[Bio-Linux] Bio-Linux Digest, Vol 78, Issue 18
Mahendra Modi
mkmodi at aau.ac.in
Mon Mar 30 08:26:53 EDT 2015
Hi Robert,
You will need to set nomodeset immediately after you see the splash screen
as the graphics chip is not sufficient to run unity desktop. Once you may
edit grub to include nomodeset and choose to run the mate terminal instead
of ubuntu. I think thats what I did to get my system going.
Mahendra
On Mon, Mar 30, 2015 at 5:47 PM, <bio-linux-request at nebclists.nerc.ac.uk>
wrote:
> Send Bio-Linux mailing list submissions to
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>
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> or, via email, send a message with subject or body 'help' to
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>
> You can reach the person managing the list at
> bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
> 1. Re: Bio-Linux Digest, Vol 78, Issue 17 (Robert Tyx)
> 2. Re: Bio-Linux on Dell R720 (Tim Booth)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Mar 2015 04:25:18 -0700
> From: Robert Tyx <robtyx at yahoo.com>
> To: "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 17
> Message-ID:
> <
> 1427714718.45474.YahooMailAndroidMobile at web140803.mail.bf1.yahoo.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,?
>
> In contrast to Mohendra, I have not been able to get BL8 to install
> successfully on a Dell R720. There's probably a way to get it to work
> (special drivers or something) but I don't know. It gets a kernel panic
> pretty quickly every time. For what it's worth, vanilla Ubuntu 14.04 LTS
> workstation does not install either, but the server version works fine. BL
> 7 works fine on this system also...
>
> Sent from Yahoo Mail on Android
>
> From:"bio-linux-request at nebclists.nerc.ac.uk" <
> bio-linux-request at nebclists.nerc.ac.uk>
> Date:Mon, Mar 30, 2015 at 7:00 AM
> Subject:Bio-Linux Digest, Vol 78, Issue 17
>
> Send Bio-Linux mailing list submissions to
> ??? bio-linux at nebclists.nerc.ac.uk
>
> To subscribe or unsubscribe via the World Wide Web, visit
> ??? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> or, via email, send a message with subject or body 'help' to
> ??? bio-linux-request at nebclists.nerc.ac.uk
>
> You can reach the person managing the list at
> ??? bio-linux-owner at nebclists.nerc.ac.uk
>
> When replying, please edit your Subject line so it is more specific
> than "Re: Contents of Bio-Linux digest..."
>
>
> Today's Topics:
>
> ? 1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 30 Mar 2015 16:08:04 +0530
> From: Mahendra Modi <mkmodi at aau.ac.in>
> To: bio-linux at nebclists.nerc.ac.uk
> Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
> Message-ID:
> ??? <CAPUhUGx419u3XA2mC2R+LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
> Content-Type: text/plain; charset="utf-8"
>
> Hi,
>
> We are running 3(three) servers with Bio-linux 8 and one of the me is a
> Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis from
> Aberdeen University helped us in customisation of the servers. We use these
> servers for NGS data analysis and Simulation studies using Gromacs.
>
> Mahendra
>
>
>
> On Sat, Mar 28, 2015 at 5:30 PM, <bio-linux-request at nebclists.nerc.ac.uk>
> wrote:
>
> > Send Bio-Linux mailing list submissions to
> >? ? ? ? bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> >? ? ? ? http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> >? ? ? ? bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> >? ? ? ? bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> >? ? 1. is it possible to install biolinux on a dell server with 64Gb
> >? ? ? RAM and 16 cores? (Stefano Campanaro)
> >? ? 2. Re: is it possible to install biolinux on a dell server with
> >? ? ? 64Gb RAM and 16 cores? (Tony Travis)
> >? ? 3. Re: is it possible to install biolinux on a dell server with
> >? ? ? 64Gb RAM and 16 cores? (Sharma, M D)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Fri, 27 Mar 2015 17:54:58 +0100
> > From: Stefano Campanaro <stefano.campanaro at gmail.com>
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID:
> >? ? ? ? <
> > CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri, 27 Mar 2015 17:19:43 +0000
> > From: Tony Travis <tony.travis at minke-informatics.co.uk>
> > To: <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> > Content-Type: text/plain; charset="windows-1252"
> >
> > On 27/03/15 16:54, Stefano Campanaro wrote:
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with 64Gb
> > > RAM and 16 cores. I would have some suggestions from users that are
> > > using bio linux on servers with similar characteristics.
> >
> > Hi, Stefano.
> >
> > I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> > 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University of
> > Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> > from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to boot
> > from RAID6 if it's not degraded.
> >
> > I've also set up Bio-Linux terminal servers many times in the past, for
> > example at the Wellcome Trust Centre for Cell Biology in Edinburgh, and
> > I helped my friends at Assam Agricultural University set up Bio-Linux 8
> > servers there for a training course we held recently.
> >
> > Bio-Linux 8 works very well as an "x2go" or SSH terminal server, thanks
> > to the efforts that Tim and his team at EOS have put into Bio-Linux 8.
> >
> > I've got 10 at SATA2 drives in each of our three Bio-Linux servers here:
> >
> > 6 at 2TB:
> >? ? ? ? RAID1 /boot
> >? ? ? ? RAID6 /, swap, /usr/local, /home, work
> >
> > 2 at 4TB:
> >? ? ? ? JBOD /backup1
> >? ? ? ? JBOD /backup2
> >
> > 2 at 4TB:
> >? ? ? ? JBOD /archive
> >? ? ? ? JBOD /scratch
> >
> > Let me know if there is anything I can do to help?
> >
> > If you boot your server from a Bio-Linux USB-stick and let me in through
> > your firewall I can install it for you remotely. I've done this several
> > times already for disaster recovery on an EU FP-6 project.
> >
> >? Tony.
> >
> > --
> > Minke Informatics Limited, Registered in Scotland - Company No. SC419028
> > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK)
> > tel. +44(0)19755 63548? ? ? ? ? ? ? ? ? ? http://minke-informatics.co.uk
> > mob. +44(0)7985 078324? ? ? ? mailto:tony.travis at minke-informatics.co.uk
> >
> >
> > ------------------------------
> >
> > Message: 3
> > Date: Fri, 27 Mar 2015 17:17:56 +0000
> > From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> > To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
> >? ? ? ? and discussion" <bio-linux at nebclists.nerc.ac.uk>,
> >? ? ? ? "bio-linux at nebclists.nerc.ac.uk" <bio-linux at nebclists.nerc.ac.uk>
> > Subject: Re: [Bio-Linux] is it possible to install biolinux on a dell
> >? ? ? ? server with 64Gb RAM and 16 cores?
> > Message-ID: <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> > Content-Type: text/plain; charset="us-ascii"
> >
> > Absolutely... I have it as you described and also with 64 cores and 512
> GB
> > of RAM..
> >
> > Sent from my HTC
> >
> > On 27 Mar 2015 16:55, Stefano Campanaro <stefano.campanaro at gmail.com>
> > wrote:
> > Hi,
> > I would install biolinux on a recently acquired DELL server with 64Gb RAM
> > and 16 cores. I would have some suggestions from users that are using bio
> > linux on servers with similar characteristics.
> > Thank you
> > Sincerely
> > --
> > Stefano
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL: <
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> > >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 16
> > *****************************************
> >
>
>
>
> --
> ________________________
> Prof. Mahendra K Modi
> Head, Agril Biotechnology & Coordinator, DIC
> Assam Agricultural University
> Jorhat 785013, India
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> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 17
> *****************************************
>
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>
> ------------------------------
>
> Message: 2
> Date: Mon, 30 Mar 2015 13:18:05 +0100
> From: Tim Booth <tbooth at ceh.ac.uk>
> To: Bio-Linux help and discussion <bio-linux at nebclists.nerc.ac.uk>
> Subject: Re: [Bio-Linux] Bio-Linux on Dell R720
> Message-ID: <1427717885.12632.5.camel at wllt1771.nerc-wallingford.ac.uk>
> Content-Type: text/plain; charset="UTF-8"
>
> Hi Robert,
>
> Strange that you should find the server version of 14.04 works but the
> desktop doesn't, because the kernel and drivers are identical. The
> server installer just puts on a different selection of packages. Is it
> possible that the Unity desktop, which uses the 3D capabilities of the
> graphics card, is triggering the crash, do you think?
>
> So does this mean you are running vanilla 14.04 from the server
> installation and installing just the Bio-Linux packages you need, or did
> you try using my upgrade script to add all the Bio-Linux stuff in one
> go?
>
> Cheers,
>
> TIM
>
> On Mon, 2015-03-30 at 12:25 +0100, Robert Tyx wrote:
> > Hi,
> > In contrast to Mohendra, I have not been able to get BL8 to install
> > successfully on a Dell R720. There's probably a way to get it to work
> > (special drivers or something) but I don't know. It gets a kernel
> > panic pretty quickly every time. For what it's worth, vanilla Ubuntu
> > 14.04 LTS workstation does not install either, but the server version
> > works fine. BL 7 works fine on this system also...
> >
> >
> >
> > Sent from Yahoo Mail on Android
> >
> >
> > ______________________________________________________________________
> > From:"bio-linux-request at nebclists.nerc.ac.uk"
> > <bio-linux-request at nebclists.nerc.ac.uk>
> > Date:Mon, Mar 30, 2015 at 7:00 AM
> > Subject:Bio-Linux Digest, Vol 78, Issue 17
> >
> >
> > Send Bio-Linux mailing list submissions to
> > bio-linux at nebclists.nerc.ac.uk
> >
> > To subscribe or unsubscribe via the World Wide Web, visit
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > or, via email, send a message with subject or body 'help' to
> > bio-linux-request at nebclists.nerc.ac.uk
> >
> > You can reach the person managing the list at
> > bio-linux-owner at nebclists.nerc.ac.uk
> >
> > When replying, please edit your Subject line so it is more specific
> > than "Re: Contents of Bio-Linux digest..."
> >
> >
> > Today's Topics:
> >
> > 1. Re: Bio-Linux Digest, Vol 78, Issue 16 (Mahendra Modi)
> >
> >
> > ----------------------------------------------------------------------
> >
> > Message: 1
> > Date: Mon, 30 Mar 2015 16:08:04 +0530
> > From: Mahendra Modi <mkmodi at aau.ac.in>
> > To: bio-linux at nebclists.nerc.ac.uk
> > Subject: Re: [Bio-Linux] Bio-Linux Digest, Vol 78, Issue 16
> > Message-ID:
> > <CAPUhUGx419u3XA2mC2R
> > +LgaSKBDTkVBc9UiqBHvn=oxQTkhrUg at mail.gmail.com>
> > Content-Type: text/plain; charset="utf-8"
> >
> > Hi,
> >
> > We are running 3(three) servers with Bio-linux 8 and one of the me is
> > a
> > Dell r520 with 2 8core Xeon processors and 128GiB RAM. Tony Travis
> > from
> > Aberdeen University helped us in customisation of the servers. We use
> > these
> > servers for NGS data analysis and Simulation studies using Gromacs.
> >
> > Mahendra
> >
> >
> >
> > On Sat, Mar 28, 2015 at 5:30 PM,
> > <bio-linux-request at nebclists.nerc.ac.uk>
> > wrote:
> >
> > > Send Bio-Linux mailing list submissions to
> > > bio-linux at nebclists.nerc.ac.uk
> > >
> > > To subscribe or unsubscribe via the World Wide Web, visit
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > > or, via email, send a message with subject or body 'help' to
> > > bio-linux-request at nebclists.nerc.ac.uk
> > >
> > > You can reach the person managing the list at
> > > bio-linux-owner at nebclists.nerc.ac.uk
> > >
> > > When replying, please edit your Subject line so it is more specific
> > > than "Re: Contents of Bio-Linux digest..."
> > >
> > >
> > > Today's Topics:
> > >
> > > 1. is it possible to install biolinux on a dell server with 64Gb
> > > RAM and 16 cores? (Stefano Campanaro)
> > > 2. Re: is it possible to install biolinux on a dell server with
> > > 64Gb RAM and 16 cores? (Tony Travis)
> > > 3. Re: is it possible to install biolinux on a dell server with
> > > 64Gb RAM and 16 cores? (Sharma, M D)
> > >
> > >
> > >
> > ----------------------------------------------------------------------
> > >
> > > Message: 1
> > > Date: Fri, 27 Mar 2015 17:54:58 +0100
> > > From: Stefano Campanaro <stefano.campanaro at gmail.com>
> > > To: bio-linux at nebclists.nerc.ac.uk
> > > Subject: [Bio-Linux] is it possible to install biolinux on a dell
> > > server with 64Gb RAM and 16 cores?
> > > Message-ID:
> > > <
> > > CAKN-0dNHyetvgYd19MOqVeuZazWQ_Z1Q5M1z73Av-L-C7S+4fQ at mail.gmail.com>
> > > Content-Type: text/plain; charset="utf-8"
> > >
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with
> > 64Gb RAM
> > > and 16 cores. I would have some suggestions from users that are
> > using bio
> > > linux on servers with similar characteristics.
> > > Thank you
> > > Sincerely
> > > --
> > > Stefano
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/2dbe225a/attachment-0001.html
> > > >
> > >
> > > ------------------------------
> > >
> > > Message: 2
> > > Date: Fri, 27 Mar 2015 17:19:43 +0000
> > > From: Tony Travis <tony.travis at minke-informatics.co.uk>
> > > To: <bio-linux at nebclists.nerc.ac.uk>
> > > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> > dell
> > > server with 64Gb RAM and 16 cores?
> > > Message-ID: <5515912F.2030803 at minke-informatics.co.uk>
> > > Content-Type: text/plain; charset="windows-1252"
> > >
> > > On 27/03/15 16:54, Stefano Campanaro wrote:
> > > > Hi,
> > > > I would install biolinux on a recently acquired DELL server with
> > 64Gb
> > > > RAM and 16 cores. I would have some suggestions from users that
> > are
> > > > using bio linux on servers with similar characteristics.
> > >
> > > Hi, Stefano.
> > >
> > > I'm running Bio-Linux 8 on three Tyan S8230-based servers with dual
> > > 8-core Opteron 6128 CPU's and 128GiB RAM in each at the University
> > of
> > > Aberdeen. I installed Bio-Linux onto a partitionable RAID6, but boot
> > > from a RAID1 because GRUB can't boot from a degraded RAID6 - OK to
> > boot
> > > from RAID6 if it's not degraded.
> > >
> > > I've also set up Bio-Linux terminal servers many times in the past,
> > for
> > > example at the Wellcome Trust Centre for Cell Biology in Edinburgh,
> > and
> > > I helped my friends at Assam Agricultural University set up
> > Bio-Linux 8
> > > servers there for a training course we held recently.
> > >
> > > Bio-Linux 8 works very well as an "x2go" or SSH terminal server,
> > thanks
> > > to the efforts that Tim and his team at EOS have put into Bio-Linux
> > 8.
> > >
> > > I've got 10 at SATA2 drives in each of our three Bio-Linux servers
> > here:
> > >
> > > 6 at 2TB:
> > > RAID1 /boot
> > > RAID6 /, swap, /usr/local, /home, work
> > >
> > > 2 at 4TB:
> > > JBOD /backup1
> > > JBOD /backup2
> > >
> > > 2 at 4TB:
> > > JBOD /archive
> > > JBOD /scratch
> > >
> > > Let me know if there is anything I can do to help?
> > >
> > > If you boot your server from a Bio-Linux USB-stick and let me in
> > through
> > > your firewall I can install it for you remotely. I've done this
> > several
> > > times already for disaster recovery on an EU FP-6 project.
> > >
> > > Tony.
> > >
> > > --
> > > Minke Informatics Limited, Registered in Scotland - Company No.
> > SC419028
> > > Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland
> > (UK)
> > > tel. +44(0)19755 63548
> > http://minke-informatics.co.uk
> > > mob. +44(0)7985 078324
> > mailto:tony.travis at minke-informatics.co.uk
> > >
> > >
> > > ------------------------------
> > >
> > > Message: 3
> > > Date: Fri, 27 Mar 2015 17:17:56 +0000
> > > From: "Sharma, M D" <M.D.Sharma at exeter.ac.uk>
> > > To: Stefano Campanaro <stefano.campanaro at gmail.com>, "Bio-Linux help
> > > and discussion" <bio-linux at nebclists.nerc.ac.uk>,
> > > "bio-linux at nebclists.nerc.ac.uk"
> > <bio-linux at nebclists.nerc.ac.uk>
> > > Subject: Re: [Bio-Linux] is it possible to install biolinux on a
> > dell
> > > server with 64Gb RAM and 16 cores?
> > > Message-ID:
> > <vackbrvwh29b5de7j29erggg.1427476673744 at email.android.com>
> > > Content-Type: text/plain; charset="us-ascii"
> > >
> > > Absolutely... I have it as you described and also with 64 cores and
> > 512 GB
> > > of RAM..
> > >
> > > Sent from my HTC
> > >
> > > On 27 Mar 2015 16:55, Stefano Campanaro
> > <stefano.campanaro at gmail.com>
> > > wrote:
> > > Hi,
> > > I would install biolinux on a recently acquired DELL server with
> > 64Gb RAM
> > > and 16 cores. I would have some suggestions from users that are
> > using bio
> > > linux on servers with similar characteristics.
> > > Thank you
> > > Sincerely
> > > --
> > > Stefano
> > > -------------- next part --------------
> > > An HTML attachment was scrubbed...
> > > URL: <
> > >
> >
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150327/3695ba87/attachment-0001.html
> > > >
> > >
> > > ------------------------------
> > >
> > > Subject: Digest Footer
> > >
> > > _______________________________________________
> > > Bio-Linux mailing list
> > > Bio-Linux at nebclists.nerc.ac.uk
> > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> > >
> > >
> > > ------------------------------
> > >
> > > End of Bio-Linux Digest, Vol 78, Issue 16
> > > *****************************************
> > >
> >
> >
> >
> > --
> > ________________________
> > Prof. Mahendra K Modi
> > Head, Agril Biotechnology & Coordinator, DIC
> > Assam Agricultural University
> > Jorhat 785013, India
> > -------------- next part --------------
> > An HTML attachment was scrubbed...
> > URL:
> > <
> http://nebclists.nerc.ac.uk/pipermail/bio-linux/attachments/20150330/ced686e3/attachment-0001.html
> >
> >
> > ------------------------------
> >
> > Subject: Digest Footer
> >
> > _______________________________________________
> > Bio-Linux mailing list
> > Bio-Linux at nebclists.nerc.ac.uk
> > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> >
> >
> > ------------------------------
> >
> > End of Bio-Linux Digest, Vol 78, Issue 17
> > *****************************************
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://environmentalomics.org/bio-linux
> +44 1491 69 2297
>
>
>
> ------------------------------
>
> Subject: Digest Footer
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
>
>
> ------------------------------
>
> End of Bio-Linux Digest, Vol 78, Issue 18
> *****************************************
>
--
________________________
Prof. Mahendra K Modi
Head, Agril Biotechnology & Coordinator, DIC
Assam Agricultural University
Jorhat 785013, India
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