[Bio-Linux] Re: Bio-Linux future directions - OS choice

[M.S YATNATTI]

Dear All,
In our view a doubts expressed by some quarters regarding RedHat is no longer being a viable option are unfounded. Because we should acknowledge the people at Red Hat Inc, who despite the massive shift in direction of their Red Hat Linux have managed to once again produce a rock solid Red Hat Fedora Linux version 1 which can be treated as Red Hat version 10, for the continuity of the Red Hat. Now this RedHat version will be continue in the name of Fedora.
Comparing Fedora and Enterprise Packages
The Fedora project was set up a "proving ground" for developing technology that can be used by RedHat, Inc to include in its Red Hat Enterprise Linux products.  Because the separation of RedHat Linux into the Fedora project and Enterprise Linux is still quite new, there is significant overlap between the packages included in the two directions.
The following bullets are intended to give you a flavor of the differences between the Fedora core software included with this and the RedHat Enterprise Linux software you can purchase from Red Hat, Inc.
* Many personal use packages in Fedora are not included in the Enterprise districbution. For example, enterprise contains fewer for playing and ripping music (no cdp, cdda2wav, cdrdao, or grip packages), fewer games (no freeciv, maelstrom or tuxracer) and fewer personal proudctivity tools (no gnucash, gnumeric, abiword, or koffice)
* Most packages in Enterprise that are not in Fedore are those that are needed particularly for high demand, high availability servers.  Enterprise packages not in Fedora include kernel software that can utilise large amounts of RAM (kernel-hugemem), tools for configuring diskless workstations (redhat-config-netboot) and monitoring tools (crash)
Although the timing of the releases of Fedora Core and Red Hat Enterprise Linux version 3 may make some version numbers different, there are literally hundreds of software packages that are the same in the two distributions.
 
Now the latest distribution contains kernel 6.2 and KDE 3.2 etc,. While building the base OS for Bio-Linux you can install and configure the latest applications available and bundle with Bioinformatics softwares.
 
In the meanwhile, debian is also a strong Linux Distribution. But any debian application is available for scientific purpose can be easily converted using alien command.
 
At the same time the entire base system need not be change for Bio-Linux frequently instead you can concentrate on adopting more Bioinformatics, Biotechnology application for integration with the base system.
 
These are our suggestions only for further thinking and deliberations.
Thanking you,
Yours Sincerely,
M.S.Yatnatti,
CEO, Biotechinfobytes,
Super computer aided Biotechnology Programme center
University of Agricultural Sciences, Hebbal Campus
Bangalore - 560 024

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Today's Topics:

1. Bio-Linux future directions - OS choice. (Dan Swan)
2. Re: Bio-Linux future directions - OS choice. (Chris Beck)
3. Re: Bio-Linux future directions - OS choice. (Dan Swan)

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Message: 1
Date: Tue, 09 Mar 2004 16:16:52 +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 directions - OS choice.

Dear All,

As you know we have been continuing to work on the development of the
Bio-Linux system and one of the recent considerations has been what
operating system to base Bio-Linux on now that Red Hat is no longer a
viable option. We would like to let you know the progress of our
evaluation and ask for any feedback you may have about the choice of
base level systems for further Bio-Linux development.

We began the evaluation by installing and working with a number of
possible base Linux systems. Through discussion with other EGTDC
members and staff from the CEH IT support team (CCS), we then narrowed 
the field to two systems for further testing, based on the requirements 
we felt most important for Bio-Linux, such as stability, future support, 
ease of updating once deployed and ease of administration.

The two base systems chosen for further evaluation were Debian,
installed from a Knoppix Live-CD, and Fedora. The evaluation consisted
of installing these systems on identical platforms, and having members
of the EGTDC at CEH Oxford work on the machines over a two week
period, noting their impressions of the systems with regards to general
usability, as well as how the systems performed when used for specific
tasks.

A full discussion of the experiences and impressions people had about
these two systems took place during the Bio-Linux strategy meeting on
March 5, 2004, which was attended by CEH Oxford EGTDC members and two
members of the local CCS staff.

A number of key points were raised about the systems during this
meeting:

KDE vs. Gnome:
Overall feelings suggested that the KDE interface of Knoppix/Debian
was preferable to the Gnome interface in Fedora. This was more to do 
with responsiveness and ease of menu configuration than look and feel.
Comments were made to the effect that the Bio-Linux look and feel could
be maintained on both platforms through the Bluecurve theme.

Apt-get vs. rpm:
The biggest difference to the two systems is the use of apt-get in
Debian versus rpm in Fedora. Comments were made that yum commands for
interacting with rpm's are very close to those of apt-get. Various
utilities were installed through apt-get on the Debian system, and
comments were positive about the interactive configuration it allows
when being updated.

Menu-based system configuration:
Comments regarding the use of menu based configuration focused on the
fact that the configuration tools for Fedora are more polished and
more comprehensive than Knoppix but that printer configuration and user
administration which were most likely to be used were present on
Knoppix.

Pre-installed packages:
There were comments regarding packages not present on Knoppix that are
present on Fedora but it was agreed that this could be easily be
remedied during remastering if a significant number of packages needed
to be added in.

Bioinformatics applications:
All bioinformatics applications were tested at a basic level on both
platforms. As expected, no significant problems were found with
Fedora as it is quite close to Bio-Linux 3.0's current base system. All
packages ran equally under Knoppix once some compatibility libraries
for C++ were installed.

Conclusions:

Overall a unanimous preference for Knoppix/Debian was expressed; some
key differences that led to this preference are outlined below:

Firstly, and very importantly, we felt that the Debian base of Knoppix
will prove to be more stable than any other distribution. This means
that the base system is likely to require major updating less often, and
that the major system updates that do become necessary are likely to be
easily executed and go smoothly.

The KDE interface, supplied by default with KDE/Debian, is crisper and
more responsive than the Gnome interface, supplied by default with
Fedora. It is also much easier to configure, which is essential both for 
the Bio-Linux development team as we endeavor to produce a user-friendly 
system, and also for users themselves to adapt their environment to best 
suit their working habits.

Another factor is that the Knoppix remastering process is well
documented and has a well supported community and will reduce the
hardware requirements for our current build methods.

We would be interested to hear from anyone that has opinions about the
continuation of development on a Knoppix-Debian system, as input from
the user community is always welcome.

We hope to release a Bio-Linux 4.0 alpha publically for feedback in the 
not too distant future, announcements will be made here.

regards,

Dan
-- 
Dr Dan Swan - Bio-Linux Developer | RHCE
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 658 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk

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Message: 2
Date: Tue, 09 Mar 2004 12:30:32 -0500
From: Chris Beck 
CC: bio-linux at ivsun01.nerc-oxford.ac.uk
Subject: Re: [Bio-Linux] Bio-Linux future directions - OS choice.

Speaking as a non-grant user I have only one caveat. It might be wise to also take into consideration the distribution that the bio 
packages are built-developed under ... if they track a fast moving distro like fedora (which will be moving to kernel 2.6 within the 
next few months then a slow moving distro like debian might fall behind. That, of course, is contingent on the pakcages in question 
being closely tied to the underlying system, if they are loosely coupled then no worries.

Cheers,
Chris

It is whispered that Dan Swan was heard, on or about 09/03/04 11:16 AM to say:

> Dear All,
> 
> 
> Firstly, and very importantly, we felt that the Debian base of Knoppix
> will prove to be more stable than any other distribution. This means
> that the base system is likely to require major updating less often, and
> that the major system updates that do become necessary are likely to be
> easily executed and go smoothly.
> 

-- 

Chris Beck / Y.A.B.A. / Fungal Genomics / CFSG / Concordia University
"We do not inherit the Earth from our Ancestors,
we borrow it from our Children."

--__--__--

Message: 3
Date: Wed, 10 Mar 2004 10:01:41 +0000
From: Dan Swan 
Reply-To: dswan at ceh.ac.uk
Organization: Centre For Ecology and Hydrology
To: Chris Beck 
CC: bio-linux at ivsun01.nerc-oxford.ac.uk
Subject: Re: [Bio-Linux] Bio-Linux future directions - OS choice.

Chris Beck wrote:
> Speaking as a non-grant user I have only one caveat. It might be wise 
> to also take into consideration the distribution that the bio packages 
> are built-developed under ... if they track a fast moving distro like 
> fedora (which will be moving to kernel 2.6 within the next few months 
> then a slow moving distro like debian might fall behind. That, of 
> course, is contingent on the pakcages in question being closely tied to 
> the underlying system, if they are loosely coupled then no worries.

In my experience bioinformatics software tends not to track the latest 
jumps in gcc versions too quickly, although this is rarely a problem as 
a quick install of the libstdc++ backwards compatibilty libraries tends 
to fix and issues. I think there is a general reaction to wait for 
platforms to be seen to be stable, I know I have not made the switch to 
a 2.6 kernel yet.

The Debian install that Knoppix does is actually very up to date as it 
tracks certain elements from testing/unstable (for those who are worried 
about those designations Debian does not describe anything as "stable" 
until it has been around for a *very* long time).

Here are the specs from my test Debian/Knoppix machine:

gcc version 3.3.3 (Debian)
This is perl, v5.8.3
Python 2.3.3
java version "1.4.2_02"
ruby 1.8.1 (2004-02-03) [i386-linux]
Linux knoppix 2.4.24-xfs
Apache/1.3.29

And from my test Fedora Core 1 machine:

gcc version 3.3.2 20031022 (Red Hat Linux 3.3.2-1)
This is perl, v5.8.3
Python 2.2.3
java version "1.4.2_03"
ruby 1.8.0 (2003-08-04) [i386-linux-gnu]
Linux fedora 2.4.22-1.2174.nptl
Apache/2.0.48

As you can see they're very close at the moment. I think it's extremely 
important to track Perl, Ruby and Python very closely with maintenance 
releases and in my experience Knoppix Debian is much more up to speed 
with this than Fedora.

With regards to the bioinformatics packages, we fully intend to create 
deb packages on i686 machines here, and then have an apt repository (we 
would have done the same for rpm/yum if we had chosen Fedora). This 
means we will test and version check the software prior to release.
Also things like BioPerl are already packaged as deb's - this removes 
the need for trying to bash through broken CPAN installs and rpm hell 
with GD under Fedora. Keeping BioPerl up to date on versions 1-3 has 
been a particular bugbear.

I hope this answers some of your concerns.

regards,

Dan

-- 
Dr Dan Swan - Bio-Linux Developer | RHCE
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR
Tel: 01865 281 658 Fax: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk


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