From humberto at hpcf.upr.edu Thu Feb 19 20:42:00 2004 From: humberto at hpcf.upr.edu (Humberto Ortiz Zuazaga) Date: Thu, 19 Feb 2004 20:42:00 -0400 Subject: [bioknoppix-discuss] Welcome, and summary of feedback Message-ID: <20040219204200.19bb8657.humberto@hpcf.upr.edu> Hello everyone, thanks for signing up to this mailing list for bioknoppix. I wanted to assure everyone that a) there really are developers, b) we've listened to the community requests, and c) we are working on bringing new and improved bioknoppix releases out soon. Carlos Rodriguez, build master extraordinare and primary developer of bioknoppix is in Vancouver Canada for two weeks for a bioinformatics workshop, so I've been handling publicity and the actual release (he posted the release announcements, then went home to pack, by the time the slashdot story came out he was in Canada). By the way, I'm using the bioknoppix distribution to teach UNIX, bioinformatics and python programming in a graduate course in bioinformatics at the University of Puerto Rico, so far, the student's reaction has been positive, even if UNIX takes a little getting used to. Our biggest problem is permanent storage of files and connecting to the Internet on networks that do not have DHCP set up, or that have winmodems. First off, we'll be making sure to get jemboss standalone working in the next release, it's a nice interface to emboss, and it's a shame we couldn't get it fixed for this first release. Next, we'll be looking at software to display protein structural data: one slashdot reader suggested Deep View Swiss PDB Viewer: http://kr.expasy.org/spdbv/ which we can redistribute without modifications. We *might* try building a Mac release, if we can get a live CD distribution working on a Mac and some hardware to test on. We'd also like to hear from you, to see what you like and dislike, or how you think we should change. In particular, we have a couple of office suites, we thought it was nice to be able to write papers as well as doing the data analysis, but recognize that other scientific live CDs like Quantian make room for more science by deleting the Office applications. Thanks for trying out bioknoppix! -- Humberto Ortiz-Zuazaga Programmer-Archaeologist High Performance Computing facility University of Puerto Rico http://www.hpcf.upr.edu/~humberto/ -------------- next part -------------- A non-text attachment was scrubbed... Name: not available Type: application/pgp-signature Size: 189 bytes Desc: not available URL: From dongfu at northwestern.edu Fri Feb 20 01:10:29 2004 From: dongfu at northwestern.edu (Dong Fu) Date: Thu, 19 Feb 2004 23:10:29 -0600 Subject: [bioknoppix-discuss] GNU R not working off the CD In-Reply-To: <20040219204200.19bb8657.humberto@hpcf.upr.edu> References: <20040219204200.19bb8657.humberto@hpcf.upr.edu> Message-ID: <19F64207-6363-11D8-ABCB-000A95CDA580@northwestern.edu> Hello Humberto, Thanks for setting up the mailing list and starting off the discussion. We have an active and eager group of bioinformatics developers here which can benefit much from a product like bioknoppix. After trying to boot off the bioknoppix CD several times, I found that the GNU R package is not working correctly for me. The GUI quickly flashes by without really launching, and the command line R complains about not being able to find libblast.so.2, which I found is in one of the directories under /usr/local. (Sorry I do not have the CD with me right now and I am using a Mac). Also the symbolic links under /usr/lib/R/etc point to some non-existing files/directories under /etc/R, which causes "R CMD config" to be not very happy. One thing I did not try is to launch it as root, which I will try when I am back at the office again. On the other hand, I was able to get the USB keydrive to work easily so I can store data files on it instead of relying on setting up the network part. It takes one second to manually mount the drive. I guess if DHCP and NFS server are both available on the network, it will be easy to transfer files, too. We would really welcome the Bioknoppix for Mac project. I checked the available Knoppix-like product on PowerPC out there, and the stable one seems to come from Gentoo Live CD instead. We will be happy to help building and testing it as we have some hardware here to use. Thanks. Dong Dong Fu System Administrator, Bioinformatics Core Robert H. Lurie Comprehensive Cancer Center of Northwestern University Chicago, IL From benhamal76 at yahoo.it Fri Feb 20 07:24:11 2004 From: benhamal76 at yahoo.it (=?iso-8859-1?q?L=20ben?=) Date: Fri, 20 Feb 2004 12:24:11 +0100 (CET) Subject: [bioknoppix-discuss] kudos to bioknoppix Message-ID: <20040220112411.44079.qmail@web60207.mail.yahoo.com> Hi everybody :-) I'm downloading and looking forward to try bioknoppix and yet I have some questions. Does bioknoppix rely on openmosix http://openmosix.sourceforge.net/ ? I ' m an openmosix fan , especially for live distros , because it lets you building a live cluster with cds wich fits in your pocket :-) Does bioknoppix comes with some data , too , i.e. to make students work on sample datasets (It would require more space but it might be worth the effort) I am trying http://www.bioteam.net/ibt/index.html wich is a bioinformatics benchmark sistem . It tests ncbi-blast , gromacs , hmmr and blat on sample datasets...at least for gromacs and ncbi-blast there should be already .deb packages so it will be effortlessy to include them and make a .deb for perl modules of ibt wich manages those tests. I' m not a big .deb fan ...infact I was doing something similar with .rpm and a live distro called Adios. If bioknoppix is is a live cluster friendly distro also mpi-blast may be interesting : http://mpiblast.lanl.gov/ sorry for my impatience ... I have a slow network and I couldn' t wait to find some of the answer directly from your wonderful distro ( wich I am pushing on all mailing list I am member of ... hope soon to see openmosix on it so I can do it with openmosix-general and devel as well ;-) best wishes ben ______________________________________________________________________ Yahoo! Mail: 6MB di spazio gratuito, 30MB per i tuoi allegati, l'antivirus, il filtro Anti-spam http://it.yahoo.com/mail_it/foot/?http://it.mail.yahoo.com/ From humberto at hpcf.upr.edu Fri Feb 20 22:06:29 2004 From: humberto at hpcf.upr.edu (Humberto Ortiz-Zuazaga) Date: Fri, 20 Feb 2004 22:06:29 -0400 Subject: [bioknoppix-discuss] kudos to bioknoppix In-Reply-To: Message from =?iso-8859-1?q?L=20ben?= of "Fri, 20 Feb 2004 12:24:11 +0100." <20040220112411.44079.qmail@web60207.mail.yahoo.com> Message-ID: <200402210206.i1L26T0e026175@daleth.hpcf.upr.edu> >>>>> "L" == =?iso-8859-1?q?L=20ben?= writes: L> Does bioknoppix rely on openmosix L> http://openmosix.sourceforge.net/ ? Not now. We've gotten this request more than once, so we'll look into it as well. L> :-) Does bioknoppix comes with some data , too , i.e. to make L> students work on sample datasets (It would require more space L> but it might be worth the effort) We have the test data for emboss, which can be used to run all of the emboss examples in every one of the man pages and tutorial. -- Humberto Ortiz Zuazaga Programmer-Archaeologist High Performance Computing facility University of Puerto Rico http://www.hpcf.upr.edu/~humberto/