Author: kono
Date: 2012-10-04 18:00:09 -0700 (Thu, 04 Oct 2012)
New Revision: 30609
Added:
new_cytoscape_website/trunk/images/advanced_search.png
new_cytoscape_website/trunk/images/cytoscape3_logo.png
new_cytoscape_website/trunk/images/cytoscape3_release_beta1.png
new_cytoscape_website/trunk/images/cytoscape_logo_left.png
new_cytoscape_website/trunk/images/edge_bend_editor.png
new_cytoscape_website/trunk/images/edge_bundling.png
new_cytoscape_website/trunk/images/network_annotation.png
new_cytoscape_website/trunk/images/network_collection.png
new_cytoscape_website/trunk/images/slides/appstore.png
new_cytoscape_website/trunk/images/slides/new_features.png
new_cytoscape_website/trunk/images/slides/title0.png
new_cytoscape_website/trunk/images/slides/title3.png
new_cytoscape_website/trunk/images/table_browser.png
new_cytoscape_website/trunk/images/welcome_screen.png
new_cytoscape_website/trunk/release_notes_3_0_0_beta.html
Modified:
new_cytoscape_website/trunk/css/main.css
new_cytoscape_website/trunk/css/slides.css
new_cytoscape_website/trunk/cy3.html
Log:
First draft of Cytoscpae 3 beta1 web page.
Modified: new_cytoscape_website/trunk/css/main.css
===================================================================
--- new_cytoscape_website/trunk/css/main.css 2012-10-04 21:22:22 UTC (rev
30608)
+++ new_cytoscape_website/trunk/css/main.css 2012-10-05 01:00:09 UTC (rev
30609)
@@ -195,6 +195,66 @@
font-size:14px;
}
+/*
+ * For Cytoscape 3 Web pages
+ */
+
+.blockfull3 {
+ display:block;
+ float:left;
+ margin:5px auto;
+ padding:5px 10px 5px 10px;
+ border-radius: 0.5em;
+ -webkit-border-radius: 0.5em;
+ -moz-border-radius: 0.5em;
+ -webkit-box-shadow: 0 1px 3px rgba(0, 0, 0, .4);
+ -moz-box-shadow: 0 1px 3px rgba(0, 0, 0, .4);
+ background: #FFF;
+
+ font: 12px/18px "Lucida Grande", "Lucida Sans Unicode", Helvetica,
Arial, Verdana, sans-serif;
+ color: #333;
+ -webkit-font-smoothing: antialiased;
+}
+
+
+.blockfull3 .section {
+ display:inline-block;
+ margin:10px 10px;
+ padding:5px 10px;
+ line-height:24px;
+}
+
+.blockfull3 p {
+ margin:10px 10px;
+ padding:5px 10px;
+ line-height:30px;
+}
+
+.blockfull3 .textright {
+ padding:5px 10px;
+ line-height:24px;
+}
+
+.blockfull3 .textright ul{
+ float:left;
+ padding-left:50px;
+ margin-bottom:20px;
+ line-height:24px;
+}
+
+.blockfull3 img {
+ border-style:none;
+}
+
+.blockfull3 .leftimg img {
+ float:left;
+}
+
+.blockfull3 .rightimg img {
+ float:right;
+}
+
+
.feeds {
height:400px;
background-color:#fff;
Modified: new_cytoscape_website/trunk/css/slides.css
===================================================================
--- new_cytoscape_website/trunk/css/slides.css 2012-10-04 21:22:22 UTC (rev
30608)
+++ new_cytoscape_website/trunk/css/slides.css 2012-10-05 01:00:09 UTC (rev
30609)
@@ -1,5 +1,5 @@
#container2 {
- font:normal 62.5%/1.5 Helvetica, Arial, sans-serif;
+ font:normal 82.5%/1.5 Helvetica, Arial, sans-serif;
letter-spacing:0;
color:#434343;
background:#ffffff;
@@ -76,11 +76,14 @@
#slides .slide img {
border:2px;
- width:560px;
- height:310px;
float:right;
}
+#slides .slide .fullimg img {
+ border:2px;
+ width:900px;
+}
+
/*
Next/prev buttons
*/
Modified: new_cytoscape_website/trunk/cy3.html
===================================================================
--- new_cytoscape_website/trunk/cy3.html 2012-10-04 21:22:22 UTC (rev
30608)
+++ new_cytoscape_website/trunk/cy3.html 2012-10-05 01:00:09 UTC (rev
30609)
@@ -44,7 +44,7 @@
<script src="js/header.js"></script>
<div id="documents">
- <div class="blockfull">
+ <div class="blockfull3">
<h2>Welcome to Cytoscape 3.0 Beta!</h2>
<div id="container2">
@@ -53,45 +53,60 @@
<div
class="slides_container">
<div
class="slide">
<div class="text">
-
<h1>Simple Workflow</h1>
-
<p>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim
veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo
consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse
cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non
proident.
-
</p>
-
<p>
-
<a href="#5" class="link">Check out the fifth slide ›</a>
-
</p>
+
<h1>Welcome!</h1>
+
<p>
+
Cytoscape 3 is a cleaner and modular new generation of
Cytoscape for future expansions. It
+
benefits both users and developers.
+
</p>
+
</div>
-
<img src="images/slides/title1.png" />
+
<img src="images/slides/title0.png" />
</div>
<div
class="slide">
<div class="text">
-
<h1>Edge Bundling</h1>
-
<p>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim
veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo
consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse
cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non
proident.
-
</p>
-
<p>
-
<a href="#5" class="link">Check out the fifth slide ›</a>
-
</p>
+
<h1>New Features</h1>
+
<p>
+
Cytoscape 3 beta has new features including:
+
<ul>
+
<li>
+
Edge Bundling
+
</li>
+
<li>
+
Network Collections
+
</li>
+
<li>
+
Visual Annotations
+
</li>
+
<li>
+
Advanced Search
+
</li>
+
<li>
+
Improved Data Table Browser
+
</li>
+
</ul>
+
</p>
+
<p>
+
<a href="release_notes_3_0_0_beta.html">Learn more about new
features ›</a>
+
</p>
</div>
-
<img src="images/slides/title2.png" />
+
<img src="images/slides/new_features.png" />
</div>
<div
class="slide">
-
<h1>New Feature: ?</h1>
-
<p>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim
veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo
consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse
cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non
proident.
-
</p>
-
<p>
-
<a href="#5" class="link">Check out the fifth slide ›</a>
-
</p>
+
<div class="text">
+
<h1>New App Store</h1>
+
<p>
+
You can install Apps directly from Cytoscape App Store.
+
</p>
+
<p>
+
<a href="http://apps.cytoscape.org/";>Visit new Cytoscape App
Store ›</a>
+
</p>
+
</div>
+
<img src="images/slides/appstore.png" />
</div>
<div
class="slide">
-
<h1>Develper Info</h1>
-
<p>
-
Lorem ipsum dolor sit amet, consectetur adipisicing elit, sed do
eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad minim
veniam, quis nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo
consequat. Duis aute irure dolor in reprehenderit in voluptate velit esse
cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non
proident.
-
</p>
-
<p>
-
<a href="#4" class="link">Check out the fourth slide ›</a>
-
</p>
+
<div class="fullimg">
+
<img src="images/cytoscape3_logo.png" />
+
</div>
</div>
</div>
</div>
@@ -99,33 +114,81 @@
</div>
</div>
- </div>
+ <h2>What is Cytoscape 3.0?</h2>
- <div class="blockleft">
- <h2>What is Cytoscape 3.0?</h2>
+ <div class="leftimg">
+ <img
src="images/cytoscape_logo_left.png" />
+ </div>
+ <div class="textright">
+ Cytoscape 3.0 is the latest
version of Cytoscape, which introduces a whole new architecture,
+ developer API and set of user
controls. Cytoscape 3.0 represents a major redesign from the
+ ground up, toward the goal of
provide a stable, extensible, high-performance platform for
+ network visualization and
analysis. The initial Beta Release will introduce users to the new
+ interfaces and features we've
been working on:
+
+ <ul>
+ <li>
+ New welcome
screen and toolbar for quick access to common actions
+ </li>
+ <li>
+ New Data Table
controls to interface with your data
+ </li>
+ <li>
+ Integrated
support for graphical annotations in networks
+ </li>
+ <li>
+ Support for
independent sets of networks within a single session
+ </li>
+ <li>
+ Advanced
network and table import controls
+ </li>
+ <li>
+ Improved
architecture and API for a more stable experience
+ </li>
+ </ul>
+
+ <p>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/";>
+ <button class="button
bigrounded orange">
+ Download
Cytoscape 3 Beta
+ </button> </a>
+ <a
href="release_notes_3_0_0_beta.html">
+ <button class="button
bigrounded blue">
+ Release Notes
+ </button> </a>
+ </p>
+ </div>
+
+ <h2>Apps for Cytoscape 3.0</h2>
<p>
- Learn about the <a
href="http://wiki.cytoscape.org/Cytoscape_3/CoreDevelopment";>Architecture,
Backward Compatibility, and API</a> of Cytoscape 3.0.
+ You can install Cytoscape 3
Apps directly from new Cytoscape App Store. Please
+ visit <a
href="http://apps.cytoscape.org/"; target="_new">apps.cytoscape.org</a>.
</p>
- <h3>What are 3.0 apps?</h3>
- <p>
- Primary documentation for
Cytoscape 3.0 <a href="http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper";>app
development</a>.
- </p>
- <br />
- <p>
- All Cytoscape 3.0 <a
href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3";>app
development tutorials</a>.
- </p>
- </div>
- <div class="blockright">
- <h2>Download Cytoscape 3 Beta</h2>
- <h4><a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1";>Cytoscape 3.0.0 User
Beta</a></h4>
-
- <h2>For App Developers</h2>
- <h4><a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/API";>Cytoscape API
3.0.0-beta3 JavaDocs</a></h4>
- <h4><a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/cytoscape-swing-app-api-3.0.0-beta3.jar";>API
JAR beta3</a></h4>
- <h4><a
href="http://chianti.ucsd.edu/svn/core3/app-developer/tags/cytoscape-3.0.0-M5";>App
Developer Project Tag</a></h4>
+ <h2>Developer Documents</h2>
+ <ul>
+ <li>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/API";>Cytoscape API
3.0.0-beta3 JavaDocs</a>
+ </li>
+ <li>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/cytoscape-swing-app-api-3.0.0-beta3.jar";>API
JAR beta3</a>
+ </li>
+ <li>
+ <a
href="http://chianti.ucsd.edu/svn/core3/app-developer/tags/cytoscape-3.0.0-beta1";>App
Developer Project Tag</a>
+ </li>
+ <li>
+ Primary documentation
for Cytoscape 3.0 <a
href="http://wiki.cytoscape.org/Cytoscape_3/AppDeveloper";>app development</a>.
+ </li>
+ <li>
+ Learn about the <a
href="http://wiki.cytoscape.org/Cytoscape_3/CoreDevelopment";>Architecture,
Backward Compatibility,
+ and API</a> of
Cytoscape 3.0.
+ </li>
+ <li>
+ All Cytoscape 3.0 <a
href="http://opentutorials.cgl.ucsf.edu/index.php/Portal:Cytoscape3";>app
development tutorials</a>.
+ </li>
+ </ul>
+
</div>
-
<script src="js/footer.js"></script>
</div>
</div>
Added: new_cytoscape_website/trunk/images/advanced_search.png
===================================================================
(Binary files differ)
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+ application/octet-stream
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+ application/octet-stream
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new_cytoscape_website/trunk/images/cytoscape3_release_beta1.png
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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===================================================================
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+ application/octet-stream
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+ application/octet-stream
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(Binary files differ)
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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+ application/octet-stream
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___________________________________________________________________
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+ application/octet-stream
Added: new_cytoscape_website/trunk/release_notes_3_0_0_beta.html
===================================================================
--- new_cytoscape_website/trunk/release_notes_3_0_0_beta.html
(rev 0)
+++ new_cytoscape_website/trunk/release_notes_3_0_0_beta.html 2012-10-05
01:00:09 UTC (rev 30609)
@@ -0,0 +1,133 @@
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN"
"http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd";>
+<html xmlns="http://www.w3.org/1999/xhtml";>
+ <head>
+ <meta http-equiv="Content-Type" content="text/html;
charset=UTF-8" />
+ <link href="css/main.css" type="text/css" rel="stylesheet"
+ media="screen">
+ <title>Cytoscape 3 Beta 1 Release Notes</title>
+ <script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jquery/1.4.2/jquery.min.js";></script>
+ <script type="text/javascript"
src="http://ajax.googleapis.com/ajax/libs/jqueryui/1.8.1/jquery-ui.min.js";></script>
+
+ <script type="text/javascript"
src="js/global_variables.js"></script>
+ <script type="text/javascript"
src="js/menu_generator.js"></script>
+ </head>
+
+ <body>
+ <div id="container">
+ <script src="js/header.js"></script>
+
+ <div id="documents">
+ <div class="blockfull3">
+ <h1>Cytoscape 3.0.0 Beta 1 Release
Notes</h1>
+
+ <img
src="images/cytoscape3_release_beta1.png" />
+
+ <h2>New Features in Cytoscape 3</h2>
+
+ <div class="section">
+ <h3>Welcome Screen</h3>
+ <div class="leftimg">
+ <img
src="images/welcome_screen.png" />
+ </div>
+ <p>
+ For convenience,
Cytoscape shows <strong><i>Welcome Screen</i></strong> at startup timewhich
provides easy way to access
+ sample data sets and
public databases.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Edge Bend Visual
Property</h3>
+ <div class="leftimg">
+ <img
src="images/edge_bend_editor.png" />
+ </div>
+ <p>
+ Edge Bend is now a
standard Visual Property. You can use it as a part of your Visual Style.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Edge Bundling</h3>
+
+ <img
src="images/edge_bundling.png" />
+
+ <p>
+ You can bundle edges by
automatic Edge Bundling. This feature is useful for dense network views.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Network Annotations</h3>
+ <div class="rightimg">
+ <img
src="images/network_annotation.png" />
+ </div>
+ <p>
+ You can add notes and
simple shapes to background or foreground of network view.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Advanced Search
Function</h3>
+ <div class="rightimg">
+ <img
src="images/advanced_search.png" />
+ </div>
+ <p>
+ From this version,
EnhancedSearch plugin is part of core. You can search networks using Lucene
syntax.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Show All feature in Data
Table Browser</h3>
+ <div class="rightimg">
+ <img
src="images/table_browser.png" />
+ </div>
+ <p>
+ By selecting <i>Show
All</i> option in Data Table Browser, you can display all network objects in the
+ table. Nodes and edges
will be selected when you select associated rows in the table.
+ </p>
+ </div>
+
+ <div class="section">
+ <h3>Network Collection</h3>
+ <div class="rightimg">
+ <img
src="images/network_collection.png" />
+ </div>
+ <p>
+ Cytoscape 3 manages
networks based on Network Collection. When you load networks to Cytoscape,
+ you can choose creating
a new set of networks or adding them to existing collection.
+ </p>
+ </div>
+
+
+ <h2>Known Issues</h2>
+ <div class="section">
+ <h3>Java Versions</h3>
+ <p>
+ You can run Cytoscape 3
on Java 6 or 7. However, there are several problems if you use
+ OpenJDK. Please use
Oracle JRE/JDK or Apple Java Virtual Machine.
+ </p>
+
+ <h3>Important Note for Mac
Users</h3>
+ <p>
+ If you run Cytoscape on
Mac OS X 10.7.5+ and 10.8+, you need to disable Gatekeeper
+ before running the
installer.
+ </p>
+ </div>
+
+ <h2>How to Report Bugs</h2>
+ <div class="section">
+ <p>
+ This version of
Cytoscape is still in beta status and your bug reports are very important
+ to improve the quality
of final version of Cytoscape 3. If you notice any problems,
+ please report them from:
+
+ <h3>Help → Report
a bug...</h3>
+ </p>
+ </div>
+
+ </div>
+ </div>
+ <script src="js/footer.js"></script>
+ </div>
+ </body>
+</html>
+
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___________________________________________________________________
Added: svn:mime-type
+ text/plain
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