{"id":28067613,"url":"https://github.com/icb-dcm/pesto","last_synced_at":"2025-05-12T16:58:31.579Z","repository":{"id":100344098,"uuid":"55497044","full_name":"ICB-DCM/PESTO","owner":"ICB-DCM","description":"PESTO: Parameter EStimation TOolbox, Bioinformatics, btx676, 2017.","archived":false,"fork":false,"pushed_at":"2020-03-02T12:42:04.000Z","size":259616,"stargazers_count":26,"open_issues_count":42,"forks_count":12,"subscribers_count":8,"default_branch":"master","last_synced_at":"2025-04-11T09:52:17.187Z","etag":null,"topics":["matlab","optimization","parameter-estimation","profile-likelihood","systems-biology","uncertainty-quantification"],"latest_commit_sha":null,"homepage":"https://doi.org/10.1093/bioinformatics/btx676","language":"MATLAB","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"bsd-3-clause","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/ICB-DCM.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":"2016-04-05T09:58:04.000Z","updated_at":"2024-04-10T08:50:58.000Z","dependencies_parsed_at":null,"dependency_job_id":"a9a442cc-edfa-4fc6-8f15-07ddf62dd2b2","html_url":"https://github.com/ICB-DCM/PESTO","commit_stats":{"total_commits":598,"total_committers":12,"mean_commits":"49.833333333333336","dds":0.6337792642140468,"last_synced_commit":"3949f150108a051ec0e627c467644290061fc494"},"previous_names":[],"tags_count":14,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ICB-DCM%2FPESTO","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ICB-DCM%2FPESTO/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ICB-DCM%2FPESTO/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/ICB-DCM%2FPESTO/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/ICB-DCM","download_url":"https://codeload.github.com/ICB-DCM/PESTO/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":253784569,"owners_count":21963895,"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":["matlab","optimization","parameter-estimation","profile-likelihood","systems-biology","uncertainty-quantification"],"created_at":"2025-05-12T16:58:30.830Z","updated_at":"2025-05-12T16:58:31.570Z","avatar_url":"https://github.com/ICB-DCM.png","language":"MATLAB","funding_links":[],"categories":[],"sub_categories":[],"readme":"# PESTO - Parameter EStimation TOolbox\n\nPESTO is a widely applicable and highly customizable toolbox for parameter estimation in MathWorks MATLAB. It offers state-of-the art algorithms for optimization and uncertainty analysis, which work in a very generic manner, treating the objective function as a black box. Hence, PESTO can be used for any parameter estimation problem, which provides an objective function in MATLAB. PESTO has been used in various computational biology [research projects](https://github.com/ICB-DCM/PESTO/wiki#references).\n\nPESTO features include:\n* Multistart optimization\n* Sampling routines\n* Profile-likelihood analysis\n* Visualization routines\n* and more\n\nThese functions are demonstrated in several systems biology examples included in the [`examples/`](examples/) directory.\n\n## Download \u0026 installation\n\nClone the PESTO repository or download the latest [release archive](https://github.com/ICB-DCM/PESTO/releases).\nThe top-level folder of the cloned repository or the unpacked archive needs to be added to the MATLAB search path (non-recursively).\n\n*Note:* Detailed instructions on how to modify your MATLAB search path are provided here: https://de.mathworks.com/help/matlab/matlab_env/add-remove-or-reorder-folders-on-the-search-path.html\n\n## Documentation\n\nPESTO usage is demonstrated in various [examples](examples/). Further documentation is available in [```doc/PESTO-doc.pdf```](doc/PESTO-doc.pdf).\n\n## Compatibility\n\nPESTO is implemented fully in MATLAB and compatible with MATLAB releases from R2014b up to at least 2017a running on Windows, Mac and Linux.\n\n## Citation\nIf you use PESTO in a projects, please cite\n* Stapor, P., Weindl, D., Ballnus, B., Hug, S., Loos, C., Fiedler, A., Krause, S., Hross, S., Fröhlich, F., Hasenauer, J. (2018). PESTO: Parameter EStimation TOolbox. Bioinformatics, 34(4), 705-707. doi: 10.1093/bioinformatics/btx676\n\n## Licensing\n\nSee [ ```LICENSE```](LICENSE) file in the PESTO source directory.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ficb-dcm%2Fpesto","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Ficb-dcm%2Fpesto","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Ficb-dcm%2Fpesto/lists"}