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<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='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.</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'> </span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Rob Anderson</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Computing Support Officer</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Centre for Population Biology</span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span style='font-size:
10.0pt;font-family:Arial;color:navy'>Imperial</span></font><font size=2
color=navy face=Arial><span style='font-size:10.0pt;font-family:Arial;
color:navy'> </span></font><font size=2 color=navy face=Arial><span
style='font-size:10.0pt;font-family:Arial;color:navy'>College</span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=2 face=Tahoma><span
lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>-----Original
Message-----<br>
<b><span style='font-weight:bold'>From:</span></b> bio-linux-admin@ivsun01.nerc-oxford.ac.uk
[mailto:bio-linux-admin@ivsun01.nerc-oxford.ac.uk] <b><span style='font-weight:
bold'>On Behalf Of </span></b>M.S YATNATTI<br>
<b><span style='font-weight:bold'>Sent:</span></b> </span></font><font size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>19
February 2004</span></font><font size=2 face=Tahoma><span lang=EN-US
style='font-size:10.0pt;font-family:Tahoma'> </span></font><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'>11:54</span></font><font
size=2 face=Tahoma><span lang=EN-US style='font-size:10.0pt;font-family:Tahoma'><br>
<b><span style='font-weight:bold'>To:</span></b>
bio-linux@ivsun01.nerc-oxford.ac.uk<br>
<b><span style='font-weight:bold'>Subject:</span></b> [Bio-Linux] Re: Bio-Linux
future versions</span></font></p>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'> </span></font></p>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Dear All, </span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Thanks for the efforts
taken by Centre For Ecology and Hydrology<br>
In our view, the direction in which center for ecology and Hydrology lead by
Dan Swan for future Bio-linux version is throught provoking.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>We have following
suggestions to make;</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>4. All databases
available opensource should be included in the Local server.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>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.</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>With regards,</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Mr.M.S.Yatnatti,</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>CEO, Biotechinfobytes,</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Super Computer Aided
Biotechnology center (SUCAB Center)</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>University of
Agricultural Sciences, Hebbal Campus,</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Bangalore - 560 024.
(India)</span></font></p>
</div>
<div>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><br>
<br>
<b><i><span style='font-weight:bold;font-style:italic'><a
href="mailto:bio-linux-request@ivsun01.nerc-oxford.ac.uk">bio-linux-request@ivsun01.nerc-oxford.ac.uk</a></span></i></b>
wrote:</span></font></p>
</div>
<blockquote style='border:none;border-left:solid #1010FF 1.5pt;padding:0cm 0cm 0cm 4.0pt;
margin-left:3.75pt;margin-top:5.0pt;margin-bottom:5.0pt'>
<p class=MsoNormal style='margin-left:36.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Send Bio-Linux mailing
list submissions to<br>
<a href="mailto:bio-linux@bioinf.ceh.ac.uk">bio-linux@bioinf.ceh.ac.uk</a><br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit<br>
<a href="http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux">http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux</a><br>
or, via email, send a message with subject or body 'help' to<br>
<a href="mailto:bio-linux-request@bioinf.ceh.ac.uk">bio-linux-request@bioinf.ceh.ac.uk</a><br>
<br>
You can reach the person managing the list at<br>
<a href="mailto:bio-linux-admin@bioinf.ceh.ac.uk">bio-linux-admin@bioinf.ceh.ac.uk</a><br>
<br>
When replying, please edit your Subject line so it is more specific<br>
than "Re: Contents of Bio-Linux digest..."<br>
<br>
<br>
Today's Topics:<br>
<br>
1. Bio-Linux future strategy (Dan Swan)<br>
<br>
--__--__--<br>
<br>
Message: 1<br>
Date: Wed, 18 Feb 2004 11:46:31 +0000<br>
From: Dan Swan <br>
<DSWAN@CEH.AC.UK>Reply-To: <a href="mailto:dswan@ceh.ac.uk">dswan@ceh.ac.uk</a><br>
Organization: Centre For Ecology and Hydrology<br>
To: <a href="mailto:bio-linux@ivsun01.nerc-oxford.ac.uk">bio-linux@ivsun01.nerc-oxford.ac.uk</a><br>
Subject: [Bio-Linux] Bio-Linux future strategy<br>
<br>
Dear all - here is a consultation document on the future of Bio-Linux - <br>
comments appreciated either on list or off list.<br>
<br>
For a breakdown on how we comnpared the distributions the delightfully <br>
coloured Excel spreadsheet can be downloaded from:<br>
<br>
<a href="http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls">http://genomics.nox.ac.uk/~dswan/Linux_comparisons.xls</a><br>
<br>
Bio-Linux future directions – OS selection.<br>
-------------------------------------------<br>
<br>
Bio-Linux 3.0 and earlier versions were based on the popular Red Hat <br>
Liinux distribution. Red Hat will be dropping support for the freely <br>
available and distributable version of the Linux operating system (OS) <br>
in April 2004. This has prompted the need to review the Linux <br>
distributions currently available and to make a decision based on this <br>
review as to the best choice for the base of future Bio-Linux development.<br>
<br>
Issues of key importance to our decision include:<br>
<br>
Compatibility with the hardware provided to Environmental Genomics <br>
Thematic Programme Awardee Labs<br>
<br>
Level of difference in administration, interface and overall feel of the <br>
system compared to the current Bio-Linux<br>
<br>
Overall level of user (and administrator)-friendliness<br>
<br>
Release schedule, automatic updating systems, versions of base system <br>
components<br>
<br>
Licensing issues for redistribution<br>
<br>
Documentation availability<br>
<br>
<br>
In addition, we will take into account the mechanism by which the OS can <br>
be distributed as distribution via hard media rather than the current <br>
situation, using SystemImager software, would free a significant amount <br>
of time for EGTDC staff providing user support, and allow distribution <br>
of the Bio-Linux system to a wider audience with no significant support <br>
cost to the EGTDC. Associated with the distribution system, some OS <br>
versions provide an easy mechanism to produce “Live CD’s”
which would <br>
allow Bio-Linux to be demonstrated easily, for example at conferences, <br>
thus raising its profile. A live CD version would also enable people to <br>
run a cut down version of Bio-Linux on machines without dedicating the <br>
machine to a Linux installation.<br>
<br>
Our testing is made up of several stages:<br>
<br>
from all the Linux distributions, choose those to be tested<br>
<br>
from those chosen, make choices for further testing based on obvious <br>
issues such as hardware incompatibility<br>
<br>
test a number of distributions further and choose two that will be <br>
tested by a larger group<br>
<br>
on the basis of all the above, decide on the OS on which to base the <br>
future development<br>
<br>
<br>
Distributions chosen for testing<br>
<br>
There are many Linux distributions available. On the basis of our <br>
requirements, some distributions were immediately excluded from <br>
consideration:<br>
<br>
Gentoo was considered to be inappropriate for the remit of Bio-Linux as <br>
the installation process allows such fine grained control an install can <br>
take upwards of a day and you must be extremely competent with Linux <br>
already.<br>
<br>
Debian was excluded on the basis that its install was too complex for <br>
people not familiar with Linux.<br>
<br>
Slackware was excluded as it lacks an integral modern system of package <br>
management (deb or rpm).<br>
<br>
Mandrake was excluded from initial consideration as it was close to <br>
receivership last year and there were worries about its long term future.<br>
<br>
The distributions reviewed include:<br>
<br>
Knoppix (a Live-CD distribution of Debian)<br>
Fedora<br>
SuSE<br>
DNALinux (a Slackware based Live-CD with some bioinformatics <br>
applications bundled)<br>
BioBrew<br>
Morphix (a “modular” Knoppix derivative )<br>
Mandrake<br>
MandrakeMove<br>
BioKnoppix<br>
<br>
Results of testing<br>
<br>
2 distributions failed to boot on our test hardware due to the inability <br>
to deal with 2 CPU machines and were immediately excluded from further <br>
consideration:<br>
<br>
DNALinux<br>
Morphix<br>
<br>
These bugs were reported to the development teams responsible.<br>
<br>
1 distribution was excluded on the basis that the Live-CD format had no <br>
option to install to disk:<br>
<br>
MandrakeMove.<br>
<br>
The remaining distributions were tested further:<br>
<br>
Knoppix<br>
Fedora<br>
SuSE<br>
BioBrew<br>
BioKnoppix<br>
<br>
A brief overview of these distributions is given here, followed by the <br>
testing results:<br>
<br>
Knoppix<br>
<br>
Knoppix is probably the oldest and best known Live-CD distribution and <br>
has a long history of customisation for various purposes (see “Related <br>
Projects” at <a href="http://www.knopper.net/knoppix-links/index-en.html">http://www.knopper.net/knoppix-links/index-en.html</a>).
<br>
Knoppix is of interest as it could be not only used as a Bio-Linux demo <br>
system at conferences, but could also be used in a teaching environment <br>
and most importantly of all can be installed onto the hard disk of a <br>
machine to give a Debian install without the pain of a traditional <br>
Debian install. It has excellent hardware detection routines.<br>
<br>
Fedora<br>
<br>
The Fedora Project is a Red-Hat-sponsored and community-supported open <br>
source project. It is also a proving ground for new technology that may <br>
eventually make its way into Red Hat products. It is not a supported <br>
product of Red Hat, Inc. Fedora Core 1 is effectively Red Hat 10. <br>
Fedora is of interest to us as this will most resemble the system <br>
Bio-Linux 3.0 and earlier are based upon. The configuration tools are <br>
largely unchanged from Red Hat 9.0. Whilst we can not make a Live-CD <br>
for Fedora we would be able to create a distribution based on it.<br>
<br>
SuSE<br>
<br>
SuSE is a German, but internationalised, distribution very much in Red <br>
Hat's image. They have a heavy focus on enterprise solutions like Red <br>
Hat and have recently been acquired by Novell as a platform for the next <br>
generation or Novell products. SuSE has a highly integrated <br>
configuration GUI, much more advanced than Red Hat's.<br>
<br>
BioBrew<br>
<br>
BioBrew is a cluster focused Linux distribution which comes with some <br>
bioinformatics software preinstalled. For the most part, the programs <br>
included form a subset of those available on Bio-Linux. BioBrew is <br>
based on NCAPI/Rocks Linux, a derivative of Red Hat Advanced Server. <br>
Bio-Brew has the look and feel of a default Red Hat 7.3 install.<br>
<br>
Bio-Knoppix<br>
<br>
A derivative of Knoppix (see above). It includes some bioinformatics <br>
tools and is in early beta development (version 0.2 currently, version <br>
0.3 was recalled due to mastering problems); essentially it is Knoppix <br>
with a new splashscreen and KDE menus for some bioinformatics software <br>
(not all of which work). If Bio-Linux 4.0 was to be derived from <br>
Knoppix we would be using a clean Knoppix base rather than a derived <br>
system such as Bio-Knoppix.<br>
<br>
Summary of some positive and negative aspects of the different distributions<br>
<br>
Knoppix<br>
<br>
Positive:<br>
<br>
1)Once installed it never has to be upgraded with CD's<br>
2)Exceedingly stable code base<br>
3)Very long release cycle<br>
4)Can be used to make a Live-CD<br>
5)Strong remastering community<br>
6)Can be made to track stable releases, or testing releases when appropriate<br>
7)Installs a perfectly configured Debian system to disk.<br>
8)Excellent hardware detection and configuration<br>
<br>
Negative:<br>
<br>
1)Not as advanced GUI for systems administration<br>
2)Debian package management system – will be unfamiliar to RPM users<br>
<br>
Fedora<br>
<br>
Positive:<br>
<br>
1)It's the closest distribution to Bio-Linux<br>
2)Has reasonably advanced GUI configurations<br>
3)Have most in house administration experience on the related RedHat <br>
platform<br>
4)Will be familiar to the Environmental Genomics user community<br>
5)Exceedingly easy to install <br>
<br>
Negative:<br>
<br>
1)Very new project, despite established base<br>
2)Focus on cutting edge -i.e. FC2 is 2.6 Kernel, 2.6 Gnome and we do not <br>
know how this will impact the software included on Bio-Linux<br>
3)Rapid release schedule: 2-3 releases a year to keep up with and remaster<br>
4)Releases not always out on date initially scheduled<br>
5)Cannot be made into a Live CD<br>
<br>
SuSE<br>
<br>
Positive:<br>
<br>
1)Exceedingly easy to install<br>
2)Centralised administration through yast2<br>
3)RPM based, therefore familiar to awardees<br>
4)Likely to be guaranteed to work with Novell products in the future.<br>
<br>
Negative:<br>
<br>
1)Licensing terms for redistribution are unclear<br>
2)There are no SuSE-derived releases on the market hence:<br>
3)There are no instructions for remastering SuSE<br>
4)Cannot be made into a Live-CD<br>
5)There is the possibility of it “pulling a Red Hat” and focusing
on <br>
Enterprise exclusively<br>
6)Will be remastering at least once a year (SuSE are slowing release <br>
dates for stability)<br>
<br>
<br>
<br>
BioBrew<br>
<br>
Positive:<br>
<br>
1)Based on Red Hat and so would be familiar to Bio-Linux users and <br>
administrators<br>
2)Large installed base <br>
3)Ready to cluster<br>
4)Already has some bioinformatics applications installed<br>
<br>
Negative:<br>
<br>
1)Cannot be made into a Live-CD<br>
2)Based on outdated version of RHAS<br>
3)Text mode install <br>
4)Not at all focused on desktop usage<br>
<br>
Bio-Knoppix<br>
<br>
<br>
This distribution has the same base list of positive and negative <br>
attributes as Knoppix, but also includes:<br>
<br>
Positive:<br>
<br>
1)Has some bioinformatics software preinstalled<br>
2)Some EMBOSS customisation has been done<br>
3)Menu customisations have been already implemented for bioinformatics <br>
software<br>
<br>
Negative:<br>
<br>
1)Current version is at 0.2 and is clearly labeled beta<br>
2)Not all menus work<br>
3)All added software, bioinformatics and non-bioinformatics, has been <br>
installed into /usr/local<br>
4)Even if we used it as a base, we'd end up ripping out everything <br>
they've done and remastering it.<br>
<br>
Linux distributions chosen for further testing<br>
<br>
On the basis of the above results, two distributions were chosen at the <br>
Bio-Linux Development strategy meeting on February 13, 2004 for further <br>
testing as potential base systems for Bio-Linux:<br>
<br>
Fedora Core 1<br>
Knoppix<br>
<br>
Testing strategy:<br>
<br>
Two machines will be set up, one for each of the above distributions. <br>
Over the next two weeks, EGTDC staff will dedicate time to work on both <br>
systems. A final decision for the distribution to be used for further <br>
Bio-Linux development will be made on February 27, 2004 on the basis of <br>
this testing.<br>
<br>
For those wishing to read up on what is happening in the Linux world <br>
there is an excellent article here on the relative market share of the <br>
top Linux variants:<br>
<br>
<a href="http://www.internetnews.com/ent-news/article.php/3313211">http://www.internetnews.com/ent-news/article.php/3313211</a><br>
-- <br>
Dr Dan Swan - Bio-Linux Developer | RHCE<br>
EGTDC, CEH, Mansfield Road, Oxford, OX1 3SR<br>
Tel: 01865 281 658 Fax: 018665 281 696<br>
<a href="http://envgen.nox.ac.uk/">http://envgen.nox.ac.uk/</a> | <a
href="mailto:dswan@ceh.ac.uk">dswan@ceh.ac.uk</a><br>
<br>
<br>
--__--__--<br>
<br>
_______________________________________________<br>
Bio-Linux mailing list<br>
<a href="mailto:Bio-Linux@bioinf.ceh.ac.uk">Bio-Linux@bioinf.ceh.ac.uk</a><br>
<a href="http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux">http://www.bioinf.ceh.ac.uk/mailman/listinfo/bio-linux</a><br>
<br>
<br>
End of Bio-Linux Digest</span></font></p>
</blockquote>
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