{"id":24529023,"url":"https://github.com/saezlab/cpt_qsptutorial","last_synced_at":"2025-04-14T17:10:56.399Z","repository":{"id":77872530,"uuid":"83438005","full_name":"saezlab/CPT_QSPtutorial","owner":"saezlab","description":"Supplementary material for CPT tutorial on logic modeling for quantitative systems pharmacology","archived":false,"fork":false,"pushed_at":"2017-05-29T14:15:07.000Z","size":109,"stargazers_count":4,"open_issues_count":0,"forks_count":3,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-03-28T05:51:02.278Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Python","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/saezlab.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}},"created_at":"2017-02-28T13:52:24.000Z","updated_at":"2019-08-05T20:27:41.000Z","dependencies_parsed_at":"2023-03-05T01:30:38.451Z","dependency_job_id":null,"html_url":"https://github.com/saezlab/CPT_QSPtutorial","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/saezlab%2FCPT_QSPtutorial","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCPT_QSPtutorial/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCPT_QSPtutorial/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FCPT_QSPtutorial/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/CPT_QSPtutorial/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248923764,"owners_count":21183954,"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":"2025-01-22T07:34:28.500Z","updated_at":"2025-04-14T17:10:56.362Z","avatar_url":"https://github.com/saezlab.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# CPT_QSPtutorial\nSupplementary material for the CPT tutorial paper:\n\nTitle: _Logic modeling in quantitative systems pharmacology_\n\nAuthors: Pauline Traynard\u003csup\u003e\\*1\u003c/sup\u003e, Luis Tobalina\u003csup\u003e\\*2\u003c/sup\u003e, Federica Eduati\u003csup\u003e*3\u003c/sup\u003e, Laurence Calzone\u003csup\u003e1\u003c/sup\u003e, Julio Saez-Rodriguez\u003csup\u003e2,3\u003c/sup\u003e\n\n\u003csup\u003e*\u003c/sup\u003e Co-first authors\n\nAffiliations:\n\u003csup\u003e1\u003c/sup\u003e Institut Curie, PSL Research University, Mines Paris Tech, Inserm, U900, F-75005, Paris, France.\n\u003csup\u003e2\u003c/sup\u003e RWTH Aachen University, Faculty of Medicine, Joint Research Centre for Computational Biomedicine, MTI2 Wendlingweg 2 D-52074 Aachen\n\u003csup\u003e3\u003c/sup\u003e European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus CB10 1SD Hinxton\n\n\n##Included files\n\n#####Construction of Prior Knowledge Network:\n_pypath_code.py_ Python code for pypath\n\n_network_extension.docx_ Description of step-by-step model extension using pypath\n\n_PriorKnowledgeNetwork.sif_ Final Prior Knowledge Network (PKN)\n\n#####Model training \n_perturbationData_LNCaP_MIDAS.csv_ Perturbation data from (Lescarbeau et al., 2014) normalised and in MIDAS format\n\n_CellNOptR_optimisation.R_ R code for optimisation with CellNOptR logic ODE\n\n#####Trained model:\n_trainedmodel.bnd_\n\n_trainedmodel.cfg_\n\n_logicODEparameters_edges.txt_\n\n_logicODEparameters_nodes.txt_\n\n\n#####MaBoSS simulations and genetic interactions:\n_table_survivalprobas.xlsx_\n_table_epistasis.xlsx_\n\n\n\n##License \nThis project is licensed under the terms of GPLv3.\n\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcpt_qsptutorial","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fcpt_qsptutorial","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fcpt_qsptutorial/lists"}