<DIV>Dear All, </DIV>
<DIV>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.</DIV>
<DIV>We have following suggestions to make;</DIV>
<DIV>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.</DIV>
<DIV>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.</DIV>
<DIV>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.</DIV>
<DIV>4. All databases available opensource should be included in the Local server.</DIV>
<DIV>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.</DIV>
<DIV>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.</DIV>
<DIV>With regards,</DIV>
<DIV>Mr.M.S.Yatnatti,</DIV>
<DIV>CEO, Biotechinfobytes,</DIV>
<DIV>Super Computer Aided Biotechnology center (SUCAB Center)</DIV>
<DIV>University of Agricultural Sciences, Hebbal Campus,</DIV>
<DIV>Bangalore - 560 024. (India)</DIV>
<DIV><BR><BR><B><I><A href="mailto:bio-linux-request@ivsun01.nerc-oxford.ac.uk">bio-linux-request@ivsun01.nerc-oxford.ac.uk</A></I></B> wrote:</DIV>
<BLOCKQUOTE class=replbq style="BORDER-LEFT: #1010ff 2px solid; MARGIN-LEFT: 5px; PADDING-LEFT: 5px">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 <DSWAN@CEH.AC.UK><BR>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>Linux 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: 01865 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</BLOCKQUOTE><p><hr SIZE=1>
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