From shou at ceh.ac.uk  Tue Dec  2 08:40:10 2008
From: shou at ceh.ac.uk (Stewart Houten)
Date: Tue, 2 Dec 2008 13:40:10 +0000
Subject: [Bio-Linux] NEBC Bio-Linux 5.0 released
Message-ID: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>

Dear all,

The NEBC is pleased to announce the release of Bio-Linux 5.0.  This
new version is based on the popular Ubuntu Linux distribution and
provides a very user-friendly desktop while continuing to deliver
access to a growing suite of bioinformatics applications.

Bio-Linux 5.0 is available on USB memory stick or as an image to
download and burn onto a DVD and is easy to install on a wide range of
computer hardware. You can also run Bio-Linux 5 as a Live system from
either the memory stick or DVD version. This is a simple way to try
out Bio-Linux.  It can also provide a practical way to deliver
teaching courses, give demonstrations or to work while away from the
office.

All PIs and CO-Is on NERC PGP grants will receive a Bio-Linux USB
stick in the post shortly.  We welcome you to try it out and would
love to hear your comments and feedback on the new release.

To find out more please visit http://nebc.nox.ac.uk/bio-linux.html.
Differences between Bio-Linux 4.0 and Bio-Linux 5.0 can be found at
http://nebc.nox.ac.uk/envgen/software/archives/000590.html.

Regards,

The NEBC Team



From rwt017 at abdn.ac.uk  Tue Dec  2 10:15:52 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Tue, 02 Dec 2008 15:15:52 +0000
Subject: [Bio-Linux] NEBC Bio-Linux 5.0 released
In-Reply-To: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>
References: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <49355128.6070805@abdn.ac.uk>

Stewart Houten wrote:
> Dear all,
> 
> The NEBC is pleased to announce the release of Bio-Linux 5.0.  This
> new version is based on the popular Ubuntu Linux distribution and
> provides a very user-friendly desktop while continuing to deliver
> access to a growing suite of bioinformatics applications.
> [...]

Hello, Stewart.

Congratulations on the release of Bio-Linux5 - I've now marked by 
'biobuntu' blue-print as 'obsolete' and will use Bio-Linux5 :-)

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From marty.gollery at gmail.com  Tue Dec  2 23:46:05 2008
From: marty.gollery at gmail.com (Martin Gollery)
Date: Tue, 2 Dec 2008 20:46:05 -0800
Subject: [Bio-Linux] NEBC Bio-Linux 5.0 released
In-Reply-To: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>
References: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>
Message-ID: <bdd10c2a0812022046m64bb5afel60404c5195ee1efd@mail.gmail.com>

I don't know much about cloud computing, but have you thought about
getting it set up as an AMI on the amazon EC2 service? That way people
could  run it with no install needed and pay only for the time that
they use.

best,
Marty

On Tue, Dec 2, 2008 at 5:40 AM, Stewart Houten <shou at ceh.ac.uk> wrote:
> Dear all,
>
> The NEBC is pleased to announce the release of Bio-Linux 5.0.  This
> new version is based on the popular Ubuntu Linux distribution and
> provides a very user-friendly desktop while continuing to deliver
> access to a growing suite of bioinformatics applications.
>
> Bio-Linux 5.0 is available on USB memory stick or as an image to
> download and burn onto a DVD and is easy to install on a wide range of
> computer hardware. You can also run Bio-Linux 5 as a Live system from
> either the memory stick or DVD version. This is a simple way to try
> out Bio-Linux.  It can also provide a practical way to deliver
> teaching courses, give demonstrations or to work while away from the
> office.
>
> All PIs and CO-Is on NERC PGP grants will receive a Bio-Linux USB
> stick in the post shortly.  We welcome you to try it out and would
> love to hear your comments and feedback on the new release.
>
> To find out more please visit http://nebc.nox.ac.uk/bio-linux.html.
> Differences between Bio-Linux 4.0 and Bio-Linux 5.0 can be found at
> http://nebc.nox.ac.uk/envgen/software/archives/000590.html.
>
> Regards,
>
> The NEBC Team
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>
> --
> 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.
>
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist



From dfield at ceh.ac.uk  Wed Dec  3 05:52:51 2008
From: dfield at ceh.ac.uk (Dawn Field)
Date: Wed, 03 Dec 2008 10:52:51 +0000
Subject: [Bio-Linux] Cloud computing
Message-ID: <s9366502.088@wpo.nerc.ac.uk>

Thanks for bringing up cloud computing.  Yes, there are academic groups starting to use cloud computing and we, as a community, should start to think about how the NERC community may/may not use cloud computing in general in the future.

Is this coming up on the radar for more people on this list?

Here is the URL to the Amazon Elastic Compute Cloud (Amazon EC2).

http://aws.amazon.com/ec2/

Cloud computing - and especially Amazon's EC2 service - is coming up more and more at major meetings where access to BIG compute power is becoming an issue.  For example, at Metagenomics 2008 in San Diego in Nov.

Interestingly it is coming up also in light of carbon budgets for big projects - shared resources cut down those costs and offload carbon use to 'others' - i.e. not your local university.  Anyway, perhaps of special interest in the NERC domain.





>>> marty.gollery at gmail.com 12/3/08 04:46:05 >>>
I don't know much about cloud computing, but have you thought about
getting it set up as an AMI on the amazon EC2 service? That way people
could  run it with no install needed and pay only for the time that
they use.

best,
Marty

On Tue, Dec 2, 2008 at 5:40 AM, Stewart Houten <shou at ceh.ac.uk> wrote:
> Dear all,
>
> The NEBC is pleased to announce the release of Bio-Linux 5.0.  This
> new version is based on the popular Ubuntu Linux distribution and
> provides a very user-friendly desktop while continuing to deliver
> access to a growing suite of bioinformatics applications.
>
> Bio-Linux 5.0 is available on USB memory stick or as an image to
> download and burn onto a DVD and is easy to install on a wide range of
> computer hardware. You can also run Bio-Linux 5 as a Live system from
> either the memory stick or DVD version. This is a simple way to try
> out Bio-Linux.  It can also provide a practical way to deliver
> teaching courses, give demonstrations or to work while away from the
> office.
>
> All PIs and CO-Is on NERC PGP grants will receive a Bio-Linux USB
> stick in the post shortly.  We welcome you to try it out and would
> love to hear your comments and feedback on the new release.
>
> To find out more please visit http://nebc.nox.ac.uk/bio-linux.html.
> Differences between Bio-Linux 4.0 and Bio-Linux 5.0 can be found at
> http://nebc.nox.ac.uk/envgen/software/archives/000590.html.
>
> Regards,
>
> The NEBC Team
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk 
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux 
>
> --
> 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.
>
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist

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




From shou at ceh.ac.uk  Wed Dec  3 05:54:55 2008
From: shou at ceh.ac.uk (Stewart Houten)
Date: Wed, 3 Dec 2008 10:54:55 +0000
Subject: [Bio-Linux] NEBC Bio-Linux 5.0 released
In-Reply-To: <bdd10c2a0812022046m64bb5afel60404c5195ee1efd@mail.gmail.com>
References: <20081202134010.GA7963@ivpcp068.nerc-oxford.ac.uk>
	<bdd10c2a0812022046m64bb5afel60404c5195ee1efd@mail.gmail.com>
Message-ID: <20081203105455.GA10734@ivpcp068.nerc-oxford.ac.uk>

Hi Marty,

On Dec 02, 2008, Martin Gollery <marty.gollery at gmail.com> wrote:
> I don't know much about cloud computing, but have you thought about
> getting it set up as an AMI on the amazon EC2 service? That way people
> could  run it with no install needed and pay only for the time that
> they use.

Thanks for pointing this out - I hadn't realised Amazon now offered
this service.  It sounds like a very interesting idea and one I will
bring up at our next developer meeting.  Of course, in the meantime
you can run a Live session with Bio-Linux 5.0 from DVD or USB key
without having to install. :-)

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



From rwt017 at abdn.ac.uk  Wed Dec  3 07:25:03 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Wed, 03 Dec 2008 12:25:03 +0000
Subject: [Bio-Linux] Cloud computing
In-Reply-To: <s9366502.088@wpo.nerc.ac.uk>
References: <s9366502.088@wpo.nerc.ac.uk>
Message-ID: <49367A9F.2000808@abdn.ac.uk>

Dawn Field wrote:
> Thanks for bringing up cloud computing.  Yes, there are academic
> groups starting to use cloud computing and we, as a community, should
> start to think about how the NERC community may/may not use cloud
> computing in general in the future.
> 
> Is this coming up on the radar for more people on this list?

Hello, Dawn.

I'm not in favour of 'cloud' computing, because I see it as an attempt 
to centralise resources and take control of resources away from the 
people who use them. The particular feature of NEBC that I admire and 
have followed in my recommendations to NuGO is the distributed resource 
you have deployed to NERC grant holders, and we have emulated in NuGO.

Although I now work in bioinformatics, I have many years experience of 
working as a biologist and, in my experience, if you take control of a 
resource away from biologists they will create their own. All too often 
this results in people using their own desktop/laptop because *they* 
control how it is used. The great virtue I see in NEBC's present 
strategy is that you *do* give control of Bio-Linux workstations to the 
biologists concerned.

The most significant change to Bio-Linux I made in deploying our NBX's 
(NuGO Black Boxes), apart from using Ubuntu, is that I've used 
server-grade PC's and use the NBX's as lab-scale servers. In that 
repect, I'm balancing the freedom of the lab to use it's own NBX server 
in the way they want to against the administrative burden of each 
biologist administering their own NBX workstation. This is not a long 
way from what you do with Bio-Linux anyway, and we hope to collaborate 
with NEBC on deployment of Bio-Linux5 on our 31 NBX's at NuGO partners.

I've now marked my 'biobuntu' blueprint as obsolete, and will use 
Bio-Linux5 on both the RINH/BioSS Beowulf and NuGO NBX servers.

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
-------------- next part --------------
An embedded message was scrubbed...
From: Tony Travis <ajt at rri.sari.ac.uk>
Subject: [Blueprint biobuntu] Bioinformatics workstation/server for Ubuntu
Date: Tue, 2 Dec 2008 15:12:45 +0000
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From dfield at ceh.ac.uk  Wed Dec  3 07:43:03 2008
From: dfield at ceh.ac.uk (Dawn Field)
Date: Wed, 03 Dec 2008 12:43:03 +0000
Subject: [Bio-Linux] Cloud computing
Message-ID: <s9367ed0.059@wpo.nerc.ac.uk>

Hi Tony,

This is the 4th or 5th time cloud computing has come to my attention in the past months, so of interest and happy to hear more thoughts about it - it is on the cusp of becoming a reality for some people.

I should note that might comment about more people talking about cloud computing is coming from the 'big groups' who are outgrowing even very big supercomputers due to the growth in metagenomic/genomic data.  

We are already working with the National GRID Service to deal with the 'big jobs' that people might want to do via Bio-Linux, but for which the hardware doesn't suffice (e.g.  big all against all homology searches of many genomes/metagenomes for example).

Tasks done by individuals are  best done 'at home' as you say, and I agree, and this is what Bio-Linux is for and always will be - to enable more people to do their own analyses.

The original post was about trying to get Bio-Linux loaded into the cloud for yet more people to use - big or little jobs, I assume...the concept of having access to software from anywhere.  Still an interesting idea.  The issue is that you have to pay and academics aren't used to that (I don't want it at all).  Perhaps, for example, in the future a teaching lab could be willing to pay a small fee to give a group of students access to a bio-linux teaching lab 'via the ether' instead of taking the time/effort to install it locally.


Dawn

>>> rwt017 at abdn.ac.uk 12/3/08 12:25:03 >>>
Dawn Field wrote:
> Thanks for bringing up cloud computing.  Yes, there are academic
> groups starting to use cloud computing and we, as a community, should
> start to think about how the NERC community may/may not use cloud
> computing in general in the future.
> 
> Is this coming up on the radar for more people on this list?

Hello, Dawn.

I'm not in favour of 'cloud' computing, because I see it as an attempt 
to centralise resources and take control of resources away from the 
people who use them. The particular feature of NEBC that I admire and 
have followed in my recommendations to NuGO is the distributed resource 
you have deployed to NERC grant holders, and we have emulated in NuGO.

Although I now work in bioinformatics, I have many years experience of 
working as a biologist and, in my experience, if you take control of a 
resource away from biologists they will create their own. All too often 
this results in people using their own desktop/laptop because *they* 
control how it is used. The great virtue I see in NEBC's present 
strategy is that you *do* give control of Bio-Linux workstations to the 
biologists concerned.

The most significant change to Bio-Linux I made in deploying our NBX's 
(NuGO Black Boxes), apart from using Ubuntu, is that I've used 
server-grade PC's and use the NBX's as lab-scale servers. In that 
repect, I'm balancing the freedom of the lab to use it's own NBX server 
in the way they want to against the administrative burden of each 
biologist administering their own NBX workstation. This is not a long 
way from what you do with Bio-Linux anyway, and we hope to collaborate 
with NEBC on deployment of Bio-Linux5 on our 31 NBX's at NuGO partners.

I've now marked my 'biobuntu' blueprint as obsolete, and will use 
Bio-Linux5 on both the RINH/BioSS Beowulf and NuGO NBX servers.

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk 
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt




From bioinformatics.lists at gmail.com  Wed Dec  3 08:56:50 2008
From: bioinformatics.lists at gmail.com (Dan Swan)
Date: Wed, 3 Dec 2008 13:56:50 +0000
Subject: [Bio-Linux] Cloud computing
In-Reply-To: <s9367ed0.059@wpo.nerc.ac.uk>
References: <s9367ed0.059@wpo.nerc.ac.uk>
Message-ID: <d606310d0812030556r73420383qf90f3ff892bc03f5@mail.gmail.com>

Hi everyone,

> This is the 4th or 5th time cloud computing has come to my attention in the past months, so of interest and happy to hear more thoughts about it - it is on the cusp of becoming a reality for some people.

Working out where it is in the Gartner hype cycle is important :)

I think the thing about AWS/EC2 is that they are already thinking
about the scientific applications - Microsoft certainly so.

Did you know AWS already offers access to scientific datasets?:

http://aws.amazon.com/publicdatasets/

The 'point' of the cloud is not to replace the racks of machines at
your local institution, although that may be a side effect - it is to
offer scalable, burstable disk/compute/whatever as and when you need
it on a 'pay per view' model.

I think what has happened is people have seen how horrendous the Grid
situation has become, and how far it has deviated from its own 'plug
in and play' mantra for access to computing resources, mired as it is
in certificates, middleware and authentication hell - and the cloud
has been borne from this.   It's a streamlined approach that offers
most of what people want without all the horribly complexity.

People whose requirements outstrip the cloud I suspect will be better
off served by existing Grid based provision.

Just my 0.02c of course :)

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 rwt017 at abdn.ac.uk  Wed Dec  3 10:01:34 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Wed, 03 Dec 2008 15:01:34 +0000
Subject: [Bio-Linux] Cloud computing
In-Reply-To: <d606310d0812030556r73420383qf90f3ff892bc03f5@mail.gmail.com>
References: <s9367ed0.059@wpo.nerc.ac.uk>
	<d606310d0812030556r73420383qf90f3ff892bc03f5@mail.gmail.com>
Message-ID: <49369F4E.4020108@abdn.ac.uk>

Dan Swan wrote:
> [...]
> I think what has happened is people have seen how horrendous the Grid
> situation has become, and how far it has deviated from its own 'plug
> in and play' mantra for access to computing resources, mired as it is
> in certificates, middleware and authentication hell - and the cloud
> has been borne from this.   It's a streamlined approach that offers
> most of what people want without all the horribly complexity.

Hello, Dan.

My experience with GRID is limited, but I agree with what you say. In 
fact, I attended a Globus level-2 system admin course given by NeSC in 
Edinburgh a few years ago, and decided on the spot not to use it, but I 
relented, and went to the myGrid 'users' workshop. This was great from 
the point of view of seeing what you can do with Taverna, but it did 
nothing to improve my view of GRID middleware. Neither did seeing how 
BLAST can be deployed on the GRID. I don't think GRID does well at a 
scale most biologists normally work at. Many bioinformatics resources 
that biologists do use are either web pages they browse, or web services 
they consume, offered at no cost by large public-funded organisations.

My own interest is in heterogenous self-organising networks of p2p 
computers. My original idea for 'biobuntu' was to use the Kerrighed 
kernel, and do GRID communication in the kernel with XtreemOS:

	http://www.xtreemos.eu/

This is the opposite of the 'Cloud', in which we would 'volunteer' our 
spare resources to the network when we don't need them locally, but use 
other people's resources when we have a big job to do. This works well 
for loosely coupled problems, for example folding at home, and I'm not 
alone in thinking that p2p is still under utilised in bioinformatics. 
The XtreemOS project is intended to support virtual organisations, and I 
think it is worth considering as an option for Bio-Linux development.

> People whose requirements outstrip the cloud I suspect will be better
> off served by existing Grid based provision.

This drives me crazy, because a lot of what biologists do is not 'BIG' 
computing and an HEP billion-dollar solution is not appropriate for all 
problems. I do realise that some problems of interest to biologists 
require huge computing resources to be thrown at them, but supporting 
what biologists actually want to do in the way that NEBC has done so far 
is probably of greater interest and value to most biologists than the 
actual hardware it runs on. In that respect, I think the issue of cloud 
computing vs. rolling your own workstation/server/cluster/GRID is less 
important than the continuing support and development of Bio-Linux :-)

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From dfield at ceh.ac.uk  Wed Dec  3 13:27:16 2008
From: dfield at ceh.ac.uk (Dawn Field)
Date: Wed, 03 Dec 2008 18:27:16 +0000
Subject: [Bio-Linux] Cloud computing
Message-ID: <s936cfa0.080@wpo.nerc.ac.uk>

Tony - thanks for the very positive words about the Bio-Linux project!

GRID is complex, and it won't be a solution for all, but again, for those who don't want to transerve the evils of it but have a big job to do, Stewart has sent out a call for case studies for work on the NGS.  He's done already of the hard work getting the plumbing working already and there is a GRID package for Bio-Linux  We just need some good biology to put through the system - where there is a need for more cycles.

As for p2p computing, we are also watching projects that harvest cycles from PCs.  For example, BOINC is of interest (http://boinc.berkeley.edu/).

Xtreemos also looks like a very worthy project, thanks for bringing it up.

Dawn


Molecular Evolution and Bioinformatics Group
Director, NERC Environmental Bioinformatics Centre

CEH Oxford
Mansfield Rd
Oxford OX1 3SR
UK

Tel : 01865 281630
Fax: 01865 281696
>>> rwt017 at abdn.ac.uk 12/03/08 3:01 PM >>>
Dan Swan wrote:
> [...]
> I think what has happened is people have seen how horrendous the Grid
> situation has become, and how far it has deviated from its own 'plug
> in and play' mantra for access to computing resources, mired as it is
> in certificates, middleware and authentication hell - and the cloud
> has been borne from this.   It's a streamlined approach that offers
> most of what people want without all the horribly complexity.

Hello, Dan.

My experience with GRID is limited, but I agree with what you say. In 
fact, I attended a Globus level-2 system admin course given by NeSC in 
Edinburgh a few years ago, and decided on the spot not to use it, but I 
relented, and went to the myGrid 'users' workshop. This was great from 
the point of view of seeing what you can do with Taverna, but it did 
nothing to improve my view of GRID middleware. Neither did seeing how 
BLAST can be deployed on the GRID. I don't think GRID does well at a 
scale most biologists normally work at. Many bioinformatics resources 
that biologists do use are either web pages they browse, or web services 
they consume, offered at no cost by large public-funded organisations.

My own interest is in heterogenous self-organising networks of p2p 
computers. My original idea for 'biobuntu' was to use the Kerrighed 
kernel, and do GRID communication in the kernel with XtreemOS:

	http://www.xtreemos.eu/

This is the opposite of the 'Cloud', in which we would 'volunteer' our 
spare resources to the network when we don't need them locally, but use 
other people's resources when we have a big job to do. This works well 
for loosely coupled problems, for example folding at home, and I'm not 
alone in thinking that p2p is still under utilised in bioinformatics. 
The XtreemOS project is intended to support virtual organisations, and I 
think it is worth considering as an option for Bio-Linux development.

> People whose requirements outstrip the cloud I suspect will be better
> off served by existing Grid based provision.

This drives me crazy, because a lot of what biologists do is not 'BIG' 
computing and an HEP billion-dollar solution is not appropriate for all 
problems. I do realise that some problems of interest to biologists 
require huge computing resources to be thrown at them, but supporting 
what biologists actually want to do in the way that NEBC has done so far 
is probably of greater interest and value to most biologists than the 
actual hardware it runs on. In that respect, I think the issue of cloud 
computing vs. rolling your own workstation/server/cluster/GRID is less 
important than the continuing support and development of Bio-Linux :-)

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt

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




From rwt017 at abdn.ac.uk  Sun Dec  7 17:10:53 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Sun, 07 Dec 2008 22:10:53 +0000
Subject: [Bio-Linux] First impressions of Bio-Linux5
Message-ID: <493C49ED.5040606@abdn.ac.uk>

Hello, Stewart.

Thanks for sending me the USB version: I've installed it on my laptop,
and I'm sending you this email from Thunderbird under Bio-Linux5  :-)

Looks like KDE with this colour scheme  ;-)

First impression of the 'live' USB version is that you should make the
'Getting started' document local: I've got a Broadcom wireless chip that
needs firmware downloading on a wired connection to get it working. If
you don't have an internet connection, you can't even read the 'Getting
started' document. The equivalent Ubuntu document is local, of course.

The Flash and Java plugins for Firefox are not installed by default:

I had problems installing the Flash plugin because the Ubuntu deb is 
broken (wrong URL for downloading the Adobe installer):

> Setting up flashplugin-nonfree (9.0.124.0ubuntu2) ...
> Downloading...
> --20:40:13--  http://fpdownload.macromedia.com/get/flashplayer/current/install_flash_player_9_linux.tar.gz
>            => `./install_flash_player_9_linux.tar.gz'
> Resolving fpdownload.macromedia.com... 88.221.170.70
> Connecting to fpdownload.macromedia.com|88.221.170.70|:80... connected.
> HTTP request sent, awaiting response... 404 Not Found
> 20:40:13 ERROR 404: Not Found.

I downloaded the Flash deb from the Adobe web site:

http://fpdownload.macromedia.com/get/flashplayer/current/install_flash_player_10_linux.deb

Then installed it manually:

	gdebi install_flash_player_10_linux.deb

I also manually installed the Sun Java plugin:

	aptitude install sun-java6-plugin

Looks like you've done a lot of work to get this out of the door!

I'll let you know how I get on with it - I'm planning to upgrade our
Beowulf servers to Bio-Linux5 over the Xmas break.

Bye,

         Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From shou at ceh.ac.uk  Tue Dec  9 12:49:58 2008
From: shou at ceh.ac.uk (Stewart Houten)
Date: Tue, 9 Dec 2008 17:49:58 +0000
Subject: [Bio-Linux] First impressions of Bio-Linux5
In-Reply-To: <493C49ED.5040606@abdn.ac.uk>
References: <493C49ED.5040606@abdn.ac.uk>
Message-ID: <20081209174958.GA8391@ivpcp068.nerc-oxford.ac.uk>

Hi Tony,

Glad you got the stick and are pleased with it so far.  Thanks also
for the feedback - I will add add them to the development issue log
and they should filter into the next minor release.  

Regards,
Stewart



From rwt017 at abdn.ac.uk  Thu Dec 11 14:09:47 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Thu, 11 Dec 2008 19:09:47 +0000
Subject: [Bio-Linux] Cloud computing...
Message-ID: <4941657B.2070003@abdn.ac.uk>

Hello, Dawn.

Re: our recent posts about cloud computing, here is a biased view that I 
completely agree with ;-)

http://www.guardian.co.uk/technology/2008/sep/29/cloud.computing.richard.stallman

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From mc at michaelcraige.com  Sat Dec 13 11:08:33 2008
From: mc at michaelcraige.com (Michael Craige)
Date: Sat, 13 Dec 2008 11:08:33 -0500
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <4941657B.2070003@abdn.ac.uk>
Message-ID: <C5694831.69BF%mc@michaelcraige.com>

I support Richard's view - it's a trap!

Michael.


> From: Tony Travis <rwt017 at abdn.ac.uk>
> Organization: Rowett Institute of Nutrition and Health
> Reply-To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
> Date: Thu, 11 Dec 2008 19:09:47 +0000
> To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
> Subject: [Bio-Linux] Cloud computing...
> 
> Hello, Dawn.
> 
> Re: our recent posts about cloud computing, here is a biased view that I
> completely agree with ;-)
> 
> http://www.guardian.co.uk/technology/2008/sep/29/cloud.computing.richard.stall
> man
> 
> Bye,
> 
> Tony.
> -- 
> Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
> and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
> tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
> mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
> 
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
> 
> -- 
> 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 morrison at cs.man.ac.uk  Wed Dec 17 10:31:33 2008
From: morrison at cs.man.ac.uk (Norman Morrison)
Date: Wed, 17 Dec 2008 15:31:33 +0000
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <C5694831.69BF%mc@michaelcraige.com>
References: <C5694831.69BF%mc@michaelcraige.com>
Message-ID: <49491B55.7070003@cs.man.ac.uk>

A bit more fuel to add to the fire:
http://www.inkspotscience.com/blog/index.php/tag/cloud-computing/

In practice, I think some kind of compromise between the two 'extremes' 
will be the likely outcome. Although it is very much a buzzword, I think 
it would be unwise to dismiss cloud computing out of hand for one simple 
reason... as Dawn mentioned, in what will be a carbon credit economy, 
relocating cyber-infrastructure to remote renewable energy sites not 
only helps the environment but can also alleviate the pressure on an 
institution that is reaching it's carbon credit cap. In essence, cloud 
computing will become a necessity driven by a carbon economy.

Tony - with Scotland's natural resources and cooler temperature enabling 
data centres to be powered and subsequently cooled (aka rainy and cold) 
- you could well end up becoming the European cloud computing hub!

Michael Craige wrote:
> I support Richard's view - it's a trap!
>
> Michael.
>
>
>   
>> From: Tony Travis <rwt017 at abdn.ac.uk>
>> Organization: Rowett Institute of Nutrition and Health
>> Reply-To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
>> Date: Thu, 11 Dec 2008 19:09:47 +0000
>> To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
>> Subject: [Bio-Linux] Cloud computing...
>>
>> Hello, Dawn.
>>
>> Re: our recent posts about cloud computing, here is a biased view that I
>> completely agree with ;-)
>>
>> http://www.guardian.co.uk/technology/2008/sep/29/cloud.computing.richard.stall
>> man
>>
>> Bye,
>>
>> Tony.
>> -- 
>> Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
>> and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
>> tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
>> mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
>>
>> _______________________________________________
>> Bio-Linux mailing list
>> Bio-Linux at envgen.nox.ac.uk
>> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>>
>> -- 
>> 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 envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>   

-- 
Norman Morrison, PhD
NEBC Ontologies & Data Standards Coordinator (http://nebc.nox.ac.uk/)
Room LF8, School of Computer Science, Kilburn Building,
University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL.
Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236




From marty.gollery at gmail.com  Wed Dec 17 10:55:50 2008
From: marty.gollery at gmail.com (Martin Gollery)
Date: Wed, 17 Dec 2008 07:55:50 -0800
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <49491B55.7070003@cs.man.ac.uk>
References: <C5694831.69BF%mc@michaelcraige.com>
	<49491B55.7070003@cs.man.ac.uk>
Message-ID: <bdd10c2a0812170755yd5c7f95i2a127898d647ee79@mail.gmail.com>

Many people do not have the funds for a BlueGene/L, nor the need for
such a thing on a regular basis, as WSU and VBI recently announced.
The throughput was very impressive, but the cost is in the millions of
dollars.

If a researcher had a job that was bigger than what he or she could
easily do on the standard BioLinux system, then a 20 CPU instance can
be started at Amazon for 80 cents (US) per hour. If there is a
deadline looming, the data could be divided into, say, ten parts and
run on ten instances for a total of 8 dollars per hour.

This does not 'lock you into a proprietary system'. Running HMMer on a
cloud today does not prevent you from running it on your own server
tomorrow, your mac the next day, and windows the next. Why would
anybody think that? A Linux instance runs like Linux.

Marty

On Wed, Dec 17, 2008 at 7:31 AM, Norman Morrison <morrison at cs.man.ac.uk> wrote:
> A bit more fuel to add to the fire:
> http://www.inkspotscience.com/blog/index.php/tag/cloud-computing/
>
> In practice, I think some kind of compromise between the two 'extremes'
> will be the likely outcome. Although it is very much a buzzword, I think
> it would be unwise to dismiss cloud computing out of hand for one simple
> reason... as Dawn mentioned, in what will be a carbon credit economy,
> relocating cyber-infrastructure to remote renewable energy sites not
> only helps the environment but can also alleviate the pressure on an
> institution that is reaching it's carbon credit cap. In essence, cloud
> computing will become a necessity driven by a carbon economy.
>
> Tony - with Scotland's natural resources and cooler temperature enabling
> data centres to be powered and subsequently cooled (aka rainy and cold)
> - you could well end up becoming the European cloud computing hub!
>
> Michael Craige wrote:
>> I support Richard's view - it's a trap!
>>
>> Michael.
>>
>>
>>
>>> From: Tony Travis <rwt017 at abdn.ac.uk>
>>> Organization: Rowett Institute of Nutrition and Health
>>> Reply-To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
>>> Date: Thu, 11 Dec 2008 19:09:47 +0000
>>> To: Bio-Linux help and discussion <bio-linux at envgen.nerc-oxford.ac.uk>
>>> Subject: [Bio-Linux] Cloud computing...
>>>
>>> Hello, Dawn.
>>>
>>> Re: our recent posts about cloud computing, here is a biased view that I
>>> completely agree with ;-)
>>>
>>> http://www.guardian.co.uk/technology/2008/sep/29/cloud.computing.richard.stall
>>> man
>>>
>>> Bye,
>>>
>>> Tony.
>>> --
>>> Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
>>> and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
>>> tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
>>> mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt
>>>
>>> _______________________________________________
>>> Bio-Linux mailing list
>>> Bio-Linux at envgen.nox.ac.uk
>>> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>>>
>>> --
>>> 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 envgen.nox.ac.uk
>> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>>
>
> --
> Norman Morrison, PhD
> NEBC Ontologies & Data Standards Coordinator (http://nebc.nox.ac.uk/)
> Room LF8, School of Computer Science, Kilburn Building,
> University of Manchester, Oxford Road, MANCHESTER, UK. M13 9PL.
> Tel: +44 (0)161 275 0646 Fax: +44 (0)161 275 6236
>
>
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at envgen.nox.ac.uk
> http://envgen.nox.ac.uk/mailman/listinfo/bio-linux
>
> --
> 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.
>
>



-- 
-- 
Martin Gollery
Senior Bioinformatics Scientist



From tbooth at ceh.ac.uk  Wed Dec 17 11:42:09 2008
From: tbooth at ceh.ac.uk (Tim Booth)
Date: Wed, 17 Dec 2008 16:42:09 +0000
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <bdd10c2a0812170755yd5c7f95i2a127898d647ee79@mail.gmail.com>
References: <C5694831.69BF%mc@michaelcraige.com>
	<49491B55.7070003@cs.man.ac.uk>
	<bdd10c2a0812170755yd5c7f95i2a127898d647ee79@mail.gmail.com>
Message-ID: <1229532129.7735.313.camel@barsukas>

But what you describe (running HMMer on Amazon, or wherever) is
'classic' GRID computing.  I don't think anyone is arguing against that
(other than complaining of the technical difficulties involved).

The buzzword 'cloud computing' seems to refer to situations where the
service provider supplies the computing power, software and storage for
every-day computing needs.  The classic example is webmail.  In this
case, you want to be very clear on your contractual relationship with
the provider.  What Stallman is basically saying is "I wouldn't have a
Hotmail or GMail account, and here's why...".

I don't entirely agree with him.  I trust my bank to look after my
money, and I would trust Google to look after my e-mail; but then my
bank is heavily regulated and backed by a deposit protection scheme.
Google isn't.

TIM

ps - Nice to see an interesting discussion on this list!

On Wed, 2008-12-17 at 07:55 -0800, Martin Gollery wrote:
> Many people do not have the funds for a BlueGene/L, nor the need for
> such a thing on a regular basis, as WSU and VBI recently announced.
> The throughput was very impressive, but the cost is in the millions of
> dollars.
> 
> If a researcher had a job that was bigger than what he or she could
> easily do on the standard BioLinux system, then a 20 CPU instance can
> be started at Amazon for 80 cents (US) per hour. If there is a
> deadline looming, the data could be divided into, say, ten parts and
> run on ten instances for a total of 8 dollars per hour.
> 
> This does not 'lock you into a proprietary system'. Running HMMer on a
> cloud today does not prevent you from running it on your own server
> tomorrow, your mac the next day, and windows the next. Why would
> anybody think that? A Linux instance runs like Linux.
> 
> Marty
> 





From rwt017 at abdn.ac.uk  Thu Dec 18 17:19:06 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Thu, 18 Dec 2008 22:19:06 +0000
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <49491B55.7070003@cs.man.ac.uk>
References: <C5694831.69BF%mc@michaelcraige.com>
	<49491B55.7070003@cs.man.ac.uk>
Message-ID: <494ACC5A.2030203@abdn.ac.uk>

Norman Morrison wrote:
> [...]
> Tony - with Scotland's natural resources and cooler temperature enabling
> data centres to be powered and subsequently cooled (aka rainy and cold)
> - you could well end up becoming the European cloud computing hub!

Hello, Norman.

Hmm... lots of clouds in Scotland :-)

Actually, I'm interested in p2p computing. Now, if the 'cloud' was p2p I 
would feel a whole lot differently about it. As it stands, the 'cloud' 
is little more than a honey trap waiting for the unwary. It's a return 
to mainframe 'bureau' computing, and users relinquishing control of the 
resources that we have seen democratised over the past 25 years.

Interestingly, though it was Micro$oft who broke IBM and DEC's monopoly 
on computing resources and presented themselves as David against IBM's 
Goliath IBM are now one of the most prominent advocates of FLOSS. DEC, 
of course did not embrace FLOSS, and paid a high price. What, I wonder, 
has this got to do with Bio-Linux? Well, quite a lot actually, because 
Bio-Linux represents the democratisation of bioinformatics resources.

In NuGO, we've built a distributed bioinformatics resource based on 
Bio-Linux. I'm very pleased to see Bio-Linux5 released, and we will be 
upgrading our 'biobuntu' (Bio-Linux4 + Ubuntu 6.06 LTS) NBX servers to 
Bio-Linux5 as soon as possible. The only obstacle to that now is getting 
GenePattern to run R properly under Ubuntu 8.04. If anyone on the list 
has got GenePattern working under Ubuntu 8.04 LTS please get in touch!

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From rwt017 at abdn.ac.uk  Thu Dec 18 17:34:56 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Thu, 18 Dec 2008 22:34:56 +0000
Subject: [Bio-Linux] Cloud computing...
In-Reply-To: <bdd10c2a0812170755yd5c7f95i2a127898d647ee79@mail.gmail.com>
References: <C5694831.69BF%mc@michaelcraige.com>	<49491B55.7070003@cs.man.ac.uk>
	<bdd10c2a0812170755yd5c7f95i2a127898d647ee79@mail.gmail.com>
Message-ID: <494AD010.30605@abdn.ac.uk>

Martin Gollery wrote:
> Many people do not have the funds for a BlueGene/L, nor the need for
> such a thing on a regular basis, as WSU and VBI recently announced.
> The throughput was very impressive, but the cost is in the millions of
> dollars.

Hello, Martin.

AFIK, the 'cloud' is based on warehouses full of COTS servers, not on 
top500 HPC clusters. You're NOT going to get 'BlueGene' performance at 
knock-down prices. You get what you pay for.

> If a researcher had a job that was bigger than what he or she could
> easily do on the standard BioLinux system, then a 20 CPU instance can
> be started at Amazon for 80 cents (US) per hour. If there is a
> deadline looming, the data could be divided into, say, ten parts and
> run on ten instances for a total of 8 dollars per hour.

Iff you are only going to run your jobs once in a while, and Stewart has 
kindly set up a virtual image of Bio-Linux with everything you want to 
use already preconfigured, and all the databases you want to access 
transparently shared between all the anonymous 'cloud' nodes you get for 
8 dollars and hour, then you are in business.

> This does not 'lock you into a proprietary system'. Running HMMer on a
> cloud today does not prevent you from running it on your own server
> tomorrow, your mac the next day, and windows the next. Why would
> anybody think that? A Linux instance runs like Linux.

The 'cloud' itself is a proprietary system. It's the opposite of HPC 
clustering. What is the point of using virtualised Bio-Linux instances 
just to 'cluster' them?  If I want to use a top500 class computer, I'll 
join the queue on a real one. However, I follow Donald Becker's example, 
and use my own DIY Bio-Linux Beowulf cluster instead :-)

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt



From rwt017 at abdn.ac.uk  Tue Dec 30 20:39:33 2008
From: rwt017 at abdn.ac.uk (Tony Travis)
Date: Wed, 31 Dec 2008 01:39:33 +0000
Subject: [Bio-Linux] USB media not automounted
Message-ID: <495ACD55.1090904@abdn.ac.uk>

Hello,

I noticed that USB media were not being automounted after installing 
Bio-Linux5 on my laptop from the Bio-Linux5 USB stick: I've traced the 
problem to two incorrect entries in the /etc/fstab created during the 
installation. It seems the installer thinks the USB stick is a CD/DVD 
drive. A work-around is to comment out the two incorrect entries at the 
end of /etc/fstab, and add a correct one for the real CD/DVD drive:

...
# /dev/sdb1       /media/cdrom0   udf,iso9660 user,noauto,exec,utf8 0 
     0
# /dev/scd0       /media/cdrom1   udf,iso9660 user,noauto,exec,utf8 0 
     0
/dev/scd0       /media/cdrom0   udf,iso9660 user,noauto,exec,utf8 0       0

I think the problem arises because there is an ISO bootable DVD image on 
the USB stick, which the installer assumes is mounted from a CD/DVD...

Merry Christmas :-)

Bye,

	Tony.
-- 
Dr. A.J.Travis, University of Aberdeen, Rowett Institute of Nutrition
and Health, Greenburn Road, Bucksburn, Aberdeen AB21 9SB, Scotland, UK
tel +44(0)1224 712751, fax +44(0)1224 716687, http://www.rowett.ac.uk
mailto:a.travis at abdn.ac.uk, http://bioinformatics.rri.sari.ac.uk/~ajt