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var nodes = [
        { name: 0, value: 0 },
        { name: 1, value: 1 },
        { name: 2, value: 2 },
        { name: 3, value: 3 }
]
var edges = [
        { source: nodes[0], target: nodes[1] },

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config.force.tick = function() {
        graphChart.links.attr({
                x1: function(d) { return d.source.x },
                y1: function(d) { return d.source.y },
                x2: function(d) { return d.target.x },
                y2: function(d) { return d.target.y } })

        graphChart.bubbles
                .selectAll('circle')
                .attr({

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(function($) {

/*
 * Author: jhsu
 *
 * This file + required modules contains all the JavaScript to run MartExplorer.
 *
 * The workflow starts from the biomart.martexplorer.init function, and ends with _stepCallback function.
 *
 * The _stepCallback function has an array (bound by closure) that maps to each of the four steps.

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function resizeHandler () {
        if (this._svg && !this._svg.empty()) {
                this._svg.attr({
                        width: $(window).width()
                        height: $(window).height()
                })
        }
}

function resize (listener, interval) {

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Weighted Network

We're going to gather gene pairs from single query results searching for genes sharing the same annotation term.

G1 A1

G2 A1 -> G1 G2 A1

G2 A3

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Enrichment

Index

1. What We need
2. Input representation within BioMart domain
3. What we want to do with it
4. Design
5. Implementation
   5.1 Ensembl IDs Translation
   5.2 Getting All the Annotations

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Exercise 2

Implement a recursive procedure (function/class, you choose) that answers to the eight-queens puzzle problem.

The eight-queens puzzle asks how to place eight queens on a chessboard so that no queen is in check from any other (i.e., no two queens are in the same row, column, or diagonal).

Spoiler: one possible solution

One possible solution is shown in figure 2.8. One way to solve the puzzle is to work across the board, placing a queen in each column. Once we have placed k - 1 queens, we must place the kth queen in a position where it does not check any of the queens already on the board. We can formulate this approach recursively: Assume that we have already generated the sequence of all possible ways to place k - 1 queens in the first k - 1 columns of the board. For each of these ways, generate an extended set of positions by placing a queen in each row of the kth column. Now filter these, keeping only th

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{
    "Gene Ontology (GO)": {
        "header": {
            "type": "annotation",
            "columns": ["id", "status", "..."],
            "display_names": ["name", "status", "..."]
        },
        "nodes": [
            { "id": "", "status": "", "start": "", "type": "term" },
            { "id": "", "foo": "", "bar": "", "type": "gene" },

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"use strict";

angular.module("martVisualEnrichment.services", [])
.factory("results",
        ["$document", "$q", "enrichmentResultsId",
        function resultsFactory ($doc, $q, containerId) {

    // I'm using a promise such that if we get data with ajax the API won't
    // change.
    var deffed = $q.defer(),

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;(function (angular) {
"use strict";

var app = angular.module("martVisualEnrichment.directives");


/**
 *
 * This implementation is highly inspired by https://github.com/angular-ui/bootstrap/blob/master/src/tabs/tabs.js
 *