{"id":20456561,"url":"https://github.com/krassowski/computational-notebooks-for-biomedical-research","last_synced_at":"2025-04-13T04:02:44.919Z","repository":{"id":93476364,"uuid":"279940794","full_name":"krassowski/computational-notebooks-for-biomedical-research","owner":"krassowski","description":"NGSeminar on the use of Jupyter and R notebooks in biomedical research","archived":false,"fork":false,"pushed_at":"2023-01-28T12:20:09.000Z","size":8651,"stargazers_count":12,"open_issues_count":3,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-26T21:03:08.586Z","etag":null,"topics":["biomedical","jupyter-notebook","jupyterlab","notebook","reproducible-research","research","rmarkdown","seminar","talk"],"latest_commit_sha":null,"homepage":"","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/krassowski.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":"2020-07-15T18:00:32.000Z","updated_at":"2024-08-04T01:15:34.000Z","dependencies_parsed_at":"2023-03-18T15:52:22.954Z","dependency_job_id":null,"html_url":"https://github.com/krassowski/computational-notebooks-for-biomedical-research","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/krassowski%2Fcomputational-notebooks-for-biomedical-research","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fcomputational-notebooks-for-biomedical-research/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fcomputational-notebooks-for-biomedical-research/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/krassowski%2Fcomputational-notebooks-for-biomedical-research/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/krassowski","download_url":"https://codeload.github.com/krassowski/computational-notebooks-for-biomedical-research/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248661703,"owners_count":21141450,"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":["biomedical","jupyter-notebook","jupyterlab","notebook","reproducible-research","research","rmarkdown","seminar","talk"],"created_at":"2024-11-15T11:23:05.764Z","updated_at":"2025-04-13T04:02:44.873Z","avatar_url":"https://github.com/krassowski.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Computational notebooks for biomedical research\n\nThe slides are available as a notebook on GitHub [`Overview.ipynb`](./Overview.ipynb). Complimentary (opinionated) slides are available in other notebooks.\n\nRun the notebooks with examples online:\n\n- For Jupyter notebook: `Examples_Jupyter_notebook.ipynb` [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/computational-notebooks-for-biomedical-research/master?urlpath=lab/tree/Examples_Jupyter_notebook.ipynb) (JupyterLab)\n- For R Markdown: `Examples_R_Markdown.Rmd` [![Binder](https://mybinder.org/badge_logo.svg)](https://mybinder.org/v2/gh/krassowski/computational-notebooks-for-biomedical-research/master?urlpath=rstudio) (RStudio)\n\nThe online environments may take some time (\u003e10 minutes) to boot up if they are run after a fresh commit or for a first time in a while.\n\n\n### Widgets screencast\n\nFor your convenience sreencasts of widgets which may be of use for biomedical researchers are embedded below:\n\n![FASTA](media/widgets/fasta.gif)\n\n![PDB](media/widgets/pdb.gif)\n\n![imaging](media/widgets/imaging.gif)\n\n![custom](media/widgets/custom.gif)\n\n\n### About\n\nThis talk was given during an [NGSeminar](https://ngschool.eu/ngseminars/) on the use of Jupyter and R notebooks in biomedical research, available to [watch on YouTube](https://www.youtube.com/watch?v=eXt4MROqTtc) and later, in an improved version for the Big Data Institute training session.\n\n### Dependencies\n\nThe Python packages used in the seminar and demonstration are listed in the [`environment.yml`](./environment.yml) file. You can install them with conda, or install specific Python requirements with pip.\n\nThe JupyterLab extensions used are listed in the `postBuild` file. You can install them by copy-pasting the line which starts with `jupyter labextension install`. In this file you will  also find the instructions on downloading the example datasets used in the presentation.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrassowski%2Fcomputational-notebooks-for-biomedical-research","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkrassowski%2Fcomputational-notebooks-for-biomedical-research","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkrassowski%2Fcomputational-notebooks-for-biomedical-research/lists"}