[Bio-Linux] Re: Bio-Linux future versions

[M.S YATNATTI]

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 
Linux 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: 01865 281 696
http://envgen.nox.ac.uk/ | dswan at ceh.ac.uk


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