From btiwari at ceh.ac.uk  Thu Mar  2 04:37:00 2006
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Thu, 02 Mar 2006 09:37:00 +0000
Subject: [Bio-Linux] Bug in GeneSpring 7.3 to be fixed in updated version -
	probably next week
Message-ID: <s406bce1.081@wpo.nerc.ac.uk>


Hello, 

This is a short note to warn you that there has been a bug found in the new version of GeneSpring where it does not parse out some GO descriptions properly. Agilent will be releasing an updated version, probably next week. As soon as it is released, I will be updating the bio-linux-genespring package.

I would recommend that anyone that has not yet updated to the new version of GeneSpring waits until the new version is released and we have made an updated bio-linux-genespring package available. We will announce the new package release on this mailing list.

Agilent knows about another small bug with the Gene List Inspector columns that will also be fixed in this update.


best wishes,

Bela



*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************





From jaa53 at cornell.edu  Mon Mar  6 14:35:36 2006
From: jaa53 at cornell.edu (Jose A. Andres)
Date: Mon, 6 Mar 2006 14:35:36 -0500 (EST)
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
Message-ID: <54340.132.236.111.89.1141673736.squirrel@webmail.cornell.edu>

Hi all,

My apologies if  my question is too basic, or if this is not the apropiate
forum it.

 I am a naive Bio-linux user and I 'd like to know if it it possible to
run Mapmaker 3.0b (a linkage analysis package)  on a Bio-Limux 4 machine.
 There is an available version of this program that runs on Sun
SPARCStations Running SunOS, but I am not sure if this is compatible with
Bio-linux.

Any suggestions?



From btiwari at ceh.ac.uk  Tue Mar  7 04:48:36 2006
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Tue, 07 Mar 2006 09:48:36 +0000
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
Message-ID: <s40d5706.059@wpo.nerc.ac.uk>

Hi

We have taken a quick look at this program and it might be possible to compile it on Bio-Linux. However, it doesn't compile "out of the box", so before we go further, we were wondering if you, or anyone else on this list involved in linkage analysis, could let us know if MapMaker3 is still a popular program. If so, what differentiates it from other software out there? 

I notice that MapMaker3 not been upated since 1993. While this does not mean it is not a valuable piece of software, it does mean that we would like feedback from people in the user community as to whether it is a program we should be looking at further or not.

cheers

Bela

*************************
Dr. Bela Tiwari
Lead Bioinformatician
NERC Environmental 
Bioinformatics Centre

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

*************************


>>> jaa53 at cornell.edu 03/06/06 7:35 pm >>>
Hi all,

My apologies if  my question is too basic, or if this is not the apropiate
forum it.

 I am a naive Bio-linux user and I 'd like to know if it it possible to
run Mapmaker 3.0b (a linkage analysis package)  on a Bio-Limux 4 machine.
 There is an available version of this program that runs on Sun
SPARCStations Running SunOS, but I am not sure if this is compatible with
Bio-linux.

Any suggestions?

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




From bioinformatics.lists at gmail.com  Tue Mar  7 06:42:50 2006
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Tue, 7 Mar 2006 11:42:50 +0000
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <s40d5706.059@wpo.nerc.ac.uk>
References: <s40d5706.059@wpo.nerc.ac.uk>
Message-ID: <d606310d0603070342q2476c02cl26cab71aa8750a97@mail.gmail.com>

On 3/7/06, Bela Tiwari <btiwari at ceh.ac.uk> wrote:
> Hi
>
> We have taken a quick look at this program and it might be possible to compile it on Bio-Linux. However, it doesn't compile "out of the box", so before we go further, we were wondering if you, or anyone else on this list involved in linkage analysis, could let us know if MapMaker3 is still a popular program. If so, what differentiates it from other software out there?
>
> I notice that MapMaker3 not been upated since 1993. While this does not mean it is not a valuable piece of software, it does mean that we would like feedback from people in the user community as to whether it is a program we should be looking at further or not.

I can't speak for the community but it is still requested at Newcastle
by people doing linkage analysis and we have it installed for use.   A
lot of linkage software is quite venerable,  I think mainly because
its robust, and works and there isn't  much need to fiddle with it
anymore!

regards,

Dan
--
Senior Research Associate, Bioinformatics Support Unit,
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
University of Newcastle upon Tyne,
Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253  (Leech offices: Rooms M.2046/M.2046A)
Tel: +44 (0)191  246 4833 (Devonshire offices: Rooms G.25/G.26)
Website: http://bioinf.ncl.ac.uk/support/



From jaa53 at cornell.edu  Tue Mar  7 08:43:43 2006
From: jaa53 at cornell.edu (Jose A. Andres)
Date: Tue, 7 Mar 2006 08:43:43 -0500 (EST)
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <d606310d0603070342q2476c02cl26cab71aa8750a97@mail.gmail.com>
References: <s40d5706.059@wpo.nerc.ac.uk>
	<d606310d0603070342q2476c02cl26cab71aa8750a97@mail.gmail.com>
Message-ID: <55182.132.236.111.89.1141739023.squirrel@webmail.cornell.edu>

Hi all,

Thanks a lot for for your quick  response and for you potential interest
in  compiling Mapmaker3 for Bio-linux.  Here at Cornell we still use this
program, and as far as I can tell is still use by many despite its "old
age".   I am not an expert myself  on this kind of analysis, so I can't
tell what the differences between Mapmaker3 and some other programs are
(I'll ask around). However,  as I understood it is quite fast, robust and
deals with  both dominant (eg AFLPs) and co-dominant (eg micros) markers. 
Apparently, it is still in good use and many projects/papers still rely on
it.

Thanks again for all your help,

/Jose Andres





From bioinformatics.lists at gmail.com  Tue Mar  7 12:12:44 2006
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Tue, 7 Mar 2006 17:12:44 +0000
Subject: [Bio-Linux] Mapmaker on Bio-linux 4?
In-Reply-To: <55182.132.236.111.89.1141739023.squirrel@webmail.cornell.edu>
References: <s40d5706.059@wpo.nerc.ac.uk>
	<d606310d0603070342q2476c02cl26cab71aa8750a97@mail.gmail.com>
	<55182.132.236.111.89.1141739023.squirrel@webmail.cornell.edu>
Message-ID: <d606310d0603070912w173c1286s94fb4c990e285ae@mail.gmail.com>

On 3/7/06, Jose A. Andres <jaa53 at cornell.edu> wrote:
> Hi all,
>
> Thanks a lot for for your quick  response and for you potential interest
> in  compiling Mapmaker3 for Bio-linux.  Here at Cornell we still use this
> program, and as far as I can tell is still use by many despite its "old
> age".   I am not an expert myself  on this kind of analysis, so I can't
> tell what the differences between Mapmaker3 and some other programs are
> (I'll ask around). However,  as I understood it is quite fast, robust and
> deals with  both dominant (eg AFLPs) and co-dominant (eg micros) markers.
> Apparently, it is still in good use and many projects/papers still rely on
> it.

Hi Jose,

just out of interest have you looked at Genehunter 2?  It's still
maintained and I'm pretty sure it has a lot (if not all) of Mapmakers
functionality.   There are a number of issues getting Mapmaker built
under Linux, at Newcastle we only offer it under OS X, where it is
available as a Fink package.

regards,

Dan


--
Senior Research Associate, Bioinformatics Support Unit,
Institute for Cell and Molecular Biosciences,
Faculty of Medical Sciences, Framlington Place,
University of Newcastle upon Tyne,
Newcastle, NE2 4HH
Tel: +44 (0)191 222 7253  (Leech offices: Rooms M.2046/M.2046A)
Tel: +44 (0)191  246 4833 (Devonshire offices: Rooms G.25/G.26)
Website: http://bioinf.ncl.ac.uk/support/



From asmo at ceh.ac.uk  Thu Mar 30 06:27:11 2006
From: asmo at ceh.ac.uk (Ashley Morley)
Date: Thu, 30 Mar 2006 12:27:11 +0100
Subject: [Bio-Linux] 
	Working with Bio-Linux 4.0 Training course - CEH Oxford, 2nd
	June 2006.
Message-ID: <s42bcec7.060@wpo.nerc.ac.uk>

Dear Colleagues,

The NERC Environmental Bioinformatics Centre (NEBC) will
be running a Working with Bio-Linux introductory course on Friday 2 June, 2006.

This is a one day course designed to introduce new users to the
Bio-Linux system. The course is divided into two sections:
Introduction to Linux and Introduction to Bioinformatics on Bio-Linux.

The course is designed so that people can work at their own pace and
discover the facilities available on Bio-Linux. Instructors from the
NEBC will be on hand to answer Bio-Linux-related questions as well as to discuss
any data management or bioinformatics analysis requirements you may
have.

The course will be held at CEH Oxford and will run from 10:30am until
5:00pm. Registration is on a first come, first serve basis. We will
hold a waiting list if demand exceeds the number of places on this
course and will schedule other courses in the near future if there is
enough interest.

You or anyone on your NERC EG or PG&P grant can register for this
course using our web registration form at:

http://envgen.nox.ac.uk/cgi-bin/showcourses.cgi 

All course notes and sample files are already available at:

http://envgen.nox.ac.uk/envgen/training/archives/000530.html 


best wishes,

The NEBC Team