{"id":17919302,"url":"https://github.com/lynnlangit/gcp-for-bioinformatics","last_synced_at":"2025-05-16T13:05:04.973Z","repository":{"id":38534320,"uuid":"190583962","full_name":"lynnlangit/gcp-for-bioinformatics","owner":"lynnlangit","description":"GCP for Bioinformatics Researchers","archived":false,"fork":false,"pushed_at":"2024-11-25T00:56:07.000Z","size":94219,"stargazers_count":258,"open_issues_count":1,"forks_count":70,"subscribers_count":15,"default_branch":"master","last_synced_at":"2025-04-03T09:08:48.452Z","etag":null,"topics":["bioinformatics","bioinformatics-analysis","bioinformatics-pipeline","bioinformatics-researchers","gcp","genomics","google","google-batch","nextflow"],"latest_commit_sha":null,"homepage":"https://www.youtube.com/playlist?list=PL4Q4HssKcxYvcixWS08UFaYIH7y4IAV0z","language":"Jupyter Notebook","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lynnlangit.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,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2019-06-06T13:13:19.000Z","updated_at":"2025-03-28T03:10:16.000Z","dependencies_parsed_at":"2025-01-01T05:04:51.700Z","dependency_job_id":"dac58e1d-0ab6-4396-ac36-273beadaeecb","html_url":"https://github.com/lynnlangit/gcp-for-bioinformatics","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/lynnlangit%2Fgcp-for-bioinformatics","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lynnlangit%2Fgcp-for-bioinformatics/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lynnlangit%2Fgcp-for-bioinformatics/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lynnlangit%2Fgcp-for-bioinformatics/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lynnlangit","download_url":"https://codeload.github.com/lynnlangit/gcp-for-bioinformatics/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248544034,"owners_count":21121878,"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":["bioinformatics","bioinformatics-analysis","bioinformatics-pipeline","bioinformatics-researchers","gcp","genomics","google","google-batch","nextflow"],"created_at":"2024-10-28T20:15:59.184Z","updated_at":"2025-04-12T09:21:06.009Z","avatar_url":"https://github.com/lynnlangit.png","language":"Jupyter Notebook","funding_links":[],"categories":[],"sub_categories":[],"readme":"# Google Cloud Platform (GCP) for Bioinformatics\n\nThis repository shows how to use Google Cloud Platform (GCP) public cloud services to scale sets of **bioinformatics data analysis** tasks. This Repo uses cloud best practices for GCP.  All examples use **genomic** sample (input) data, tools and pipelines.  Use cases included here as examples are called by any and all of the following terms:\n- genomic-scale data workflows or pipelines\n- bioinformatics primary, secondary or tertiary analysis \n- distributed cloud-based batch jobs\n\n\u003cimg src=\"https://github.com/lynnlangit/gcp-for-bioinformatics/raw/master/images/learn-gcp.png\" width=\"390\" align=\"right\"\u003e\n\nThis content is intended for researchers - in particular, this guide is for those who are **NEW to working with GCP**.  You have a number of options on how to use the materials provided in this course.  A summary is shown below left.\n\n\nThis Repo includes content you can read, watch or run:  \n\n- 📗 **READ** - one page of this Repo (MD page)\n- 📺 **WATCH** -  linked YouTube screencasts\n- 📙 **RUN** - Jupyter Notebook example\n- :octocat: **TRY** - linked GitHub Repos\n- 📘 **EXPAND** - linked (external) resources\n- 🔍 **SCAN** - search a list in this Repo\n\nNOTE: If you are looking for AWS guidance, see my **'aws-for-bioinformatics'** Repo/Course at [link](https://github.com/lynnlangit/aws-for-bioinformatics)\n\n---\n\n### 📺 Click below to WATCH 'Lynn's Welcome Video' (4 min) on YouTube\n\n[![Welcome to GCP for Bioinformatics](http://img.youtube.com/vi/YoFkSVDlN6k/0.jpg)](http://www.youtube.com/watch?v=YoFkSVDlN6k \"Welcome to GCP for Bioinformatics\")\n\n---\n\n### Why would I choose to use a public cloud vendor for bioinformatics?\n\n⭐️ **SAVE MONEY** run (and pay for) scalable analysis jobs only when you need to run them  \n⭐️ **SAVE TIME** use vendor-managed infrastructure \u0026 best-practice patterns for fast repeatable research   \n📗 **READ** the [FAQ for GCP bioinformatics](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/1_FAQ.md) for this Repo  \n📕 **READ** Nature article: [\"Cloud computing for genomic data analysis and collaboration\"](https://www.nature.com/articles/nrg.2017.113)  \n📗 **READ** the top 4 most [common use cases](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/3_USER-STORIES.md) for using the public cloud for bioinformatics researchers\n\n\n### Bioinformatics wanting more advanced GCP content?\nIf you would like to learn **more advanced concepts** (including script examples and patterns) about working with Google Cloud Platform, see my Repo `gcp-essentials` --\u003e [link](https://github.com/lynnlangit/gcp-essentials)\n\n---\n\n### New to Bioinformatics?\n\nIf you are **NEW to bioinformatics** and have a computational background...\n- :octocat: **REVIEW** my bioinformatics concepts tools and terms \n  - Designed for experienced cloud practioners who are **NEW to Bioinformatics**\n  - The 'student notes repo' is named `Team Teri` - [link](https://github.com/lynnlangit/TeamTeri#who-is-teri) to 'who is Teri?'\n  - This Repo includes links to explanations of bioinformatics concepts, tools and platforms - [link](https://github.com/lynnlangit/TeamTeri)\n\n----\n\n### Contibutions\n\nWe love contributions! See this [short style guide](https://github.com/lynnlangit/gcp-for-bioinformatics/blob/master/CONTRIBUTING.md) when making pull requests to this repo.\n\n---\n\n\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flynnlangit%2Fgcp-for-bioinformatics","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flynnlangit%2Fgcp-for-bioinformatics","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flynnlangit%2Fgcp-for-bioinformatics/lists"}