cytoscape-discuss Google Group

Re: Cytoscape IDE 0.2.2 for Eclipse 3.5 Galileo Released

2009-11-09T07:16:57Z

Keiichiro :
The cytoscape wiki is server still down.

How to create a graph and increment node and edge's size during creation

2009-11-07T16:03:49Z

Hi,
someone has an example of how to do this thing with cytoscape classes?
I cannot enter Cytoscape plugin and can't find anyone posted a
question like mine.
I explored Cytoscape API but really I can't solve the problem. Someone
says me to use a VisualStyle but it's not possible only with methods

PSICQUIC Universal Client Test Release

2009-11-07T02:16:49Z

Hi.
Here is the alpha version of PSICQUIC Universal client for Cytoscape.
[link]
PSICQUIC is a standardized web service for molecular interaction
databases. Major interaction data providers are involving this
project and you can search latest datasets from multiple databases by

Re: [Cytoscape-discuss] Re: What does an edge mean?

2009-11-06T19:59:37Z

Satyajit,

You prob need to load external attribute data. Actually if you just
want to see pathways, you could go to use DAVID.
For interactions, try Cytoscape MIMI plugin

Gang

Re: [Cytoscape-discuss] Re: What does an edge mean?

2009-11-06T18:21:30Z

Hi
I have a list of 15 proteins. want to see their
1. interaction among themselves
2. what pathways they are involved
kindly guide me.
Satyajit Patra

Re: [Cytoscape-discuss] What does an edge mean?

2009-11-06T15:41:55Z

Depends on the database, experiment, type of interaction. In the case of
protein-protein interactions, you have two (hopefully) independent
experiments that indicate an interaction between these two proteins.
Often experiments text different interaction properties. One identifies
binding, the other phosphorylation of the bound proteins (one a kinase,

What does an edge mean?

2009-11-06T11:14:26Z

Am new to Cytoscape....

Taking for example a protein-protein interaction network created from
multiple databases,

If two nodes are connected by two edges what does this mean?

Does it mean that there are 2 separate experiments to supporting the
interaction?

or does it mean that there are 2 separate data sources (which in

Re: Export TexFlame graph in Cytoscape compatible XGMML format

2009-11-06T06:02:19Z

Thanks for pointing to unlock option for node "width" and "height" in
cytoscape. We have incorporated your comment in our Cytoscape Help
page (Section 3B).

Thanks.
Ravikumar

Re: [Cytoscape-discuss] Re: Data Panel modify

2009-11-05T13:15:10Z

Thanks Peng,

This code is quite diferent to understand for me, may be who can help me,
and say in wich class or method i need to change

Mindaugas

2009/10/30 Peng-Liang Wang <plw...@bioeng.ucsd.edu>

Re: [Cytoscape-discuss] Re: Cytoscape Tutorial Video for Users and Developers

2009-11-04T21:23:37Z

Hi.
Thanks for your feedback.
Plugin developer's guide for Eclipse users is one of our TODO items.

Currently, we are developing both Cytoscape 3 series and 2 series, and
not much documentation or sample code is available for 3, so first,
I'll try to make some plugin developer tutorials for 3.

Re: [Cytoscape-discuss] Re: Setting Attributes to nodes and edges dimensions and visualizing them

2009-11-04T12:07:14Z

Sorry,
I'm trying to study these classes but I can't understand how to use them. Do you have a simple example of how to do it?
And what does means "continuous mapping programatically", how can I do it?
thanks again

______________________________ __
To: cytoscape-discuss@googlegroups .com

Re: [Cytoscape-discuss] Cytoscape Tutorial Video for Users and Developers

2009-11-04T12:47:39Z

Very nice idea and useful tutorial, thanks

It would be great if it were a video tutorial how to create or modify core
plugins from source and make jars file :)

Mindaugas

2009/11/4 Keiichiro Ono <kei...@gmail.com>

Cytoscape Tutorial Video for Users and Developers

2009-11-04T02:26:40Z

Hi.
We are planning to make some tutorial video for both users and
developers something like the following:
For Users:
[link]
For Developers:
[link]
Please let me know if you have any comments. Answers for the
following question is very helpful:
- What kind of information/tutorial do you need?

Plug-in Development in Eclipse

2009-11-03T23:58:43Z

Hi,

I have a question regarding how to set up Eclipse to develop Cytoscape
plug-ins. I've followed the directions in the tutorial here:
[link]. I know this is
from 2005 but I can't find any other relevant documentation.

I have set up everything as the tutorial says and the plug-in loads

Re: [Cytoscape-discuss] Export TexFlame graph in Cytoscape compatible XGMML format

2009-11-03T19:26:30Z

One quick comment.
By default, Cytoscape uses "node size" instead of "node width" and
"height," so the diagram looks better if you unlock it. You can do it
from the default view editor (check box on the bottom-left).

Kei

2009/11/3 Keiichiro Ono <kei...@gmail.com>:

--
Keiichiro Ono k...@ucsd.edu