From mith at ceh.ac.uk  Fri Feb 10 08:36:41 2006
From: mith at ceh.ac.uk (Milo Thurston)
Date: Fri, 10 Feb 2006 13:36:41 +0000
Subject: [Bio-Linux] New Bio-Linux packages
Message-ID: <200602101336.k1ADagiS027809@ivpcp076.nox.ac.uk>

Dear All,
I've recently produced some new packages that may be of interest (thanks to Stewart for 
checking them over), as follows:

bio-linux-yamap:
A first-pass annotation tool for metagenomics. 
http://www.genomics.ceh.ac.uk/yamap/

bio-linux-msatfinder:
A perl script for finding microsatellites.
http://www.genomics.ceh.ac.uk/msatfinder/

bio-linux-trnascan;
An application to search for tRNA genes in genomic sequence.
http://www.genetics.wustl.edu/eddy/tRNAscan-SE/

bio-linux-tetra:
A graphical application for comparing tetranucleotide frequencies between sequences.
The Linux version is a bit older than the Mac version, unfortunately.
http://www.megx.net/tetra_new/html/download.html

bio-linux-ocount:
A command line oligonucleotide frequency calculator.
http://www.megx.net/tetra_new/html/download.html

Also, the following package produced by CCS at CEH Ox. is available.

bio-linux-big-blast:
Sanger's script for chopping up sequences, blasting the parts and re-assembling
them.


Milo.

--
Dr. Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR.
'phone 01865 281975,  fax 01865 281696.
http://www.genomics.ceh.ac.uk/lab/


From jmof1 at st-andrews.ac.uk  Thu Feb 16 07:21:50 2006
From: jmof1 at st-andrews.ac.uk (Jorge Fernandes)
Date: Thu, 16 Feb 2006 12:21:50 +0000
Subject: [Bio-Linux] ? Fast remote desktop for Bio-Linux using FreeNX ?
In-Reply-To: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk>
References: <1133172500.14790.11.camel@ivpcp044.nox.ac.uk>
Message-ID: <6.2.3.4.0.20060216122118.01d431a0@bute.st-and.ac.uk>

Hi Tim,

I have just installed FreeNX on our Bio-Linux machine but I can not 
get remote access to it through my Windows client. There is always a 
connection error and I get the following message:
NX> 203 NXSSH running with pid: 3996
NX> 285 Enabling check on switch command
NX> 285 Enabling skip of SSH config files
nxssh: 138.251.161.20/: no address associated with name

Any idea of what might be the problem? Thanks in advance for your help.

Cheers,

Jorge


Jorge M. O. Fernandes, PhD
Research Fellow
Fish Muscle Research Group
Gatty Marine Laboratory
University of St Andrews
Tel.:+ 44 1334 463449/463488
Fax:+ 44 1334 463443
Web: http://www.st-andrews.ac.uk/%7Efmrg/Jorge%27s%20webpage/index.html




At 10:08 28/11/2005, you wrote:
>Hi All,
>
>Nic here suggested trying FreeNX for remote connections into Bio-Linux
>machines.  The system promises a full-speed remote desktop even over a
>home broadband connection, has clients for Windows, Mac and Linux and is
>available at no cost.  I tried it myself this weekend and was very
>impressed.  If you are running remote applications on a Bio-Linux
>machine and finding them slow, then FreeNX may be the answer.  It also
>allows you to run a remote session on a Windows machine without
>installing software like Exceed.  I have put instructions on how to set
>it up on our website:
>
>http://envgen.nox.ac.uk/envgen/software/archives/000506.html#freenx
>
>The homepage for the FreeNX project is:
>
>http://freenx.berlios.de/
>
>NX was developed by NoMachine:
>
>http://nomachine.com
>
>Please let me know if you do try NX and find it useful.
>
>Thanks,
>
>TIM
>
>--
>Tim Booth <tbooth at ceh.ac.uk>
>NEBC at CEH Oxford
>
>_______________________________________________
>Bio-Linux mailing list
>Bio-Linux at bioinf.ceh.ac.uk
>http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux

Jorge M. O. Fernandes, PhD
Research Fellow
Fish Muscle Research Group
Gatty Marine Laboratory
University of St Andrews
Tel.:+ 44 1334 463449/463488
Fax:+ 44 1334 463443
Web: http://www.st-andrews.ac.uk/%7Efmrg/Jorge%27s%20webpage/index.html 



From btiwari at ceh.ac.uk  Thu Feb 16 08:14:18 2006
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Thu, 16 Feb 2006 13:14:18 +0000
Subject: [Bio-Linux] ? Fast remote desktop for Bio-Linux using
	FreeNX ?
Message-ID: <s3f47ad3.016@wpo.nerc.ac.uk>

Hi Jorge,

Are you able to connect to your Bio-Linux machine using ssh (e.g. using putty client) from your Windows machine?


cheers

Bela 

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

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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


>>> jmof1 at st-andrews.ac.uk 02/16/06 12:21 pm >>>
Hi Tim,

I have just installed FreeNX on our Bio-Linux machine but I can not 
get remote access to it through my Windows client. There is always a 
connection error and I get the following message:
NX> 203 NXSSH running with pid: 3996
NX> 285 Enabling check on switch command
NX> 285 Enabling skip of SSH config files
nxssh: 138.251.161.20/: no address associated with name

Any idea of what might be the problem? Thanks in advance for your help.

Cheers,

Jorge


Jorge M. O. Fernandes, PhD
Research Fellow
Fish Muscle Research Group
Gatty Marine Laboratory
University of St Andrews
Tel.:+ 44 1334 463449/463488
Fax:+ 44 1334 463443
Web: http://www.st-andrews.ac.uk/%7Efmrg/Jorge%27s%20webpage/index.html 






-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.




From jmof1 at st-andrews.ac.uk  Thu Feb 16 10:01:57 2006
From: jmof1 at st-andrews.ac.uk (Jorge Fernandes)
Date: Thu, 16 Feb 2006 15:01:57 +0000
Subject: [Bio-Linux] ? Fast remote desktop for Bio-Linux using
  FreeNX ?
In-Reply-To: <s3f47ad3.016@wpo.nerc.ac.uk>
References: <s3f47ad3.016@wpo.nerc.ac.uk>
Message-ID: <6.2.3.4.0.20060216150002.01d68168@bute.st-and.ac.uk>

Hi Bela,

Nice chatting to you earlier on. :o)

I have just spoken to a very nice lady from IT, who told me that she 
would enable port 22 on our BioLinux machine. Could you please try to 
access my computer through NX again (IP: 138.251.161.20)? Thank you in advance.

Cheers,

Jorge


At 13:14 16/02/2006, you wrote:
>Hi Jorge,
>
>Are you able to connect to your Bio-Linux machine using ssh (e.g. 
>using putty client) from your Windows machine?
>
>
>cheers
>
>Bela
>
>*************************
>Dr. Bela Tiwari
>Lead Bioinformatician
>NERC Environmental
>Bioinformatics Centre
>
>CEH Oxford
>Mansfield Road
>Oxford, OX1 3SR
>01865 281975
>
>*************************
>
>
> >>> jmof1 at st-andrews.ac.uk 02/16/06 12:21 pm >>>
>Hi Tim,
>
>I have just installed FreeNX on our Bio-Linux machine but I can not
>get remote access to it through my Windows client. There is always a
>connection error and I get the following message:
>NX> 203 NXSSH running with pid: 3996
>NX> 285 Enabling check on switch command
>NX> 285 Enabling skip of SSH config files
>nxssh: 138.251.161.20/: no address associated with name
>
>Any idea of what might be the problem? Thanks in advance for your help.
>
>Cheers,
>
>Jorge
>
>
>Jorge M. O. Fernandes, PhD
>Research Fellow
>Fish Muscle Research Group
>Gatty Marine Laboratory
>University of St Andrews
>Tel.:+ 44 1334 463449/463488
>Fax:+ 44 1334 463443
>Web: http://www.st-andrews.ac.uk/%7Efmrg/Jorge%27s%20webpage/index.html
>
>
>
>
>
>
>--
>This message (and any attachments) is for the recipient only. NERC
>is subject to the Freedom of Information Act 2000 and the contents
>of this email and any reply you make may be disclosed by NERC unless
>it is exempt from release under the Act. Any material supplied to
>NERC may be stored in an electronic records management system.
>
>
>_______________________________________________
>Bio-Linux mailing list
>Bio-Linux at bioinf.ceh.ac.uk
>http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux

Jorge M. O. Fernandes, PhD
Research Fellow
Fish Muscle Research Group
Gatty Marine Laboratory
University of St Andrews
Tel.:+ 44 1334 463449/463488
Fax:+ 44 1334 463443
Web: http://www.st-andrews.ac.uk/%7Efmrg/Jorge%27s%20webpage/index.html 



From btiwari at ceh.ac.uk  Fri Feb 17 07:26:41 2006
From: btiwari at ceh.ac.uk (Bela Tiwari)
Date: Fri, 17 Feb 2006 12:26:41 +0000
Subject: [Bio-Linux] GeneSpring version 7.3 available for Bio-Linux - not an
 automatic update
Message-ID: <s3f5c115.030@wpo.nerc.ac.uk>

Hello Bio-Linux System Administrators,

This message will only be pertinent to those of you running GeneSpring on your Bio-Linux machines.

Version 7.3 of GeneSpring is now available for Bio-Linux. We recommend that you upgrade as soon as possible as there are many new features in this version and users will not be able to load new data into Signet (aka GeneSpring Workgroup), the associated database, until they are running version 7.3 of GeneSpring.

The new version of GeneSpring will NOT be installed via automatic nightly update. We have done this to make sure that system administrators have the chance to back up their data before proceeding. The easiest way to proceed with the installation is to log on as manager and type:

sudo apt-get update

and then type

sudo apt-get install bio-linux-genespring

Our  web documentation for GeneSpring has been updated. Of particular importance are changes we have implemented with regards to file permissions. Please read the following information on our FAQ to make sure you understand the default setup for the new version of GeneSpring:

http://envgen.nox.ac.uk/envgen/software/archives/000366.html#permissions 


There are several issues to be aware of BEFORE proceeding with the upgrade of GeneSpring:

1) We HIGHLY recommend that you back up your GeneSpring data directory before starting the upgrade. The data directory on a default Bio-Linux machine is at /home/db/SiliconGenetics/GeneSpring/data.  The NEBC is not responsible for any of your data, so please ensure you back up.

2) Our experience has been that version 7.3 of GeneSpring works on Bio-Linux when installed on a "clean" system.  It also works when upgrading - that is, installing on a machine where GeneSpring is already in use.  However, on one of the machines I upgraded at the NEBC, I did see a conflict, where GeneSpring reported that it could not recognise the normalization scenario I was using. 
To solve this, I moved my "old" GeneSpring/data directory elsewhere and installed the new version of GeneSpring. This creates a new GeneSpring/data directory into which I then moved important files from the old version.
I cannot say what the root cause of this was, but on the basis of this, you may wish to consider "backing up" your old data directory by moving it somewhere else, installing the new bio-linux-genespring package, and then copying your user's files (and your LicenseKey.txt file) from the old GeneSpring/data folder into the new one.  I can't say whether this is really necessary or not, but I have my suspicions that things may work better this way. You'll have to decide for yourself whether to believe my hunch about this or not. Sorry I cannot provide any more concrete advice about this.

3) Agilent has not officially released GeneSpring 7.3 for Linux. As GeneSpring is a java file, it should work fine on any platform. We have endeavored to test the bio-linux-genespring package, but exhaustive testing of version 7.3 has not been done on the Linux platform by Agilent. 

If you do notice anything strange about how GeneSpring is running, please let us know. If it is problem with our package, we will fix it and alert other users right away. If it is a problem with Agilent's software, we will inform them immediately. 


Please do contact us (helpdesk at envgen.nox.ac.uk) if you experience any problems with the new version of GeneSpring.


best wishes,

Bela

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

CEH Oxford
Mansfield Road
Oxford, OX1 3SR
01865 281975

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



-- 
This message (and any attachments) is for the recipient only. NERC
is subject to the Freedom of Information Act 2000 and the contents
of this email and any reply you make may be disclosed by NERC unless
it is exempt from release under the Act. Any material supplied to
NERC may be stored in an electronic records management system.




From mith at ceh.ac.uk  Mon Feb 20 08:31:14 2006
From: mith at ceh.ac.uk (Milo Thurston)
Date: Mon, 20 Feb 2006 13:31:14 +0000
Subject: [Bio-Linux] Distributed computing
In-Reply-To: Your message of "Tue, 10 Jan 2006 18:01:13 GMT."
             <1136916073.10518.134.camel@ivpcp044.nox.ac.uk> 
Message-ID: <200602201331.k1KDVFlq028959@ivpcp076.nox.ac.uk>

Dear All,
I just spotted this link concerning the "Berkeley Open Infrastructure for 
Network Computing". 
http://boinc.berkeley.edu/
Given the requirements for setting up one's own project it might not be
of much use to us right now, but you may find it interesting.
http://boinc.berkeley.edu/parallelize.php
Milo.
--
Dr. Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR.
'phone 01865 281975,  fax 01865 281696.
http://www.genomics.ceh.ac.uk/lab/


From ajt at rri.sari.ac.uk  Mon Feb 20 10:06:43 2006
From: ajt at rri.sari.ac.uk (Tony Travis)
Date: Mon, 20 Feb 2006 15:06:43 +0000
Subject: [Bio-Linux] Distributed computing
In-Reply-To: <200602201331.k1KDVFlq028959@ivpcp076.nox.ac.uk>
References: <200602201331.k1KDVFlq028959@ivpcp076.nox.ac.uk>
Message-ID: <43F9DB03.2060202@rri.sari.ac.uk>

Milo Thurston wrote:
> Dear All,
> I just spotted this link concerning the "Berkeley Open Infrastructure for 
> Network Computing". 
> http://boinc.berkeley.edu/
> Given the requirements for setting up one's own project it might not be
> of much use to us right now, but you may find it interesting.
> http://boinc.berkeley.edu/parallelize.php

Hello, Milo.

I tried using the boinc client for the seti @ home project:

	http://setiathome.ssl.berkeley.edu/

However, we're now folding proteins - that's more appropriate for RRI!

http://fah-web.stanford.edu/cgi-bin/main.py?qtype=userpage&username=RowettResearchInstitute

What did you have in mind for boinc under Bio-Linux?

I'm interested in P2P computing + P2P databases. As you might remember 
from my recent visit to NEBC, I want to create a Bio-Linux based 'black 
box' for my NuGO work. Do you think boinc might be useful to spread the 
computational burden of analysing DNA microarray data, for example?

	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 mith at ceh.ac.uk  Mon Feb 20 10:22:13 2006
From: mith at ceh.ac.uk (Milo Thurston)
Date: Mon, 20 Feb 2006 15:22:13 +0000
Subject: [Bio-Linux] Distributed computing 
In-Reply-To: Your message of "Mon, 20 Feb 2006 15:06:43 GMT."
             <43F9DB03.2060202@rri.sari.ac.uk> 
Message-ID: <200602201522.k1KFMDJ8030828@ivpcp076.nox.ac.uk>

Tony,
Thanks for your reply.

>Do you think boinc might be useful to spread the 
>computational burden of analysing DNA microarray data, for example?

That sort of thing, or perhaps the annotation work that metashark
might undertake. I intend to discuss this further with Dawn to see
if we can come up with something interesting enough (to those outside
the community) to gain access to the full resources.
If you have any suggestions, please let me know.
Thanks,
Milo.

--
Dr. Milo Thurston, CEH Oxford, Mansfield Road, Oxford, OX1 3SR.
'phone 01865 281975,  fax 01865 281696.
http://www.genomics.ceh.ac.uk/lab/


From shou at ceh.ac.uk  Mon Feb 20 13:28:28 2006
From: shou at ceh.ac.uk (Stewart Houten)
Date: Mon, 20 Feb 2006 18:28:28 +0000
Subject: [Bio-Linux] New mailing list address
Message-ID: <20060220182828.GA14596@ivpcp068.nerc-oxford.ac.uk>

Dear All,

This is just a quick note to let you know that the Bio-Linux mailing
list has been moved to a new home to help us better deal with
excessive spam.

If you would like to update your address book, the new address for
posting to the list is:

bio-linux at envgen.nox.ac.uk

and the archives of previous posts can now be viewed at:

http://envgen.nox.ac.uk/pipermail/bio-linux/

Thanks for your cooperation.

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