[Bio-Linux] Bio-Linux future directions - OS choice.

[Dan Swan]

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