-
Notifications
You must be signed in to change notification settings - Fork 30
/
competitions.html
369 lines (320 loc) · 19.4 KB
/
competitions.html
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
<!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">
<meta name="description" content="">
<meta name="author" content="">
<!-- Le styles -->
<link href="assets/css/bootstrap.css" rel="stylesheet">
<link href="assets/css/bootstrap-responsive.css" rel="stylesheet">
<link href="assets/css/nrnb.css" rel="stylesheet">
<!-- HTML5 shim, for IE6-8 support of HTML5 elements -->
<!--[if lt IE 9]>
<script src="http://html5shim.googlecode.com/svn/trunk/html5.js"></script>
<![endif]-->
<!-- Fav and touch icons -->
<link rel="shortcut icon" href="assets/ico/favicon.ico">
<link rel="apple-touch-icon-precomposed" sizes="144x144"
href="assets/ico/apple-touch-icon-144-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="114x114"
href="assets/ico/apple-touch-icon-114-precomposed.png">
<link rel="apple-touch-icon-precomposed" sizes="72x72"
href="assets/ico/apple-touch-icon-72-precomposed.png">
<link rel="apple-touch-icon-precomposed"
href="assets/ico/apple-touch-icon-57-precomposed.png">
<script src="https://www.w3schools.com/lib/w3.js"></script>
</head>
<body>
<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="#e-tab" data-toggle="tab">CyREST</a></li>
<li><a href="#d-tab" data-toggle="tab">Animation</a></li>
<li><a href="#c-tab" data-toggle="tab">Launch Challenges</a></li>
<li><a href="#b-tab" data-toggle="tab">Bug Bounty</a></li>
</ul>
<div class="tab-content">
<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" target="_blank">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" 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>
</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></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>
<!-- end tab-pane -->
<div class="tab-pane" id="d-tab">
<h4>
<a href="http://nrnb.org/competition-2016.html" target="blank">Animation Cytoscape Challenge Feb 2016</a>
</h4>
<h3>Winners</h3>
<h4>Best demonstration of cyAnimator</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span4">
<div class="thumbnail">
<iframe width="360" src="https://www.youtube.com/embed/6nXR4tOWH7k?rel=0 " frameborder="0" allowfullscreen></iframe>
<p><b>1st - Srikanth B. - TieDIE Subnetworks</b><p>The TieDIE algorithm computes a subnetwork of gene and protein interactions that connect genomic perturbations to gene expression changes characteristic of cancer subtypes. The pathways derived using the TieDIE app(algorithm) predict interlinking genes(linker nodes, yellow ones in animation) that may correspond to essential components of cancer signaling and may provide a mechanistic explanation of tumor behavior and suggest subtype-specific drug targets.
</p><p>Subnetworks were generated on a GBM pathway by tuning the size parameter(from a lesser value to desirable size of subnetwork). The idea of the animation of subnetworks using CyAnimator is that it helps biologists for a closer and intuitive inspection of the events.
</p>
</div>
</li>
<li class="span4">
<div class="thumbnail">
<iframe width="360" src="https://www.youtube.com/embed/ozdLo7o-Ya0?rel=0 " frameborder="0" allowfullscreen></iframe>
<p><b>2nd - Adam T. - The Cell Ontology</b><p>I parsed the Cell Type Ontology using the is_a relation for edges, animated the transitions between a few different layouts, and set it to a reggae beat.</p>
</div>
</li>
<li class="span4">
<div class="thumbnail">
<iframe width="360" src="https://www.youtube.com/embed/kSLfL1EacR4?rel=0 " frameborder="0" allowfullscreen></iframe>
<p><b>3rd - Mohammed F. - Heuristic to Travelling Salesman Problem</b><p>CySpanningTree app has a feature that creates Hamiltonian cycle using pre-order traversal. Pre-order traversal on a minimum spanning tree is one of the heuristic solutions for Travelling Salesman Problem. This video created using CyAnimator shows how the app traverses on minimum spanning tree to create a cycle.</p>
</div>
</li>
</ul>
</div>
<h4>Most valuable Cytoscape feature suggestion</h4>
<div class="row-fluid">
<ul>
<li><b>1st - Mark F. - Automatic Node Annotation</b><p>Automatically import node annotations. By default, node annotations like gene ID, gene symbol, UniProt ID, GO terms, PFAM IDs, PDB IDs, ProSite ID, would automatically be imported. (The MyGene.info web service has a pretty comprehensive list of annotations). By default, all linkouts should work. </p></li>
<li><b>2nd - Adam T. - Drop Files</b><p>The first feature I'd like to add to Cytoscape is a drop event handler so that tables, graphs, images and annotations can be dragged in from the desktop.</p></li>
</ul>
</div>
</div>
<!-- end tab-pane -->
<div class="tab-pane active" id="e-tab">
<h4>
<a href="http://nrnb.org/competition-2017.html" target="blank">Cytoscape v3.5 CyREST Challenge June 2017</a>
</h4>
<h3>Winners</h3>
<h4>R</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span6">
<div class="thumbnail">
<a href="images/grimes_cyrest.png" target="_blank"><img src="images/grimes_cyrest.png"
alt="Mark Grimes" /></a>
<p><b>Mark Grimes:</b> Shows how derive multiple results from a valuable biological
network, to compose visualizations and get them into a standalone browser display.</p>
</div>
</li>
<li class="span6">
<div class="thumbnail">
<a href="images/isserlin_cyrest.png" target="_blank"><img src="images/isserlin_cyrest.png"
alt="Ruth Isserlin" /></a>
<p><b>Ruth Isserlin:</b> Extensive cell-cell interaction calculations in Python followed by simple but elegant styling and layout.</p>
</div>
</li>
</ul>
</div>
<h4>Python</h4>
<div class="row-fluid">
<ul class="thumbnails">
<li class="span6">
<div class="thumbnail">
<a href="images/lima_cyrest2.gif" target="_blank"><img src="images/lima_cyrest2.gif"
alt="Leandro Lima" /></a>
<p><b>Leandro Lima:</b> Mined skateboarding data and produced simple visualization.
Shows data acquisition and basic CyREST usage.</p>
</div>
</li>
<li class="span6">
<div class="thumbnail">
<a href="images/konig_cyrest.gif" target="_blank"><img src="images/konig_cyrest.gif"
alt="Matthias König" /></a>
<p><b>Matthias König :</b> Uses SBML and time course simulation to produce animated pathway (using cy3sbml & roadrunner).</p>
</div>
</li>
</ul>
</div>
<!-- end tab-pane -->
</div>
<!-- end tab-content -->
</div>
</div>
</div>
<footer></footer>
<script>
w3.includeHTML();
</script>
<!-- For Navbar -->
<script src="assets/js/jquery-1.11.0.min.js"></script>
<script src="assets/js/bootstrap.min.js"></script>
<script src="assets/js/page_setup.js"></script>
<script>
$(function () {
var activeTab = $('[href=' + location.hash + ']');
activeTab && activeTab.tab('show');
window.scrollTo(0, 0);
});
</script>
<script type="text/javascript">
var _gaq = _gaq || [];
_gaq.push([ '_setAccount', 'UA-19386719-1' ]);
_gaq.push([ '_trackPageview' ]);
(function () {
var ga = document.createElement('script');
ga.type = 'text/javascript';
ga.async = true;
ga.src = ('https:' == document.location.protocol ? 'https://ssl'
: 'http://www')
+ '.google-analytics.com/ga.js';
var s = document.getElementsByTagName('script')[0];
s.parentNode.insertBefore(ga, s);
})();
</script>
</body>
</html>