Author: maxfranz
Date: 2010-09-14 12:19:13 -0700 (Tue, 14 Sep 2010)
New Revision: 21842
Modified:
cytoscapeweb/trunk/website/src/php/content/faq.php
Log:
Modified: cytoscapeweb/trunk/website/src/php/content/faq.php
===================================================================
--- cytoscapeweb/trunk/website/src/php/content/faq.php 2010-09-14 18:29:30 UTC
(rev 21841)
+++ cytoscapeweb/trunk/website/src/php/content/faq.php 2010-09-14 19:19:13 UTC
(rev 21842)
@@ -4,10 +4,13 @@
<p class="question">What does Cytoscape Web do?</p>
<p class="answer">Cytoscape Web is a network visualisation
library that you can use to embed
- networks onto a webpage.</p>
+ networks onto a webpage. It is not a stand alone application
for users; it is a tool for developers to
+ display networks on the web.</p>
<p class="question">What are the minimum system requirements
for end users?</p>
- <p class="answer">End users need a modern browser with the
Flash plugin installed.</p>
+ <p class="answer">End users need a modern browser with the
Flash plugin installed.
+ Cytoscape Web is tested on Chrome (OS X, Windows, Linux),
Firefox (OS X, Windows, Linux),
+ Safari (OS X), and Internet Explorer (Windows).</p>
<p class="question">What is the license of Cytoscape Web?</p>
<p class="answer">Cytoscape Web is an open source project under
the
@@ -15,7 +18,9 @@
<p class="question">How do I reference Cytoscape Web?</p>
<p class="answer">You can find reference information and the
publication itself on
- <a
href="http://www.ncbi.nlm.nih.gov/pubmed/20656902";>Pubmed</a>.</p>
+ <a
href="http://www.ncbi.nlm.nih.gov/pubmed/20656902";>Pubmed</a>. If you want to
link to
+ Cytoscape web, please see the
+ <a href="about#section/Linking_back_to_Cytoscape_Web">About
section</a>.</p>
<h1>Development background</h1>
@@ -45,12 +50,15 @@
<h1>Loading networks</h1>
<p class="question">What network formats does Cytoscape Web
support?</p>
- <p class="answer">Cytoscape Web supports GraphML, XGMML, and
SIF.</p>
+ <p class="answer">Cytoscape Web supports
+ <a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html"; >GraphML</a>,
+ <a href="http://www.cs.rpi.edu/~puninj/XGMML/"; >XGMML</a>, and
+ <a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
>SIF</a>.</p>
<p class="question">My favourite network format isn't
supported? What can I do?</p>
<p class="answer">You can either write some code that
translates your networks into a
supported format on-the-fly, or you could add it to Cytoscape
Web itself. Cytoscape Web
- is an open source project, so feel free to check out the source
and try things out!</p>
+ is an open source project, so feel free to check out the <a
href="download#section/Source_Code">source</a> and try things out!</p>
<p class="question">Can I load a network from Javascript
objects instead of a file?</p>
<p class="answer">No, but the next question may interest
you.</p>
@@ -62,17 +70,23 @@
Note that these functions are slow when applied in iteration on
many elements.</p>
<p class="question">Can I load a network from a URL?</p>
- <p class="answer">Use AJAX to pull the file you want into a
string in Javascript, and then pass that string
- to Cytoscape Web.</p>
+ <p class="answer">Cytoscape Web does not support this feature
directly, but you can implement
+ yourself easily.
+ Use AJAX to pull the file you want into a string in Javascript,
and then pass that string
+ to Cytoscape Web. <a href="http://jquery.com";>jQuery</a> is a
good library for this.</p>
<h1>Interacting with Cytoscape Web</h1>
<p class="question">I added a listener, changed the data
schema, filtered, or called some function on Cytoscape Web. Why isn't it
working?</p>
- <p class="answer">You need to call new, ready, and draw in that
order with listeners within
- the ready callback. See the <a
href="tutorial#section/Interacting_with_Cytoscape_Web">tutorial</a> for an
example.</p>
+ <p class="answer">You need to call new, ready, and draw in that
order with interactions with Cytoscape Web within
+ the ready callback. All interaction with Cytoscape Web occurs
within the callback function passed to the ready function.
+ See the <a
href="tutorial#section/Interacting_with_Cytoscape_Web">tutorial</a> for an
example.</p>
<p class="question">What formats can I export the network
to?</p>
- <p class="answer">GraphML, SIF, XGMML, PDF, and PNG are
supported.</p>
+ <p class="answer">PDF, PNG,
+ <a
href="http://graphml.graphdrawing.org/primer/graphml-primer.html"; >GraphML</a>,
+ <a href="http://www.cs.rpi.edu/~puninj/XGMML/"; >XGMML</a>, and
+ <a
href="http://cytoscape.wodaklab.org/wiki/Cytoscape_User_Manual/Network_Formats/";
>SIF</a> are supported.</p>
<h1>Customizing visual styles</h1>
@@ -80,7 +94,7 @@
<p class="answer">See the <a
href="documentation/visual_style">API reference</a>.</p>
<p class="question">Can I change the visual style after the
network has been drawn?</p>
- <p class="answer">Yes.</p>
+ <p class="answer">Yes, use <a
href="documentation#section/visualStyle">visualStyle</a>.</p>
<p class="question">How do I set the visual style to be
dependent on the network data?</p>
<p class="answer">Use a <a
href="documentation/mappers">mapper</a>.</p>
@@ -109,10 +123,10 @@
<h1>Layouts</h1>
<p class="question">What layouts does Cytoscape Web support?</p>
- <p class="answer">See the <a
href="documentation/layout">API</a>.</p>
+ <p class="answer">Several; see the <a
href="documentation/layout">API</a> for details.</p>
<p class="question">Can I customize the layout parameters?</p>
- <p class="answer">Yes, see the <a
href="documentation/layout">API</a>.</p>
+ <p class="answer">Yes, see the <a
href="documentation/layout">API</a> for details.</p>
<p class="question">Why is the force-directed layout not
animated?</p>
<p class="answer">It's computationally expensive such that
large networks become unresponsive
@@ -122,5 +136,7 @@
<p class="answer">Yes, see weightAttr in the <a
href="documentation/layout">API</a>.</p>
<p class="question">Can I use my own custom layout
algorithm?</p>
- <p class="answer">Yes, calculate your layout and pass it to
Cytoscape Web as a preset layout.</p>
+ <p class="answer">Yes, calculate your layout and pass it to
Cytoscape Web as a preset layout.
+ You can calculate it on the client side with Javascript or on
the server side with Java, PHP,
+ and so on.</p>
</div>
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