biojs

BioJS 2.0

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TL;DR: you can browse the registry at biojs.io.

Contents

1. 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?
• Support
  4.1 Get involved
  4.2. Contact
  4.3. More questions?
  4.4. Documentation
• 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.

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. 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.

1. 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.

2.2. How to search for a package

biojs.io

(Find it on github: Frontend repo, backend repo).

2.3. What do I need to use a package?

A web browser. For convenience you can grab a recent CDN version of

• all parsers
• all visualization components

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".

2.4. How do I use a package?

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.

2.5. How to build a BioJS package

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.

1. Developing packages

---

3.1. What do I need to develop?

• git
• npm

Detailed installation instructions.

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

To bootstrap a new project you can use the BioJS slush generator.

npm install -g slush slush-biojs
mkdir biojsAWesome && cd biojsAwesome
slush biojs

3.3. How to use snippets/examples?

↝ read our sniper.

3.4 Guidelines

• 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.

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

3.6. Gold standards

Our gold standards 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.

↝ Learn more

1. Support

---

4.1. Get involved

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)!

↝ Get involved

Here are some general ideas:

• Browse our issue list (or [all BioJS repositories][issue_all]) for ideas
• Propose your own ideas
• Ask on gitter, our mailing list or irc

↝ more information

4.2. Contact

↝ There are many ways to contact us

For technical queries (questions, suggestions, proposal or bug reports) Github issues are preferred.

4.3. More questions

↝ We have a community-based wiki. Some topics include:

• Common error messages
• FAQ
• Migration

4.4. Documentation

We maintain a learning platform edu.biojs.net.

Pull requests are welcome.

Contents:

• BioJS 2 101 tutorial series.

1. License

---

Apache 2