{"id":21274784,"url":"https://github.com/maayanlab/biojupies","last_synced_at":"2026-03-12T06:41:00.854Z","repository":{"id":37777888,"uuid":"108299932","full_name":"MaayanLab/biojupies","owner":"MaayanLab","description":"Automated generation of tailored bioinformatics Jupyter Notebooks via a user interface.","archived":false,"fork":false,"pushed_at":"2025-06-09T16:59:16.000Z","size":70991,"stargazers_count":119,"open_issues_count":85,"forks_count":30,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-12-06T20:21:55.440Z","etag":null,"topics":["bioinformatics","cloud","dcppc","jupyter","notebook","pipeline","rna-seq","systems-biology"],"latest_commit_sha":null,"homepage":"http://biojupies.cloud","language":"HTML","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/MaayanLab.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"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":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-10-25T17:03:36.000Z","updated_at":"2025-10-05T15:47:43.000Z","dependencies_parsed_at":"2023-01-24T20:30:45.961Z","dependency_job_id":"2c8f6f2b-8bdb-4266-946e-218f2dc71ea9","html_url":"https://github.com/MaayanLab/biojupies","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/MaayanLab/biojupies","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/MaayanLab","download_url":"https://codeload.github.com/MaayanLab/biojupies/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/MaayanLab%2Fbiojupies/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":30417557,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-03-12T06:40:58.731Z","status":"ssl_error","status_checked_at":"2026-03-12T06:40:40.296Z","response_time":114,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: 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":["bioinformatics","cloud","dcppc","jupyter","notebook","pipeline","rna-seq","systems-biology"],"created_at":"2024-11-21T09:25:31.640Z","updated_at":"2026-03-12T06:41:00.838Z","avatar_url":"https://github.com/MaayanLab.png","language":"HTML","funding_links":[],"categories":[],"sub_categories":[],"readme":"# BioJupies\n![Notebooks Generated](https://img.shields.io/badge/dynamic/json.svg?url=https://amp.pharm.mssm.edu/biojupies/api/stats?obj=notebook\u0026label=notebooks%20generated\u0026query=$.n\u0026colorB=blue)\n![Datasets Available](https://img.shields.io/badge/RNA--seq%20datasets%20available-9145-green.svg)\n![Plugins](https://img.shields.io/badge/analysis%20plugins-14-yellow.svg)\n\nAutomated generation of Jupyter Notebooks for RNA-seq data analysis via user interface (http://biojupies.cloud).\n\nSource code for the RNA-seq analysis plugins available at https://github.com/MaayanLab/biojupies-plugins.\n\n### Overview\n1. [What is BioJupies?](#what-is-biojupies)\n2. [How can I generate notebooks using BioJupies?](#how-can-i-generate-a-notebook-using-biojupies)\n3. [How can I upload my own RNA-seq data to BioJupies?](#how-can-i-upload-my-rna-seq-data-to-biojupies)\n4. [What analyses can BioJupies perform?](#what-analyses-can-biojupies-perform)\n5. [Can I contribute my RNA-seq analysis tools?](#can-i-contribute-my-rna-seq-analysis-tools)\n6. [How can I download and rerun my notebooks?](#how-can-i-download-and-rerun-my-notebooks)\n7. [References](#references)\n\n## What is BioJupies?\nBioJupies is a web server which allows users to automatically generate Jupyter Notebooks from RNA-seq datasets through an intuitive interface, with no knowledge of coding required. It can be accessed for free from http://biojupies.cloud.\n![Screenshot of the BioJupies website landing page.](img/website.png)\n\n## How can I generate a notebook using BioJupies?\n\nGenerating a notebook using BioJupies requires three steps:\n\n![Screenshot of the BioJupies website landing page.](img/workflow.png)\n\n1. First, **select an RNA-seq dataset** you with to analyze. You can upload FASTQ files, gene expression tables, or use a search engine to browse over 6,000 public datasets published in the [Gene Expression Omnibus](https://www.ncbi.nlm.nih.gov/geo/) and processed by [ARCHS4](https://amp.pharm.mssm.edu/archs4/).\n2. Second, **add one or more computational tools** to analyze the data. BioJupies currently supports 14 plugins to perform exploratory data analysis, differential gene expression, enrichment analysis, and small molecule queries.\n3. Third, **generate the notebook** with the desired settings. The notebook will be served to you through a URL, and can be easily downloaded and rerun on your local computer.\n\n\u003cbr\u003e\n\n## How can I upload my RNA-seq data to BioJupies?\nUsers can upload their RNA-seq datasets for analysis at https://amp.pharm.mssm.edu/biojupies/upload.\n\n![Screenshot of the BioJupies upload page.](img/upload.png)\n\nBioJupies currently supports uploading **RNA-seq datasets in the FASTQ format** or **tables of gene-level counts**.\n\n**Note**: While the user may successfully generate a notebook from normalized gene expression counts or microarray data tables, the tools are **NOT** yet optimized to handle such data. Such results should be interpreted with caution.\n\nThe Enrichment Analysis and Small Molecule Query plugins currently support datasets uploaded with **gene symbols** as row identifiers. When uploading datasets with different identifiers (e.g. ENSEMBL IDs, Entrez IDs), please note that these plugins may return empty results.\n\n\u003cbr\u003e\n\n## What analyses can BioJupies perform?\nBioJupies currently provides **14 RNA-seq data analysis plugins**, divided \ninto four categories. For more information about the plugins, visit https://github.com/MaayanLab/biojupies-plugins.\n\n![Screenshot of the BioJupies upload page.](img/tools.png)\n\n## Can I contribute my RNA-seq analysis tools?\nDevelopers are welcome to contribute their own RNA-seq data analysis plugins for integration in BioJupies. Once integrated, the plugin will be made available to all users for notebook generation and published on the BioJupies plugins [GitHub repository](https://github.com/MaayanLab/biojupies-plugins).\n\nTo contribute your plug-in, please visit https://amp.pharm.mssm.edu/biojupies/contribute.\n\n\u003cbr\u003e\n\n## How can I download and rerun my notebooks?\nAfter generating a notebook, users can download and execute it locally using the `maayanlab/biojupies-notebooks` Docker container.\n\nTo do this, the following steps are required:\n1. Pull the latest version of the Docker container from the console:\n\n``` bash \ndocker pull maayanlab/biojupies-notebooks\n```\n\n2. Identify the notebook's unique ID (a 9-character alphanumeric string) from its URL - e.g. `5DAHiejHN`.\n\n![Screenshot of the a BioJupies notebook UID.](img/notebook_uid.png)\n\n3. Launch the Docker container.\n\n``` bash \ndocker run -it -p 8888:8888 -e NOTEBOOK_UID=5DAHiejHN maayanlab/biojupies-notebooks\n```\n\n**Note: replace `5DAHiejHN` with the UID of the notebook you wish to rerun.**\n\n4. Access the local Jupyter Notebook server from your browser at port 8888.\n\n![Screenshot of the a local Jupyter Server.](img/local_server.png)\n\n5. Execute and customize your notebook from the Jupyter server.\n\n![Screenshot of the a local Jupyter Server.](img/local_notebook.png)\n\nFor more information about reusing notebooks, see https://amp.pharm.mssm.edu/biojupies/docker.\n\n\u003cbr\u003e\n\n## References\nBioJupies is available as a pre-print on **BioRxiv**:\n[BioJupies: Automated Generation of Interactive Notebooks for RNA-seq Data Analysis in the Cloud](http://dx.doi.org/10.1016/j.cels.2018.10.007) Torre, D., Lachmann, A., and Ma’ayan, A. (Cell Systems, 2018)\n\n## License\nThis project is licensed under the Apache-2.0 License - see the [LICENSE.md](LICENSE.md) file for details","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fbiojupies","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmaayanlab%2Fbiojupies","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmaayanlab%2Fbiojupies/lists"}