[Bio-Linux] Re: Bio-Linux future versions
Anderson, Rob A
robert.anderson at imperial.ac.uk
Thu Feb 19 07:30:00 EST 2004
It seems that you are asking for a lot of something that is being given
away for free. Remember that EGTDC have to install, test and support
every package that they include in BioLinux and that takes resources.
Would your organization contribute the necessary resources for EGTDC to
be able to include and support all the packages you request (and any
interaction between them)? From a support point of view it is much
simpler to include a core set of applications that cover most of the
tasks people using a BioLinux box are likely to use, and then allow them
to install and support their own specific packages on top of that.
There is nothing to stop you installing your own extra applications on
top of the BioLinux 3 distribution.
Rob Anderson
Computing Support Officer
Centre for Population Biology
Imperial College
-----Original Message-----
From: bio-linux-admin at ivsun01.nerc-oxford.ac.uk
[mailto:bio-linux-admin at ivsun01.nerc-oxford.ac.uk] On Behalf Of M.S
YATNATTI
Sent: 19 February 2004 11:54
To: bio-linux at ivsun01.nerc-oxford.ac.uk
Subject: [Bio-Linux] Re: Bio-Linux future versions
Dear All,
Thanks for the efforts taken by Centre For Ecology and Hydrology
In our view, the direction in which center for ecology and Hydrology
lead by Dan Swan for future Bio-linux version is throught provoking.
We have following suggestions to make;
1. It is suggested that the Bio-Linux version can continue on Redhat 9
or Fedora 1 as in our view it does not make much difference for open
source community whether Redhat goes commercial and support Fedora
project. THe Redhat 9 will continue in the name of Fedora 1 (Instead of
Redhat 10), The linux community is mature and strong enough to support
its continuity worldwide.
2. The Bio-Linux Future versions should contain OSCAR, GLOBUS, CONDOR,
OPEN MOSIX, Sun Grid Engine(All must be included) user should have
choice to use whatever he needs in whatever contest.
3. Bio-Linux should contain almost all Biotechnology, Bioinformatics,
Medical informatics, Chem-informatics, proteomics, Bio-chemistry,
chemistry, inlcuding visualization, modelling, graphic multi-media
utilities and applications.All applications either they are RPM or tar.
files can be installed in the system instead of converting all
applications into rpm and making a installable distribution of Bio-Linux
in CDs. As this will take still some time to take to convert all
scientific application to RPM format. We are building up Bio-Linux in
this direction.
4. All databases available opensource should be included in the Local
server.
5. With regard to districution of this type of Bio-linux system can be
made in CDs or hard-discs by cloning the entire system on the hard disc
or on CDs. Linux has many such utilities. SYstem Imager is very much
fine when the installation is done at a Local LAN to 100s of nodes to
build a cluster. But with regard with the internet installation it will
have still bandwidth problem.
6. We request Dan Swan to send atleast Bio-Linux 3 cloning on CDs by
using Linux utilities for Backup or system recovery or cloning the
hard-discs by using free linux softwares.
With regards,
Mr.M.S.Yatnatti,
CEO, Biotechinfobytes,
Super Computer Aided Biotechnology center (SUCAB Center)
University of Agricultural Sciences, Hebbal Campus,
Bangalore - 560 024. (India)
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Today's Topics:
1. Bio-Linux future strategy (Dan Swan)
--__--__--
Message: 1
Date: Wed, 18 Feb 2004 11:46:31 +0000
From: Dan Swan
Reply-To: dswan at ceh.ac.uk
Organization: Centre For Ecology and Hydrology
To: bio-linux at ivsun01.nerc-oxford.ac.uk
Subject: [Bio-Linux] Bio-Linux future strategy
Dear all - here is a consultation document on the future of
Bio-Linux -
comments appreciated either on list or off list.
For a breakdown on how we comnpared the distributions the
delightfully
coloured Excel spreadsheet can be downloaded from:
http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls
Bio-Linux future directions - OS selection.
-------------------------------------------
Bio-Linux 3.0 and earlier versions were based on the popular Red
Hat
Liinux distribution. Red Hat will be dropping support for the
freely
available and distributable version of the Linux operating
system (OS)
in April 2004. This has prompted the need to review the Linux
distributions currently available and to make a decision based
on this
review as to the best choice for the base of future Bio-Linux
development.
Issues of key importance to our decision include:
Compatibility with the hardware provided to Environmental
Genomics
Thematic Programme Awardee Labs
Level of difference in administration, interface and overall
feel of the
system compared to the current Bio-Linux
Overall level of user (and administrator)-friendliness
Release schedule, automatic updating systems, versions of base
system
components
Licensing issues for redistribution
Documentation availability
In addition, we will take into account the mechanism by which
the OS can
be distributed as distribution via hard media rather than the
current
situation, using SystemImager software, would free a significant
amount
of time for EGTDC staff providing user support, and allow
distribution
of the Bio-Linux system to a wider audience with no significant
support
cost to the EGTDC. Associated with the distribution system, some
OS
versions provide an easy mechanism to produce "Live CD's" which
would
allow Bio-Linux to be demonstrated easily, for example at
conferences,
thus raising its profile. A live CD version would also enable
people to
run a cut down version of Bio-Linux on machines without
dedicating the
machine to a Linux installation.
Our testing is made up of several stages:
from all the Linux distributions, choose those to be tested
from those chosen, make choices for further testing based on
obvious
issues such as hardware incompatibility
test a number of distributions further and choose two that will
be
tested by a larger group
on the basis of all the above, decide on the OS on which to base
the
future development
Distributions chosen for testing
There are many Linux distributions available. On the basis of
our
requirements, some distributions were immediately excluded from
consideration:
Gentoo was considered to be inappropriate for the remit of
Bio-Linux as
the installation process allows such fine grained control an
install can
take upwards of a day and you must be extremely competent with
Linux
already.
Debian was excluded on the basis that its install was too
complex for
people not familiar with Linux.
Slackware was excluded as it lacks an integral modern system of
package
management (deb or rpm).
Mandrake was excluded from initial consideration as it was close
to
receivership last year and there were worries about its long
term future.
The distributions reviewed include:
Knoppix (a Live-CD distribution of Debian)
Fedora
SuSE
DNALinux (a Slackware based Live-CD with some bioinformatics
applications bundled)
BioBrew
Morphix (a "modular" Knoppix derivative )
Mandrake
MandrakeMove
BioKnoppix
Results of testing
2 distributions failed to boot on our test hardware due to the
inability
to deal with 2 CPU machines and were immediately excluded from
further
consideration:
DNALinux
Morphix
These bugs were reported to the development teams responsible.
1 distribution was excluded on the basis that the Live-CD format
had no
option to install to disk:
MandrakeMove.
The remaining distributions were tested further:
Knoppix
Fedora
SuSE
BioBrew
BioKnoppix
A brief overview of these distributions is given here, followed
by the
testing results:
Knoppix
Knoppix is probably the oldest and best known Live-CD
distribution and
has a long history of customisation for various purposes (see
"Related
Projects" at
http://www.knopper.net/knoppix-links/index-en.html).
Knoppix is of interest as it could be not only used as a
Bio-Linux demo
system at conferences, but could also be used in a teaching
environment
and most importantly of all can be installed onto the hard disk
of a
machine to give a Debian install without the pain of a
traditional
Debian install. It has excellent hardware detection routines.
Fedora
The Fedora Project is a Red-Hat-sponsored and
community-supported open
source project. It is also a proving ground for new technology
that may
eventually make its way into Red Hat products. It is not a
supported
product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat
10.
Fedora is of interest to us as this will most resemble the
system
Bio-Linux 3.0 and earlier are based upon. The configuration
tools are
largely unchanged from Red Hat 9.0. Whilst we can not make a
Live-CD
for Fedora we would be able to create a distribution based on
it.
SuSE
SuSE is a German, but internationalised, distribution very much
in Red
Hat's image. They have a heavy focus on enterprise solutions
like Red
Hat and have recently been acquired by Novell as a platform for
the next
generation or Novell products. SuSE has a highly integrated
configuration GUI, much more advanced than Red Hat's.
BioBrew
BioBrew is a cluster focused Linux distribution which comes with
some
bioinformatics software preinstalled. For the most part, the
programs
included form a subset of those available on Bio-Linux. BioBrew
is
based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced
Server.
Bio-Brew has the look and feel of a default Red Hat 7.3 install.
Bio-Knoppix
A derivative of Knoppix (see above). It includes some
bioinformatics
tools and is in early beta development (version 0.2 currently,
version
0.3 was recalled due to mastering problems); essentially it is
Knoppix
with a new splashscreen and KDE menus for some bioinformatics
software
(not all of which work). If Bio-Linux 4.0 was to be derived from
Knoppix we would be using a clean Knoppix base rather than a
derived
system such as Bio-Knoppix.
Summary of some positive and negative aspects of the different
distributions
Knoppix
Positive:
1)Once installed it never has to be upgraded with CD's
2)Exceedingly stable code base
3)Very long release cycle
4)Can be used to make a Live-CD
5)Strong remastering community
6)Can be made to track stable releases, or testing releases when
appropriate
7)Installs a perfectly configured Debian system to disk.
8)Excellent hardware detection and configuration
Negative:
1)Not as advanced GUI for systems administration
2)Debian package management system - will be unfamiliar to RPM
users
Fedora
Positive:
1)It's the closest distribution to Bio-Linux
2)Has reasonably advanced GUI configurations
3)Have most in house administration experience on the related
RedHat
platform
4)Will be familiar to the Environmental Genomics user community
5)Exceedingly easy to install
Negative:
1)Very new project, despite established base
2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and
we do not
know how this will impact the software included on Bio-Linux
3)Rapid release schedule: 2-3 releases a year to keep up with
and remaster
4)Releases not always out on date initially scheduled
5)Cannot be made into a Live CD
SuSE
Positive:
1)Exceedingly easy to install
2)Centralised administration through yast2
3)RPM based, therefore familiar to awardees
4)Likely to be guaranteed to work with Novell products in the
future.
Negative:
1)Licensing terms for redistribution are unclear
2)There are no SuSE-derived releases on the market hence:
3)There are no instructions for remastering SuSE
4)Cannot be made into a Live-CD
5)There is the possibility of it "pulling a Red Hat" and
focusing on
Enterprise exclusively
6)Will be remastering at least once a year (SuSE are slowing
release
dates for stability)
BioBrew
Positive:
1)Based on Red Hat and so would be familiar to Bio-Linux users
and
administrators
2)Large installed base
3)Ready to cluster
4)Already has some bioinformatics applications installed
Negative:
1)Cannot be made into a Live-CD
2)Based on outdated version of RHAS
3)Text mode install
4)Not at all focused on desktop usage
Bio-Knoppix
This distribution has the same base list of positive and
negative
attributes as Knoppix, but also includes:
Positive:
1)Has some bioinformatics software preinstalled
2)Some EMBOSS customisation has been done
3)Menu customisations have been already implemented for
bioinformatics
software
Negative:
1)Current version is at 0.2 and is clearly labeled beta
2)Not all menus work
3)All added software, bioinformatics and non-bioinformatics, has
been
installed into /usr/local
4)Even if we used it as a base, we'd end up ripping out
everything
they've done and remastering it.
Linux distributions chosen for further testing
On the basis of the above results, two distributions were chosen
at the
Bio-Linux Development strategy meeting on February 13, 2004 for
further
testing as potential base systems for Bio-Linux:
Fedora Core 1
Knoppix
Testing strategy:
Two machines will be set up, one for each of the above
distributions.
Over the next two weeks, EGTDC staff will dedicate time to work
on both
systems. A final decision for the distribution to be used for
further
Bio-Linux development will be made on February 27, 2004 on the
basis of
this testing.
For those wishing to read up on what is happening in the Linux
world
there is an excellent article here on the relative market share
of the
top Linux variants:
http://www.internetnews.com/ent-news/article.php/3313211
--
Dr Dan Swan - Bio-Linux Developer | RHCE
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 658 Fax: 018665 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk
--__--__--
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