{"id":22668524,"url":"https://github.com/lanl/pybnf","last_synced_at":"2025-04-12T11:08:27.519Z","repository":{"id":45559146,"uuid":"125790189","full_name":"lanl/PyBNF","owner":"lanl","description":"An application for parameterization of biological models available in SBML and BNGL formats. Features include parallelization, metaheuristic optimization algorithms, and an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm.","archived":false,"fork":false,"pushed_at":"2023-12-13T22:00:54.000Z","size":120883,"stargazers_count":24,"open_issues_count":48,"forks_count":18,"subscribers_count":5,"default_branch":"master","last_synced_at":"2025-04-12T11:08:17.222Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lanl.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","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":"2018-03-19T02:23:27.000Z","updated_at":"2025-02-21T21:18:34.000Z","dependencies_parsed_at":"2023-10-12T10:41:21.348Z","dependency_job_id":null,"html_url":"https://github.com/lanl/PyBNF","commit_stats":null,"previous_names":[],"tags_count":17,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FPyBNF","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FPyBNF/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FPyBNF/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lanl%2FPyBNF/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lanl","download_url":"https://codeload.github.com/lanl/PyBNF/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248557828,"owners_count":21124167,"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":"2024-12-09T15:15:37.283Z","updated_at":"2025-04-12T11:08:27.486Z","avatar_url":"https://github.com/lanl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"![alt text](docs/Logo1.png \"PyBioNetFit\")\n\nPyBioNetFit (PyBNF) is a general-purpose program for parameterizing biological models specified using the BioNetGen\nrule-based modeling language (BNGL) or the Systems Biology Markup Language (SBML). PyBioNetFit offers a suite of\nparallelized metaheuristic algorithms (differential evolution, particle swarm optimization, scatter search) for\nparameter optimization. In addition to model parameterization, PyBNF supports uncertainty quantification by\nbootstrapping or Bayesian approaches, and model checking. PyBNF includes an adaptive Markov chain Monte Carlo (MCMC) sampling algorithm, which supports Bayesian inference. PyBNF includes the Biological Property Specification Language\n(BPSL) for defining qualitative data for use in parameterization or checking. It runs on most Linux and macOS\nworkstations as well on computing clusters.\n\nFor documentation, refer to [Documentation_PyBioNetFit.pdf](Documentation_PyBioNetFit.pdf) or the online documentation at \u003chttps://pybnf.readthedocs.io/en/latest/\u003e.\n\nPyBioNetFit is released under the BSD-3 license. For more information, refer to the\n[LICENSE](LICENSE). LANL code designation: C18062\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flanl%2Fpybnf","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flanl%2Fpybnf","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flanl%2Fpybnf/lists"}