{"id":19015267,"url":"https://github.com/americocunhajr/sobios","last_synced_at":"2025-04-23T01:43:55.530Z","repository":{"id":80385282,"uuid":"251503138","full_name":"americocunhajr/SoBioS","owner":"americocunhajr","description":"SoBioS is an easy-to-run Matlab code to compute Sobol' indices for biological systems.","archived":false,"fork":false,"pushed_at":"2025-04-04T18:56:43.000Z","size":15502,"stargazers_count":6,"open_issues_count":0,"forks_count":1,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-04-17T18:22:58.729Z","etag":null,"topics":["bioinformatics","biomathematics","computational-biology","dynamical-systems","global-sensitivity-analysis","nonlinear-dynamics","sensitivity-analysis","sobol-indices","uerj","ufrj"],"latest_commit_sha":null,"homepage":"https://americocunhajr.github.io/SoBioS","language":"MATLAB","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/americocunhajr.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":"2020-03-31T04:49:26.000Z","updated_at":"2025-04-04T18:56:46.000Z","dependencies_parsed_at":"2024-11-08T19:50:00.245Z","dependency_job_id":null,"html_url":"https://github.com/americocunhajr/SoBioS","commit_stats":null,"previous_names":[],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/americocunhajr%2FSoBioS","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/americocunhajr%2FSoBioS/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/americocunhajr%2FSoBioS/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/americocunhajr%2FSoBioS/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/americocunhajr","download_url":"https://codeload.github.com/americocunhajr/SoBioS/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":250354292,"owners_count":21416749,"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":["bioinformatics","biomathematics","computational-biology","dynamical-systems","global-sensitivity-analysis","nonlinear-dynamics","sensitivity-analysis","sobol-indices","uerj","ufrj"],"created_at":"2024-11-08T19:36:34.031Z","updated_at":"2025-04-23T01:43:55.510Z","avatar_url":"https://github.com/americocunhajr.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"## Sobol' Indices for Biological Systems\n\n**SoBioS: Sobol' Indices for Biological Systems** is an easy-to-use Matlab code designed for Sobol' indices-based global sensitivity analysis of biological systems. Developed with an educational approach, **SoBioS** is intuitive and user-friendly, making it an excellent tool for researchers and students in the field of systems biology.\n\n\u003cp align=\"center\"\u003e\n\u003cimg src=\"logo/SobolIndices.png\" width=\"60%\"\u003e\n\u003c/p\u003e\n\n### Table of Contents\n- [Overview](#overview)\n- [Features](#features)\n- [UQLab dependency](#uqlab-dependency)\n- [Usage](#usage)\n- [Documentation](#documentation)\n- [Authors](#authors)\n- [Citing SoBioS](#citing-sobios)\n- [License](#license)\n- [Institutional support](#institutional-support)\n- [Funding](#funding)\n\n### Overview\n**SoBioS** was developed as a pedagogical tool to teach the basics of global sensitivity analysis of biological systems via Sobol' indices. A tutorial explaining the theory and practical aspects behind the **SoBioS** package is provided in the following book chapter:\n- **M. Tosin, A.M.A. Côrtes, A. Cunha Jr**, *A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models*, in Networks in Systems Biology: Applications for Disease Modeling, Computational Biology, vol. 32, Springer, Cham, 2020. \u003ca href=\"https://doi.org/10.1007/978-3-030-51862-2_6\" target=\"_blank\"\u003eDOI\u003c/a\u003e. \n\n### Features\n- Global sensitivity analysis using Sobol' indices\n- Easy-to-run Matlab implementation\n- Educational style code for easy understanding\n- Includes example cases and detailed comments\n\n### UQLab dependency\nIn order to use the **SoBioS** code, it is necessary to have UQLab package installed:\n\u003ca href=\"https://www.uqlab.com\" target=\"_blank\"\u003ehttps://www.uqlab.com\u003c/a\u003e. \n\nThis external package is free for academic use.\n\n### Usage\nThis package includes the following modules:\n- SoBioS_CaseName.m - main file for the simulation (use servaral resourses from UQLab package);\n- QoI_CaseName.m - function to compute the Quantity of Interest (QoI).\n\nTo get started with **SoBioS**, follow these steps:\n1. Clone the repository:\n   ```bash\n   git clone https://github.com/americocunhajr/SoBioS.git\n   ```\n2. Navigate to the code directory:\n   ```bash\n   cd SoBioS/SoBioS-1.0\n   ```\n3. To run a simulation, execute the main file corresponding to your case:\n   ```bash\n   SoBioS_CaseName\n   ```\n\n### Documentation\nThe routines in SoBioS are well-commented to explain their functionality. Each routine includes a description of its purpose, as well as inputs and outputs. Detailed documentation can be found within the code comments and the provided tutorial.\n\n### Authors\n- Michel Tosin\n- Adriano Côrtes\n- Americo Cunha\n\n### Citing SoBioS\nIf you use **SoBioS** in your research, please cite the following publication:\n- *Tosin M., Côrtes A.M.A., Cunha A. (2020) A Tutorial on Sobol’ Global Sensitivity Analysis Applied to Biological Models. In: da Silva F.A.B., Carels N., Trindade dos Santos M., Lopes F.J.P. (eds) Networks in Systems Biology: Applications for Disease Modeling. Computational Biology, vol 32. Springer, Cham https://doi.org/10.1007/978-3-030-51862-2_6*\n\n```\n@incollection{Tosin2020SoBioS,\n   author    = {M. Tosin and A. M. A. C\\ˆ{o}rtes and A. {Cunha~Jr}},\n   title     = {A {T}utorial on {S}obol’ {G}lobal {S}ensitivity {A}nalysis {A}pplied to {B}iological {M}odels},\n   editor    = {F.A.B. {da Silva} and N. Carels and M. {Trindade dos Santos} and F.J.P. Lopes},\n   booktitle = {Networks in Systems Biology: Applications for Disease Modeling},\n   publisher = {Springer International Publishing},\n   address   = {Cham},\n   year      = {2020},\n   pages     = {93-118},\n   doi       = {https://doi.org/10.1007/978-3-030-51862-2_6},\n}\n```\n\n### License\n\n**SoBioS** is released under the MIT license. See the LICENSE file for details. All new contributions must be made under the MIT license.\n\n\u003cimg src=\"logo/mit_license_red.png\" width=\"10%\"\u003e \n\n### Institutional support\n\n\u003cimg src=\"logo/logo_uerj.png\" width=\"12%\"\u003e \u0026nbsp; \u0026nbsp; \u003cimg src=\"logo/logo_ufrj.png\" width=\"8%\"\u003e\n\n### Funding\n\n\u003cimg src=\"logo/faperj.png\" width=\"20%\"\u003e \u0026nbsp; \u0026nbsp; \u003cimg src=\"logo/cnpq.png\" width=\"20%\"\u003e \u0026nbsp; \u0026nbsp; \u003cimg src=\"logo/capes.png\" width=\"10%\"\u003e\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Famericocunhajr%2Fsobios","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Famericocunhajr%2Fsobios","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Famericocunhajr%2Fsobios/lists"}