{"id":22308582,"url":"https://github.com/sysbiochalmers/salb-gem","last_synced_at":"2025-03-26T01:28:25.494Z","repository":{"id":39406363,"uuid":"177741819","full_name":"SysBioChalmers/Salb-GEM","owner":"SysBioChalmers","description":"GEM for Streptomyces albidoflavus (S.albus J1074)","archived":false,"fork":false,"pushed_at":"2021-04-21T17:47:13.000Z","size":32195,"stargazers_count":0,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-30T22:51:19.321Z","etag":null,"topics":[],"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":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":"2019-03-26T08:07:46.000Z","updated_at":"2021-04-21T17:42:37.000Z","dependencies_parsed_at":"2022-09-08T13:22:56.750Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/Salb-GEM","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FSalb-GEM","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FSalb-GEM/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FSalb-GEM/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FSalb-GEM/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/Salb-GEM/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245571111,"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":"2024-12-03T20:14:29.273Z","updated_at":"2025-03-26T01:28:25.477Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Salb-GEM: genome-scale metabolic model for _Streptomyces albus_ J1074\n\n[![Version](https://badge.fury.io/gh/SysBioChalmers%2FSalb-GEM.svg)](https://badge.fury.io/gh/SysBioChalmers%2FSalb-GEM) [![Zenodo](https://zenodo.org/badge/177741819.svg)](https://zenodo.org/badge/latestdoi/177741819) [![Gitter chat](https://badges.gitter.im/SysBioChalmers/Salb-GEM.svg)](https://gitter.im/SysBioChalmers/Salb-GEM)\n\n#### Brief Model Description\n\nThis repository entails the genome-scale metabolic model (GEM) SalbGEM for *Streptomyces albidoflavus*, previously and more commonly recognized under the name *S. albus J1074*. \n\n#### Organism Information\n\n*S. albus* J1074 is recognized as an effective host for heterologous production of natural products and secondary metabolites. Its fast growth and an efficient genetic system based on a naturally minimized genome have been attributed for the strain's advantage in expression of biosynthetic pathways for a variety of natural products including antibiotics and flavonoids ([Zaburannyi et al., 2014](https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-15-97), [Marin et al., 2017](https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0207278)).\n\n#### Main Model Descriptors:\n\n|Taxonomy | Template Model | Reactions | Metabolites| Genes |\n|:-------:|:--------------:|:---------:|:----------:|:-----:|\n|_Streptomyces albus J1074_|[Sco-GEM](https://github.com/SysBioChalmers/Sco-GEM)|2231|1872|1381|\n\nThis repository is administered by Cheewin Kittikunapong, Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.\n\n### Installation\n\n#### Recommended Software:\n* A functional Matlab installation (MATLAB 7.3 or higher).\n* [RAVEN Toolbox 2](https://github.com/SysBioChalmers/RAVEN) for MATLAB (required for contributing to development). \n* libSBML MATLAB API ([version 5.16.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/)  is recommended).\n* [Gurobi Optimizer for MATLAB](http://www.gurobi.com/registration/download-reg).\n\n#### Installation Instructions\n* Clone the [master](https://github.com/SysBioChalmers/Salb-GEM) branch from [SysBioChalmers GitHub](https://github.com/SysBioChalmers).\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### Citation\n\n* All model releases will be archived on [Zenodo](https://doi.org/10.5281/zenodo.3693406).\n* The associated manuscript is in preparation and will be available for citations in the near future.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fsalb-gem","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fsalb-gem","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fsalb-gem/lists"}