From n.haigh at sheffield.ac.uk Tue Aug 15 09:02:49 2006 From: n.haigh at sheffield.ac.uk (Nathan S. Haigh) Date: Tue, 15 Aug 2006 13:02:49 +0000 Subject: [Bio-Linux] Workshop: Recent Advances in Statistical Genetics and Bioinformatics Message-ID: <44E1C5F9.7000908@sheffield.ac.uk> I have recently been made aware of this workshop which is to take place in Cambridge on 11-15th Dec inclusive and thought it worth a post to the list. Further details can be found here: http://www.newton.cam.ac.uk/programmes/SCB/scbw02.html Kind regards Nathan From a.j.pemberton at bham.ac.uk Fri Aug 18 06:28:17 2006 From: a.j.pemberton at bham.ac.uk (Tony Pemberton) Date: Fri, 18 Aug 2006 11:28:17 +0100 Subject: [Bio-Linux] Monitor change Message-ID: Dear Biolinux users, Can anyone tell me how to reset the defualt refresh rate on Bio-Linux 4? I have chnaged to a newer monitor but this needs the lower 60Hz refresh rate. I tried logging in as myself on the system and could switch to a viewable rate by using the old monitor, but when I logout the refresh rate changes back to 75Hz, Regards, Tony Pemberton *********************************************************************** Mr. A. Pemberton Tel:+44 121 414 3388 School of Biosciences, Fax:+44 121 414 5925 The University of Birmingham Email:a.j.pemberton at bham.ac.uk Birmingham B15 2TT U.K. *********************************************************************** From jaa53 at cornell.edu Mon Aug 21 14:35:36 2006 From: jaa53 at cornell.edu (Jose Andres) Date: Mon, 21 Aug 2006 14:35:36 -0400 Subject: [Bio-Linux] bioinformatics system menu question In-Reply-To: References: Message-ID: <05D3EDEC-A369-4701-B10F-C1F3A35E60B2@cornell.edu> Hi all, Currently the bioinformatics system menu of the task bar in my bio- linux machine only shows a small fraction of the programs (n=6) its used to showed (e.g. gap, pergap, act, etc... all gone!). Any idea on what went wrong? Is there any way I can put them back into the menu? I've been searching on the info but could not find any reference. Thanks a bunch, /Jose On Mar 30, 2006, at 6:27, Ashley Morley wrote: > Dear Colleagues, > > The NERC Environmental Bioinformatics Centre (NEBC) will > be running a Working with Bio-Linux introductory course on Friday 2 > June, 2006. > > This is a one day course designed to introduce new users to the > Bio-Linux system. The course is divided into two sections: > Introduction to Linux and Introduction to Bioinformatics on Bio-Linux. > > The course is designed so that people can work at their own pace and > discover the facilities available on Bio-Linux. Instructors from the > NEBC will be on hand to answer Bio-Linux-related questions as well > as to discuss > any data management or bioinformatics analysis requirements you may > have. > > The course will be held at CEH Oxford and will run from 10:30am until > 5:00pm. Registration is on a first come, first serve basis. We will > hold a waiting list if demand exceeds the number of places on this > course and will schedule other courses in the near future if there is > enough interest. > > You or anyone on your NERC EG or PG&P grant can register for this > course using our web registration form at: > > http://envgen.nox.ac.uk/cgi-bin/showcourses.cgi > > All course notes and sample files are already available at: > > http://envgen.nox.ac.uk/envgen/training/archives/000530.html > > > best wishes, > > The NEBC Team > > > _______________________________________________ > Bio-linux mailing list > Bio-linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From shou at ceh.ac.uk Wed Aug 23 05:15:24 2006 From: shou at ceh.ac.uk (Stewart Houten) Date: Wed, 23 Aug 2006 10:15:24 +0100 Subject: [Bio-Linux] bioinformatics system menu question In-Reply-To: <05D3EDEC-A369-4701-B10F-C1F3A35E60B2@cornell.edu> References: <05D3EDEC-A369-4701-B10F-C1F3A35E60B2@cornell.edu> Message-ID: <20060823091524.GB8535@ivpcp068.nerc-oxford.ac.uk> Hi Jose, I can't offer an explanation of why they disappeared other than to say KDE does strange things at times. To refresh the menus you might try the command "update-menus" from a terminal. This should rebuild the menus from the entries in /etc/menu. If this doesn't work let me know off the list. Regards, Stewart -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ From jaa53 at cornell.edu Thu Aug 24 11:30:41 2006 From: jaa53 at cornell.edu (Jose Andres) Date: Thu, 24 Aug 2006 11:30:41 -0400 Subject: [Bio-Linux] condor cluster In-Reply-To: <20060823091524.GB8535@ivpcp068.nerc-oxford.ac.uk> References: <05D3EDEC-A369-4701-B10F-C1F3A35E60B2@cornell.edu> <20060823091524.GB8535@ivpcp068.nerc-oxford.ac.uk> Message-ID: Hi all, I'd like to use Biolinux to establish a local network of computers (most of them running Windows or Mac OS) that will allow us to use some applications (e.g. omegaMap, Paup) on a "grid mode" or as in a serial node cluster. If I understood some of the documentation I've been reading you can do it using the version of condor implemented in our bio-linux machines. Is that right? Does anyone have experience on this type of networks? Are they difficult to set up? I am quite naive with this issues and I'd really appreciate any comments/ suggestions you might have. Cheers, /Jose On Aug 23, 2006, at 5:15, Stewart Houten wrote: > Hi Jose, > > I can't offer an explanation of why they disappeared other than to say > KDE does strange things at times. > > To refresh the menus you might try the command "update-menus" from a > terminal. This should rebuild the menus from the entries in /etc/ > menu. > > If this doesn't work let me know off the list. > > Regards, > Stewart > -- > Dr Stewart Houten, Bio-Linux Developer > NEBC, CEH, Mansfield Road, Oxford, OX1 3SR > http://nebc.nox.ac.uk/ > > _______________________________________________ > Bio-linux mailing list > Bio-linux at envgen.nox.ac.uk > http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From N.H.Mann at warwick.ac.uk Thu Aug 24 16:19:35 2006 From: N.H.Mann at warwick.ac.uk (Nick Mann) Date: Thu, 24 Aug 2006 21:19:35 +0100 Subject: [Bio-Linux] condor cluster (Out of office) Message-ID: This is an automated reply to your email. I am away from the Department until 18th September. I will deal with all my emails on return. Regards Nick Mann Professor Nicholas Mann Department of Biological Sciences University of Warwick Coventry CV4 7AL From bioinformatics.lists at gmail.com Fri Aug 25 05:28:06 2006 From: bioinformatics.lists at gmail.com (Dan Swan) Date: Fri, 25 Aug 2006 10:28:06 +0100 Subject: [Bio-Linux] condor cluster In-Reply-To: References: <05D3EDEC-A369-4701-B10F-C1F3A35E60B2@cornell.edu> <20060823091524.GB8535@ivpcp068.nerc-oxford.ac.uk> Message-ID: On 8/24/06, Jose Andres wrote: > Hi all, > > I'd like to use Biolinux to establish a local network of computers > (most of them running Windows or Mac OS) that will allow us to use > some applications (e.g. omegaMap, Paup) on a "grid mode" or as in a > serial node cluster. If I understood some of the documentation I've > been reading you can do it using the version of condor implemented in > our bio-linux machines. Is that right? Does anyone have experience > on this type of networks? Are they difficult to set up? I am quite > naive with this issues and I'd really appreciate any comments/ > suggestions you might have. Hi Jose, You can certainly use your Bio-Linux workstation as the central manager for a Condor pool - the necessary software is already installed. I run a (large) mixed Condor pool at Newcastle with a Linux central manager. You can send jobs to your Windows and Mac OS machines from the Bio-Linux machine, this is not a problem, you can specify which resources a job needs (OS, architechture, installed programs) using Condor requirements expressions. By and large the only jobs you are going to send to the Windows machines are Java jobs, or Windows executables. Similarly the only things you are going to send to Linux machines are Linux executables, Java jobs or shell/Perl scripts. The same goes for OS X - OS X executables, Java jobs or shell/Perl scripts. Unless you have Windows, UNIX and OS X versions of PAUP you're most likely to be limited to running it on a single OS. Most likely OS X if the researchers here are anything to go by ;) Omegamap appears to be Windows only anyway. However you're best to sticking with applications that can be scripted - or run from the command line. Whilst it's possible to launch GUI applications under Condor, you're effectively unable to interact with them. Condor is relatively easy to set up, but can be occasionally frustrating to troubleshoot due to the rather uninformative errors it first seems to generate. Once you have the central manager machine running, it is very simple to set up clients to join the pool. If you have a lot of Windows machines managed by Active Directory, you'll probably want an MSI build of Condor - your local IT people should be able to help you with this. Condor is backed by an excellent community mailing list (https://lists.cs.wisc.edu/mailman/listinfo/condor-users) Currently the OS X and Windows builds do not support 'checkpointing' - allowing jobs to be stopped and restarted part of the way through the computation, so this may impact on your turnover of jobs. The best advice I can give is to configure the central manager on your Bio-Linux machine (which shouldn't require much effort) and then get a 'sacrificial' Windows and Mac machine, and set them up as 'execute' nodes. For the purposes of testing, it's best that these machines are infrequently used, otherwise you will be sat waiting for your submitted jobs to complete until people stop using the machines. In practice as your pool becomes larger this becomes less of a problem - but you'll definitely want to do your initial testing on a small, completely idle, pool of machines. If I can help you any further, please get in touch, I spend a fair p -- Senior Research Associate, Bioinformatics Support Unit, Institute for Cell and Molecular Biosciences, Faculty of Medical Sciences, Framlington Place, University of Newcastle upon Tyne, Newcastle, NE2 4HH Tel: +44 (0)191 222 7253 (Leech offices: Rooms M.2046/M.2046A) Tel: +44 (0)191 246 4833 (Devonshire offices: Rooms G.25/G.26) Website: http://bioinf.ncl.ac.uk/support/