Announcing Cytoscape v3.0.2 release

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Barry Demchak

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Jul 31, 2013, 8:31:34 PM7/31/13
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=+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+

 

Hello Cytoscapers -

 

We're very pleased and excited to formally release Cytoscape v3.0.2, effective immediately!

 

We encourage you to give it a try!

 

To get a copy for yourself, surf to http://cytoscape.org

 

Before downloading v3.0.2, we urge you to orient yourself by reading our updated Welcome Letter (http://cytoscape.org/cy3_welcome_letter_v9.pdf) and the Release Notes (http://cytoscape.org/releasenotes.html).

 

We now encourage new users, casual users, and power users to download and use Cytoscape v3.0.2 going forward.  (v3.0.2 addresses some rare data loss events and issues important to Google Summer of Code developers. A list of issues addressed is contained at the end of the Welcome Letter.)

 

You can install v3.0.2 on the same workstation as your existing v2.x, v3.0.1, and v3.0.0 Cytoscape, and we hope you will decide to use v3.0.2 *instead* of older versions very soon. (Support for v2.x will continue, but will diminish over time.)

 

Tell all your friends ... THIS IS BIG NEWS!!

 

 

vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv

: Barry Demchak, PhD

: UC San Diego

: Department of Medicine

: Pharmaceutical Sciences Building, Room 4107

: https://sosa.ucsd.edu/confluence/display/~bdemchak/Home

: Land line: (858) 822-4756, Mobile: (858) 452-8700

^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

 

Tim Hull

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Aug 1, 2013, 1:44:24 PM8/1/13
to cytoscape...@googlegroups.com, snehangs...@igp.uu.se, cytoscap...@googlegroups.com, cytoscape...@googlegroups.com, cyto...@googlegroups.com, Barry Demchak, Jason Montojo, Scooter Morris
Hi,

Given the symptoms you're seeing and the fact that you're on a Mac, this looks like it could be a result of the broken Java update Apple put out a few weeks ago. Could you run the following command in a Terminal window to check what version of Java you have installed?

/usr/libexec/java_home -v 1.6 -exec java -version

If the output contains “xM4508”, you have the broken version. If it contains "xM4509", this is probably a different issue...

If you do have the bad version, try downloading and installing the update from Apple:

<http://support.apple.com/kb/DL1572> (OS X 10.7, 10.8+)
<http://support.apple.com/kb/DL1573> (OS X 10.6-only)

On the other hand, if you have the latest version installed and this still occurs, you may want to try deleting the CytoscapeConfiguration directory to clear the bundle cache and running Cytoscape again (note that you will have to reinstall any plugins after doing this.)

Let me know if you are still having the problem after trying these things...

Tim


On Thu, Aug 1, 2013 at 1:30 AM, Snehangshu Kundu <snehangs...@igp.uu.se> wrote:
Dear Cytoscape supporting team,

I downloaded the latest version but the icons/options are not active. Please find the screenshot for the same.
it will be highly appreciated if you can help me in this regard.

Best regards,

SNEHANGSHU KUNDU,PH.D
RESEARCHER
Department of Immunology, Genetics and Pathology (IGP)
Rudbeck Laboratory,C11, PLAN 3
Dag Hammarskjöldsv. 20
Uppsala University
SE-751 85 UPPSALA
SWEDEN
MOBILE- +46 (0)727124714
OFFICE NO +46 18 4714829
FAX- +46-18-55 89 31
Alt.ID: snehans...@gmail.com
Web Site: www.igp.uu.se



On 1 aug 2013, at 02:31, Barry Demchak <idekerlab...@gmail.com> wrote:

=+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+ =+=+
 
Hello Cytoscapers -
 
We're very pleased and excited to formally release Cytoscape v3.0.2, effective immediately!
 
We encourage you to give it a try!
 
To get a copy for yourself, surf to http://cytoscape.org
 
Before downloading v3.0.2, we urge you to orient yourself by reading our updated Welcome Letter (http://cytoscape.org/cy3_welcome_letter_v9.pdf) and theRelease Notes (http://cytoscape.org/releasenotes.html).
 
We now encourage new users, casual users, and power users to download and use Cytoscape v3.0.2 going forward.  (v3.0.2 addresses some rare data loss events and issues important to Google Summer of Code developers. A list of issues addressed is contained at the end of the Welcome Letter.)
 
You can install v3.0.2 on the same workstation as your existing v2.x, v3.0.1, and v3.0.0 Cytoscape, and we hope you will decide to use v3.0.2 *instead* of older versions very soon. (Support for v2.x will continue, but will diminish over time.)
 
Tell all your friends ... THIS IS BIG NEWS!!
 
 
vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv
: Barry Demchak, PhD
: UC San Diego
: Department of Medicine
: Pharmaceutical Sciences Building, Room 4107
: Land line: (858) 822-4756, Mobile: (858) 452-8700
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 

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Davide Cittaro

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Aug 1, 2013, 2:54:01 PM8/1/13
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I've downloaded 3.0.2 version and, apparently, the import procedure from web services is broken (I have all data banks in red with "Server returns error, try again later" message. It was working today with 3.0.1. Also, launching 3.0.1 doesn't solve the issue 
$ java -version
java version "1.7.0_25"
Java(TM) SE Runtime Environment (build 1.7.0_25-b15)
Java HotSpot(TM) 64-Bit Server VM (build 23.25-b01, mixed mode)
$ uname -a
Darwin r702954.station 12.4.0 Darwin Kernel Version 12.4.0: Wed May  1 17:57:12 PDT 2013; root:xnu-2050.24.15~1/RELEASE_X86_64 x86_64

d

Tim Hull

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Aug 2, 2013, 4:16:13 PM8/2/13
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I'm not seeing any issues like what you report - what specific import option in Cytoscape are you trying to use? Also, can you send a screenshot showing the problem?

Tim


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