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TL;DR: you can browse the registry at biojs.io.
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
- Essentials
1.1. Objectives
1.2. What is BioJS
1.3. Why is there nothing in this repo?
- Packages
2.1. What is a package?
2.2. How to search for a package
2.3. What do I need to use a package?
2.4. How do I use a package?
2.5. How to build a BioJS package - Developing packages
3.1. What do I need to develop?
3.2. How to create a package?
3.3. How to use snippets/examples?
3.4. Guidelines
3.5 I need the functionality X
3.6. Gold standards
3.7. How to publish a package?
3.8. How can I report a package? - Support
4.1 Get involved
4.2. Contact
4.3. More questions?
4.4. Documentation - License
- Essentials
- Represent consistently biological information across different projects
- Ease discovery, test and integration of graphical components
- Standardize and facilitate components development
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.
For BioJS 2.0 every component is a separate github repository. To search for a package, visit our registry. This repo is kept as intro guide and discussion repo. Feel free to open an issue (questions, suggestions, proposal or bug reports here) or to submit a component wish.
However you are still invited to show your interest in this project by starring this repo.
- Packages
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.
(Find it on github: Frontend repo, backend repo).
A web browser. For convenience you can grab a recent CDN version of
Normally the author provides also provides you with a minimized version of his component, but you can always easily build it yourself by running "npm run build-browser".
In general the README.md of each project should explain you how to interact with it.
For visualization components you can just copy the JSBin or Codepen example.
You can also add it as a dependency of your project by using npm install <package> --save.
Clone the package an run
npm install # this downloads all the dependencies of a package
npm test # optional
npm run build-browser # this will generate a JS file usuable in every browser (normally in the build folder)
Working examples of the component can be found in the snippets folder of a package.
- Developing packages
Detailed installation instructions.
Even tough you can easily install node on Windows, a Unix-like OS is generally a more productive development enviroment.
↝ read our guide
To bootstrap a new project you can use the BioJS slush generator.
npm install -g slush slush-biojs
mkdir biojsAWesome && cd biojsAwesome
slush biojs
↝ read our sniper.
- Events (Convention for the Observer pattern)
- CSS dependencies
- JS dependencies (=npm packages)
- Reusable modules
- example snippets
Especially the snippets should give one a quick start on how to use a component.
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.
Our gold standards are conventions we highly encourage you to follow (especially for JS beginners). They will help you to create a great package!
Just publish it on npm.
Either open an issue in their repository or use io-ratings.
- Support
Whether you want to write your own component and just submit it onto our BioJS registry or help to increase our ecosystem - we value your contribution(s)!
Here are some general ideas:
- Browse our issue list (or all BioJS repositories) for ideas
- Propose your own ideas
- Ask on gitter, our mailing list or irc
↝ There are many ways to contact us
For technical queries (questions, suggestions, proposal or bug reports) Github issues are preferred.
↝ We have a community-based wiki. Some topics include:
We maintain a learning platform edu.biojs.net.
Pull requests are welcome.
Contents:
- License