cytoscape-discuss Google Group

Plugin name doesn't appear in Cytoscape plugin menù

2009-12-17T10:44:14Z

Hi all,
I writed so many times on this forum and so much of you answered me
helping each time. Now my plugin is completed with a Java GUI. I
followed this steps:
1) compiled without warnings the jar file
2) opened the jar and inserted the manifest file:
Manifest-Version: 1.0
Ant-Version: Apache Ant 1.7.0

PSICQUIC Universal Web Service Client Plugin beta release

2009-12-15T21:25:59Z

Hi everyone.

If you need to access public interaction databases from Cytoscape,
this might be interesting.

PSICUQIC is a standardized web service API for biological interaction
network databases:

[link]

The advantage of standardized web service API is that we (client

Manage two or more net in an only session

2009-12-12T11:58:59Z

Hi all,
I write code to create two nets that I would view in an only session
on cytoscape.

CyNetwork graph1 = Cytoscape.createNetwork("graph 1", false);//Il
nostro grafo
final CyNetworkView cyView;

CyNetwork graph2 = Cytoscape.createNetwork("graph 2", false);//
Il nostro grafo

Cytoscape Scripting Engine Plugins Updated

2009-12-07T22:17:10Z

Hi everyone.

All of Cytoscape-compatible scripting engines have been updated. The
following binaries are included in the plugins:

Ruby - JRuby 1.4.0
Python - Jython 2.5.1
Groovy - Groovy 1.6.7
JavaScript - Rhino 1.7.2

Sample Scripts are available here:

[link]

Re: [cytoscape-helpdesk] Re: Disease-protein network

2009-12-05T11:05:35Z

Dear researchers,

My research group developed a web server (BioNet) that allow to
collect the proteins associated with a specific disease from OMIM site
[[link]] and use these data to generate
protein-protein interaction network from the site STRING
[[link]]. The archives can be saved in different

Listener for Layout calls

2009-12-02T09:54:28Z

Hi all,

is there a way in Cytoscape to listen for layout events? I'd like my
plugin to remember which layout was performed last by the user so that
when the plug-in adds nodes the same layout can be performed.

Kind regards,

Jan
Delft University of Technology

How to get all edges of a node

2009-12-02T14:42:27Z

How can I do this? I've added an attribute for every edge that
indicates its name and I would to retrieve the list of all edge for
every node.
Thanks
Franktwis

Re: [Cytoscape-discuss] Using Cytoscape plugin to open GSEA enrichment results

2009-12-05T16:18:57Z

Hi Francesco,

The 'Excel" files that are generated by GSEA are in fact tab-separated
text files with an .xls file-extension.

Hm, this sounds more like you have encoding issues ( Unix/Mac/Windows
newlines or ASCII/ANSI/UTF8 encoding).

Try to inspect both files ecoding with a good text-editor (don't know

Layout code

2009-11-30T17:50:27Z

Howdy,
Just a trivial query, really. When I set up new networks in cytoscape
(programmatically) all the nodes get added on top of each other. I
can't find the code that allows me to set a network layout, for
example I'd like find the code that imposes the GridLayout to a
network.

Kind regards

jactive module

2009-11-30T14:11:14Z

Hi!!!
I am quries to know whether jactive module can be run outside
cytoscape. Is thier anyway that I can run simultenously many jactive
modules i.e. 1000 with some program? How it is possible to do so?
Do please Answer!
Regards
Amitabh
Amitabh Sharma
Postdoctoral Research Fellow
Diabetes and Cardiovascular Disease, Genetic Epidemiology

Degree sorted circle layout - Problem

2009-11-28T18:19:00Z

hi all!

I have a problem with creating degree attribute for my network. When I
run Degree Sorted Layout the attribute is not created.
I'm running Cytoscape 2.6.3 on Windows XP with the Java version
1.6.0_15.
I tried to do the same with oldest version of Cytoscape, but this
problem also occured.

AUTO: Out of office, returning Monday, November 30 (returning 11/30/2009)

2009-11-26T16:01:51Z

I am out of the office until 11/30/2009.

I am currently out of the office, with limited access to my email. I will
be returning on Monday If you need immediate assistance, please forward
your message to eStrat...@sial.com
Take care, and Happy Thanksgiving!
Kristy
x4559

Note: This is an automated response to your message "[Cytoscape-discuss]

Adding a Frame to my plugin for Cytoscape

2009-11-26T11:06:52Z

hi all,
I would to start my plugin in Cytoscape with a GUI that gives
possibilities to initialize a Net that I build after in the code. How
can I do it? Have I simply use swing or awt in Java or there is a
cytoscape class to extend?
Is there an example for doing it?
thanks

Xxx Sexy hot lady’s aviation us Indian Pakistani Chinese USA Indonesian Malaysian Singapore Russian photos

2009-11-20T20:18:14Z

Xxx Sexy hot lady’s aviation us Indian Pakistani Chinese USA
Indonesian Malaysian Singapore Russian photos
[link]

cytoscape wiki

2009-11-18T21:01:52Z

Hi Everyone,

Just a quick note that the Cytoscape Wiki is back in action. You can follow
the various links on the home page, or go directly to the root of the wiki
here: [link] If you notice any links still
pointing to the old installation just drop me a line and I will fix them.