From dfield at ceh.ac.uk  Thu May  8 09:30:30 2008
From: dfield at ceh.ac.uk (Dawn Field)
Date: Thu, 08 May 2008 14:30:30 +0100
Subject: [Bio-Linux] Ubuntu question
Message-ID: <s8230ea0.028@wpo.nerc.ac.uk>

Many thanks for all the replies to the question about local versus central use of the Bio-Linux documentation system - it was largely used locally.

A new query:

Ubuntu is very similar (derived from) to Debian and very user-friendly - how many of you have experiences with it?

Stewart is working on a DVD Install disk for Bio-Linux 5 and it will most likely be Ubuntu based...we are interested in views on future advance if you have them.

Also, any testers out there once it's ready?   Anyone with a spare machine?

best to all,

Dawn




From sujai.kumar at ed.ac.uk  Thu May  8 09:42:58 2008
From: sujai.kumar at ed.ac.uk (Sujai Kumar)
Date: Thu, 8 May 2008 14:42:58 +0100
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <s8230ea0.028@wpo.nerc.ac.uk>
References: <s8230ea0.028@wpo.nerc.ac.uk>
Message-ID: <ce64fe350805080642o3d1877abo17bc545c2d98fb71@mail.gmail.com>

Hi Dawn/Stewart

Ubuntu should be fun. I've run it before and been happy with the
interface/support/knowledgebase, as has one other user in our lab.
We'd be happy to test Bio-Linux 5 for you.

- Sujai

On Thu, May 8, 2008 at 2:30 PM, Dawn Field <dfield at ceh.ac.uk> wrote:
> Many thanks for all the replies to the question about local versus central use of the Bio-Linux documentation system - it was largely used locally.
>
>  A new query:
>
>  Ubuntu is very similar (derived from) to Debian and very user-friendly - how many of you have experiences with it?
>
>  Stewart is working on a DVD Install disk for Bio-Linux 5 and it will most likely be Ubuntu based...we are interested in views on future advance if you have them.
>
>  Also, any testers out there once it's ready?   Anyone with a spare machine?
>
>  best to all,
>
>  Dawn
>
>
>  _______________________________________________
>  Bio-Linux mailing list
>  Bio-Linux at envgen.nox.ac.uk
>  http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>
>



-- 
Sujai Kumar
Bioinformatics
The Ashworth Laboratories
King's Buildings Campus
University of Edinburgh
EH9 3JT, UK
+44 131 650 7403

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336



From arantza.rico at plants.ox.ac.uk  Thu May  8 10:06:40 2008
From: arantza.rico at plants.ox.ac.uk (Arantza Rico)
Date: Thu, 08 May 2008 15:06:40 +0100
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <ce64fe350805080642o3d1877abo17bc545c2d98fb71@mail.gmail.com>
References: <s8230ea0.028@wpo.nerc.ac.uk>
	<ce64fe350805080642o3d1877abo17bc545c2d98fb71@mail.gmail.com>
Message-ID: <482308F0.9010103@plants.ox.ac.uk>

I use ubuntu at home and I like it very much

At my office we have a spare biolinux machine or otherwise I'm happy to 
test it in mine

Best

Arantza

Sujai Kumar wrote:
> Hi Dawn/Stewart
>
> Ubuntu should be fun. I've run it before and been happy with the
> interface/support/knowledgebase, as has one other user in our lab.
> We'd be happy to test Bio-Linux 5 for you.
>
> - Sujai
>
> On Thu, May 8, 2008 at 2:30 PM, Dawn Field <dfield at ceh.ac.uk> wrote:
>   
>> Many thanks for all the replies to the question about local versus central use of the Bio-Linux documentation system - it was largely used locally.
>>
>>  A new query:
>>
>>  Ubuntu is very similar (derived from) to Debian and very user-friendly - how many of you have experiences with it?
>>
>>  Stewart is working on a DVD Install disk for Bio-Linux 5 and it will most likely be Ubuntu based...we are interested in views on future advance if you have them.
>>
>>  Also, any testers out there once it's ready?   Anyone with a spare machine?
>>
>>  best to all,
>>
>>  Dawn
>>
>>
>>  _______________________________________________
>>  Bio-Linux mailing list
>>  Bio-Linux at envgen.nox.ac.uk
>>  http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>>
>>
>>     
>
>
>
>   

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From petwa at pml.ac.uk  Fri May  9 09:40:04 2008
From: petwa at pml.ac.uk (Peter Walker)
Date: Fri, 9 May 2008 14:40:04 +0100
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <s8230ea0.028@wpo.nerc.ac.uk>
Message-ID: <7546D505C3AF304280B10C3D8B8DFD3902257945@burgh.npm.ac.uk>

One of the things on my todo list is an evaluation of Ubuntu 8.04. I
have used previous releases and been very impressed.
We generally have spare machines for testing so I would be happy to give
it a go here. 
Will there be a Wubi install of Bio-Linux?

Cheers,

Pete

> -----Original Message-----
> From: bio-linux-bounces at envgen.nerc-oxford.ac.uk 
> [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf 
> Of Dawn Field
> Sent: 08 May 2008 14:30
> To: bio-linux at envgen.nerc-oxford.ac.uk
> Cc: Peter.Dawyndt at UGent.be
> Subject: [Bio-Linux] Ubuntu question
> 
> Many thanks for all the replies to the question about local 
> versus central use of the Bio-Linux documentation system - it 
> was largely used locally.
> 
> A new query:
> 
> Ubuntu is very similar (derived from) to Debian and very 
> user-friendly - how many of you have experiences with it?
> 
> Stewart is working on a DVD Install disk for Bio-Linux 5 and 
> it will most likely be Ubuntu based...we are interested in 
> views on future advance if you have them.
> 
> Also, any testers out there once it's ready?   Anyone with a 
> spare machine?
> 
> best to all,
> 
> Dawn
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> 



From dfield at ceh.ac.uk  Mon May 12 07:43:24 2008
From: dfield at ceh.ac.uk (Dawn Field)
Date: Mon, 12 May 2008 12:43:24 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
Message-ID: <s8283b7a.012@wpo.nerc.ac.uk>

Many thanks for all the replies about Ubuntu - there seems to be strong interest and support for it in the community, and lots of offers for testing Bio-Linux 5.   This is really helpful.

The next question is about desktops - Bio-Linux has traditionally used KDE.

How do you feel about GNOME versus KDE - we're asking because there are some good reasons to consider switching to GNOME for the next release and we are looking for the pros/cons of both.

best to all,

Dawn






From bioinformatics.lists at gmail.com  Mon May 12 10:04:59 2008
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Mon, 12 May 2008 15:04:59 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <s8283b7a.012@wpo.nerc.ac.uk>
References: <s8283b7a.012@wpo.nerc.ac.uk>
Message-ID: <d606310d0805120704u51f0d1c7g4209f9f48631faef@mail.gmail.com>

2008/5/12 Dawn Field <dfield at ceh.ac.uk>:
> Many thanks for all the replies about Ubuntu - there seems to be strong interest and support for it in the community, and lots of offers for testing Bio-Linux 5.   This is really helpful.
>
>  The next question is about desktops - Bio-Linux has traditionally used KDE.
>
>  How do you feel about GNOME versus KDE - we're asking because there are some good reasons to consider switching to GNOME for the next release and we are looking for the pros/cons of both.

Hi everyone,

firstly I think the move to Ubuntu is an excellent idea!  I'm not
sticking my oar in here, but as a long term KDE user I would like to
at least place a vote for switching to GNOME in the next release.  KDE
3.5 I do think is an excellent desktop environment, but recently
having trialled the 'future' of KDE (namely KDE's 4.0 and 4.1) I'm
worried that KDE is about to enter a age of 'style over substance'.
KDE 4 is not intuitive to KDE 3.5 users, who would have little
difficulty adapting to GNOME.  We've been using GNOME on Hardy Heron
in preference to our KDE3.5 desktops on Feisty, and pretty much
everyone has made the switch (I am sure KDE3.5 is still the default in
Hardy Kubuntu anyway).  4.X now looks like a horribly mismash of the
worst bits of XP/Vista (convoluted start menus) combined with some
poorly implemented OS X gloss.  The taskbar does not function
*remotely* like the taskbar in any other window manager I have ever
used - in fact losing so much accustomed functionality it is rendered
almost superfluous.   There was (at last check) no way to drag a
quicklaunch icon from the KDE menu to the taskbar.  There are terrible
issues with icon sets, icon placement and sizes on the desktop, and
it's all too easy to accidentally rotate desktop icons - a piece of
functionality I have never, ever desired.  The amount of mouse
waggling to get it back to being lined up could result in many man
hours of lost work..

I never thought I'd step away from KDE, but I have!  GNOME is also a
better choice these days for those who prefer their OSX style screen
layout.

Looking forward to seeing version 5.  Any chance of a server as well
as a desktop build? :)

Dan
-- 
Bioinformatics Support Unit || http://bsu.ncl.ac.uk/
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
Newcastle University, Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A - Mon/Wed)
Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26 - Thu/Fri)



From Peter.Dawyndt at UGent.be  Fri May  9 10:07:06 2008
From: Peter.Dawyndt at UGent.be (Peter Dawyndt)
Date: Fri, 09 May 2008 16:07:06 +0200
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <s8230ea0.029@wpo.nerc.ac.uk>
References: <s8230ea0.029@wpo.nerc.ac.uk>
Message-ID: <48245A8A.1060309@UGent.be>

Dear Dawn,

Many of our co-workers are working on either Debian or Ubuntu, where 
Ubuntu seems like the most popular of the two on desktop systems. The 
minor difference between the two seems to be that Ubuntu has more 
frequent software releases than Debian, but with it comes that it's also 
slightly less stable (won't be much of a problem). I have been using 
Bio-Linux mainly for teaching purposes and would be happy to test out 
the new version.

Best regards,

Peter

Dawn Field wrote:
> Many thanks for all the replies to the question about local versus central use of the Bio-Linux documentation system - it was largely used locally.
>
> A new query:
>
> Ubuntu is very similar (derived from) to Debian and very user-friendly - how many of you have experiences with it?
>
> Stewart is working on a DVD Install disk for Bio-Linux 5 and it will most likely be Ubuntu based...we are interested in views on future advance if you have them.
>
> Also, any testers out there once it's ready?   Anyone with a spare machine?
>
> best to all,
>
> Dawn
>
>
>   


-- 
-----------------------------------------------------------
The StrainInfo.net bioportal has been officially released.
Check it out at www.straininfo.net or www.straininfo.be
-----------------------------------------------------------
Prof. Dr. Peter Dawyndt

Ghent University
Department of Applied Mathematics and Computer Science
Krijgslaan 281 S9
B-9000 Ghent
Belgium

Tel: (32)9.264.47.79
Fax: (32)9.264.49.95
Email: Peter.Dawyndt at UGent.be
-----------------------------------------------------------



From arantza.rico at plants.ox.ac.uk  Wed May 14 05:34:55 2008
From: arantza.rico at plants.ox.ac.uk (Arantza Rico)
Date: Wed, 14 May 2008 10:34:55 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <s8283b7a.012@wpo.nerc.ac.uk>
References: <s8283b7a.012@wpo.nerc.ac.uk>
Message-ID: <482AB23F.4040303@plants.ox.ac.uk>

I prefer Gnome, is simpler and nicer



Dawn Field wrote:
> Many thanks for all the replies about Ubuntu - there seems to be strong interest and support for it in the community, and lots of offers for testing Bio-Linux 5.   This is really helpful.
>
> The next question is about desktops - Bio-Linux has traditionally used KDE.
>
> How do you feel about GNOME versus KDE - we're asking because there are some good reasons to consider switching to GNOME for the next release and we are looking for the pros/cons of both.
>
> best to all,
>
> Dawn
>
>
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>   

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From ajt at rri.sari.ac.uk  Thu May 15 06:10:01 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Thu, 15 May 2008 11:10:01 +0100
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <s8230ea0.028@wpo.nerc.ac.uk>
References: <s8230ea0.028@wpo.nerc.ac.uk>
Message-ID: <482C0BF9.1090905@rri.sari.ac.uk>

Dawn Field wrote:
> [...]
> Ubuntu is very similar (derived from) to Debian and very
> user-friendly - how many of you have experiences with it?
> 
> Stewart is working on a DVD Install disk for Bio-Linux 5 and it will
> most likely be Ubuntu based...we are interested in views on future
> advance if you have them.

Hello, Dawn.

Yes, I have created 'biobuntu' from your Debian Bio-Linux:

	https://blueprints.launchpad.net/ubuntu/+spec/biobuntu

> Also, any testers out there once it's ready?   Anyone with a spare
> machine?

I'm happy to be a tester, and I've got a spare machine to run it on.

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From ajt at rri.sari.ac.uk  Thu May 15 06:16:21 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Thu, 15 May 2008 11:16:21 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <s8283b7a.012@wpo.nerc.ac.uk>
References: <s8283b7a.012@wpo.nerc.ac.uk>
Message-ID: <482C0D75.1050704@rri.sari.ac.uk>

Dawn Field wrote:
> Many thanks for all the replies about Ubuntu - there seems to be
> strong interest and support for it in the community, and lots of
> offers for testing Bio-Linux 5.   This is really helpful.
> 
> The next question is about desktops - Bio-Linux has traditionally
> used KDE.
> 
> How do you feel about GNOME versus KDE - we're asking because there
> are some good reasons to consider switching to GNOME for the next
> release and we are looking for the pros/cons of both.

Hello, Dawn.

We use Bio-Linux under Gnome on our Beowulf cluster and our NuGO 'Black 
Boxes' (Ubuntu + Bio-Linux = 'biobuntu'). I can't see any advantage in 
using KDE these days because Gnome has been greatly improved in recent 
releases. Supporting both might be a waste of time that could be used 
for other aspects of Bio-Linux/biobuntu development!

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From ajt at rri.sari.ac.uk  Thu May 15 06:21:21 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Thu, 15 May 2008 11:21:21 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <d606310d0805120704u51f0d1c7g4209f9f48631faef@mail.gmail.com>
References: <s8283b7a.012@wpo.nerc.ac.uk>
	<d606310d0805120704u51f0d1c7g4209f9f48631faef@mail.gmail.com>
Message-ID: <482C0EA1.2080805@rri.sari.ac.uk>

Dan Swan wrote:
> [...]
> Looking forward to seeing version 5.  Any chance of a server as well
> as a desktop build? :)

Hello, Dan.

I run 'biobuntu' as a server on our Beowulf cluster and NBX's. Just did 
an Ubuntu server install and "aptitude install ubuntu-desktop". We do 
NOT use the console login to run Bio-Linux programs - All done with VNC, 
or web browsers from Windows/Mac/Linux clients:

	http://bioinformatics.rri.sari.ac.uk
	http://nbx2.nugo.org

Please consider signing up for my Ubuntu 'blueprint':

	https://blueprints.launchpad.net/ubuntu/+spec/biobuntu

Thanks,

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From H.Schaefer at warwick.ac.uk  Thu May 15 07:25:24 2008
From: H.Schaefer at warwick.ac.uk (Schaefer, Hendrik)
Date: Thu, 15 May 2008 12:25:24 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <s8283b7a.012@wpo.nerc.ac.uk>
Message-ID: <85B7D5F07C58694E9AC91EE423ED15794E6508@pear.hri.warwick.ac.uk>

Hi Dawn,

I cannot really give you an educated opinion on KDE vs Gnome other than that I do not mind as I do not really use the functions of the desktops.

As long as I can start the programs I need through a terminal I am fine.

Cheers,
Hendrik



--
Dr Hendrik Sch?fer
Warwick HRI
University of Warwick
Wellesbourne, CV35 9EF
United Kingdom
 
Phone (office): +44 (0)2476 575 052
Phone: +44 (0)2476 526 659 or +44 (0)2476 575 086
Email: H.Schaefer at warwick.ac.uk
 
 


> -----Original Message-----
> From: bio-linux-bounces at envgen.nerc-oxford.ac.uk 
> [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf 
> Of Dawn Field
> Sent: 12 May 2008 12:43
> To: bio-linux at envgen.nerc-oxford.ac.uk
> Cc: Peter.Dawyndt at ugent.be
> Subject: [Bio-Linux] next question: KDE or GNOME?
> 
> 
> Many thanks for all the replies about Ubuntu - there seems to 
> be strong interest and support for it in the community, and 
> lots of offers for testing Bio-Linux 5.   This is really helpful.
> 
> The next question is about desktops - Bio-Linux has 
> traditionally used KDE.
> 
> How do you feel about GNOME versus KDE - we're asking because 
> there are some good reasons to consider switching to GNOME 
> for the next release and we are looking for the pros/cons of both.
> 
> best to all,
> 
> Dawn
> 
> 
> 
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk 
> http://envgen.nox.ac.uk/mailman/listinfo/bio-> linux
> 



From Simon.Wagstaff at liverpool.ac.uk  Thu May 15 07:30:59 2008
From: Simon.Wagstaff at liverpool.ac.uk (Wagstaff, Simon)
Date: Thu, 15 May 2008 12:30:59 +0100
Subject: [Bio-Linux] next question: KDE or GNOME?
In-Reply-To: <s8283b7a.012@wpo.nerc.ac.uk>
References: <s8283b7a.012@wpo.nerc.ac.uk>
Message-ID: <1F5F98FBDEA9184EA157995B3E9A9075015A5D89@EVSSTAFF1.livad.liv.ac.uk>

I prefer GNOME over KDE because it's simpler.

Simon

-----Original Message-----
From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Dawn Field
Sent: 12 May 2008 12:43
To: bio-linux at envgen.nerc-oxford.ac.uk
Cc: Peter.Dawyndt at UGent.be
Subject: [Bio-Linux] next question: KDE or GNOME?

Many thanks for all the replies about Ubuntu - there seems to be strong interest and support for it in the community, and lots of offers for testing Bio-Linux 5.   This is really helpful.

The next question is about desktops - Bio-Linux has traditionally used KDE.

How do you feel about GNOME versus KDE - we're asking because there are some good reasons to consider switching to GNOME for the next release and we are looking for the pros/cons of both.

best to all,

Dawn




_______________________________________________
Bio-Linux mailing list
Bio-Linux at envgen.nox.ac.uk
http://envgen.nox.ac.uk/mailman/listinfo/bio-linux



From pasko at biol.uni.wroc.pl  Thu May 15 09:12:16 2008
From: pasko at biol.uni.wroc.pl (=?ISO-8859-2?Q?=A3ukasz_Pa=B6ko?=)
Date: Thu, 15 May 2008 15:12:16 +0200
Subject: [Bio-Linux] Odp:  next question: KDE or GNOME?
Message-ID: <D6BF9321-0D28-4A5F-9885-3BC428727DBF@biol.uni.wroc.pl>

GNOME please :)
Best regards
Lukasz Pasko


~~~~
dr Lukasz Pasko
Department of Vertebrate Zoology
and Laboratory of DNA Analysis
Institute of Zoology
University of Wroclaw
Sienkiewicz street  21
50-335 Wroclaw
Poland



From vanallsburg at hope.edu  Tue May 13 13:22:05 2008
From: vanallsburg at hope.edu (Paul Van Allsburg)
Date: Tue, 13 May 2008 13:22:05 -0400
Subject: [Bio-Linux]  Ubuntu question
Message-ID: <4829CE3D.6030409@hope.edu>

Hi Dawn,

I'd like to help with any ubuntu testing!  I've got a dozen+ machines in 
a classroom/lab that I can work with.  Lately I've been playing with the 
8.04 release installing apps from the NEBC repository.  I'm curious to 
see if I can make a VM appliance out of the finished product and run it 
in a vm player. 

Cheers,
Paul

-- 
Paul Van Allsburg       
Computational Science & Modeling Facilitator
Natural Sciences Division,  Hope College
35 East 12th Street
Holland, Michigan 49423
616-395-7292 
http://www.hope.edu/academic/csm/





From caj23 at leicester.ac.uk  Tue May 20 11:31:56 2008
From: caj23 at leicester.ac.uk (Clive A. Jones)
Date: Tue, 20 May 2008 16:31:56 +0100 (BST)
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <17978765.931211297229501.JavaMail.root@zimbra>
Message-ID: <7168210.951211297516163.JavaMail.root@zimbra>

Hi Dawn,

----- "Dawn Field" <dfield at ceh.ac.uk> wrote:

> Stewart is working on a DVD Install disk for Bio-Linux 5 and it will
> most likely be Ubuntu based...we are interested in views on future
> advance if you have them.

Can all of the bio-* packages be made available in the repository as 
source packages?  We will need to rebuild those packages for Debian if 
you move to Ubuntu. The availability of source packages will also enable 
us to update packages to slightly more recent versions as the need arises, 
without us building the packages from scratch.

I've tried adding the following repository:

deb-src http://envgen.nox.ac.uk/bio-linux/ unstable bio-linux

but no joy. 

We currently install the bio-linux packages on a shared service used 
by many departments, and changing to Ubuntu isn't an option for us.

Best Regards,

Clive.


-- 
Clive Jones - Unix Systems Administrator, caj23 at le.ac.uk
Network Support Services, ITS, University of Leicester.
Tel: 0116 2525133



From shou at ceh.ac.uk  Thu May 22 08:57:11 2008
From: shou at ceh.ac.uk (Stewart Houten)
Date: Thu, 22 May 2008 13:57:11 +0100
Subject: [Bio-Linux] Ubuntu question
In-Reply-To: <7168210.951211297516163.JavaMail.root@zimbra>
References: <17978765.931211297229501.JavaMail.root@zimbra>
	<7168210.951211297516163.JavaMail.root@zimbra>
Message-ID: <20080522125711.GA8235@ivpcp068.nerc-oxford.ac.uk>

Hi Clive,

The plan is to maintain the package repository as it is, with Debian
binary packages, and to move the base system on to Ubuntu for fresh
installs.  Our packages currently work on Ubuntu and in future we will
be building and testing our package updates with both systems in mind.

This should mean that anyone like yourself who is happy with their
current Bio-Linux 4 setup and doesn't wish to upgrade won't have to.

Regards,
Stewart 
--
Dr Stewart Houten, Bio-Linux Developer
NEBC, CEH, Mansfield Road, Oxford, OX1 3SR
http://nebc.nox.ac.uk/ 



From shou at ceh.ac.uk  Wed May 28 12:03:30 2008
From: shou at ceh.ac.uk (Stewart Houten)
Date: Wed, 28 May 2008 17:03:30 +0100
Subject: [Bio-Linux] Glimmer usage on Bio-Linux
Message-ID: <20080528160330.GA20961@ivpcp068.nerc-oxford.ac.uk>

Hi all,

I would like to hear from anyone using the program Glimmer on
Bio-Linux, and in particular from anyone who calls it from within
pipeline (such as Yamap).  

There are a few compatibility issues between version 3.02 and the
previous one which may have consequences for pipeline tools and I
would just like to gauge the potential effects before releasing an
upgraded Bio-Linux package.

Regards,
Stewart 
--
Dr Stewart Houten, Bio-Linux Developer
NEBC, CEH, Mansfield Road, Oxford, OX1 3SR
http://nebc.nox.ac.uk/ 



From ajt at rri.sari.ac.uk  Wed May 28 17:35:29 2008
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Wed, 28 May 2008 22:35:29 +0100
Subject: [Bio-Linux] Glimmer usage on Bio-Linux
In-Reply-To: <20080528160330.GA20961@ivpcp068.nerc-oxford.ac.uk>
References: <20080528160330.GA20961@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <483DD021.5070308@rri.sari.ac.uk>

Stewart Houten wrote:
> Hi all,
> 
> I would like to hear from anyone using the program Glimmer on
> Bio-Linux, and in particular from anyone who calls it from within
> pipeline (such as Yamap).  

Hello, Stewart.

Ah! good news :-)

Yes, I was using Glimmer2 in YAMAP, but I've downloaded and compiled 
Glimmer3 from source. I've been using Glimmer3 separately from YAMAP.

> There are a few compatibility issues between version 3.02 and the
> previous one which may have consequences for pipeline tools and I
> would just like to gauge the potential effects before releasing an
> upgraded Bio-Linux package.

I would be very interested in beta-testing your new package!

	Tony.
-- 
Dr. A.J.Travis,                     |  mailto:ajt at rri.sari.ac.uk
Rowett Research Institute,          |    http://www.rri.sari.ac.uk/~ajt
Greenburn Road, Bucksburn,          |   phone:+44 (0)1224 712751
Aberdeen AB21 9SB, Scotland, UK.    |     fax:+44 (0)1224 716687



From jaa53 at cornell.edu  Wed May 28 21:02:37 2008
From: jaa53 at cornell.edu (Jose Andres)
Date: Wed, 28 May 2008 21:02:37 -0400
Subject: [Bio-Linux] EigenSoft on biolinux?
In-Reply-To: <483DD021.5070308@rri.sari.ac.uk>
References: <20080528160330.GA20961@ivpcp068.nerc-oxford.ac.uk>
	<483DD021.5070308@rri.sari.ac.uk>
Message-ID: <719EFE7B-E443-44A5-861E-0EC4533D0CFB@cornell.edu>

Hello,

I would like to use the software package EIGENSOFT 2.0, which applies  
principal components analyses to multi-locus genotype data.  This  
software could also be useful for many other BioLinux users.  Will  
you please tell me whether this software is compatible with BioLinux  
and whether it can be integrated into the platform? EIGENSOFT is  
already distributed as a linux package so it might be really easy to  
implement (please check the link bellow)


http://genepath.med.harvard.edu/~reich/Software.htm

Thank you!


/Jose Andres



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