{"id":22308649,"url":"https://github.com/sysbiochalmers/enzymeconstrained_humanmodels","last_synced_at":"2025-08-16T19:12:04.903Z","repository":{"id":39406411,"uuid":"103944041","full_name":"SysBioChalmers/EnzymeConstrained_humanModels","owner":"SysBioChalmers","description":"Collection of scripts for enhancing humanGEM based models with kinetic and proteomics constraints and specialized simulation utilities.","archived":false,"fork":false,"pushed_at":"2020-02-16T15:23:47.000Z","size":486606,"stargazers_count":2,"open_issues_count":1,"forks_count":0,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-06-05T17:47:00.411Z","etag":null,"topics":["enzyme-constraints","genome-scale-models","kinetics","proteomics-data-integration","systems-biology"],"latest_commit_sha":null,"homepage":"","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"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":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2017-09-18T13:40:31.000Z","updated_at":"2024-09-19T02:06:38.000Z","dependencies_parsed_at":"2022-09-08T09:42:46.702Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/EnzymeConstrained_humanModels","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"purl":"pkg:github/SysBioChalmers/EnzymeConstrained_humanModels","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEnzymeConstrained_humanModels","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEnzymeConstrained_humanModels/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEnzymeConstrained_humanModels/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEnzymeConstrained_humanModels/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/EnzymeConstrained_humanModels/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FEnzymeConstrained_humanModels/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":270758366,"owners_count":24640224,"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":"2025-08-16T02:00:11.002Z","response_time":91,"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":["enzyme-constraints","genome-scale-models","kinetics","proteomics-data-integration","systems-biology"],"created_at":"2024-12-03T20:14:50.675Z","updated_at":"2025-08-16T19:12:04.875Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Enzyme-constrained Human1 GEMs\nThis directory contains an automated pipeline for constructing cell-specific enzyme-constrained GEMs (ecGEMs) derived from Human-GEM (v1.3.0) based on transcriptomics and proteomics datasets.\n\n### Required Software:\n* A functional Matlab installation (MATLAB 7.3 and higher)\n* The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN) (version 2.3.0)\n* For generating some figures, a functional [R installation](https://www.r-project.org/) (version 3.6.1)\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 simulation\n\n## Regenerating the ecGEMs:\nThe ecGEMs are already present in the `models/` subdirectory, but the scripts and data necessary to regenerate the models are available here. The master script for generating the ecGEMs from the tINIT GEMs (provided in the `/models/humanGEM_cellLines/11models.mat` file) is `generate_human_ecModels_NCI60.m`, located in the `/ComplementaryScripts` directory. Run this `generate_human_ecModels_NCI60` script in MATLAB to regenerate the 11 ecGEMs.\n\n## Flux variability analysis\nFlux variability analysis (FVA) (corresponding to the results presented in Fig. 5B) can be run using the `comparativeFVA_humanModels.m` function in the `ComplementaryScripts/Simulation` subdirectory. Specify the name of the model (cell line) for which FVA is to be run; for example:\n\n`results = comparativeFVA_humanModels('HOP62');`\n\n## Prediction of growth and metabolite exchange rates:\nTo use the ecGEMs and non-ecGEMs to predict growth rates and metabolite exchange rates with increasing levels of constraints (as shown in Figs. 5C and 5D), run the `predict_cellLines_gRates.m` script in the `ComplementaryScripts` subdirectory.\n\n\n## Generating plots for Figure 5\nThe R script used to generate plots shown in Fig. 5 of the main text is `plot_ecGEM_results.R`, located in the `ComplementaryScripts` subdirectory.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fenzymeconstrained_humanmodels","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fenzymeconstrained_humanmodels","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fenzymeconstrained_humanmodels/lists"}