\n* Python user:\n  * Python 2.7, 3.4, 3.5 or 3.6\n  * [cobrapy](https://github.com/opencobra/cobrapy)\n\n### Required Software - Contributor:\n\n* Both of the previous Matlab requirements.\n* The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN).\n* A [git wrapper](https://github.com/manur/MATLAB-git) added to the search path.\n\n### Dependencies - Recommended Software:\n* For Matlab, the [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/) (version 5.17.0 is recommended).\n* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.\n\n### Installation Instructions\n* For users: Clone it from [`master`](https://github.com/SysBioChalmers/yeast-GEM) in the Github repo, or just download [the latest release](https://github.com/SysBioChalmers/yeast-GEM/releases).\n* For contributors: Fork it to your Github account, and create a new branch from [`devel`](https://github.com/SysBioChalmers/yeast-GEM/tree/devel).\n\n## Usage\n**Explain how strain specific models can be generated**\n\n## Model Files\n\n**Include explanation that a yeast-GEM derived pan-submodel and a non-S288c pan-submodel are kept separately (with the first one being automatically generated from yeast-GEM), while the final pan model combines these two submodels **\nThe model is available in `.xml`, `.txt`, `.yml`, `.mat` and `.xlsx` (the last 2 extensions only in `master`). Additionally, the following 2 files are available:\n* `dependencies.txt`: Tracks versions of toolboxes \u0026 SBML used for saving the model.\n\n## Complementary Scripts\n**Should include following Matlab scripts:**\n* Convert yeast-GEM to pan-submodel\n* Combine pan-submodels into one pan-model\n* Generate strain specific models from pan-model and table matching genes with panIDs\n* Potential gap-filling to result in a functional model\n\n## Complementary Data\n** Should include the following:**\n* Pan-genome data, matching panIDs with strain specific gene IDs\n\n## Contributors\n\n* [Eduard J. Kerkhoven](https://www.chalmers.se/en/staff/Pages/Eduard-Kerkhoven.aspx) ([@edkerk](https://github.com/edkerk)), Chalmers University of Technology, Sweden\n* [Feiran Li](https://www.chalmers.se/en/staff/Pages/feiranl.aspx) ([@feiranl](https://github.com/feiranl)), Chalmers University of Technology, Sweden\n* [Hongzhong Lu](https://www.chalmers.se/en/Staff/Pages/luho.aspx) ([@hongzhonglu](https://github.com/hongzhonglu)), Chalmers University of Technology, Sweden\n* [Benjamín J. Sánchez](https://www.chalmers.se/en/staff/Pages/bensan.aspx) ([@BenjaSanchez](https://github.com/benjasanchez)), Chalmers University of Technology, Sweden\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fpanyeast-gem","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fpanyeast-gem","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fpanyeast-gem/lists"}