{"id":24529118,"url":"https://github.com/saezlab/shinycnor","last_synced_at":"2025-08-22T22:40:20.206Z","repository":{"id":77872956,"uuid":"179712473","full_name":"saezlab/ShinyCNOR","owner":"saezlab","description":"Shiny application for the CellNOptR packages","archived":false,"fork":false,"pushed_at":"2022-06-10T14:35:52.000Z","size":379,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-01-22T07:37:41.721Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"R","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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-04-05T15:56:18.000Z","updated_at":"2022-09-05T18:58:32.000Z","dependencies_parsed_at":null,"dependency_job_id":"b3dcfea5-a47c-4ea2-a86d-a2285f020a80","html_url":"https://github.com/saezlab/ShinyCNOR","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%2FShinyCNOR","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FShinyCNOR/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FShinyCNOR/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/saezlab%2FShinyCNOR/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/saezlab","download_url":"https://codeload.github.com/saezlab/ShinyCNOR/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":243769949,"owners_count":20345215,"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":"2025-01-22T07:34:51.306Z","updated_at":"2025-03-15T17:45:26.959Z","avatar_url":"https://github.com/saezlab.png","language":"R","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Welcome to the Shiny application for the CellNOpt packages\nCellNOpt (from CellNetOptimizer; a.k.a. CNO) is a software used for creating logic-based models of signal transduction networks using different logic formalisms (Boolean, probabilistic logic, or differential equations). CellNOpt uses information on signaling pathways encoded as a Prior Knowledge Network, and trains it against high-throughput biochemical data to create cell-specific models.\n\n### Implemented Approaches\nShinyCNOR is still under development, and the following approaches are implemented or in the process of being implemented.\n\n#### CellNOptR\n\u003ca href=\"https://github.com/saezlab/CellNOptR/\" target=\"_blank\"\u003eCellNOptR\u003c/a\u003e for Boolean formalism. It contains the core functions as well as the boolean and steady states version. It implements the workflow described in Saez-Rodriguez et al Mol Sys Bio 2009, with extended capabilities for multiple time points.\n\n#### CNORprob\n\u003ca href=\"https://github.com/saezlab/CNORprob/\" target=\"_blank\"\u003eCNORprob\u003c/a\u003e for Probablistic Logic formalism. It is a probabilistic logic variant of CellNOpt which allows for quantitative optimisation of logical network for (quasi-)steady-state data. The core optimisation pipeline is derived from FALCON: a toolbox for the fast contextualization of logical networks.\n\n#### CNORode\n\u003ca href=\"https://github.com/saezlab/CNORode/\" target=\"_blank\"\u003eCNORode\u003c/a\u003e for logic-based ODE formalism. It is an ODE add-on to CellNOptR. It is based on the method of (Wittmann et al BMC Sys Bio 2009), also implemented in the tool Odefy (Krusiek et al BMC Bioinf 2010).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fshinycnor","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsaezlab%2Fshinycnor","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsaezlab%2Fshinycnor/lists"}