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competitions.html
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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="utf-8">
<title>NRNB: Competitions</title>
<meta name="viewport" content="width=device-width, initial-scale=1.0">
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<div class="belt white">
<div class="container">
<div class="section">
<H3>Competitions</H3>
<p>
NRNB sponsors a variety of competitions for the communities around
network biology tools. These competitions range from app development
to bug bounties. Check out ongoing competitions and the results of
past competitions below. Also feel free to <a
href="mailto:[email protected]">suggest a competition</a>.
</p>
<ul class="nav nav-tabs" id="tabs">
<li class="active"><a href="#c-tab" data-toggle="tab">Launch Challenges</a></li>
<li><a href="#b-tab" data-toggle="tab">Bug Bounty</a></li>
<li><a href="#a-tab" data-toggle="tab">App Development</a></li>
</ul>
<div class="tab-content">
<div class="tab-pane" id="a-tab">
<iframe src="http://apps.cytoscape.org/help/competitions"
width="100%" height="500" frameborder="0" scrolling="auto"></iframe>
</div>
<div class="tab-pane" id="b-tab">
<div class="span8 offset1" style="text-align: center;">
<h4>
<a href="http://cytoscape.org/cy3_bug_bounty.html">February
Bug Bounty 2013</a>
</h4>
<h3>Winners</h3>
<ul style="list-style-type:none">
<b>
<li><big>Giovanni Dall'Olio - 47 points</big></li>
<li>Carol Scalice - 20 points</li>
<li>Anna Dieckmann - 10 points</li>
<li>Dirk - 10 points</li>
<li>Hideo Matsuda - 10 points</li>
<li>Navin Rauniyar - 10 points</li>
<li>Ramayya - 10 points</li>
<li>Savvas Genitsaris - 10 points</li>
<li>Michael Heuer - 8 points</li>
</b>
</ul>
</div>
</div>
<!-- end tab-pane -->
<div class="tab-pane active" id="c-tab">
<h4>
<a href="http://www.cytoscape.org/cy32_launch_challenge.html" target="blank">Cytoscape 3.2 Launch Challenge November 2014</a>
</h4>
<h3>Winners</h3>
<h4>Best example of using Cytoscape for Biology</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span4">
<div class="thumbnail">
<a href="images/kelder.png" target="_blank"><img src="images/kelder.png"
alt="Thomas Kelder" /></a>
<p><b>1st - Thomas Kelder:</b> The Food - Genomics - Disease landscape: A network linking food ingredients with
human disease through underlying molecular interactions.</p>
<div>
</li>
<li class="span4">
<div class="thumbnail">
<a href="images/grimes.png" target="_blank"><img src="images/grimes.png"
alt="Mark Grimes" /></a>
<p><b>2nd - Mark Grimes:</b> Co-cluster correlation network of phoshporylated proteins in
neuroblastoma samples.</p>
</div>
</li>
<li class="span4">
<div class="thumbnail">
<a href="images/kalaiarasan.png" target="_blank"><img src="images/kalaiarasan.png"
alt="Ponnusamy Kalaiarasan" /></a>
<p><b>3rd - Ponnusamy Kalaiarasan:</b> Crosstalk among the modules and hubs in the apoptosis
protein-protein interaction network.</p>
</div>
</li>
</ul>
</div>
<h4>Most novel use of Cytoscape</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span3">
<div class="thumbnail">
<a href="images/vaitsis.png" target="_blank"><img src="images/vaitsis.png"
alt="Christos Vaitsis" /></a>
<p><b>1st - Christos Vaitsis:</b> Mapping of learning outcomes and teaching
methods of one course in an undergraduate medical program.</p>
<div>
</li>
<li class="span3">
<div class="thumbnail">
<a href="images/lima.png" target="_blank"><img src="images/lima.png"
alt="Leandro Lima" /></a>
<p><b>2nd - Leandro Lima:</b> Network of citations constructed using BioPython/PubMed API.</p>
<div>
</li>
<li class="span3">
<div class="thumbnail">
<a href="../images/hallam.png" target="_blank"><img src="images/hallam.png"
alt="Steven Hallam" /></a>
<p><b>3rd - Steven Hallam:</b> The image combines network analysis with single-cell genomic
sequencing to infer metabolic interactions between uncultivated microbes inhabiting salt stratified
Sakinaw Lake.</p>
<div>
</li>
<li class="span3">
<div class="thumbnail">
<a href="images/bell.png" target="_blank"><img src="images/bell.png"
alt="Sherilyn Bell" /></a>
<p><b>3rd - Sherilyn Bell:</b> Using Cytoscape to visualize commercial personal DNA testing data
such as chromosome start and end points, genetic distance, surnames etc. </p>
<div>
</li>
</ul>
</div>
<h4>Most aesthetically pleasing network visualization in Cytoscape</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span4">
<div class="thumbnail">
<a href="images/mosca.png" target="_blank"><img src="images/mosca.png"
alt="Roberto Mosca" /></a>
<p><b>1st - Roberto Mosca:</b> The binary protein-protein interaction landscape
of Escherichia coli. Cytoscape used to generate the networks.</p>
<div>
</li>
<li class="span4">
<div class="thumbnail">
<a href="images/himmelstein.png" target="_blank"><img src="images/himmelstein.png"
alt="Daniel Himmelstein" /></a>
<p><b>2nd - Daniel Himmelstein: </b>Heterogeneous Network Visualization with Cytoscape: An
Integrative Approach to the Genetics of Complex Human Disease.</p>
</div>
</li>
<li class="span4">
<div class="thumbnail">
<a href="images/haider.png" target="_blank"><img src="images/haider.png"
alt="Shazia Haider" /></a>
<p><b>3rd - Shazia Haider:</b> Protein-protein interaction network of apoptosis
regulatory protein coding genes.</p>
</div>
</li>
</ul>
</div>
<h4>Most valuable feature to add to Cytoscape</h4>
<ul style="list-style-type:none">
<li><b>1st - Gordon Bean: </b><p>Provide a “wizard” user interface for simple styles based on common data-driven
visualizations to:
<ul>
<li>Teach the user about basic visual style techniques, such as mapping
discrete colors to discrete node classes and using edge weights to denote edge score or strength.</li>
<li>Ask the user to select attributes that match these criteria (Cytoscape can scan data for each
attribute to loosely determine what attributes might be appropriate - i.e. continuous, discrete,
pass-through, etc).</li>
<li>Automatically bind these attributes to sensible style properties that match the rest of the style
theme.</li>
</ul>
</p></li>
<li><b>2nd - Mark Fortner: </b><p>Use Oracle JavaFX packager for Cytoscape installers, which package the required
version of Java with the application, thus cutting down on the amount of headscratching by users.</p></li>
<li><b>3rd - Srikanth Bezawada: </b><p>
<ul>
<li>Provide case studies on social network data and visualizing transportation networks data.</li>
<li>Implement generic feature to allow an app to be run on a large set of networks
and allow for efficient extraction of app results to compare networks on a large scale.</li>
</ul></p></li>
<li><b>3rd - Thomas Pfau: </b><p>Implement edges with multiple sources and targets to allow for programmatic
representation of more complex interactions. For example, they could be used to represent Gene-Protein-Reaction
relationships without necessitating the introduction of Enzyme subunits.</p></li>
</ul>
</div>
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