From ecabot@yahoo.com Mon Apr 14 10:49:43 2003
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Date: Mon, 14 Apr 2003 10:49:41 -0700 (PDT)
From: "Eric L. Cabot" <ecabot@yahoo.com>
To: sockeye-announce@bcgsc.ca
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Subject: [Sockeye-announce] Can't start fresh install of Sockeye 0.8.2 
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I am posting this here because I cannot successfully start Sockeye 0.8.2,
and hence have no way to select the problem/suggestion reporting tool from
the main menu.

I just downloaded and installed Sockey 0.8.2 under Suse Linux 8.0 (i386).
Attempts to launch Sockeye result in the following
InvocationTargetException:

java.lang.NoSuchMethodError
	at ca.bcgsc.sockeye.config.Configuration.init(Configuration.java:92)
	at ca.bcgsc.sockeye.config.Configuration.read(Configuration.java:57)
	at ca.bcgsc.sockeye.gui.Sockeye.<init>(Sockeye.java:48)
	at ca.bcgsc.sockeye.gui.Sockeye.main(Sockeye.java:141)
	at java.lang.reflect.Method.invoke(Native Method)
	at com.zerog.lax.LAX.launch(Unknown Source)
	at com.zerog.lax.LAX.main(Unknown Source)

Was there some crucial installation step that I missed?  During the
download, an applet tried to run on my machine but access was not granted,
since it was not something that I expected. In retrospect, this was from
ZeroG and I wonder if this might have been part of the installer. 

__________________________________________________
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From smontgom@bcgsc.bc.ca Mon Apr 14 16:12:17 2003
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Date: Mon, 14 Apr 2003 16:12:11 -0700
From: Stephen Montgomery <smontgom@bcgsc.bc.ca>
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cc: sockeye-announce@bcgsc.ca
Subject: [Sockeye-announce] Sockeye bug fix.
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We believe we have identified the current bug in the Sockeye release 
0.82.  This has to do with the InstallAnywhere configuration not 
correctly setting the target Java VM (ie the one that comes with your 
Sockeye installation).  Our untestable opinion at this point is that 
changing your sockeye.lax file entry to below

 lax.nl.current.vm=jre/bin/java

should fix this problem.  Please confirm if that isn't the case.  You 
may need to go into your jre/bin folder and change all the files to 
executable.  Your install left them as r+w only.

Thanks for reporting this install bug.  Feel free to contact the Sockeye 
development group about further errors at this.

Cheers,
Stephen

From grobertson@bcgsc.ca Thu May 29 15:24:28 2003
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From: Gordon Robertson <grobertson@bcgsc.ca>
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Subject: [Sockeye-announce] Sockeye 0.8.4 now available
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Date: Thu, 29 May 2003 22:24:31 -0000
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A new prerelease version of Sockeye is now available for Linux or 
Windows. A 'Changes' document is available on the download page and in 
the online help. Installers are available with and without bundled 
Java/Java3D.


Gordon Robertson
Gene Regulation (Informatics) - BCGSC

From grobertson@bcgsc.ca  Wed Jan 28 11:22:24 2004
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Date: Wed, 28 Jan 2004 11:22:23 -0800
From: Gordon Robertson <grobertson@bcgsc.ca>
Organization: Michael Smith Genome Sciences Centre
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Subject: [Sockeye-announce] Sockeye 1.1 released
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Sockeye v1.1 is available as of Monday, 26 January, 2004, from www.bcgsc.ca/gc/bomge. The latest version of the 3D genome visualisation software is available for Linux and Windows. Each version has a bundled Java 1.4.x/Java3D 1.3.x; each is available as an InstallAnywhere installer or as Java WebStart. Solaris and Mac OS X versions will be available soon. 

This version offers improved functionality for comparative genomics in an improved user interface. 'On-demand annotations' with 'semantic zooming' permit querying very large genomic regions. DNA sequences for pairs or sets of related regions can be aligned using several methods, sequence conservation profiles and conserved regions are dynamically configurable from an alignment, and a basepair-level viewer for alignments is available. Sequences can be scanned with known TFBS weight matrices that are accessed by a catalog browser from user-extensible libraries. 

A change list and release notes are available from the download page. A Documentation page offers How-to's and an FAQ.

-- 
Gordon Robertson
Gene Regulation (Informatics)
Canada's Michael Smith Genome Sciences Centre
Vancouver BC Canada
www.bcgsc.ca
Voice: 604-707-5900 ext 5416



From klin@bcgsc.ca  Fri May 28 14:33:53 2004
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Date: Fri, 28 May 2004 14:30:53 -0700
From: Keven Lin <klin@bcgsc.ca>
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Subject: [Sockeye-announce] Sockeye 1.2 Release
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Sockeye 1.2 Release Note

The release notes for Sockeye 1.2 contain a summery of recent changes 
made to the Sockeye project based on the 1.2 beta development branch.  
This document list applicable fixes that were issued since the last release

Two ways to get Sockeye 1.2:

 - via Java Webstart (http://coast.bcgsc.ca:8080/webstart)
 - Sockeye installers for Linux, Solaris and Windows are currently 
available to download on FlintBox (http://www.flintbox.ca)

What's New
-------------

- Sockey 1.2 Online Help 
(http://coast.bcgsc.bc.ca:8080/sockeyehelp/1.2/index.html)
- Primer Prediction
- Rearrangement alignment (Shuffle-LAGAN, Mauve)
- New algorithms for alignment (Dialign, T-Coffee, Conreal) and motif 
discovery (MotifSampler, (w)consensus, MEME)
- Improved session management
- Set Operation Dialog
- Masked sequence
- Improve Ensembl query performance
- Loading orthologues in Ensembl v18 or Higher
- Scalability improvement: indirect database connection

User Support and Feedback
-----------------------------

There are several excellent resources to help support users and gather 
feedbacks:

- Sockeye Online Help 
(http://coast.bcgsc.ca:8080/sockeyehelp/1.2/index.html)
- Feedback box in Sockeye.  In Sockeye, select Tools -> 
Suggestions/Problems



Sockeye Development Team

From klin@bcgsc.ca  Fri May 28 15:02:53 2004
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Date: Fri, 28 May 2004 14:59:54 -0700
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Subject: [Sockeye-announce] [Fwd: Sockeye on MSN messenger]
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Date: Wed, 26 May 2004 11:40:17 -0700
From: Maik Hassel <mhassel@bcgsc.bc.ca>
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Hey everybody,

in order to provide faster help and online guidance to outside(!!!) 
users, we have sockeye (our team) reachable by MSN messenger

sockeye-help@bcgsc.ca


Maik

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