{"payload":{"pageCount":4,"repositories":[{"type":"Public","name":"GECKO","owner":"SysBioChalmers","isFork":false,"description":"Toolbox for including enzyme constraints on a genome-scale model.","topicNames":["systems-biology","toolbox","data-integration","proteomics","kinetics","enzyme-constraints","matlab"],"topicsNotShown":0,"allTopics":["systems-biology","toolbox","data-integration","proteomics","kinetics","enzyme-constraints","matlab"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":2,"issueCount":11,"starsCount":63,"forksCount":43,"license":"MIT License","participation":[1,0,0,7,8,8,6,3,0,0,0,2,2,0,0,0,0,0,0,0,0,0,0,0,0,0,6,0,0,0,0,0,2,1,4,2,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-27T10:00:19.669Z"}},{"type":"Public","name":"RAVEN","owner":"SysBioChalmers","isFork":false,"description":"The RAVEN Toolbox for genome scale model reconstruction, curation and analysis.","topicNames":["systems-biology","metabolic-models","metabolic-reconstruction","constraint-based-modeling","metabolic-engineering","gap-filling","human-metabolism","genome-scale-models","sysbio"],"topicsNotShown":0,"allTopics":["systems-biology","metabolic-models","metabolic-reconstruction","constraint-based-modeling","metabolic-engineering","gap-filling","human-metabolism","genome-scale-models","sysbio"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":1,"issueCount":6,"starsCount":97,"forksCount":52,"license":"Other","participation":[0,0,0,18,10,0,5,2,0,0,0,0,0,0,0,0,0,0,0,0,2,5,0,0,0,2,0,0,0,0,0,0,0,0,0,0,0,5,3,1,0,0,0,0,0,0,0,0,8,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-27T09:36:47.364Z"}},{"type":"Public","name":"yeast-GEM","owner":"SysBioChalmers","isFork":false,"description":"The consensus GEM for Saccharomyces cerevisiae","topicNames":["python","biology","matlab","systems-biology","consensus","reconstruction","hacktoberfest","yeast","metabolic-models","genome-scale-models"],"topicsNotShown":2,"allTopics":["python","biology","matlab","systems-biology","consensus","reconstruction","hacktoberfest","yeast","metabolic-models","genome-scale-models","saccharomyces-cerevisiae","standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":30,"starsCount":87,"forksCount":42,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-23T23:06:47.180Z"}},{"type":"Public","name":"Yarrowia_Multifactor","owner":"SysBioChalmers","isFork":false,"description":"Data and scripts used for the RNA-seq analysis of Yarrowia lipolytica (fat-free strain and urea utilisation)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,4,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,3,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-14T07:21:47.984Z"}},{"type":"Public","name":"Human-GEM","owner":"SysBioChalmers","isFork":false,"description":"The generic genome-scale metabolic model of Homo sapiens","topicNames":["human-metabolism","genome-scale-models","standard-gem"],"topicsNotShown":0,"allTopics":["human-metabolism","genome-scale-models","standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":4,"issueCount":73,"starsCount":85,"forksCount":39,"license":"Creative Commons Attribution 4.0 International","participation":[19,55,30,64,54,22,10,4,6,8,0,4,4,3,0,0,7,12,9,12,36,27,10,16,6,1,0,6,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-09T22:40:39.905Z"}},{"type":"Public","name":"sysbio.se","owner":"SysBioChalmers","isFork":false,"description":"The sysbio.se source code","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"CSS","color":"#563d7c"},"pullRequestCount":0,"issueCount":1,"starsCount":0,"forksCount":2,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-05-07T13:25:33.598Z"}},{"type":"Public","name":"BrainMetabolismModeling","owner":"SysBioChalmers","isFork":false,"description":"Modeling of the energy metabolism of the brain","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,1,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,1,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-14T20:01:38.997Z"}},{"type":"Public","name":"hanpo-GEM","owner":"SysBioChalmers","isFork":false,"description":"Draft genome-scale model of Hansenula polymorpha (Ogataea polymorpha; Pichia angusta)","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":1,"starsCount":4,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2024-01-05T14:16:34.726Z"}},{"type":"Public","name":"GEMsforTrophicLevels","owner":"SysBioChalmers","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":2,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-19T14:30:36.173Z"}},{"type":"Public","name":"Worm-GEM","owner":"SysBioChalmers","isFork":false,"description":"Genome-scale model for Caenorhabditis elegans","topicNames":["standard-gem"],"topicsNotShown":0,"allTopics":["standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-10T15:52:42.812Z"}},{"type":"Public","name":"Fruitfly-GEM","owner":"SysBioChalmers","isFork":false,"description":"Genome scale model for Drosophila melanogaster","topicNames":["standard-gem"],"topicsNotShown":0,"allTopics":["standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":1,"starsCount":6,"forksCount":3,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-10T15:44:52.501Z"}},{"type":"Public","name":"Zebrafish-GEM","owner":"SysBioChalmers","isFork":false,"description":"Genome-scale model for Danio rerio","topicNames":["standard-gem"],"topicsNotShown":0,"allTopics":["standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":4,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-10T15:37:11.762Z"}},{"type":"Public","name":"Rat-GEM","owner":"SysBioChalmers","isFork":false,"description":"Genome-scale model for Rattus norvegicus","topicNames":["standard-gem"],"topicsNotShown":0,"allTopics":["standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-10T15:26:40.356Z"}},{"type":"Public","name":"Mouse-GEM","owner":"SysBioChalmers","isFork":false,"description":"Genome-scale model for Mus musculus","topicNames":["standard-gem"],"topicsNotShown":0,"allTopics":["standard-gem"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":1,"starsCount":6,"forksCount":5,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-10T15:22:29.542Z"}},{"type":"Public","name":"TMEModeling","owner":"SysBioChalmers","isFork":false,"description":"Modeling of the tumor microenvironment using a diffusion model for upptake constraints.","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":0,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-12-06T14:26:22.412Z"}},{"type":"Public","name":"Human-GEM-guide","owner":"SysBioChalmers","isFork":false,"description":"Guide for Human-GEM","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-28T12:43:51.010Z"}},{"type":"Public","name":"pcSecYeast","owner":"SysBioChalmers","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":0,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-11-03T03:29:44.420Z"}},{"type":"Public","name":"KMG060-Systems-Biology-course","owner":"SysBioChalmers","isFork":false,"description":"KMG060 Systems Biology course - repo for students","topicNames":["systems-biology","rna-seq-analysis","metabolic-models","flux-balance-analysis","enzyme-constraints"],"topicsNotShown":0,"allTopics":["systems-biology","rna-seq-analysis","metabolic-models","flux-balance-analysis","enzyme-constraints"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":3,"starsCount":1,"forksCount":7,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-09-23T13:24:25.200Z"}},{"type":"Public","name":"sybil","owner":"SysBioChalmers","isFork":false,"description":"Efficient Constrained Based Modelling in R","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":1,"starsCount":6,"forksCount":1,"license":"GNU General Public License v3.0","participation":[0,0,0,0,0,0,0,0,0,3,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-02T05:25:35.509Z"}},{"type":"Public","name":"sybil-SBML","owner":"SysBioChalmers","isFork":false,"description":"SBML (Systems Biology Markup Language) integration in sybil","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"R","color":"#198CE7"},"pullRequestCount":0,"issueCount":2,"starsCount":4,"forksCount":0,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-08-01T19:31:34.861Z"}},{"type":"Public","name":"DLKcat","owner":"SysBioChalmers","isFork":false,"description":"Deep learning and Bayesian approach applied to enzyme turnover number for the improvement of enzyme-constrained genome-scale metabolic models (ecGEMs) reconstruction","topicNames":["deep-learning","bayesian","kinetics","enzyme-constraints","enzyme-turnover-number","kcat"],"topicsNotShown":0,"allTopics":["deep-learning","bayesian","kinetics","enzyme-constraints","enzyme-turnover-number","kcat"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":1,"starsCount":112,"forksCount":50,"license":null,"participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-07-04T15:32:14.006Z"}},{"type":"Public","name":"Human-maps","owner":"SysBioChalmers","isFork":false,"description":"Human1 metabolic maps","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":null,"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-04-08T11:49:55.832Z"}},{"type":"Public","name":"CellFactory-ecYeastGEM","owner":"SysBioChalmers","isFork":false,"description":"Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.","topicNames":["yeast","constraint-based-modeling","enzyme-constraints","cell-factory"],"topicsNotShown":0,"allTopics":["yeast","constraint-based-modeling","enzyme-constraints","cell-factory"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":1,"issueCount":6,"starsCount":0,"forksCount":1,"license":"Creative Commons Attribution 4.0 International","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-28T17:24:23.218Z"}},{"type":"Public","name":"ecFactory","owner":"SysBioChalmers","isFork":false,"description":"A constraint-based method for prediction of metabolic engineering targets using ecModels of metabolism","topicNames":["metabolic-models","enzyme-constraints","microbes","cell-factory"],"topicsNotShown":0,"allTopics":["metabolic-models","enzyme-constraints","microbes","cell-factory"],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":1,"issueCount":0,"starsCount":7,"forksCount":3,"license":"GNU General Public License v3.0","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-03-14T12:21:29.057Z"}},{"type":"Public","name":"bacterial-exclusion-prediction","owner":"SysBioChalmers","isFork":false,"description":"Estimating the anti-bacterial property of surfaces based on SEM images","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"Rust","color":"#dea584"},"pullRequestCount":0,"issueCount":0,"starsCount":2,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-21T22:45:22.346Z"}},{"type":"Public","name":"HGTphyloDetect","owner":"SysBioChalmers","isFork":false,"description":"HGTphyloDetect is a versatile toolbox to identify horizontal gene transfer (HGT) events combined with phylogenetic analysis.","topicNames":["systems-biology","phylogenetics","horizontal-gene-transfer","sequence-analysis","evolutionary-biology","high-throughput-pipeline"],"topicsNotShown":0,"allTopics":["systems-biology","phylogenetics","horizontal-gene-transfer","sequence-analysis","evolutionary-biology","high-throughput-pipeline"],"primaryLanguage":{"name":"Python","color":"#3572A5"},"pullRequestCount":0,"issueCount":0,"starsCount":28,"forksCount":5,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-02-11T18:59:28.400Z"}},{"type":"Public","name":"Penicillium-GEMs","owner":"SysBioChalmers","isFork":false,"description":"","topicNames":["genome-scale-models"],"topicsNotShown":0,"allTopics":["genome-scale-models"],"primaryLanguage":{"name":"Perl","color":"#0298c3"},"pullRequestCount":0,"issueCount":1,"starsCount":1,"forksCount":1,"license":"Other","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2023-01-27T13:32:23.800Z"}},{"type":"Public","name":"SingleCellModeling","owner":"SysBioChalmers","isFork":false,"description":"Code for the publication \"Generation and analysis of context-specific genome-scale metabolic models derived from single-cell RNA-Seq data\"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"MATLAB","color":"#e16737"},"pullRequestCount":0,"issueCount":0,"starsCount":5,"forksCount":1,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-21T17:49:47.895Z"}},{"type":"Public","name":"Yeast-Species-GEMs","owner":"SysBioChalmers","isFork":false,"description":"A universal metabolic model knowledge database (pan-GEM) for current existing yeast species with genome sequence, based on which we will build the GEMs of high quality for each yeast species.","topicNames":["pan-metabolic-model","pan-genome-annotation","strain-specific-metabolic-model","pathway-conservation-analysis","yeast-species"],"topicsNotShown":0,"allTopics":["pan-metabolic-model","pan-genome-annotation","strain-specific-metabolic-model","pathway-conservation-analysis","yeast-species"],"primaryLanguage":{"name":"Pep8","color":"#C76F5B"},"pullRequestCount":0,"issueCount":7,"starsCount":6,"forksCount":4,"license":"MIT License","participation":[0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0],"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-07T05:40:18.793Z"}},{"type":"Public","name":"GAGome-MCED","owner":"SysBioChalmers","isFork":false,"description":"","topicNames":[],"topicsNotShown":0,"allTopics":[],"primaryLanguage":{"name":"HTML","color":"#e34c26"},"pullRequestCount":0,"issueCount":0,"starsCount":1,"forksCount":0,"license":"MIT License","participation":null,"lastUpdated":{"hasBeenPushedTo":true,"timestamp":"2022-12-06T09:17:58.578Z"}}],"repositoryCount":100,"userInfo":null,"searchable":true,"definitions":[],"typeFilters":[{"id":"all","text":"All"},{"id":"public","text":"Public"},{"id":"source","text":"Sources"},{"id":"fork","text":"Forks"},{"id":"archived","text":"Archived"},{"id":"template","text":"Templates"}],"compactMode":false},"title":"Repositories"}