cytoscape-announce Google Group

Random Network Plugin Beta Release

pjmcs...@gmail.com (Patrick McSweeney) — Wed, 13 Aug 2008 16:48:03 UT

Hello everyone,
We are very excited to release the Beta version of the Random
Network Plugin, a Google Summer of Code Project. Our plugin can be
used for three main tasks:
(1) Creating random networks according to three main models
(erdos-renyi, watts-strogatz, barabasi-albert).
(2) Create a degree(in/out) preserved randomization of an existing networks.

Cytoscape programming job

msm...@ucsd.edu (Mike Smoot) — Mon, 14 Jul 2008 18:25:39 UT

Hi Everyone,
We're hiring a full-time Cytoscape developer here at UCSD. Here is the job
posting:
[link]
Please contact me off list if you have any questions!
thanks,
Mike

CCMB/NCIBI MiMI plugin 3.0 release

jg11...@gmail.com (Jing Gao) — Tue, 17 Jun 2008 19:59:46 UT

The CCMB/NCIBI MiMI plugin 3.0 was released on June 16 2008 to
Cytoscape using the latest
version of mimiR2/geneR2 and pubmed_08n databases.

You can download MiMI plugin 3.0 from here:
[link]

MiMI plugin 3.0 has the following improvements:

1. Faster performance due to the use of pre-computed tables for gene

Cytoscape retreat registration and hotel block

gary.ba...@utoronto.ca (Gary Bader) — Mon, 16 Jun 2008 14:23:04 UT

Hi everyone,
Please remember to register for the Cytoscape retreat, Toronto July 16-19.
[link]
If you were having trouble registering, an issue with the site has
recently been fixed.
Hotel
-----
We've negotiated a special rate at the Delta Chelsea hotel for the

CentiScaPe release: Centralities for Cytoscape

giovanni.scard...@gmail.com (giovanni scardoni) — Mon, 19 May 2008 15:55:31 UT

Release 1.0 of the CentiScaPe plug-in, a plug-in to calculate network
centralities.
CentiScaPe is available at:
[link] <[link]>
Complex biological networks, such as intracellular signaling networks, are
modeled by the evolution to accomplish a variety of different regulatory

Cytoscape retreat registration now open! July 16-19, Toronto

gary.ba...@utoronto.ca (Gary Bader) — Thu, 15 May 2008 14:58:42 UT

On 16th – 19th July 2008 we will be hosting the 6th Annual Cytoscape
Retreat at the Donnelly Centre for Cellular and Biomolecular Research,
University of Toronto, Canada.
[link]
I'm pleased to announce that the Cytoscape retreat registration site is

Cytoscape software engineer, Pasteur Institute, Paris (France)

be...@pasteur.fr (Benno Schwikowski) — Wed, 23 Apr 2008 10:20:38 UT

The Systems Biology Group at the Pasteur Institute in Paris (France)
has one-year vacancy for a software engineer. In collaboration with a
number of groups in the United States, we are developing Cytoscape,
the most popular open-source software platform for visualization and
analysis of interaction networks. The person we are looking for will

Save the date: Cytoscape retreat July 16-19, 2008 - Toronto

gary.ba...@utoronto.ca (Gary Bader) — Wed, 16 Apr 2008 14:15:37 UT

On 16th – 19th July 2008 we will be hosting the 6th Annual Cytoscape
Retreat at the Donnelly Centre for Cellular and Biomolecular Research,
University of Toronto, Canada.
[link]
This year’s meeting is particularly exciting since it is the first time

JavaScriptEngine Plugin v0.01

kei...@gmail.com (Keiichiro Ono) — Wed, 16 Apr 2008 00:32:56 UT

Hi.
For JavaScript programmers, I've created another scripting engine for
Cytoscape. JavaScriptEngine Plugin 0.01 is also a technology preview
for future version of Cytoscape. This plugin is based on Rhino 1.7.1:
[link]
and BSF 2.4.0, so you can use this in both Java 5 and 6. You can

Ruby Scripting Engine Plugin 0.02 Released

kei...@gmail.com (Keiichiro Ono) — Tue, 15 Apr 2008 02:12:16 UT

Hi.
I've updated RubScriptingEngine, a plugin to access Cytoscape's Java
objects directly from ruby scripting language. This is an
experimental plugin for evaluating scripting engines and final version
will be released with Cytoscape 3.0. Currently, I'm planning to
support JavaScript, Python, and Ruby.

Cytoscape 2.6.0!

msm...@ucsd.edu (Mike Smoot) — Fri, 11 Apr 2008 19:56:03 UT

Hi Everyone,
The Cytoscape team is proud to announce the release of Cytsocape version
2.6.0! Cytoscape is an open-source software platform for visualizing
interaction networks and integrating these interactions with other state
data.
You can download version 2.6.0 here:
[link]<[link]>

Web Service Clients for Pathway Commons, IntAct, BioMart, and NCBI (BioGRID, HPRD, BIND)

kei...@gmail.com (Keiichiro Ono) — Mon, 24 Mar 2008 19:59:15 UT

Hi.
From version 2.6.0, Cytoscape supports several external databases
through web services. This means you can access
interaction/annotation data directly from Cytoscape Desktop. Please
read the following document to learn how to use this feature:
[link]

NetworkAnalyzer Release 2.5.2

yas...@mpi-inf.mpg.de (Yassen Assenov) — Thu, 20 Mar 2008 14:30:10 UT

Release 2.5.2 of the Cytoscape plugin NetworkAnalyzer.
NetworkAnalyzer computes various topology parameters.
To get further information and to download the plugin,
go to [link]
NetworkAnalyzer 2.5.2 is tested to work with Cytoscape 2.5.2
New features are the computation of closeness and

Cytoscape 2.6 beta 2

msm...@ucsd.edu (Mike Smoot) — Fri, 14 Mar 2008 22:45:51 UT

Hi Everyone,
I've just released the second beta of Cytoscape 2.6. We encourage everyone,
plugin writers in particular, to give it a try. This would be a *great*
time for plugin writers to update their version compatibility for 2.6! The
install bundles are available here: [link]

Attn: Students - Google Summer of Code applications are due March 31st

ap...@gladstone.ucsf.edu (Alexander Pico) — Mon, 10 Mar 2008 21:10:13 UT

Want to write open source code?
Want to make money?
Want to do both?
In 2007 alone, Google Summer of Code brought together 900 students and
nearly 1500 mentors across 90 countries to contribute to over 130 different
open source software projects. We¹re looking for mentors and students to
join us in making 2008 the best Summer of Code yet! We¹ll be offering