cytoscape-announce Google Group

urgent request for your support by Sept 18th

msm...@ucsd.edu (Mike Smoot) — Thu, 03 Sep 2009 17:58:40 UT

(on behalf of Trey Ideker)
Dear Cytoscape Users,
In order to continue development and support of the Cytoscape
application, we rely heavily on grant support from the NIH. We are
right now in the process of preparing an application to add support
to Cytoscape as part of an NCRR National Resource for Network

Release of CyThesaurus, a Cytoscape plugin for ID mapping

jianjiong....@gmail.com (Jianjiong Gao) — Wed, 02 Sep 2009 20:49:52 UT

Dear Everyone,
I am exited to announce the release of a new Cytoscape
plugin--CyThesaurus, from a project of Google Summer of Code 2009.
CyThesaurus is a plugin for performing ID mapping/translation for
Cytoscape networks. In this version, the plugin supports translating
node attributes in networks from source ID types to the target ID

MetScape release 1.0

jg11...@gmail.com (Jing Gao) — Tue, 01 Sep 2009 20:18:21 UT

The CCMB/NCIBI MetScape 1.0 was released on September 1 2009 to
Cytoscape!
MetScape 1.0 is verified to work in Cytoscape v2.6.x. Please visit
MetScape website for more information [link].

Version 1.0 has the following new features:

Allow Compound Name Search
-Besides KEGG IDs, users are allowed to enter compound names to

annoying features in Cytoscape

msm...@ucsd.edu (Mike Smoot) — Thu, 30 Jul 2009 18:22:08 UT

Hi Everyone,
The Cytoscape team is preparing to work on a bug-fix release for Cytoscape
2.6.x and we're particularly interested in quashing "annoying" bugs and
features. Is there anything that is confusing or doesn't seem to make
sense? Something that behaves much differently than you expect? Is there a

hiring a Cytoscape Programmer

msm...@ucsd.edu (Mike Smoot) — Fri, 17 Jul 2009 19:13:12 UT

Hi Everyone,
Just a quick announcement that we're looking to hire an experienced Java
developer to work on Cytoscape here at UC San Diego. The job posting is
here:
[link]
Contact me directly with any questions.
thanks,
Mike

Cytoscape 2.6.3

msm...@ucsd.edu (Mike Smoot) — Tue, 30 Jun 2009 22:50:19 UT

Hi Everyone,
The Cytoscape team would like to announce the arrival of version 2.6.3 of
Cytoscape. This release addresses bugs introduced because of Apple's recent
security upgrade for OS X. Specifically, this release fixes the problems
of:
- Misshapen windows and panels within windows.
- Disappearing menus.

Cytoscape Birds of a Feather (BoF) at ISMB/ECCB 2009

maita...@gmail.com (Maital Ashkenazi) — Tue, 23 Jun 2009 14:28:55 UT

Hi Everyone,
We are organizing a Birds of a Feather (BoF) meeting during ISMB/ECCB 2009
conference. Users and plugin developers are invited to join core developers
for Cytoscape discussion. We are particularly interested in getting
feedback on users’ experiences, problems, and bugs that we can fix.

Google Summer of Code 2009

ap...@gladstone.ucsf.edu (Alexander Pico) — Thu, 26 Mar 2009 22:17:53 UT

We are looking for students to help build Cytoscape, GenMAPP and
WikiPathways through the Google Summer of Code 2009 program. If you
are a student and are interested in open source and biology, then you
should apply!
[link]

MetScape released

jg11...@gmail.com (Jing Gao) — Mon, 16 Mar 2009 15:57:08 UT

The CCMB/NCIBI MetScape was released on March 13 2009 to Cytoscape!

You can Download MetScape from Cytoscape plugins websit at
[link]. MetScape is
verified to work in Cytoscape v2.6, v2.6.1 and v2.6.2.

MetScape is a Cytoscape plugin which is used to visualize and analyze

Cytoscape release 2.6.2!

msm...@ucsd.edu (Mike Smoot) — Mon, 02 Mar 2009 19:10:38 UT

Hi Everyone,
The Cytoscape team is proud to announce the release of Cytoscape 2.6.2!
This release consists of bug fixes and should be fully compatible with all
2.6.x plugins.. Some of issues that have been addressed with this release
include:
- Fixed the webstart on Mac OS X problem.
- Fixed Linkout for Linux when no default browser is set.

Cytoscape programming position

msm...@ucsd.edu (Mike Smoot) — Sat, 29 Nov 2008 16:09:03 UT

Hi Everyone,
We're looking for an experienced Java programmer to work on the Cytoscape
project at UCSD. If you're interested, please apply here:
[link]
thanks,
Mike

Release 2.0 of DomainGraph plugin

de...@mpi-inf.mpg.de (Dorothea Emig) — Mon, 17 Nov 2008 16:53:23 UT

DomainGraph decomposes protein interaction networks into their
underlying domain interactions. Gene networks can be loaded to
visualize the encoded proteins and their domain compositions.
Additionally, DomainGraph supports the integration of Affymetrix Exon
Array data. Genes, proteins and domains containing differentially

New Tutorial: Integrate Networks and Annotations by Web Services

kei...@gmail.com (Keiichiro Ono) — Tue, 14 Oct 2008 01:20:54 UT

Hi everyone.
A new tutorial about data integration with web service clients is
available in Cytoscape web site:
[link]
Some of the sections are not finished yet, but you can learn how to
use web service clients to import public data sets and annotations

Announcing ExpressionCorrelation plugin

gary.ba...@utoronto.ca (Gary Bader) — Wed, 08 Oct 2008 15:15:21 UT

The ExpressionCorrelation plug-in creates a network from gene expression
data.
It computes a similarity network from either the genes or conditions in
a gene expression matrix. The nodes in the similarity network represent
genes or conditions. The edges represent the similarity between vectors

First release of clusterMaker

scoo...@cgl.ucsf.edu (Scooter Morris) — Tue, 23 Sep 2008 23:12:48 UT

The UCSF RBVI is happy to announce the first release of clusterMaker, a
Cytoscape plugin for creating and visualizing clusters within Cytoscape
networks. This initial release provides support for hierarchical,
k-means, MCL, and FORCE clusters. The hierarchical and k-means clusters
are based on the Cluster 3.0 C sources from the Laboratory of DNA