{"id":22308520,"url":"https://github.com/sysbiochalmers/ecfactory","last_synced_at":"2025-06-14T20:37:05.046Z","repository":{"id":87216064,"uuid":"504143894","full_name":"SysBioChalmers/ecFactory","owner":"SysBioChalmers","description":"A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism","archived":false,"fork":false,"pushed_at":"2024-11-15T07:38:02.000Z","size":368,"stargazers_count":8,"open_issues_count":2,"forks_count":4,"subscribers_count":1,"default_branch":"main","last_synced_at":"2024-11-15T08:28:14.192Z","etag":null,"topics":["cell-factory","enzyme-constraints","metabolic-models","microbes"],"latest_commit_sha":null,"homepage":"","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"gpl-3.0","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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2022-06-16T12:18:08.000Z","updated_at":"2024-11-15T07:38:07.000Z","dependencies_parsed_at":null,"dependency_job_id":"5a71f06c-9363-4196-84aa-03b9a4c37802","html_url":"https://github.com/SysBioChalmers/ecFactory","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%2FecFactory","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FecFactory/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FecFactory/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FecFactory/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/ecFactory/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":227990287,"owners_count":17852266,"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":["cell-factory","enzyme-constraints","metabolic-models","microbes"],"created_at":"2024-12-03T20:14:16.854Z","updated_at":"2025-06-14T20:37:05.018Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ecFactory: A multi-step method for prediction of metabolic engineering gene targets\n\n![fig1](https://user-images.githubusercontent.com/26483972/175298382-c3ceb172-bf59-4eb7-85e6-aa0ec60928c9.jpg)\n\nThe ecFactory method is a series of sequential steps for identification of metabolic engineering gene targets. These targets show which genes should be subject to overexpression, modulated expression (knock-down) or deletion (knock-out), with the objective of increasing production of a given metabolite. This method was developed by combining the principles of the FSEOF algorithm (flux scanning with enforced objective function) together with the features of GECKO enzyme-constrained metabolic models (ecModels), which incorporate enzymes as part of genome-scale metabolic networks.\n\n## Required Software\n* A functional Matlab installation (MATLAB 7.3 or higher). \n* The [RAVEN toolbox for MATLAB](https://github.com/SysBioChalmers/RAVEN).\n* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.\n* [Git](https://git-scm.com/downloads)\n\n## Installation\n\nClone this repository into an accesible directory in your computer. No further steps are needed.\n\n## Tutorial\n\nA case study for prediction of metabolic engineering targets for increased production of 2-phenylethanol in *S. cerevisiae* cells using [ecYeastGEM](https://github.com/SysBioChalmers/yeast-GEM) and the **ecFactory** method is explained in detail in a MATLAB live script. To run this example, open the [live script](https://github.com/SysBioChalmers/ecFactory-case-studies/blob/main/code/find_gene_targets.mlx) in MATLAB and run it! with this, you will see the outputs of the method scripts in real time. \n\n* An additional case study for prediction of gene targets for enhanced heme production in *S. cerevisiae* has been added. Validation of a subset of the predicted gene targets can be seen [in this publication](https://doi.org/10.1073/pnas.2108245119).\n\nAll the relevant outputs of the method are stored in the `tutorials/results` folder in this repository.\n\nLast update: 2025-02-12\n\nThis repository is administered by [Iván Domenzain](https://github.com/IVANDOMENZAIN), Division of Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology.\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fecfactory","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fecfactory","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fecfactory/lists"}