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Modularity
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101
101/modularity/
15

This is a short tutorial on the basics of using and reusing BioJS components -- it should take you about 5 minutes to complete.

  1. Install node & npm

{% alert warn %} You need to install node before you can start to rock. See the getting started guide for more info. {% endalert %}

How does the LEGO-System of BioJS work? We recommend you use a Unix terminal and a text editor!

  1. Your first easy BioJS Component

Make a new folder and create a new file called index.js. Now we create a simple BioJS component which adds two numbers and can be reused!

function biojs101(a,b) {
    return a+b;
}

console.log(biojs101(1,2));

module.exports = biojs101;

Congratulations, you wrote your first BioJS Component! Run

node index.js

to run this file! It should show you 3.

  1. Reuse your component

Create a second file called reuse.js which is in the same folder as index.js

Type in:

var reuse = require("./index");

console.log(reuse(3,6));

Congratulations! You reused your first BioJS function in the source code! Check for yourself, type in:

node reuse.js

It will show you 3 (because of console.log in index.js) and 9.

{% hlblock info %} Are you interested in how require works? {% endhlblock %}

  1. Reusing current BioJS components!

BioJS offers a lot of common parsers and algorithms for reuse.

Open your reuse.js file and type in

var parser = require("biojs-io-newick").parse_newick;

Now you included a newick parser for testing. Checkout the documentation for newick parser to see for yourself. To download the BioJS component, just type

npm install biojs-io-newick --save

into your terminal. Now you can look up: You have a node_module folder next to your index file. It has the source code of biojs-io-newick inside! Ok, get back to your reuse.js. Now add the following into reuse.js:

var newick = "(homo_sapiens:1,(mus_musculus:2,danio_rerio:17):4);"
var parsed_data = parser(newick);
console.log(parsed_data);

Now run again

node reuse.js

You should see the following:

{ children:
   [ { name: 'homo_sapiens', branch_length: 1 },
     { name: '', children: [Object], branch_length: 4 } ],
  name: '' }

Congratulations! You parsed a string by reusing a common BioJS algorithm.

  1. Reuse your component in the web

It is super easy to reuse your component and built on top of it.

We have created a very simple tree visualization by using this parser.

Have a look at it

{% hlblock info %} We can create more interactive and fancy visualizations. For a component using the Newick parser, have a look at TnT {% endhlblock %}