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Last active August 29, 2015 14:15
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scialog pre-conference network
Raw
README.md

This is a quick visualization of the Scialog pre-conference network. Orange nodes are theorists, blue nodes are experimentalists, and yellow circles are both experimentalists and theorists. For simplicity, this only displays the bidirectional links between pairs of scientists where the thickness of the line joining two scientists corresponds with how strongly they know each other.

To run this in development, just use python's simple server:

python -m SimpleHTTPServer
Raw
index.html
<html>
<head>
<link rel="stylesheet" type="text/css" href="style.css">
</head>
<body>
<script src="//d3js.org/d3.v3.min.js"></script>
<script src="//rawgit.com/mbostock/d3/master/lib/colorbrewer/colorbrewer.js"></script>
<script src="viz.js"></script>
</body>
</html>
Raw
pre-conference.json
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],
"multigraph": false,
"nodes": [
{
"department": "National Blood, Heart & Lung Institute",
"id": "justin.taraska@nih.gov",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Applied Physics and Molecular and Cellular Biology",
"id": "dan.needleman@gmail.com",
"seniority": "jr",
"theory_or_exp": ""
},
{
"department": "Physics",
"id": "pankajm@bu.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Bioengineering",
"id": "kchuang@stanford.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Physics",
"id": "schmit@phys.ksu.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "aparna@brandeis.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "modsps@rit.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Chemistry",
"id": "vhuxter@email.arizona.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
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"id": "kondev@brandeis.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Biology",
"id": "nihal.altan-bonnet@nih.gov",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "emszcollins@gmail.com",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "jsbiteen@umich.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "tjha@illinois.edu",
"seniority": "sr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "cox@physics.ucdavis.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Bioengineering",
"id": "ashokp@engr.colostate.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Applied Physics",
"id": "jonuchic@ucsd.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Biology",
"id": "laub@mit.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Biochemistry & Molecular Biology",
"id": "golding@bcm.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Physics",
"id": "icisse@MIT.EDU",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "randerson@sandiego.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "mcm@physics.syr.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Physics - Cellular Biophysics",
"id": "gardel@uchicago.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "tg2@princeton.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "jengland@mit.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Theoretical Physics",
"id": "Kingshuk.Ghosh@du.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "spresse@iupui.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Biology",
"id": "Kenneth.Dill@stonybrook.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Chemistry",
"id": "gruebele@scs.uiuc.edu",
"seniority": "sr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "ddube@bowdoin.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Mechanical Engineering",
"id": "valentine@engineering.ucsb.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Rowland Institute",
"id": "sanchez@rowland.harvard.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Biology",
"id": "brian.hammer@biology.gatech.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "banu.ozkan@asu.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Chemistry",
"id": "scott.brewer@fandm.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "seppe@illinois.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Quantitative Biology",
"id": "jkinney@cshl.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Biophysics",
"id": "sveatch@umich.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "clonderg@haverford.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "rossj@physics.umass.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Computational Biology",
"id": "xavierj@mskcc.org",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Applied Physics",
"id": "dsfisher@stanford.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Chemistry",
"id": "mcotten@hamilton.edu",
"seniority": "sr",
"theory_or_exp": "e"
},
{
"department": "Systems Biology",
"id": "gabor.balazsi@stonybrook.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "hgoodson@nd.edu",
"seniority": "sr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "raghu@uoregon.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics & Molecular Biology",
"id": "jun@ucsd.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Molecular Biology",
"id": "gsuel@ucsd.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Chemistry",
"id": "CEGELSKI@STANFORD.EDU",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "System Biologist / Immunologist ",
"id": "altanbog@mskcc.org",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Systems Biology",
"id": "egarner@fas.harvard.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Genetics",
"id": "churchman@genetics.med.harvard.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Physics",
"id": "gore@mit.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Genetics & Cell Biology",
"id": "mrust@uchicago.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Kavli Institute of Theoretical Physics",
"id": "shraiman@kitp.ucsb.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Molecular & Human Genetics",
"id": "Chenghang.Zong@bcm.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "agopinathan@ucmerced.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "sunb@physics.oregonstate.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "mmanning@syr.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "Dinah.Loerke@du.edu",
"seniority": "jr",
"theory_or_exp": "b"
},
{
"department": "Physics",
"id": "daltman@willamette.edu",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "arielamir@physics.harvard.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Chemistry",
"id": "hernandez@gatech.edu",
"seniority": "sr",
"theory_or_exp": "t"
},
{
"department": "Physics",
"id": "korolev@bu.edu",
"seniority": "jr",
"theory_or_exp": "t"
},
{
"department": "Biological Engineering",
"id": "pblainey@broadinstitute.org",
"seniority": "jr",
"theory_or_exp": "e"
},
{
"department": "Physics",
"id": "motter@northwestern.edu",
"seniority": "jr",
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}
]
}
Raw
style.css
.node {
stroke: #fff;
stroke-width: 1.5px;
}
.link {
stroke: #999;
stroke-opacity: .6;
}
Raw
viz.js
var width = 960,
height = 500;
//var color = d3.scale.category20();
var color = d3.scale.ordinal()
.domain(["t", "b", "e"])
.range(colorbrewer.RdYlBu[3]);
var force = d3.layout.force()
.charge(-250)
.linkDistance(50)
.size([width, height]);
var svg = d3.select("body").append("svg")
.attr("width", width)
.attr("height", height);
function get_key(link) {
var key = link.source + '-' + link.target;
if (link.source > link.target) {
key = link.target + '-' + link.source;
}
return key;
}
d3.json("pre-conference.json", function(error, graph) {
console.log(color("t"), color("b"), color("e"));
// get the list of sr people so we can omit them
var seniors = [];
graph.nodes.forEach(function (node, i) {
seniors.push(node.seniority==='sr');
// also exclude person for which we don't have information
if (! node.theory_or_exp) {
seniors[seniors.length-1] = true;
}
})
// filter to only include links in the graph that are bidirectional and
// between jr people to make this less of a total mess
var counter = {}, weights = {};
graph.links.forEach(function (link) {
var key = get_key(link);
if (counter[key] === undefined) {
counter[key] = 0;
weights[key] = 0;
}
if (! (seniors[link.source] || seniors[link.target])) {
counter[key] += 1;
weights[key] += link.weight;
}
});
graph._links = [];
graph.links.forEach(function (link) {
var key = get_key(link);
if (counter[key] === 2) { // && weights[key]>2) { // also filter by weight?
link.weight = weights[key] / 2;
graph._links.push(link)
counter[key] = 0;
}
})
graph.links = graph._links;
force.nodes(graph.nodes)
.links(graph.links)
.start();
var link = svg.selectAll(".link")
.data(graph.links)
.enter().append("line")
.attr("class", "link")
.style("stroke-width", function(d) { return d.weight; });
var node = svg.selectAll(".node")
.data(graph.nodes)
.enter().append("circle")
.attr("class", "node")
.attr("r", function (d) {if (d.seniority==='jr') return 5; return 0;})
.style("fill", function(d) { return color(d.theory_or_exp); })
.call(force.drag);
node.append("title")
.text(function(d) { return d.id; });
force.on("tick", function() {
link.attr("x1", function(d) { return d.source.x; })
.attr("y1", function(d) { return d.source.y; })
.attr("x2", function(d) { return d.target.x; })
.attr("y2", function(d) { return d.target.y; });
node.attr("cx", function(d) { return d.x; })
.attr("cy", function(d) { return d.y; });
});
});
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