Author: kono
Date: 2010-09-10 09:45:00 -0700 (Fri, 10 Sep 2010)
New Revision: 21785
Added:
new_cytoscape_website/trunk/images/people/jm1.jpg
new_cytoscape_website/trunk/images/people/trey.png
new_cytoscape_website/trunk/images/screenshots/kegg1.png
new_cytoscape_website/trunk/images/screenshots/rdf1.png
new_cytoscape_website/trunk/images/screenshots/twitterVisualization1.png
new_cytoscape_website/trunk/images/screenshots/visualMapping1.png
new_cytoscape_website/trunk/images/top_slides/cytoscapeDesktop1.png
new_cytoscape_website/trunk/images/top_slides/pdbCustomGraphics.png
new_cytoscape_website/trunk/images/top_slides/pieChart.png
Modified:
new_cytoscape_website/trunk/css/main.css
new_cytoscape_website/trunk/css/navigation.css
new_cytoscape_website/trunk/development_team.html
new_cytoscape_website/trunk/index.html
new_cytoscape_website/trunk/js/footer.js
new_cytoscape_website/trunk/news.html
new_cytoscape_website/trunk/what_is_cytoscape.html
new_cytoscape_website/trunk/who_is_using.html
Log:
Updated based on Trey's requests.
Modified: new_cytoscape_website/trunk/css/main.css
===================================================================
--- new_cytoscape_website/trunk/css/main.css 2010-09-10 00:44:24 UTC (rev
21784)
+++ new_cytoscape_website/trunk/css/main.css 2010-09-10 16:45:00 UTC (rev
21785)
@@ -52,7 +52,7 @@
#header {
color:#fff;
height:100px;
- margin: 3px auto;
+ margin: 3px auto 0px auto;
padding: 10px 10px 5px 10px;
background-image:url(../images/cytoscape_title.png);
line-height: 100%;
@@ -94,6 +94,11 @@
background:#F2F2F2;
}
+#footer p {
+ font-size:10px;
+ margin: 5px 0 5px 0;
+}
+
/* general content box: Full width */
.blockfull {
display:block;
@@ -217,11 +222,11 @@
}
.introbox .button {
- margin:20px auto;
+ margin:5px auto;
+ width:225px;
padding:auto 5px !important;
- float:left;
- font-size:14px !important;
- line-height:20px !important;
+ font-size:18px !important;
+ line-height:22px !important;
}
/* News Feed box by Tumblr */
@@ -244,7 +249,6 @@
.news h3, .news h4, .news h5, .news p {
margin:15px 20px;
-
}
.news .entry img {
@@ -256,6 +260,7 @@
padding:5px 10px;
}
+
/* Accordion box */
.startnav {
float:right;
@@ -266,6 +271,10 @@
margin: 15px 15px;
}
+
+
+
+
/* Link icons for social media */
#linkIcons li {
margin:60px 0px 0px 0px;
@@ -286,10 +295,11 @@
}
.feed {
- width:940px !important;
+ width:370px !important;
height:auto;
- float:left;
- margin-top:0;
+ margin-top:10px;
+ margin-bottom:10px;
+ margin-left:10px;
}
.feed h2 {
@@ -329,7 +339,6 @@
#tumblr {
margin: 0px auto 10px 0;
padding: 0 0;
-
}
#tumblr #posts {
@@ -342,7 +351,6 @@
background:#fff;
display:block;
width:100%;
-
padding:15px 0;
margin:0 0 10px 0;
border-radius: 0.7em;
@@ -353,8 +361,6 @@
border:solid 1px #666;
}
-
-
#tumblr img, #tumblr #bottom {
display:block;
margin: 10px auto;
@@ -441,7 +447,7 @@
background: #f1f1f1;
}
-#downleft, #downright{
+#downleft, #downright {
height:510px;
}
@@ -450,7 +456,6 @@
line-height:30px;
}
-
#download ul li {
font-size:14px;
padding-left: 70px;
@@ -497,7 +502,7 @@
#people .blockfull .column {
width:33%;
- height:520px;
+ height:360px;
position:relative;
float:left;
}
@@ -552,7 +557,7 @@
}
#community h1, #community h2, #community h3, #documents h1, #documents h2,
#documents h3, #documents h4 {
- margin:10px 15px;
+ margin:15px 15px 15px 10px ;
}
#community .blockfull, #documents .blockfull {
@@ -607,7 +612,7 @@
}
#community .mailinglist {
- height:200px;
+ height:230px;
padding:5px 15px;
}
@@ -658,7 +663,7 @@
}
#documents .blockleft, #documents .blockright {
- height:320px;
+ height:340px;
}
#documents .blockleft img, #documents .blockright img {
@@ -686,3 +691,12 @@
background: -moz-linear-gradient(top, #f9f9f9, #dadada); /* for firefox
3.6+ */
border: solid 1px #9d9d9d;
}
+
+.guide p {
+ margin:20px auto;
+}
+
+.guide .button {
+ margin:5px auto;
+ float:right;
+}
Modified: new_cytoscape_website/trunk/css/navigation.css
===================================================================
--- new_cytoscape_website/trunk/css/navigation.css 2010-09-10 00:44:24 UTC
(rev 21784)
+++ new_cytoscape_website/trunk/css/navigation.css 2010-09-10 16:45:00 UTC
(rev 21785)
@@ -10,7 +10,7 @@
#nav {
z-index:1000;
- margin:10px 0 10px 0;
+ margin:3px 0 4px 0;
height:36px;
padding: 0px 6px 0;
line-height: 100%;
Modified: new_cytoscape_website/trunk/development_team.html
===================================================================
--- new_cytoscape_website/trunk/development_team.html 2010-09-10 00:44:24 UTC
(rev 21784)
+++ new_cytoscape_website/trunk/development_team.html 2010-09-10 16:45:00 UTC
(rev 21785)
@@ -17,24 +17,22 @@
<div class="blockfull">
<h1>Cytoscape Consortium</h1>
<div class="column">
- <div class="institute"><a href=""><img
src="images/logo/agilent_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/isb_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/unilever_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.home.agilent.com";><img
src="images/logo/agilent_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.utoronto.ca/";><img
src="images/logo/toronto_logo_web.png" /></a></div>
</div>
<div class="column">
- <div class="institute"><a href=""><img
src="images/logo/ucsf_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/pasteur_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/toronto_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.ucsf.edu/";><img
src="images/logo/ucsf_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.pasteur.fr";><img
src="images/logo/pasteur_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.mskcc.org";><img
src="images/logo/mskcc_logo_web.png" /></a></div>
</div>
<div class="column">
- <div class="institute"><a href=""><img
src="images/logo/ucsd_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/ncibi_logo_web.png" /></a></div>
- <div class="institute"><a href=""><img
src="images/logo/mskcc_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.ucsd.edu/";><img
src="images/logo/ucsd_logo_web.png" /></a></div>
+ <div class="institute"><a href="http://www.systemsbiology.org/";><img
src="images/logo/isb_logo_web.png" /></a></div>
</div>
</div>
<div class="blockfull">
<h1>Board of Directors</h1>
- <div class="person"> <a href="http://chianti.ucsd.edu/idekerlab/";> <img
src="images/people/trey.jpg"></img>
+ <div class="person"> <a
href="http://chianti.ucsd.edu/idekerlab/pages/ideker.html";> <img
src="images/people/trey.png"></img>
<div class="name">Trey Ideker</div>
</a> </div>
<div class="person"> <a
href="http://cbio.mskcc.org/people/info/chris_sander.html";><img
src="images/people/chris_s.jpg"></img>
@@ -47,10 +45,7 @@
<div class="person"><a
href="http://www.pasteur.fr/recherche/unites/Biolsys/benno/";><img
src="images/people/benno.jpg"></img>
<div class="name">Benno Schwikowski</div>
</a></div>
- <div class="person"><a href="http://www.unilever.com/";><img
src="images/people/yeyejide.jpg"></img>
- <div class="name">Yeyejide Adeleye</div>
- </a></div>
- <div class="person"><a
href="http://www.agilent.com/labs/research/mtl/projects/sysbio.html";><img
src="images/people/annette.jpg"></img>
+ <div class="person"><a href="http://www.home.agilent.com";><img
src="images/people/annette.jpg"></img>
<div class="name">Annette Adler</div>
</a> </div>
<div class="person"><a href="http://baderlab.org/";><img
src="images/people/gary.jpg"></img>
@@ -62,7 +57,7 @@
<div class="person"><a
href="http://www.systemsbiology.org/Scientists_and_Research/Faculty_Groups/Shmulevich_Group";><img
src="images/people/ilya.jpg"></img>
<div class="name">Ilya Schmulevich</div>
</a> </div>
- <div class="person"><a href="http://www.systemsbiology.org/";><img
src="images/people/NO_PHOTO_YET.jpg"></img>
+ <div class="person"><a href=""><img
src="images/people/NO_PHOTO_YET.jpg"></img>
<div class="name">Louis Coffman</div>
</a> </div>
</div>
@@ -123,10 +118,16 @@
</a></div>
</div>
<div class="group">
+ <h3>University of Toronto (Ontario, Canada)</h3>
+ <div class="person"> <a href="http://baderlab.org/";><img
src="images/people/jm1.jpg"></img>
+ <div class="name">Jason Montojo</div>
+ </a></div>
+ <div class="person"> <a href="http://baderlab.org/";><img
src="images/people/NO_PHOTO_YET.jpg"></img>
+ <div class="name"></div>
+ </a></div>
+ </div>
+ <div class="group">
<h3>Other Institutes</h3>
- <div class="person"> <a href="#"><img
src="images/people/mathieu.jpg"></img>
- <div class="name">Mathieu Michaud</div>
- </a></div>
<div class="person"> <a href="#"><img
src="images/people/piet.jpg"></img>
<div class="name">Piet Molenaar</div>
</a></div>
@@ -159,7 +160,7 @@
</ul>
</div>
<div class="blockfull">
- <h2>Past Developers and Directors</h2>
+ <h2>Past Developers, Directors, and Funding Agencies</h2>
<ul>
<li>Chris Workman</li>
<li>Aditya Vailaya</li>
@@ -178,6 +179,9 @@
<li>Paul Shannon</li>
<li>Jonathan Wang</li>
<li>Robert Sheridan</li>
+ <li>Yeyejide Adeleye</li>
+ <li>Mathieu Michaud</li>
+ <li>
</ul>
</div>
</div>
Added: new_cytoscape_website/trunk/images/people/jm1.jpg
===================================================================
(Binary files differ)
Property changes on: new_cytoscape_website/trunk/images/people/jm1.jpg
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/people/trey.png
===================================================================
(Binary files differ)
Property changes on: new_cytoscape_website/trunk/images/people/trey.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/screenshots/kegg1.png
===================================================================
(Binary files differ)
Property changes on: new_cytoscape_website/trunk/images/screenshots/kegg1.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/screenshots/rdf1.png
===================================================================
(Binary files differ)
Property changes on: new_cytoscape_website/trunk/images/screenshots/rdf1.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/screenshots/twitterVisualization1.png
===================================================================
(Binary files differ)
Property changes on:
new_cytoscape_website/trunk/images/screenshots/twitterVisualization1.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/screenshots/visualMapping1.png
===================================================================
(Binary files differ)
Property changes on:
new_cytoscape_website/trunk/images/screenshots/visualMapping1.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/top_slides/cytoscapeDesktop1.png
===================================================================
(Binary files differ)
Property changes on:
new_cytoscape_website/trunk/images/top_slides/cytoscapeDesktop1.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/top_slides/pdbCustomGraphics.png
===================================================================
(Binary files differ)
Property changes on:
new_cytoscape_website/trunk/images/top_slides/pdbCustomGraphics.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Added: new_cytoscape_website/trunk/images/top_slides/pieChart.png
===================================================================
(Binary files differ)
Property changes on: new_cytoscape_website/trunk/images/top_slides/pieChart.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Modified: new_cytoscape_website/trunk/index.html
===================================================================
--- new_cytoscape_website/trunk/index.html 2010-09-10 00:44:24 UTC (rev
21784)
+++ new_cytoscape_website/trunk/index.html 2010-09-10 16:45:00 UTC (rev
21785)
@@ -2,6 +2,12 @@
<html xmlns="http://www.w3.org/1999/xhtml";>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+ <meta name="keywords" content="Cytoscape, visualization, interaction
network,
+ software, genetic, gene, expression, protein interaction,
graph, bioinformatics,
+ computational biology, Whitehead Institute, Institute for
Systems Biology,
+ microarray analysis, clustering, pathways, integration,
algorithm,
+ statistical analysis, gene regulation, complex networks, social
networks"/>
+
<title>An Open Source Platform for Complex-Network Analysis and
Visualization</title>
<!-- Main CSS for all pages. -->
@@ -57,96 +63,210 @@
<body>
<div id="container">
<script src="js/header.js"></script>
-
<div id="slides" class="galleryview">
+
+ <div class="panel"> <a name="desc-00" title="Cytoscape 2.8.0"
href="images/top_slides/cytoscapeDesktop1.png"> <img
src="images/top_slides/cytoscapeDesktop1.png" width="700px" /> </a>
+ <div class="panel-overlay">
+ <h2>Cytoscape 2.8.0</h2>
+ <div id="desc-00">Cytoscape 2.8.0 supports custom graphics,
functions, and commands.</div>
+ </div>
+ </div>
+
<div class="panel"> <a name="desc-01" title="Module Finders"
href="images/top_slides/network1.png"> <img
src="images/top_slides/network1.png" width="700px" /> </a>
<div class="panel-overlay">
- <h2>Module Finders</h2>
- <div id="desc-01">Module Finders. Click image to view full-size
image</div>
+ <h2>Module Finding</h2>
+ <div id="desc-01">Cytoscape supports nested network structure.
You can easily visualize relationship of modules in the network.</div>
</div>
</div>
<div class="panel"> <a name="desc-02" title="Human Interactome"
href="images/top_slides/humanInteractome1.png"> <img
src="images/top_slides/humanInteractome1.png" width="700px"/> </a>
<div class="panel-overlay">
- <h2>Human Interactome</h2>
- <div id="desc-02">Test 2. Click image to view full-size
image</div>
+ <h2>Large Scale Data Visualization</h2>
+ <div id="desc-02">With Cytoscape and modern workstations, you can
handle large scale networks such as human interactome or social network
datasets.</div>
</div>
</div>
- <div class="panel"> <a name="desc-03" title="Custom Graphics"
href="images/top_slides/customGraphics1.png"> <img
src="images/top_slides/customGraphics1.png" width="700px" /> </a>
+ <div class="panel"> <a name="desc-03" title="Custom Graphics support"
href="images/top_slides/pdbCustomGraphics.png"> <img
src="images/top_slides/pdbCustomGraphics.png" width="700px" /> </a>
<div class="panel-overlay">
- <h2>Custom Graphics Mapping</h2>
- <div id="desc-03">Custom Graphics function. Click image for full
size view.</div>
+ <h2>Custom Graphics 1</h2>
+ <div id="desc-03">From Cytoscape 2.8.0, you can map up to nine
images per node.</div>
</div>
</div>
+ <div class="panel"> <a name="desc-04" title="Chart Mapping"
href="images/top_slides/pieChart.png"> <img
src="images/top_slides/pieChart.png" width="700px" /> </a>
+ <div class="panel-overlay">
+ <h2>Custom Graphics 2</h2>
+ <div id="desc-03">Mapping charts to node is one of the most common
usecase of Custom Graphics. You can map charts generated web services such as
Google Chart API.</div>
+ </div>
+ </div>
+
<ul class="filmstrip">
- <li><img src="images/top_slides/network1.png" width="70" height="40"
alt="Module Finders" title="Module Finders" /></li>
- <li><img src="images/top_slides/humanInteractome1.png" width="70"
height="40" alt="Human Interactome" title="Human Interactome" /></li>
- <li><img src="images/top_slides/customGraphics1.png" width="70"
height="40" alt="Custom Graphics" title="Custom Graphics" /></li>
+ <li><img src="images/top_slides/cytoscapeDesktop1.png"
width="70" height="40" alt="Cytoscape 2.8.0" title="Cytoscape 2.8.0" /></li>
+ <li><img src="images/top_slides/network1.png" width="70"
height="40" alt="Module Finders" title="Module Finders" /></li>
+ <li><img src="images/top_slides/humanInteractome1.png"
width="70" height="40" alt="Human Interactome" title="Human Interactome" /></li>
+ <li><img src="images/top_slides/pdbCustomGraphics.png"
width="70" height="40" alt="Custom Graphics" title="Custom Graphics" /></li>
+ <li><img src="images/top_slides/pieChart.png" width="70"
height="40" alt="Custom Graphics" title="Custom Graphics" /></li>
</ul>
</div>
<div class="introbox">
<h3>Network Data Integration, Analysis, and Visualization in a Box</h3>
- <p> Cytoscape is an open source software platform for visualizing
complex-networks and integrating these networks with any type of attribute
data. A lot of <a href="plugins.html">plugins</a> are available for various
kinds of problem domains, especially for bioinformatics and systems biology.
</p>
+ <p> Cytoscape is an open source software platform for visualizing
complex-networks and integrating these with any type of attribute data. A lot
of <a href="plugins.html">plugins</a> are available for various kinds of
problem domains, including bioinformatics, social network analysis, and
semantic web. </p>
<p> <a href="what_is_cytoscape.html">Learn More...</a> </p>
+
<a href="download.html">
- <button class="button blue">Download Cytoscape v2.7.0</button>
+ <button class="button medium blue">Download Cytoscape
Now</button>
</a>
- <ul>
- <li><a href="#">Release Note</a></li>
- <li><a href="#">System Requirments</a></li>
- </ul>
+
+ <a href="#start">
+ <button class="button medium green">Where to Start?</button>
+ </a>
+
</div>
+ <!-- Support Cytoscape -->
+ <div class="blockfull">
+ <h2>How to Cite Cytoscape</h2>
+ <p><strong>Cytoscape project needs your support!</strong> Please cite
either of the following papers when you use Cytoscape in your publications. It
is very important to make the Cytoscape project sustainable.</p>
+ <div class="pub">
+ <div class="author"> Melissa S Cline, Michael Smoot, Ethan Cerami,
+ Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas,
Iliana
+ Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers,
Ruth
+ Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere,
John
+ Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya
Vailaya,
+ Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin
+ Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J
Warner,
+ Trey Ideker & Gary D Bader</div>
+ <div class="title"> Integration of biological networks and gene
expression data using Cytoscape </div>
+ <div class="source"> Nature Protocols 2, 2366 - 2382 (2007)
Published online: 27 September
+ 2007 | doi:10.1038/nprot.2007.324 </div>
+ <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947979";> [PubMed
+ entry]</a> </div>
+ <div class="pub">
+ <div class="author">Shannon P, Markiel A, Ozier O, Baliga NS, Wang
+ JT, Ramage D, Amin N, Schwikowski B, Ideker T. </div>
+ <div class="title">Cytoscape: a software environment for integrated
models of
+ biomolecular interaction networks.</div>
+ <div class="source"> Genome Research 2003 Nov; 13(11):2498-504 </div>
+ <a href="http://www.genome.org/cgi/content/full/13/11/2498";>
[Abstract] </a> <a href="http://www.genome.org/cgi/reprint/13/11/2498";> [PDF]
</a> <a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgicmd=Retrieve&db=PubMed&list_uids=14597658&dopt=Abstract";>
[PubMed entry]</a> </div>
+ </div>
+
<!-- News -->
<div class="news">
- <iframe id="frame" src="news.html" height="545" width="428"
frameborder="0" scrolling="auto">
- </iframe>
+ <iframe id="frame" src="news.html" height="545" width="428"
frameborder="0" scrolling="auto"> </iframe>
</div>
- <div class="startnav">
+ <!-- Where to start -->
+ <div class="startnav" id="start">
<h2>Where to Start?</h2>
<div class="guide">
- <h1><a href="#">Biologists</a></h1>
+ <h1><a href="#">Biology</a></h1>
<div>
- <h4>With Cytoscape, you can...</h4>
+ <p>Cytoscape was developed for biological researches, and it
supports a lot of usecases including:</p>
<ul>
<li>Load Protein-Protein interaction data sets in various
formats</li>
<li>Integrate annotation data, such as Gene Ontology, to the
network</li>
<li>Analyze your network with plugins</li>
+ <li>Visualize and analyze human-curated pathway datasets such as
KEGG.</li>
</ul>
- <a href="http://www.cytoscape.org/"; target="_new">
- <button class="button blue">Quick Start Guide</button>
- </a> </div>
- <h1><a href="#">Social Scientists</a></h1>
+
+ <p>
+ <div class="panel">
+ <a name="vizmap" title="Visual Mapping"
href="images/screenshots/visualMapping1.png">
+ <img src="images/screenshots/visualMapping1.png"
width="420px"/>
+ </a>
+ </div>
+ </p>
+
+ <p>
+ <div class="panel">
+ <a name="kegg" title="KEGG Data Import"
href="images/screenshots/kegg1.png">
+ <img src="images/screenshots/kegg1.png" width="420px"/>
+ </a>
+ </div>
+ </p>
+
+ <p>
+ <a href="http://cytoscape.wodaklab.org/wiki/Presentations";
target="_new">
+ <button class="button green">Online Tutorial</button>
+ </a>
+ </p>
+ </div>
+
+ <h1><a href="#">Social Science</a></h1>
<div>
+ <p>You can analyze and visualize network of people
interactively on Cytoscape:</p>
<ul>
- <li>Build Cytoscape from source code</li>
- <li>Develop a plugin</li>
- <li>Learn Cytoscape API</li>
+ <li>Import your network data from spreadsheet</li>
+ <li>Write your own web crawler in scripting languages within
Cytoscape</li>
+ <li>Calculate network statistics using plugins</li>
</ul>
- <a href="http://www.cytoscape.org/"; target="_new">
- <button class="button gray">Developers Tutorial</button>
- </a> </div>
- <h1><a href="#">Computer Scientists</a></h1>
+
+ <div class="panel">
+ <a name="twitter" title="Twitter Social Network Visualization"
href="images/screenshots/twitterVisualization1.png">
+ <img src="images/screenshots/twitterVisualization1.png"
width="420px"/>
+ </a>
+ </div>
+ <p>
+ <a href="http://cytoscape.wodaklab.org/wiki/Presentations";
target="_new">
+ <button class="button green">Online Tutorial</button>
+ </a> </p>
+
+ </div>
+ <h1><a href="#">Semantic Web</a></h1>
<div>
+ Since semantic web data sets are esentially graphs, you can use
Cytoscape as a workbench for RDF data:
<ul>
- <li>List item one</li>
- <li>List item two</li>
- <li>List item three</li>
+ <li>Load and visualize RDF</li>
+ <li>Reasoning by plugins</li>
+ <li>Use as a platform to develop your own semantic web
applicaitons</li>
</ul>
+
+ <p>
+ <div class="panel">
+ <a name="rdf" title="RDF Data Visualization"
href="images/screenshots/rdf1.png">
+ <img src="images/screenshots/rdf1.png" width="420px"/>
+ </a>
+
+ </div>
+ </p>
+ <p>
+ <a href="http://cytoscape.wodaklab.org/wiki/Presentations";
target="_new">
+ <button class="button green">Online Tutorial</button>
+ </a>
+ </p>
+
</div>
- <h1><a href="#">Plugin Developers</a></h1>
+
+ <h1><a href="#">General Complex Network Analysis</a></h1>
<div>
- <p>Plugin Developer start guide</p>
+ <p>Cytoscape is a domain-independent platform, and you can use
it as a powerful tool for complex network analysis in general.</p>
+ <ul>
+ <li>Calculate statistics for networks</li>
+ <li>Import data files from other network analysis tools such as
igraph, pajek, or graphviz (by standard file formats like GML)</li>
+ </ul>
+
+ <p>
+ <a href="http://cytoscape.wodaklab.org/wiki/Presentations";
target="_new">
+ <button class="button green">Online Tutorial</button>
+ </a>
+ </p>
</div>
+ <h1><a href="#">Plugin Development</a></h1>
+ <div>
+ <p>Cytoscape is an expandable platform. You can write your own
plugins to implement new features for Cytoscape.</p>
+
+ <ul>
+ <li>Build Cytoscape from source code</li>
+ <li>Develop a plugin</li>
+ <li>Cytoscape API</li>
+ </ul>
+
+ <p>
+ <a
href="http://cytoscape.wodaklab.org/wiki/cytoscape_developer_tutorial";
target="_new">
+ <button class="button gray">Plugin Developers Tutorial</button>
+ </a>
+ </p>
+ </div>
</div>
</div>
- <div class="feed">
- <h2>Aggregated Cytoscape News by <a
href="http://friendfeed.com/cytoscape";>FriendFeed</a></h2>
- <script type="text/javascript"
src="http://friendfeed.com/embed/widget/cytoscape?v=3&num=10&hide_logo=1&width=900";></script>
- <noscript>
- <a href="http://friendfeed.com/cytoscape";><img alt="View my
FriendFeed" style="border:none;"
src="http://friendfeed.com/embed/widget/cytoscape?v=3&num=10&hide_logo=1&width=900&format=png"/></a>
- </noscript>
- </div>
+
<script src="js/footer.js"></script>
</div>
</body>
Modified: new_cytoscape_website/trunk/js/footer.js
===================================================================
--- new_cytoscape_website/trunk/js/footer.js 2010-09-10 00:44:24 UTC (rev
21784)
+++ new_cytoscape_website/trunk/js/footer.js 2010-09-10 16:45:00 UTC (rev
21785)
@@ -1,2 +1,6 @@
// Footer
-document.write('<div id="footer">©2001-2010 Cytoscape Consotrium</div>');
\ No newline at end of file
+document.write('<div id="footer"><p>Funding for Cytoscape is provided by a
federal grant from the U.S. ' +
+ '<a href="http://www.nigms.nih.gov";>National Institute of General
Medical Sciences (NIGMS)</a> ' +
+ 'of the <a href="http://www.nih.gov";>National Institutes of Health
(NIH)</a> under award ' +
+ 'number GM070743-01 and the U.S. <a href="http://www.nsf.gov";>National
Science Foundation ' +
+ '(NSF) </a>.</p><p>©2001-2010 Cytoscape Consotrium</p></div>');
Modified: new_cytoscape_website/trunk/news.html
===================================================================
--- new_cytoscape_website/trunk/news.html 2010-09-10 00:44:24 UTC (rev
21784)
+++ new_cytoscape_website/trunk/news.html 2010-09-10 16:45:00 UTC (rev
21785)
@@ -26,15 +26,23 @@
padding:2px 15px;
background:#999;
}
-
-
</style>
</head>
<body>
<div class="frame">
- <h3>Latest News <a href="http://cytoscape.tumblr.com/";
target="_top"><img src="images/icon/tumblr.png"/></a></h3>
+
+ <h3>Featured Cytoscape News <a href="http://cytoscape.tumblr.com/";
target="_top"><img src="images/icon/tumblr.png"/></a></h3>
+
<script type="text/javascript"
src="http://cytoscape.tumblr.com/api/read/json";></script>
<script type="text/javascript" src="js/tumblr_feed.js"></script>
</div>
+
+<div class="feed">
+ <h2>Aggregated News Feed by <a
href="http://friendfeed.com/cytoscape";>FriendFeed</a></h2>
+ <script type="text/javascript"
src="http://friendfeed.com/embed/widget/cytoscape?v=3&num=10&hide_logo=1&width=280";></script>
+ <noscript>
+ <a href="http://friendfeed.com/cytoscape";><img alt="View my FriendFeed"
style="border:none;"
src="http://friendfeed.com/embed/widget/cytoscape?v=3&num=10&hide_logo=1&width=900&format=png"/></a>
+ </noscript>
+</div>
</body>
</html>
\ No newline at end of file
Modified: new_cytoscape_website/trunk/what_is_cytoscape.html
===================================================================
--- new_cytoscape_website/trunk/what_is_cytoscape.html 2010-09-10 00:44:24 UTC
(rev 21784)
+++ new_cytoscape_website/trunk/what_is_cytoscape.html 2010-09-10 16:45:00 UTC
(rev 21785)
@@ -146,8 +146,8 @@
3.0, please visit <a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_3.0";>developer's
wiki page</a>. </p>
</div>
+ <script src="js/footer.js"></script>
</div>
- <script src="js/footer.js"></script>
-</div>
+
</body>
</html>
Modified: new_cytoscape_website/trunk/who_is_using.html
===================================================================
--- new_cytoscape_website/trunk/who_is_using.html 2010-09-10 00:44:24 UTC
(rev 21784)
+++ new_cytoscape_website/trunk/who_is_using.html 2010-09-10 16:45:00 UTC
(rev 21785)
@@ -15,12 +15,16 @@
<script src="js/header.js"></script>
<div id="documents">
<div class="blockleft">
- <h1>Who is Using Cytoscape?</h1>
- <p>Cytoscae is used by ....</p>
+ <h1>Featured Publications</h1>
+ <p>
+ <h2>Cell</h2>
+ <h2>Nature</h2>
+ <h2>Science</h2>
+ </p>
</div>
<div class="blockright">
<h1>Research Using Cytoscape</h1>
- <p><strong>As of June 2010, 501 publications are citing <a
+ <p><strong>Many publications are citing <a
href="http://www.genome.org/cgi/content/full/13/11/2498";>Shannon et
al. (2003)</a>.</strong></p>
<ul id="paragraph">
@@ -33,39 +37,13 @@
<li><a
href="http://highwire.stanford.edu/cgi/searchresults?fulltext=cytoscape&andorexactfulltext=and&author1=&pubdate_year=&volume=&firstpage=&src=hw&searchsubmit=redo&resourcetype=1&search=Search&fmonth=Jan&fyear=1844&tmonth=Jul&tyear=2007&fdatedef=1+January+1844&tdatedef=24+Jul+2007";>
Link to HighWire Press</a></li>
</ul>
- <h3><a href="">Featured Publications</a></h3>
- <h2>Let us know about your publication</h2>
+ <h2>Let us know about your publication!</h2>
<p>If you have a publication which makes use of Cytoscape,
please let us know by sending an email to the <a
href="http://groups-beta.google.com/group/cytoscape-discuss";>
cytoscape-discuss </a> mailing list or use <a href="community.html">other
social media</a>.</p>
</div>
<div class="blockfull">
- <h1>Publication about Cytoscape</h1>
- <p><strong>Please cite any of the following papers when you use
Cytoscape in your publications. It is very important to make Cytoscape project
sustainable!</strong></p>
- <div class="pub">
- <div class="author"> Melissa S Cline, Michael Smoot, Ethan Cerami,
- Allan Kuchinsky, Nerius Landys, Chris Workman, Rowan Christmas,
Iliana
- Avila-Campilo, Michael Creech, Benjamin Gross, Kristina Hanspers,
Ruth
- Isserlin, Ryan Kelley, Sarah Killcoyne, Samad Lotia, Steven Maere,
John
- Morris, Keiichiro Ono, Vuk Pavlovic, Alexander R Pico, Aditya
Vailaya,
- Peng-Liang Wang, Annette Adler, Bruce R Conklin, Leroy Hood, Martin
- Kuiper, Chris Sander, Ilya Schmulevich, Benno Schwikowski, Guy J
Warner,
- Trey Ideker & Gary D Bader</div>
- <div class="title"> Integration of biological networks and gene
expression data using Cytoscape </div>
- <div class="source"> Nature Protocols 2, 2366 - 2382 (2007) Published
online: 27 September
- 2007 | doi:10.1038/nprot.2007.324 </div>
- <a href="http://www.ncbi.nlm.nih.gov/pubmed/17947979";> [PubMed
- entry]</a> </div>
- <div class="pub">
- <div class="author">Shannon P, Markiel A, Ozier O, Baliga NS, Wang
- JT, Ramage D, Amin N, Schwikowski B, Ideker T. </div>
- <div class="title">Cytoscape: a software environment for integrated
models of
- biomolecular interaction networks.</div>
- <div class="source"> Genome Research 2003 Nov; 13(11):2498-504 </div>
- <a href="http://www.genome.org/cgi/content/full/13/11/2498";>
[Abstract] </a> <a href="http://www.genome.org/cgi/reprint/13/11/2498";> [PDF]
</a> <a
href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgicmd=Retrieve&db=PubMed&list_uids=14597658&dopt=Abstract";>
[PubMed entry]</a> </div>
- </div>
- <div class="blockfull">
<h2>Share Your Works!</h2>
<p>If you have Cytoscape-related publications, news/blog articles, or
artworks, share them with others by <a href="community.html">social media
services</a>.</p>
</div>
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