cytoscape-discuss Google Group

Re: Server down?

francescomusacc...@gmail.com (Franktwis) — Tue, 10 Nov 2009 17:32:07 UT

I'm very grateful for your help Oliver!!!
Thanks a lot!
Francesco

Re: [Cytoscape-discuss] Re: Server down?

ostue...@gmail.com (Oliver Stueker) — Tue, 10 Nov 2009 15:36:16 UT

Hi,

The current API is still online at [link]

And while the wiki is still down, you can try to find what you want in
the Google Cache:
e.g.:
[link]
[link]

Re: Server down?

francescomusacc...@gmail.com (Franktwis) — Tue, 10 Nov 2009 14:06:30 UT

Hi.. the server is still down as I can see! Isn't there another place
where I can find instructions on how to use Cytoscape APIs?
Thanks a lot

Re: [Cytoscape-discuss] Re: Cytoscape IDE 0.2.2 for Eclipse 3.5 Galileo Released

k...@ucsd.edu (Keiichiro Ono) — Mon, 09 Nov 2009 22:55:09 UT

Sorry, but we are still working on this problem and not sure when we
can fix the wiki.
I'll let you know when it's back.

Kei

2009/11/8 Fengbo Xie <fengbo....@gmail.com>:

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

Cytoscape Core Developer Team: [link]
UCSD School of Medicine Trey Ideker Lab: [link]

Server down?

francescomusacc...@gmail.com (Franktwis) — Mon, 09 Nov 2009 14:38:02 UT

HI all, since 4-5 days ago, I'm trying to read pages of plugin
tutorial but I retrieve always a Internal Server Error. What's
happening? When will be restored the service?
thanks

Re: Cytoscape IDE 0.2.2 for Eclipse 3.5 Galileo Released

fengbo....@gmail.com (Fengbo Xie) — Mon, 09 Nov 2009 07:16:57 UT

Keiichiro :
The cytoscape wiki is server still down.

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

francescomusacc...@gmail.com (Franktwis) — Sat, 07 Nov 2009 16:03:49 UT

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

kei...@gmail.com (Keiichiro Ono) — Sat, 07 Nov 2009 02:16:49 UT

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?

paladinj...@gmail.com (Gang Su) — Fri, 06 Nov 2009 19:59:37 UT

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?

sapa...@ucsd.edu (Satyajit Patra) — Fri, 06 Nov 2009 18:21:30 UT

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?

christian.fo...@utsouthwestern.edu (Christian Forst) — Fri, 06 Nov 2009 15:41:55 UT

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?

martinmacgu...@googlemail.com (Martin MacGuill) — Fri, 06 Nov 2009 11:14:26 UT

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

sreebash...@gmail.com (Ravi) — Fri, 06 Nov 2009 06:02:19 UT

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

minr...@gmail.com (Mindaugas Razbadauskas) — Thu, 05 Nov 2009 13:15:10 UT

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

kei...@gmail.com (Keiichiro Ono) — Wed, 04 Nov 2009 21:23:37 UT

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.