{"id":13704265,"url":"https://github.com/biojs/biojs","last_synced_at":"2025-05-05T09:33:34.511Z","repository":{"id":48178479,"uuid":"11845905","full_name":"biojs/biojs","owner":"biojs","description":"🔬A library of JavaScript components to represent biological data","archived":false,"fork":false,"pushed_at":"2021-10-11T22:47:13.000Z","size":44869,"stargazers_count":484,"open_issues_count":57,"forks_count":121,"subscribers_count":70,"default_branch":"master","last_synced_at":"2024-05-09T09:32:16.832Z","etag":null,"topics":["biojs","biology","javascript","visualisation"],"latest_commit_sha":null,"homepage":"http://biojs.net/","language":null,"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/biojs.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}},"created_at":"2013-08-02T15:05:19.000Z","updated_at":"2024-04-26T01:11:36.000Z","dependencies_parsed_at":"2022-08-23T09:50:13.806Z","dependency_job_id":null,"html_url":"https://github.com/biojs/biojs","commit_stats":null,"previous_names":[],"tags_count":3,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojs%2Fbiojs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojs%2Fbiojs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojs%2Fbiojs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/biojs%2Fbiojs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/biojs","download_url":"https://codeload.github.com/biojs/biojs/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":224439851,"owners_count":17311539,"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":["biojs","biology","javascript","visualisation"],"created_at":"2024-08-02T21:01:06.577Z","updated_at":"2024-11-13T11:31:07.610Z","avatar_url":"https://github.com/biojs.png","language":null,"readme":"BioJS 2.0\n=========\n\n```\n\n88888888ba  88                     88  ad88888ba      ad888888b,  \n88      \"8b \"\"                     88 d8\"     \"8b    d8\"     \"88  \n88      ,8P                        88 Y8,                    a8P  \n88aaaaaa8P' 88  ,adPPYba,          88 `Y8aaaaa,           ,d8P\"   \n88\"\"\"\"\"\"8b, 88 a8\"     \"8a         88   `\"\"\"\"\"8b,       a8P\"      \n88      `8b 88 8b       d8         88         `8b     a8P'        \n88      a8P 88 \"8a,   ,a8\" 88,   ,d88 Y8a     a8P    d8i\"          \n88888888P\"  88  `\"YbbdP\"'   \"Y8888P\"   \"Y88888P\"     88888888888 \n\n ```\n\n[![Version](http://img.shields.io/badge/npm-v2.0.0_alpha-orange.svg?style=flat)](#) [![Build Status](http://img.shields.io/travis/biojs/edu.svg?style=flat)](https://travis-ci.org/biojs/edu)  [![License: Apache 2](http://img.shields.io/hexpm/l/plug.svg?style=flat)](https://github.com/biojs/biojs/blob/master/LICENSE) [![DOI](https://zenodo.org/badge/6143/biojs/biojs.png)](http://dx.doi.org/10.5281/zenodo.11893)\n\n[![Slack](https://img.shields.io/badge/slack-join%20chat-E01563.svg)](http://biojs-slackin.herokuapp.com/)\n[![Gitter](https://badges.gitter.im/BioJS.png)](https://gitter.im/biojs/biojs)   [![IRC](https://img.shields.io/badge/irc-%23biojs-yellow.svg)](https://kiwiirc.com/client/irc.freenode.net/biojs)\n\n\n**TL;DR:** you can browse the [registry][registry] at [biojs.net][registry].\n\n*Guy Yachdav, Tatyana Goldberg, Sebastian Wilzbach, David Dao, Iris Shih, Saket Choudhary, Steve Crouch, Max Franz, Alexander García, Leyla J García, Björn A Grüning, Devasena Inupakutika, Ian Sillitoe, Anil S Thanki, Bruno Vieira, José M Villaveces, Maria V Schneider, Suzanna Lewis, Steve Pettifer, Burkhard Rost, and Manuel Corpas*  \n__[Anatomy of BioJS, an open source community for the life sciences][BioJS-elife]__  \neLife 2015;4:e07009\n[BioJS-elife]: http://elifesciences.org/content/4/e07009\n\nContents\n----------\n\n1. [Essentials](#1-essentials)  \n 1.1. [Objectives](#11-objectives)    \n 1.2. [What is BioJS](#12-what-is-biojs)  \n 1.3. [Why is there nothing in this repo?](#13-why-is-there-nothing-in-this-repo)  \n* [Packages](#2-packages)  \n  2.1. [What is a package?](#21-what-is-a-package)  \n  2.2. [How to search for a package](#22-how-to-search-for-a-package)  \n* [Developing packages](#3-developing-packages)  \n  3.1. [What do I need to develop?](#31-what-do-i-need-to-develop)  \n  3.2. [How to create a package?](#32-how-to-create-a-package)  \n  3.3. [How to use snippets/examples?](#33-how-to-use-snippets)  \n  3.4. [Guidelines](#34-guidelines)  \n  3.5  [I need the functionality X](#35-i-need-the-functionality-x)  \n  3.6. [Gold standards](#36-gold-standards)    \n  3.7. [How to publish a package?](#37-how-to-publish-a-package)   \n* [Support](#4-support)  \n  4.1  [Get involved](#41-get-involved)  \n  4.2. [Contact](#42-contact)   \n  4.3. [More questions?](#43-more-questions)  \n  4.4. [Documentation](#44-documentation)  \n* [License](#5-license)  \n\n1. Essentials\n--------------\n\n### 1.1. Objectives\n\n* Represent consistently biological information across different projects\n* Ease discovery, test and integration of graphical components\n* Standardize and facilitate components development\n\n### 1.2. What is BioJS?\n\nBioJS builds a infrastructure, guidelines and tools to __avoid the reinvention of the wheel in life sciences__ (= \"Docker for Bio web components\"). Our community builds modules than can be reused by anyone and makes them available for download via a centralised [registry][registry].\n\n### 1.3. Why is there nothing in this repo?\n\nFor BioJS 2.0 every component is a separate github repository. To search for a package, visit our [registry][registry].\nThis repo is kept as intro guide and discussion repo. Feel free to open an [issue][issue] (questions, suggestions, proposal or bug reports here) or [to submit a component wish][wishlist].\n\nHowever you are still invited to show your interest in this project by __starring__ this repo.\n\n2. Packages\n-------------\n\n### 2.1. What is a package?\n\nA __tiny building block__ like a FASTA parser or a visualization piece. If it obeys the rule _\"do one thing and do it well\"_ , then it is (most likely) a package. The BioJS packages are published on the JavaScript package manager [npm](npmjs.org).\n\n## 2.2. How to search for a package\n\nVisit the [biojs.net][registry] registry to search for components. \n\n(Find it on github: [Frontend repo][registryui], [backend repo][registry-workmen]).\n\n3. Developing packages\n-----------------------\n\n### 3.1. What do I need to develop?\n\n* [git](https://try.github.io/levels/1/challenges/1)\n* [npm](http://nodejs.org/download/)\n\n\n[Detailed installation instructions](http://edu.biojs.net/101/getting_started).\n\nEven tough you can easily install node on Windows, a Unix-like OS is generally a more productive development enviroment.\n\n### 3.2. How to create a package?\n\n↝ read our [guide][101]\n\nTo bootstrap a new project you can use the BioJS [slush generator](https://github.com/biojs/slush-biojs).\n\n```\nnpm install -g slush slush-biojs\nmkdir biojsAWesome \u0026\u0026 cd biojsAwesome\nslush biojs\n```\n\n### 3.3. How to use snippets/examples?\n\n↝ read our [sniper][sniper].\n\n### 3.4  Guidelines \u003ca name=guidelines\u003e\u003c/a\u003e\n\n* [Events](https://github.com/biojs/biojs/wiki/BioJS-events) (Convention for the [Observer](https://github.com/biojs/biojs-events) pattern)\n* [CSS dependencies](https://github.com/biojs/biojs/wiki/Adding-CSS-stylesheets)\n* [JS dependencies](https://github.com/biojs/biojs/wiki/I-need-a-npm-module-for-X) (=npm packages)\n* [Reusable modules](https://github.com/biojs/biojs/wiki/Gotchas-about-reusability)\n* [example snippets][sniper]\n\nEspecially the snippets should give one a quick start on how to use a component.\n\n### 3.5. I need the functionality X\n\nYou are now ready to enjoy the benefits of npm. For common use cases (requests, drag and drop, promises) you will always find plenty of npm modules.\n\n↝ [Learn more](https://github.com/biojs/biojs/wiki/I-need-a-npm-module-for-X)\n\n### 3.6. Gold standards\n\nOur [gold standards](http://edu.biojs.net/details/conventions) are conventions we highly encourage you to follow (especially for JS beginners). They will help you to create a great package!\n\n### 3.7. How to publish a package?\n\nJust publish it on [npm](npmjs.org).\n\n↝ [Learn more](https://github.com/biojs/biojs/wiki/Gotchas-about-the-BioJS-registry)\n\n### 3.8. How can I report defective components?\n\nWe'd recommend opening an issue in their repository directly. \n\n4. Support\n----------\n\n### 4.1. Get involved\n\nWhether you want to [write your own component](#4-developing-packages) and just [submit](#46-how-to-publish-a-package) it onto our BioJS registry or help to increase our ecosystem -  we __value__ your contribution(s)!\n\n↝ [Get involved](http://biojs.net/get_involved.html)\n\nHere are some general ideas:\n\n* Browse our [issue list](https://github.com/biojs/organisation/issues)\n* Ask on [gitter](https://gitter.im/biojs/biojs)\n\n↝ [more information](./CONTRIBUTING.md)\n\n### 4.2. Contact\n\n↝ [There are many ways to contact us](http://biojs.net/get_involved.html)\n\nFor technical queries (questions, suggestions, proposal or bug reports) [Github issues](https://github.com/biojs/biojs/issues) are preferred.\n\n### 4.3. More questions\n\n↝ We have a community-based [wiki][wiki].\nSome topics include:\n\n - [Common error messages](https://github.com/biojs/biojs/wiki/Common-error-messages)\n - [FAQ](https://github.com/biojs/biojs/wiki/FAQ)\n - [Migration][migration]\n\n### 4.4. Documentation\n\nWe maintain a learning platform [edu.biojs.net](http://edu.biojs.net/).\n\n[Pull requests](https://github.com/biojs/tutorials) are welcome.\n\nContents:\n  - [BioJS 2 101 tutorial series][101].\n\n5. License\n----------\n\n[Apache 2](http://www.apache.org/licenses/LICENSE-2.0)\n\n\n[101]: http://edu.biojs.net/101/intro\n[gitter]: https://gitter.im/biojs/biojs\n[groups]: https://groups.google.com/forum/#!forum/biojs\n[irc]: http://webchat.freenode.net/?channels=biojs \n[issue]: https://github.com/biojs/biojs/issues\n[issues_all]: https://github.com/search?l=\u0026o=desc\u0026q=user%3Abiojs+state%3Aopen\u0026ref=advsearch\u0026s=created\u0026type=Issues\u0026utf8=%E2%9C%93 \n[publishit]: http://edu.biojs.net/101/publish_it\n[migration]: https://github.com/biojs/biojs/wiki/biojs1-biojs2-migration\n[registry]: http://biojs.net\n[registryui]: https://github.com/biojs/biojs-frontend\n[registry-workmen]: https://github.com/biojs/biojs-backend\n[sniper]: https://github.com/greenify/biojs-sniper\n[wiki]: https://github.com/biojs/biojs/wiki\n[wishlist]: https://github.com/biojs/biojs/issues/new?title=%5BWish%5D\u0026body=%3E+Try+to+be+as+detailed+as+possible.+Why+do+you+need+it%3F+What+data+does+it+use%3F+What+should+the+user+experience%3F%0A%0A%0A%3E+Complexity+%28approx.+estimate+in+dates%29\n","funding_links":[],"categories":["Visualization"],"sub_categories":["Genome Browsers / Gene Diagrams"],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojs%2Fbiojs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbiojs%2Fbiojs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbiojs%2Fbiojs/lists"}