{"id":22308551,"url":"https://github.com/sysbiochalmers/proteomereallocationforfastgrowth","last_synced_at":"2025-07-08T12:41:58.284Z","repository":{"id":39406512,"uuid":"265607428","full_name":"SysBioChalmers/ProteomeReallocationForFastGrowth","owner":"SysBioChalmers","description":"Collection of data and scripts for analyzing the proteome allocation of yeast grown in rich and minimal medium","archived":false,"fork":false,"pushed_at":"2020-08-19T16:51:02.000Z","size":2256,"stargazers_count":0,"open_issues_count":0,"forks_count":0,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-01-30T22:51:18.405Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"R","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","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","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2020-05-20T15:26:22.000Z","updated_at":"2020-08-19T16:51:05.000Z","dependencies_parsed_at":"2022-09-08T13:22:59.789Z","dependency_job_id":null,"html_url":"https://github.com/SysBioChalmers/ProteomeReallocationForFastGrowth","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%2FProteomeReallocationForFastGrowth","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FProteomeReallocationForFastGrowth/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FProteomeReallocationForFastGrowth/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/SysBioChalmers%2FProteomeReallocationForFastGrowth/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/SysBioChalmers","download_url":"https://codeload.github.com/SysBioChalmers/ProteomeReallocationForFastGrowth/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":245571063,"owners_count":20637274,"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":"2024-12-03T20:14:21.042Z","updated_at":"2025-03-26T01:28:20.239Z","avatar_url":"https://github.com/SysBioChalmers.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"# ProteomeReallocationForFastGrowth\nThis repository contains a collection of supplementary data and scripts for analyzing and visualizing the data pertaining to the study:\n\n_Proteome re-allocation from amino acid biosynthesis to ribosomes enables yeast to grow faster in rich media._\n\nIn this study, _Saccharomyces cerevisiae_ strain CEN.PK113-7D was cultivated in bioreactors with glucose as carbon source with or without supplementation of amino acids, both aerobically and anaerobically.\n\nThe main script **Organize_filter_and_quantify_proteomics.R** is used to normalize the TMT data into mass-percentages. The result of running this script is 6 data files named glu_proteomics_\\*.csv that are used throughout the analysis. Input data for the script are **TMT_aerobic_cultures.csv**, **TMT_anaerobic_cultures.csv** and **ref2824_iBAQ_unique_peptides.csv**. For the iBAQ-file, fmol/ug amounts and Uniprot accessions were obtained from the proteomics analysis and matched to gene names obtained from Uniprot. All original proteomics data can be obtained from the [PRIDE database](https://www.ebi.ac.uk/pride/) using accession numbers PXD018361 and PXD012803.\n\n  ### Required software\n  - R studio (version 1.0.136 or later)\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fproteomereallocationforfastgrowth","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsysbiochalmers%2Fproteomereallocationforfastgrowth","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsysbiochalmers%2Fproteomereallocationforfastgrowth/lists"}