https://github.com/biojs/biojs
Tip revision: c91b69fe786751be09d8398a3ad8ef9188861245 authored by James McLaughlin on 11 October 2021, 22:47:13 UTC
Change URL to biojs.net
Change URL to biojs.net
Tip revision: c91b69f
README.md
BioJS 2.0
=========
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[](#) [](https://travis-ci.org/biojs/edu) [](https://github.com/biojs/biojs/blob/master/LICENSE) [](http://dx.doi.org/10.5281/zenodo.11893)
[](http://biojs-slackin.herokuapp.com/)
[](https://gitter.im/biojs/biojs) [](https://kiwiirc.com/client/irc.freenode.net/biojs)
**TL;DR:** you can browse the [registry][registry] at [biojs.net][registry].
*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*
__[Anatomy of BioJS, an open source community for the life sciences][BioJS-elife]__
eLife 2015;4:e07009
[BioJS-elife]: http://elifesciences.org/content/4/e07009
Contents
----------
1. [Essentials](#1-essentials)
1.1. [Objectives](#11-objectives)
1.2. [What is BioJS](#12-what-is-biojs)
1.3. [Why is there nothing in this repo?](#13-why-is-there-nothing-in-this-repo)
* [Packages](#2-packages)
2.1. [What is a package?](#21-what-is-a-package)
2.2. [How to search for a package](#22-how-to-search-for-a-package)
* [Developing packages](#3-developing-packages)
3.1. [What do I need to develop?](#31-what-do-i-need-to-develop)
3.2. [How to create a package?](#32-how-to-create-a-package)
3.3. [How to use snippets/examples?](#33-how-to-use-snippets)
3.4. [Guidelines](#34-guidelines)
3.5 [I need the functionality X](#35-i-need-the-functionality-x)
3.6. [Gold standards](#36-gold-standards)
3.7. [How to publish a package?](#37-how-to-publish-a-package)
* [Support](#4-support)
4.1 [Get involved](#41-get-involved)
4.2. [Contact](#42-contact)
4.3. [More questions?](#43-more-questions)
4.4. [Documentation](#44-documentation)
* [License](#5-license)
1. Essentials
--------------
### 1.1. Objectives
* Represent consistently biological information across different projects
* Ease discovery, test and integration of graphical components
* Standardize and facilitate components development
### 1.2. What is BioJS?
BioJS 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].
### 1.3. Why is there nothing in this repo?
For BioJS 2.0 every component is a separate github repository. To search for a package, visit our [registry][registry].
This 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].
However you are still invited to show your interest in this project by __starring__ this repo.
2. Packages
-------------
### 2.1. What is a package?
A __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).
## 2.2. How to search for a package
Visit the [biojs.net][registry] registry to search for components.
(Find it on github: [Frontend repo][registryui], [backend repo][registry-workmen]).
3. Developing packages
-----------------------
### 3.1. What do I need to develop?
* [git](https://try.github.io/levels/1/challenges/1)
* [npm](http://nodejs.org/download/)
[Detailed installation instructions](http://edu.biojs.net/101/getting_started).
Even tough you can easily install node on Windows, a Unix-like OS is generally a more productive development enviroment.
### 3.2. How to create a package?
↝ read our [guide][101]
To bootstrap a new project you can use the BioJS [slush generator](https://github.com/biojs/slush-biojs).
```
npm install -g slush slush-biojs
mkdir biojsAWesome && cd biojsAwesome
slush biojs
```
### 3.3. How to use snippets/examples?
↝ read our [sniper][sniper].
### 3.4 Guidelines <a name=guidelines></a>
* [Events](https://github.com/biojs/biojs/wiki/BioJS-events) (Convention for the [Observer](https://github.com/biojs/biojs-events) pattern)
* [CSS dependencies](https://github.com/biojs/biojs/wiki/Adding-CSS-stylesheets)
* [JS dependencies](https://github.com/biojs/biojs/wiki/I-need-a-npm-module-for-X) (=npm packages)
* [Reusable modules](https://github.com/biojs/biojs/wiki/Gotchas-about-reusability)
* [example snippets][sniper]
Especially the snippets should give one a quick start on how to use a component.
### 3.5. I need the functionality X
You 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.
↝ [Learn more](https://github.com/biojs/biojs/wiki/I-need-a-npm-module-for-X)
### 3.6. Gold standards
Our [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!
### 3.7. How to publish a package?
Just publish it on [npm](npmjs.org).
↝ [Learn more](https://github.com/biojs/biojs/wiki/Gotchas-about-the-BioJS-registry)
### 3.8. How can I report defective components?
We'd recommend opening an issue in their repository directly.
4. Support
----------
### 4.1. Get involved
Whether 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)!
↝ [Get involved](http://biojs.net/get_involved.html)
Here are some general ideas:
* Browse our [issue list](https://github.com/biojs/organisation/issues)
* Ask on [gitter](https://gitter.im/biojs/biojs)
↝ [more information](./CONTRIBUTING.md)
### 4.2. Contact
↝ [There are many ways to contact us](http://biojs.net/get_involved.html)
For technical queries (questions, suggestions, proposal or bug reports) [Github issues](https://github.com/biojs/biojs/issues) are preferred.
### 4.3. More questions
↝ We have a community-based [wiki][wiki].
Some topics include:
- [Common error messages](https://github.com/biojs/biojs/wiki/Common-error-messages)
- [FAQ](https://github.com/biojs/biojs/wiki/FAQ)
- [Migration][migration]
### 4.4. Documentation
We maintain a learning platform [edu.biojs.net](http://edu.biojs.net/).
[Pull requests](https://github.com/biojs/tutorials) are welcome.
Contents:
- [BioJS 2 101 tutorial series][101].
5. License
----------
[Apache 2](http://www.apache.org/licenses/LICENSE-2.0)
[101]: http://edu.biojs.net/101/intro
[gitter]: https://gitter.im/biojs/biojs
[groups]: https://groups.google.com/forum/#!forum/biojs
[irc]: http://webchat.freenode.net/?channels=biojs
[issue]: https://github.com/biojs/biojs/issues
[issues_all]: https://github.com/search?l=&o=desc&q=user%3Abiojs+state%3Aopen&ref=advsearch&s=created&type=Issues&utf8=%E2%9C%93
[publishit]: http://edu.biojs.net/101/publish_it
[migration]: https://github.com/biojs/biojs/wiki/biojs1-biojs2-migration
[registry]: http://biojs.net
[registryui]: https://github.com/biojs/biojs-frontend
[registry-workmen]: https://github.com/biojs/biojs-backend
[sniper]: https://github.com/greenify/biojs-sniper
[wiki]: https://github.com/biojs/biojs/wiki
[wishlist]: https://github.com/biojs/biojs/issues/new?title=%5BWish%5D&body=%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
