cytoscape-helpdesk Google Group

node coordinates

dlnot...@gmail.com (Daniel Luis Notari) — Tue, 10 Nov 2009 13:12:05 UT

I am developing a plugin to Cystoscape but I have a problem with the
coordinates to the viewport. Cytoscape has many layouts to represent in
a window a protein network. I need to know how does Cytoscape attributes
x and y coordinates for each node (protein)?

Somebody can help me?

thanks

Re: [cytoscape-helpdesk] Re: Problem with the online tutorials

projectb...@gmail.com (swaraj basu) — Tue, 10 Nov 2009 05:41:27 UT

Hello,
You can find and excellent tutorial in the form of this
publication :[link]

Re: [cytoscape-helpdesk] error

projectb...@gmail.com (swaraj basu) — Tue, 10 Nov 2009 05:38:47 UT

If you are using Cytoscape 2.6.3, try once 2.6.2

error

reshmisur...@gmail.com (Reshmi Suresh) — Mon, 09 Nov 2009 06:46:04 UT

hi,
when i enter web services and enter the pathway details and show
interaction of particular gene.., then error comes.."see log for details"
wht should i do ?

Broken link for Cytoscape tutorials?

clineonther...@gmail.com (Melissa Cline) — Wed, 04 Nov 2009 20:08:49 UT

Hi folks,

Greetings from Argentina, where I'm on sabbatical for a couple of
months... I just received a lovely, polite email from someone who
apologized for contacting me while I'm away, but was desperately
trying to get to the Cytoscape tutorials. At the moment, the link
from cytoscape.org appears to be broken. Would someone do the honors

Re: [cytoscape-helpdesk] online tutorials problem

maita...@gmail.com (Maital Ashkenazi) — Wed, 04 Nov 2009 07:08:16 UT

Hi,

Temporarily, the tutorials are not available, as well as other material on
Cytoscape wiki. We are aware of this problem and working to fix it.
In the meanwhile try using Cytoscape User Manual, available here:
[link]

Hope this helps,
Maital

Re: [cytoscape-helpdesk] Problem with the online tutorials

k...@ucsd.edu (Keiichiro Ono) — Tue, 03 Nov 2009 21:38:10 UT

Hi.
Due to our web hosting company's server upgrade, connection to
cytoscape.org and wiki is unstable now. I'll let you know when it's
back.

Sorry for the inconveniences.

Kei

2009/11/3 Shady Saad <shady.s...@gmail.com>:

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

Cytoscape Core Developer Team: [link]

Problem with the online tutorials

shady.s...@gmail.com (Shady Saad) — Tue, 03 Nov 2009 21:29:01 UT

Hi, I'm a PhD student, currently learning to use cytoscape but I have
a problem with the online tutorials.
Everytime I try to open the tutorials I receive the following message
"
Internal Server Error
The server encountered an internal error or misconfiguration and was
unable to complete your request.

online tutorials problem

shadshou...@yahoo.com (shady saad) — Tue, 03 Nov 2009 21:21:26 UT

Dear Sir,
I'm a PhD student, currently learning to use cytoscape but I have a problem with the online tutorials.
I receive the following message "
Internal Server ErrorThe server encountered an internal error or misconfiguration and was unable to complete your request.
Please contact the server administrator, or webmaster and inform them of the time the error occurred, and anything you might have done that may have caused the error.

Re: [cytoscape-helpdesk] List-type attributes

k...@ucsd.edu (Keiichiro Ono) — Tue, 03 Nov 2009 19:06:45 UT

Hi.
Manual editor for attributes does not support List/Map attributes. I
recommend to edit data table in spreadsheet applications, and then use
Table Import function.

Thanks.
Kei

2009/10/22 Russ <russell.h...@liv.ac.uk>:

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

Cytoscape Core Developer Team: [link]

Re: [cytoscape-helpdesk] python scripting

k...@ucsd.edu (Keiichiro Ono) — Tue, 03 Nov 2009 18:50:04 UT

Hi.
In general, Cytoscape Scripting feature uses JVM implementation of
scripting languages, such as Jython, JRuby, or Rhino. You can
directly access Cytoscape public Java API from scripting languages:

[link]

Thanks.
Kei

2009/10/23 David Epstein <david...@umich.edu>:

Re: [cytoscape-helpdesk] List-type attributes

projectb...@gmail.com (swaraj basu) — Tue, 03 Nov 2009 09:30:57 UT

Hello,
Better use import attributes from table function.

Re: [cytoscape-helpdesk] python scripting

projectb...@gmail.com (swaraj basu) — Tue, 03 Nov 2009 09:28:59 UT

Hello,
you can create nodes from cytoscape editor in the cytoscape
control panel.

opening cytoscape

jean-charles.mar...@univmed.fr (jean-charles.martin) — Thu, 29 Oct 2009 13:06:36 UT

Dear cytoscape users ,
I’m not new in cytoscape, but I got several troubles
1) while opening the 2.6.3 version: The first use is ok, but when I
want to re-open cytoscape, then I’m unable to do so and the following error
message appears (I upgraded the java version, but nothing changed):
java.lang.NullPointerException

Re: [cytoscape-helpdesk] filters need to be reset?

plw...@bioeng.ucsd.edu (Peng-Liang Wang) — Wed, 28 Oct 2009 16:43:51 UT

Hi david,

Can you please report a bug at Cytoscape bugtracker?
[link].

Please give step by step instuctions to reproduce the bug. If I can
reproduce the probem, I can fix it.

Thanks,

Peng