Author: kono Date: 2012-12-18 11:28:36 -0800 (Tue, 18 Dec 2012) New Revision: 31017
Added:
new_cytoscape_website/trunk/release_notes_3_0_0.html
Modified:
new_cytoscape_website/trunk/cy3.html
Log:
Minor update had been done for Cytoscape 3 release.
Modified: new_cytoscape_website/trunk/cy3.html
===================================================================
--- new_cytoscape_website/trunk/cy3.html 2012-12-18 18:55:10 UTC (rev
31016)
+++ new_cytoscape_website/trunk/cy3.html 2012-12-18 19:28:36 UTC (rev
31017)
@@ -42,11 +42,9 @@
<body>
<div id="container">
<script src="js/header.js"></script>
-
<div id="documents">
<div class="blockfull3">
- <h2>Welcome to Cytoscape 3.0 Beta!</h2>
-
+ <h2>Welcome to Cytoscape 3.0.0</h2>
<div id="container2">
<div id="example">
<div id="slides">
@@ -66,7 +64,7 @@
<div class="text">
<h1>New Features</h1>
<p>
-
Cytoscape 3 beta has new features including:
+
Cytoscape 3 has new features including:
<ul>
<li>
Edge Bundling
@@ -86,7 +84,7 @@
</ul>
</p>
<p>
-
<a href="release_notes_3_0_0_beta.html">Learn more about new
features ›</a>
+
<a href="release_notes_3_0_0.html">Learn more about new
features ›</a>
</p>
</div>
<img src="images/slides/new_features.png" />
@@ -148,11 +146,11 @@
</ul>
<p>
- <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0-beta1/";>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0/";>
<button class="button
bigrounded2 orange">
- Download
Cytoscape 3 Beta
+ Download
Cytoscape 3
</button> </a>
- <a
href="release_notes_3_0_0_beta.html">
+ <a
href="release_notes_3_0_0.html">
<button class="button
bigrounded2 blue">
Release Notes
</button> </a>
@@ -184,13 +182,13 @@
<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>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0/API";>Cytoscape API 3.0.0
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>
+ <a
href="http://chianti.ucsd.edu/cytoscape-3.0.0/cytoscape-swing-app-api-3.0.0.jar";>API
JAR 3.0.0</a>
</li>
<li>
- <a
href="http://chianti.ucsd.edu/svn/core3/app-developer/tags/cytoscape-3.0.0-beta1";>App
Developer Project Tag</a>
+ <a
href="http://chianti.ucsd.edu/svn/core3/app-developer/tags/cytoscape-3.0.0";>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>.
@@ -203,10 +201,9 @@
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>
</body>
-</html>
+</html>
\ No newline at end of file
Added: new_cytoscape_website/trunk/release_notes_3_0_0.html
===================================================================
--- new_cytoscape_website/trunk/release_notes_3_0_0.html
(rev 0)
+++ new_cytoscape_website/trunk/release_notes_3_0_0.html 2012-12-18
19:28:36 UTC (rev 31017)
@@ -0,0 +1,154 @@
+<!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 3.0.0 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 Release Notes</h1>
+
+ <img
src="images/cytoscape3_release_beta1.png" />
+
+ <h2>New Features in Cytoscape 3</h2>
+
+ <div class="section">
+ <h3>Updated 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>User Manual</h2>
+ <div class="section">
+ <p>
+ User manual for
Cytoscape 3 is available
+ <a
href="http://wiki.cytoscape.org/Cytoscape_3/UserManual";>here</a>.
+ </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>Windows XP Problems</h3>
+ <p>
+ (Need to describe XP
problems)
+ </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>
+ Your bug reports are
very important
+ to improve quality of
future versions of Cytoscape 3. If you notice any problems,
+ please report them from:
+
+ <h3>Help → Report
a bug...</h3>
+ </p>
+ </div>
+
+ <h2>Need Help?</h2>
+ <div class="section">
+ <p>
+ We need your feedback
to improve Cytoscape 3! Please send your questions and comments
+ to our <a
href="https://groups.google.com/forum/?fromgroups#!forum/cytoscape-helpdesk";>
+ mailing list</a>.
+ </p>
+ </div>
+
+ </div>
+ </div>
+ <script src="js/footer.js"></script>
+ </div>
+ </body>
+</html>
+
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