{"id":17485681,"url":"https://github.com/mtefagh/qfca","last_synced_at":"2025-03-28T14:40:38.113Z","repository":{"id":160510791,"uuid":"106218487","full_name":"mtefagh/qfca","owner":"mtefagh","description":"Compressed biological systems of tens of thousands of biochemical reactions by a hierarchical organization of pathways which speeds up the downstream analysis up to 3 times in addition to saving memory and storage space","archived":false,"fork":false,"pushed_at":"2022-01-05T09:30:05.000Z","size":2930,"stargazers_count":2,"open_issues_count":0,"forks_count":1,"subscribers_count":0,"default_branch":"master","last_synced_at":"2024-10-19T05:22:37.966Z","etag":null,"topics":["fca","qfca"],"latest_commit_sha":null,"homepage":"https://mtefagh.github.io/qfca/","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/mtefagh.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","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":"2017-10-08T23:51:32.000Z","updated_at":"2023-02-17T11:30:55.000Z","dependencies_parsed_at":null,"dependency_job_id":"e01ab7ad-9ff6-4aef-95f0-f6e9ac3e200c","html_url":"https://github.com/mtefagh/qfca","commit_stats":{"total_commits":34,"total_committers":2,"mean_commits":17.0,"dds":0.1470588235294118,"last_synced_commit":"25fcc1bce21e1a98f76328b757c35337ab9cc564"},"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtefagh%2Fqfca","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtefagh%2Fqfca/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtefagh%2Fqfca/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/mtefagh%2Fqfca/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/mtefagh","download_url":"https://codeload.github.com/mtefagh/qfca/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246049605,"owners_count":20715510,"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":["fca","qfca"],"created_at":"2024-10-19T02:08:28.850Z","updated_at":"2025-03-28T14:40:38.066Z","avatar_url":"https://github.com/mtefagh.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"Quantitative Flux Coupling Analysis\n====\n\nIntroduction\n----\n*Quantitative flux coupling analysis* (QFCA) is a quantitative approach to identify and remove the redundancies of the steady-state flux cone. The full description and theory of the algorithm implemented by QFCA is discussed in the associated papers. When referencing QFCA, please cite the followings:\n- Tefagh, M., \u0026 Boyd, S. P. (2019). Quantitative flux coupling analysis. J. Math. Biol., 78(5), 1459-1484. [https://doi.org/10.1007/s00285-018-1316-9](https://doi.org/10.1007/s00285-018-1316-9)\n- Tefagh, M., \u0026 Boyd, S. P. (2019). Metabolic network reductions. bioRxiv, 499251. [https://doi.org/10.1101/499251](https://doi.org/10.1101/499251)\n\nQuick Start\n----\nThe following example uses the `QFCA` function to compute the table of **flux coupling relations** and the list of **blocked reactions** for the [core *E. coli* model](http://systemsbiology.ucsd.edu/Downloads/EcoliCore) and also returns the **reduced metabolic network**.\n```matlab\nload('ecoli_core_model.mat');\n[reduced_net, fctable, blocked] = QFCA(model, true, 'linprog');\n```\nThe output of the above code is as follows.\n```matlab\nOriginal number of:\n\tmetabolites = 72;\treactions = 95;\tnonzero elements = 360\nOriginal number of:\n\treversible reactions = 59;\tirreversible reactions = 36\nIdentifying the blocked reactions and removing them from the network: 0.034\nReduced number of:\n\tmetabolites = 72;\treactions = 95;\tnonzero elements = 360\nFinding the full coupling relations: 0.008\nReduced number of:\n\tmetabolites = 34;\treactions = 60;\tnonzero elements = 236\nCorrecting the reversibility types: 0.037\nFinding the directional and partial coupling relations: 0.411\nInferring by the transitivity of full coupling relations: 0.000\nMetabolic network reductions postprocessing: 0.001\nReduced number of:\n\tmetabolites = 30;\treactions = 58;\tnonzero elements = 224\nThe number of solved:\n\tlinear programs = 54;\tsystems of linear equations = 8\n```\nFurthermore, the `directionallyCoupled` function can be utilized as a stand-alone function to find **fictitious metabolite** certificates.\n\nLicense\n----\n*QFCA* is distributed under the [GNU General Public License v3.0](http://www.gnu.org/copyleft/gpl.html).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmtefagh%2Fqfca","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmtefagh%2Fqfca","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmtefagh%2Fqfca/lists"}