{"id":44454443,"url":"https://github.com/biosimulators/biosimulators_tutorials","last_synced_at":"2026-02-12T17:09:18.839Z","repository":{"id":123976508,"uuid":"409823566","full_name":"biosimulators/Biosimulators_tutorials","owner":"biosimulators","description":"Tutorials for BioSimulators","archived":false,"fork":false,"pushed_at":"2023-05-01T14:39:46.000Z","size":1795,"stargazers_count":2,"open_issues_count":3,"forks_count":0,"subscribers_count":7,"default_branch":"dev","last_synced_at":"2025-09-09T16:39:30.305Z","etag":null,"topics":["biosimulations","biosimulators","combine","computational-biology","jupyter","mathematical-modeling","numerical-simulation","omex","sbml","sed-ml","systems-biology","tutorial"],"latest_commit_sha":null,"homepage":"https://tutorial.biosimulators.org","language":"Jupyter Notebook","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/biosimulators.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":"CONTRIBUTING.md","funding":null,"license":"LICENSE","code_of_conduct":"CODE_OF_CONDUCT.md","threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":"GOVERNANCE.md","roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null,"zenodo":null,"notice":null,"maintainers":null,"copyright":null,"agents":null,"dco":null,"cla":null}},"created_at":"2021-09-24T03:49:48.000Z","updated_at":"2023-09-25T16:35:30.000Z","dependencies_parsed_at":"2025-09-09T15:31:37.856Z","dependency_job_id":"cf23a279-dc3d-47a9-8e06-8c91c8525eeb","html_url":"https://github.com/biosimulators/Biosimulators_tutorials","commit_stats":null,"previous_names":[],"tags_count":5,"template":false,"template_full_name":null,"purl":"pkg:github/biosimulators/Biosimulators_tutorials","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosimulators%2FBiosimulators_tutorials","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosimulators%2FBiosimulators_tutorials/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosimulators%2FBiosimulators_tutorials/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosimulators%2FBiosimulators_tutorials/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biosimulators","download_url":"https://codeload.github.com/biosimulators/Biosimulators_tutorials/tar.gz/refs/heads/dev","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biosimulators%2FBiosimulators_tutorials/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":29373841,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-02-12T08:51:36.827Z","status":"ssl_error","status_checked_at":"2026-02-12T08:51:26.849Z","response_time":55,"last_error":"SSL_read: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"can_crawl_api":true,"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":["biosimulations","biosimulators","combine","computational-biology","jupyter","mathematical-modeling","numerical-simulation","omex","sbml","sed-ml","systems-biology","tutorial"],"created_at":"2026-02-12T17:09:18.505Z","updated_at":"2026-02-12T17:09:18.835Z","avatar_url":"https://github.com/biosimulators.png","language":"Jupyter Notebook","readme":"[![Binder](https://mybinder.org/badge_logo.svg)](https://tutorial.biosimulators.org/)\n[![All Contributors](https://img.shields.io/github/all-contributors/biosimulators/Biosimulators_tutorials/HEAD)](#contributors-)\n\n![Logo](https://raw.githubusercontent.com/biosimulations/Biosimulations/dev/libs/shared/assets/src/assets/images/biosimulators-logo/logo-white.svg)\n\n# BioSimulators tutorials\n\nThis repository contains Jupyter notebooks with tutorials for the Python APIs for the simulation tools registered with BioSimulators and a Jupyter notebook server for running the notebooks.\n\nThe tutorials are located in the [`tutorials`](tutorials) subdirectory. The [README](tutorials/README.md) in this directory summarizes the content of the tutorials.\n\n## Getting started\n\n### Running the tutorials online with Binder\nThe easiest way to run the tutorials is with Binder. Simply open https://tutorial.biosimulators.org/ in your browser.\n\n### Running the tutorials on your own machine\nRun the following command to download the tutorials:\n```\ndocker pull ghcr.io/biosimulators/tutorials\n```\n\nRun the following command to launch a Jupyter notebook server at http://localhost:8888 for the tutorials in this repository:\n```\ndocker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter notebook --ip=0.0.0.0 --port=8888\n```\n\nAlternatively, run the following command to launch a Jupyter lab server at http://localhost:8888 for the tutorials in this repository:\n```\ndocker run -it --rm -p 8888:8888 ghcr.io/biosimulators/tutorials jupyter lab --ip=0.0.0.0 --port=8888\n```\n\n## License\n\nThis package is released under the [MIT license](LICENSE).\n\n## Development team\n\nThis package was developed by the [Karr Lab](https://www.karrlab.org) at the Icahn School of Medicine at Mount Sinai in New York as part of the [Center for Reproducible Biomodeling Modeling](https://reproduciblebiomodels.org) with assistance from the contributors listed [here](CONTRIBUTORS.md).\n\n- [Bilal Shaikh](https://www.bshaikh.com)\n- [Jonathan Karr](https://www.karrlab.org)\n\n## Funding\n\nThis package was developed with support from the National Institute for Bioimaging and Bioengineering (award P41EB023912).\n\n## Questions and comments\n\nPlease contact us at [info@biosimulators.org](mailto:info@biosimulators.org) with any questions or comments.\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulators%2Fbiosimulators_tutorials","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiosimulators%2Fbiosimulators_tutorials","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiosimulators%2Fbiosimulators_tutorials/lists"}