genemania-announce Google Group

Announcing the two month old GeneMANIA release!

quaid.mor...@utoronto.ca (Quaid Morris) — Thu, 20 Dec 2012 17:44:41 UT

*Some of you probably noticed that about two months ago, the GeneMANIA
website underwent a major user interface re-design and had added new search
features. We hope these changes have improved your GeneMANIA experience but
please provide us any feedback that you have about them.

The best way to find out about the changes is to try them out for yourself

Try out the new beta of GeneMANIA!

gary.ba...@utoronto.ca (Gary Bader) — Fri, 21 Sep 2012 16:08:21 UT

[link]

The GeneMANIA website has undergone a major user interface re-design and has new search features. We hope these changes will enhance your GeneMANIA experience and we are now in beta testing so you can try them out and provide feedback to us.

Website design improvements:

New GeneMANIA plugin data set (version 2012-05-25)

jrr...@gmail.com (Jason Montojo) — Fri, 01 Jun 2012 19:36:15 UT

*Hi everyone,*
*
*
*Some GeneMANIA users reported differences in prediction results between
the web site, and the Cytoscape plugin and command line tools. We traced
the cause of these differences to the plugin data’s co-expression networks
having more interactions than the web site’s. The website optimizes the

GeneMANIA Cytoscape plugin 2.5 now available

jrr...@gmail.com (Jason Montojo) — Sat, 12 May 2012 14:22:07 UT

We are pleased to announce the release of version 2.5 of the GeneMANIA
Cytoscape plugin and command line tools for really fast gene function
prediction. This release contains bug fixes and no new features. Extend
and analyze your gene lists using our database of over 260 million
interactions spanning 1,400 networks. You can also perform predictions on

GeneMANIA is back up

quaid.mor...@gmail.com (Quaid Morris) — Sun, 25 Mar 2012 21:08:10 UT

One of our switches malfunctioned this morning, so GeneMANIA was down for a
couple hours today. Switch is fixed and we are back online.

GeneMANIA PSICQUIC webservice now available

gary.ba...@utoronto.ca (Gary Bader) — Thu, 16 Feb 2012 17:00:54 UT

Hello,
We are pleased to announce our GeneMANIA ([link]) PSICQUIC webservice, which allows you to query millions of GeneMANIA functional interactions from your own software and scripts and multiple software that support the standard PSICQUIC molecular interaction query service (such as the Cytoscape PSICQUIC client plugin). It is accessible through [link] or through the PSICQUIC Registry: [link]

Re: New GeneMANIA data release.

jrr...@gmail.com (Jason Montojo) — Sat, 07 Jan 2012 13:29:40 UT

Hi folks,
This data release is now available for the GeneMANIA Cytoscape plugin. You
can select either "Choose Another Data Set" or "Check for Data Updates"
from the menu to install it. Command line users can do the same through
the Data Admin tool.
Thanks,
Jason

New GeneMANIA data release.

gary.ba...@utoronto.ca (Gary Bader) — Fri, 06 Jan 2012 04:50:27 UT

Hello,
We are pleased to announce a new GeneMANIA data release. The major changes are:
1. We have added iRefIndex as a replacement to Pathway Commons data source for physical interactions. This solves an issue where some protein interactions derived from large-scale proteomics studies were too highly connected to each other. iRefIndex compiles physical interactions from the same sources as Pathway Commons (and more). However, some of the interaction numbers may change slightly compared to our previous version of GeneMANIA due to differences in data processing between data sources. Pathway Commons is still used for Pathway information from Reactome, NCI/Nature PID, HumanCyc, IMID and the MSKCC Cancer Cell Map.

GeneMANIA Cytoscape plugin 2.3 now available

jrr...@gmail.com (Jason Montojo) — Tue, 20 Dec 2011 22:09:08 UT

We are pleased to announce the release of version 2.3 of the
GeneMANIA Cytoscape plugin and command line tools for really fast gene
function predictions. Extend and analyze your gene lists using our
database of over 400 million interactions spanning 1,300 networks. You can
also perform predictions on your own data by importing networks and

It’s now easier to refine your query in GeneMANIA

gary.ba...@utoronto.ca (Gary Bader) — Sat, 10 Sep 2011 17:41:41 UT

Hello,
We’ve added a new feature to GeneMANIA that allows you to refine your search by selecting nodes in your results page.
The new query menu in the network display area of the results gives you the option to add selected genes to your query; remove them from the query; or re-query using only the selected genes. Before you had to type to refine your query.

New GeneMANIA data release

quaid.mor...@gmail.com (Quaid Morris) — Fri, 12 Aug 2011 19:26:34 UT

We are pleased to announce a new GeneMANIA data release and some minor
changes to the website.
The major changes are:
1) We have added Rat to the list of organisms we support. We have 140
networks for rat, including 80 non-co-expression networks. We will be
continuing to add new organisms over time.

Announcing Version 2.2 of The GeneMANIA Cytoscape Plugin for Gene Function Prediction

jrr...@gmail.com (Jason Montojo) — Fri, 22 Jul 2011 11:48:08 UT

We are pleased to announce the release of version 2.2 of the GeneMANIA
Cytoscape plugin and command line tools. This release includes
numerous bug fixes and a handful of new features. You can install
this new release through Cytoscape's plugin manager. Read below for
more details.
New Features:
* The plugin now provides access to three different types of data sets:

Announcing GeneMANIA 3.0

quaid.mor...@gmail.com (Quaid Morris) — Thu, 19 May 2011 17:27:02 UT

We are pleased to announce the release of a new version of GeneMANIA.
You’ll find this version of GeneMANIA faster and more responsive!
We’ve also given GeneMANIA a fresh, new look and a fresh set of features.
The export options have been greatly improved and there is a new report,
which gives you a live view of the report while you select which sections

Please help us test the next version of GeneMANIA!

gary.ba...@utoronto.ca (Gary Bader) — Fri, 15 Apr 2011 01:58:05 UT

Please help us test the next version of GeneMANIA! It will only take a few seconds (and about 30 minutes of your computer’s idle time).
Simply visit [link] with your favourite web browser. Visiting this site will automatically run our test suite on our site from your computer. Any problems it finds with our site will be sent back to us so that we can fix them. The tests take about 30 minutes to finish. Your participation will be a big help to the GeneMANIA project -- by running the tests in your browser, we can detect browser and operating system specific problems that would be difficult for us to detect otherwise.

Announcing Version 2.1 of The GeneMANIA Cytoscape Plugin for Gene Function Prediction

jrr...@gmail.com (Jason Montojo) — Mon, 21 Mar 2011 14:42:44 UT

The GeneMANIA Cytoscape Plugin version 2.1 features the following changes:
New Features - Cytoscape:
* Users now have the option to download a specific data set from the
website, instead of only the latest.
* Reworked network descriptions to provide more provenance and linkouts.
* Added "Attributes..." button on result page that allows users to