[Bio-Linux] Bio-Linux future versions
M.S YATNATTI
biotechinfobytes at yahoo.com
Fri Feb 20 00:25:48 EST 2004
Dear Sir
It seems that you are mixing the two issues which are very seprate, one is you provide under GPL and other is support at cost.
General user will never ask the support from you Because you provide Bio-Linux 3 Under GPL. After that what user does is his risk. Ours was general responce to future versions of Bio-Linux.It is upto you to consider or reject in the intrest of Linux community under GPL.
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. RE: Re: Bio-Linux future versions (Anderson, Rob A)
--__--__--
Message: 1
Subject: RE: [Bio-Linux] Re: Bio-Linux future versions
Date: Thu, 19 Feb 2004 12:30:00 -0000
From: "Anderson, Rob A"
To:
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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.
=20
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
=20
Dear All,=20
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)
bio-linux-request at ivsun01.nerc-oxford.ac.uk wrote:
Send Bio-Linux mailing list submissions to
bio-linux at bioinf.ceh.ac.uk
=09
To subscribe or unsubscribe via the World Wide Web, visit
http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux
or, via email, send a message with subject or body 'help' to
bio-linux-request at bioinf.ceh.ac.uk
=09
You can reach the person managing the list at
bio-linux-admin at bioinf.ceh.ac.uk
=09
When replying, please edit your Subject line so it is more
specific
than "Re: Contents of Bio-Linux digest..."
=09
=09
Today's Topics:
=09
1. Bio-Linux future strategy (Dan Swan)
=09
-- __--__--
=09
Message: 1
Date: Wed, 18 Feb 2004 11:46:31 +0000
From: Dan Swan=20
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
=09
Dear all - here is a consultation document on the future of
Bio-Linux -=20
comments appreciated either on list or off list.
=09
For a breakdown on how we comnpared the distributions the
delightfully=20
coloured Excel spreadsheet can be downloaded from:
=09
http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls
=09
Bio-Linux future directions - OS selection.
-------------------------------------------
=09
Bio-Linux 3.0 and earlier versions were based on the popular Red
Hat=20
Liinux distribution. Red Hat will be dropping support for the
freely=20
available and distributable version of the Linux operating
system (OS)=20
in April 2004. This has prompted the need to review the Linux=20
distributions currently available and to make a decision based
on this=20
review as to the best choice for the base of future Bio-Linux
development.
=09
Issues of key importance to our decision include:
=09
Compatibility with the hardware provided to Environmental
Genomics=20
Thematic Programme Awardee Labs
=09
Level of difference in administration, interface and overall
feel of the=20
system compared to the current Bio-Linux
=09
Overall level of user (and administrator)-friendliness
=09
Release schedule, automatic updating systems, versions of base
system=20
components
=09
Licensing issues for redistribution
=09
Documentation availability
=09
=09
In addition, we will take into account the mechanism by which
the OS can=20
be distributed as distribution via hard media rather than the
current=20
situation, using SystemImager software, would free a significant
amount=20
of time for EGTDC staff providing user support, and allow
distribution=20
of the Bio-Linux system to a wider audience with no significant
support=20
cost to the EGTDC. Associated with the distribution system, some
OS=20
versions provide an easy mechanism to produce "Live CD's" which
would=20
allow Bio-Linux to be demonstrated easily, for example at
conferences,=20
thus raising its profile. A live CD version would also enable
people to=20
run a cut down version of Bio-Linux on machines without
dedicating the=20
machine to a Linux installation.
=09
Our testing is made up of several stages:
=09
from all the Linux distributions, choose those to be tested
=09
from those chosen, make choices for further testing based on
obvious=20
issues such as hardware incompatibility
=09
test a number of distributions further and choose two that will
be=20
tested by a larger group
=09
on the basis of all the above, decide on the OS on which to base
the=20
future development
=09
=09
Distributions chosen for testing
=09
There are many Linux distributions available. On the basis of
our=20
requirements, some distributions were immediately excluded from=20
consideration:
=09
Gentoo was considered to be inappropriate for the remit of
Bio-Linux as=20
the installation process allows such fine grained control an
install can=20
take upwards of a day and you must be extremely competent with
Linux=20
already.
=09
Debian was excluded on the basis that its install was too
complex for=20
people not familiar with Linux.
=09
Slackware was excluded as it lacks an integral modern system of
package=20
management (deb or rpm).
=09
Mandrake was excluded from initial consideration as it was close
to=20
receivership last year and there were worries about its long
term future.
=09
The distributions reviewed include:
=09
Knoppix (a Live-CD distribution of Debian)
Fedora
SuSE
DNALinux (a Slackware based Live-CD with some bioinformatics=20
applications bundled)
BioBrew
Morphix (a "modular" Knoppix derivative )
Mandrake
MandrakeMove
BioKnoppix
=09
Results of testing
=09
2 distributions failed to boot on our test hardware due to the
inability=20
to deal with 2 CPU machines and were immediately excluded from
further=20
consideration:
=09
DNALinux
Morphix
=09
These bugs were reported to the development teams responsible.
=09
1 distribution was excluded on the basis that the Live-CD format
had no=20
option to install to disk:
=09
MandrakeMove.
=09
The remaining distributions were tested further:
=09
Knoppix
Fedora
SuSE
BioBrew
BioKnoppix
=09
A brief overview of these distributions is given here, followed
by the=20
testing results:
=09
Knoppix
=09
Knoppix is probably the oldest and best known Live-CD
distribution and=20
has a long history of customisation for various purposes (see
"Related=20
Projects" at
http://www.knopper.net/knoppix-links/index-en.html).=20
Knoppix is of interest as it could be not only used as a
Bio-Linux demo=20
system at conferences, but could also be used in a teaching
environment=20
and most importantly of all can be installed onto the hard disk
of a=20
machine to give a Debian install without the pain of a
traditional=20
Debian install. It has excellent hardware detection routines.
=09
Fedora
=09
The Fedora Project is a Red-Hat-sponsored and
community-supported open=20
source project. It is also a proving ground for new technology
that may=20
eventually make its way into Red Hat products. It is not a
supported=20
product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat
10.=20
Fedora is of interest to us as this will most resemble the
system=20
Bio-Linux 3.0 and earlier are based upon. The configuration
tools are=20
largely unchanged from Red Hat 9.0. Whilst we can not make a
Live-CD=20
for Fedora we would be able to create a distribution based on
it.
=09
SuSE
=09
SuSE is a German, but internationalised, distribution very much
in Red=20
Hat's image. They have a heavy focus on enterprise solutions
like Red=20
Hat and have recently been acquired by Novell as a platform for
the next=20
generation or Novell products. SuSE has a highly integrated=20
configuration GUI, much more advanced than Red Hat's.
=09
BioBrew
=09
BioBrew is a cluster focused Linux distribution which comes with
some=20
bioinformatics software preinstalled. For the most part, the
programs=20
included form a subset of those available on Bio-Linux. BioBrew
is=20
based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced
Server.=20
Bio-Brew has the look and feel of a default Red Hat 7.3 install.
=09
Bio-Knoppix
=09
A derivative of Knoppix (see above). It includes some
bioinformatics=20
tools and is in early beta development (version 0.2 currently,
version=20
0.3 was recalled due to mastering problems); essentially it is
Knoppix=20
with a new splashscreen and KDE menus for some bioinformatics
software=20
(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=20
system such as Bio-Knoppix.
=09
Summary of some positive and negative aspects of the different
distributions
=09
Knoppix
=09
Positive:
=09
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
=09
Negative:
=09
1)Not as advanced GUI for systems administration
2)Debian package management system - will be unfamiliar to RPM
users
=09
Fedora
=09
Positive:
=09
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=20
platform
4)Will be familiar to the Environmental Genomics user community
5)Exceedingly easy to install=20
=09
Negative:
=09
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=20
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
=09
SuSE
=09
Positive:
=09
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.
=09
Negative:
=09
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=20
Enterprise exclusively
6)Will be remastering at least once a year (SuSE are slowing
release=20
dates for stability)
=09
=09
=09
BioBrew
=09
Positive:
=09
1)Based on Red Hat and so would be familiar to Bio-Linux users
and=20
administrators
2)Large installed base=20
3)Ready to cluster
4)Already has some bioinformatics applications installed
=09
Negative:
=09
1)Cannot be made into a Live-CD
2)Based on outdated version of RHAS
3)Text mode install=20
4)Not at all focused on desktop usage
=09
Bio-Knoppix
=09
=09
This distribution has the same base list of positive and
negative=20
attributes as Knoppix, but also includes:
=09
Positive:
=09
1)Has some bioinformatics software preinstalled
2)Some EMBOSS customisation has been done
3)Menu customisations have been already implemented for
bioinformatics=20
software
=09
Negative:
=09
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=20
installed into /usr/local
4)Even if we used it as a base, we'd end up ripping out
everything=20
they've done and remastering it.
=09
Linux distributions chosen for further testing
=09
On the basis of the above results, two distributions were chosen
at the=20
Bio-Linux Development strategy meeting on February 13, 2004 for
further=20
testing as potential base systems for Bio-Linux:
=09
Fedora Core 1
Knoppix
=09
Testing strategy:
=09
Two machines will be set up, one for each of the above
distributions.=20
Over the next two weeks, EGTDC staff will dedicate time to work
on both=20
systems. A final decision for the distribution to be used for
further=20
Bio-Linux development will be made on February 27, 2004 on the
basis of=20
this testing.
=09
For those wishing to read up on what is happening in the Linux
world=20
there is an excellent article here on the relative market share
of the=20
top Linux variants:
=09
http://www.internetnews.com/ent-news/article.php/3313211
--=20
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
=09
=09
-- __--__--
=09
_______________________________________________
Bio-Linux mailing list
Bio-Linux at bioinf.ceh.ac.uk
http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux
=09
=09
End of Bio-Linux Digest
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style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>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.
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Rob Anderson
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Computing Support =
Officer
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Centre for Population =
Biology
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Imperialsize=3D2
color=3Dnavy face=3DArial>style=3D'font-size:10.0pt;font-family:Arial;
color:navy'> face=3DArial> =
style=3D'font-size:10.0pt;font-family:Arial;color:navy'>Collegeont>
face=3DTahoma>lang=3DEN-US style=3D'font-size:10.0pt;font-family:Tahoma'>-----Original
Message-----
From: =
bio-linux-admin at ivsun01.nerc-oxford.ac.uk
[mailto:bio-linux-admin at ivsun01.nerc-oxford.ac.uk] style=3D'font-weight:
bold'>On Behalf Of M.S YATNATTI
Sent: size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'>19
February 2004lang=3DEN-US
style=3D'font-size:10.0pt;font-family:Tahoma'> size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'>11:54size=3D2 face=3DTahoma>style=3D'font-size:10.0pt;font-family:Tahoma'>
To:
bio-linux at ivsun01.nerc-oxford.ac.uk
Subject: [Bio-Linux] Re: =
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