From shou at ceh.ac.uk Tue Jul 8 18:52:10 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Tue, 8 Jul 2008 23:52:10 +0100 Subject: [Bio-Linux] Request for testers of Bio-Linux 5 (beta) Message-ID: <20080708225210.GA7417@ivpcp068.nerc-oxford.ac.uk> Dear all, I would like to invite all members of this list to participate in the testing of the beta release of what will become the version 5 release of Bio-Linux. A number of you have already offered your time and resources to assisting with this effort but it may be worth casting the net once more to see if others are interested in helping out. A BETA version is now available for download from the NEBC website [1] which contains *most* of the packages in our the regular repository and some customisations. This version is not intended for regular use or as a replacement for your current Bio-Linux installation, but if you do have a spare machine which you are happy to reinstall it then I would appreciate your comments. All feedback and suggestions would be welcomed but in particular I would like to hear of: - Runtime issues with Bio-Linux software packages - Customisation suggestions (graphics and branding) - General comments on Gnome and Ubuntu I appreciate that this list is generally low-volume and not strictly a "dev" list so I would like to suggest that feedback might be best coordinated through the NEBC helpdesk [helpdesk at nebc.nox.ac.uk]. Thanks in advance. Stewart [1] http://nebc.nox.ac.uk/downloads/bio-linux-5.01-beta.iso c363ca29d9ef1cc07c5f8e7b7302847c bio-linux-5.01-beta.iso -- Dr Stewart Houten, Bio-Linux Developer NEBC, CEH, Mansfield Road, Oxford, OX1 3SR http://nebc.nox.ac.uk/ From shou at ceh.ac.uk Wed Jul 9 03:49:39 2008 From: shou at ceh.ac.uk (Stewart Houten) Date: Wed, 9 Jul 2008 08:49:39 +0100 Subject: [Bio-Linux] Request for testers of Bio-Linux 5 (beta) In-Reply-To: <20080708225210.GA7417@ivpcp068.nerc-oxford.ac.uk> References: <20080708225210.GA7417@ivpcp068.nerc-oxford.ac.uk> Message-ID: <20080709074939.GA14345@ivpcp068.nerc-oxford.ac.uk> Hi all, Sending this at night was bound to be problematic. The image is actually ~2.2G and the correct md5sum is. 2da58f1779dcf23ee437a255d54a70e8 bio-linux-5.01-beta.iso > [1] http://nebc.nox.ac.uk/downloads/bio-linux-5.01-beta.iso > c363ca29d9ef1cc07c5f8e7b7302847c bio-linux-5.01-beta.iso Regards, Stewart From dfield at ceh.ac.uk Tue Jul 29 08:26:06 2008 From: dfield at ceh.ac.uk (Dawn Field) Date: Tue, 29 Jul 2008 13:26:06 +0100 Subject: [Bio-Linux] top five uses of Bio-Linux? Message-ID: ** High Priority ** Dear All, (Sorry for any cross-posting using two lists). The alpha Bio-Linux 5.0 image was posted a while back and Stewart reports several downloads. If you have feedback, including a successful install at this early stage, we'd be happy to hear it. A newer version should go up in early August. The web docs will come last. We've had discussions of the added-value features of Bio-Linux and would be happy to hear community thoughts on this issue. Q: What are your top-five uses for Bio-Linux (could be re-phrased as "what are your top-five favorate features of Bio-Linux") answers could include things like: - ease of installation (turn-key installation of a full system) - past combination of Debian/KDE or new deployment of Ubuntu/Gnome - knowing collaborators have the same local system - access to support through the NEBC helpdesk - access to online documentation - access to courses (materials) - access to particular packages, or a large suite of packages (e.g. do you use Bio-Linux primarily for blast, stats, or phylogenetics, etc? what about Partigene? genespring?) - you use the repository to build other systems - the documentation system - a built-in firewall, secure system - logging software - fact that things like partitioning and backups are built into the system - use of condor to build clusters (have you built a cluster?) - using Bio-Linux to build teaching labs, teach students, use in demonstrations - full-featured programming/database development environment - future access to the National Grid Service (NGS) - interactions with NEBC bioinformatics about analyses/projects you are running/developing on Bio-Linux - other... Any features that are not currently in Bio-Linux that you'd like to see can also be included! best, Dawn From dasp at ceh.ac.uk Tue Jul 29 08:28:34 2008 From: dasp at ceh.ac.uk (David Spurgeon) Date: Tue, 29 Jul 2008 13:28:34 +0100 Subject: [Bio-Linux] top five uses of Bio-Linux? Message-ID: I will be out of the office from July 22 until August 18. Between August the 4 and August 8 I will be accessing E-mail, but unless urgen may not be able to respond until later. >>> bio-linux 07/29/08 13:26 >>> ** High Priority ** Dear All, (Sorry for any cross-posting using two lists). The alpha Bio-Linux 5.0 image was posted a while back and Stewart reports several downloads. If you have feedback, including a successful install at this early stage, we'd be happy to hear it. A newer version should go up in early August. The web docs will come last. We've had discussions of the added-value features of Bio-Linux and would be happy to hear community thoughts on this issue. Q: What are your top-five uses for Bio-Linux (could be re-phrased as "what are your top-five favorate features of Bio-Linux") answers could include things like: - ease of installation (turn-key installation of a full system) - past combination of Debian/KDE or new deployment of Ubuntu/Gnome - knowing collaborators have the same local system - access to support through the NEBC helpdesk - access to online documentation - access to courses (materials) - access to particular packages, or a large suite of packages (e.g. do you use Bio-Linux primarily for blast, stats, or phylogenetics, etc? what about Partigene? genespring?) - you use the repository to build other systems - the documentation system - a built-in firewall, secure system - logging software - fact that things like partitioning and backups are built into the system - use of condor to build clusters (have you built a cluster?) - using Bio-Linux to build teaching labs, teach students, use in demonstrations - full-featured programming/database development environment - future access to the National Grid Service (NGS) - interactions with NEBC bioinformatics about analyses/projects you are running/developing on Bio-Linux - other... Any features that are not currently in Bio-Linux that you'd like to see can also be included! best, Dawn _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From keith.jolley at medawar.ox.ac.uk Tue Jul 29 08:53:39 2008 From: keith.jolley at medawar.ox.ac.uk (Keith Jolley) Date: Tue, 29 Jul 2008 13:53:39 +0100 Subject: [Bio-Linux] top five uses of Bio-Linux? In-Reply-To: References: Message-ID: <488F12D3.9060002@medawar.ox.ac.uk> Hi Dawn, For me it would be (in descending order): - knowing collaborators have the same local system: we mirror web databases for MLST. Apart from apache and postgresql, this system requires BLAST, EMBOSS, BioPerl and various Perl libraries. Knowing these are installed and in a standard location makes this relatively simple. - I use the repository to build other systems: I haven't used the standard image now for a while as our hardware is too variable. Installing Debian and then the Bio-Linux debs is straightforward and works fine on everything I've tried it on. - I use Bio-Linux to build teaching labs, teach students, use in demonstrations: We run a course which involves participants assembling sequence data using Staden and STARS. They can connect to one of our Bio-Linux machines using NX client, and freenx server. - Ease of installation - Full-featured programming/database development environment Best wishes Keith Dawn Field wrote: > ** High Priority ** > > Dear All, > > (Sorry for any cross-posting using two lists). > > The alpha Bio-Linux 5.0 image was posted a while back and Stewart > reports several downloads. If you have feedback, including a > successful install at this early stage, we'd be happy to hear it. A > newer version should go up in early August. The web docs will come > last. > > We've had discussions of the added-value features of Bio-Linux and > would be happy to hear community thoughts on this issue. > > Q: What are your top-five uses for Bio-Linux (could be re-phrased as > "what are your top-five favorate features of Bio-Linux") -- Dr. Keith Jolley The Peter Medawar Building for Pathogen Research University of Oxford, UK From lister at liverpool.ac.uk Tue Jul 29 09:13:14 2008 From: lister at liverpool.ac.uk (Rosin, Angela) Date: Tue, 29 Jul 2008 14:13:14 +0100 Subject: [Bio-Linux] top five uses of Bio-Linux? In-Reply-To: References: Message-ID: I've tried to download it but I had some problems... I've a machine ready to test it but I'll wait for the next version. Ang -----Original Message----- From: bio-linux-bounces at envgen.nerc-oxford.ac.uk [mailto:bio-linux-bounces at envgen.nerc-oxford.ac.uk] On Behalf Of Dawn Field Sent: 29 July 2008 13:26 To: bio-linux at envgen.nerc-oxford.ac.uk Cc: envgen-dev at envgen.nerc-oxford.ac.uk Subject: [Bio-Linux] top five uses of Bio-Linux? Importance: High ** High Priority ** Dear All, (Sorry for any cross-posting using two lists). The alpha Bio-Linux 5.0 image was posted a while back and Stewart reports several downloads. If you have feedback, including a successful install at this early stage, we'd be happy to hear it. A newer version should go up in early August. The web docs will come last. We've had discussions of the added-value features of Bio-Linux and would be happy to hear community thoughts on this issue. Q: What are your top-five uses for Bio-Linux (could be re-phrased as "what are your top-five favorate features of Bio-Linux") answers could include things like: - ease of installation (turn-key installation of a full system) - past combination of Debian/KDE or new deployment of Ubuntu/Gnome - knowing collaborators have the same local system - access to support through the NEBC helpdesk - access to online documentation - access to courses (materials) - access to particular packages, or a large suite of packages (e.g. do you use Bio-Linux primarily for blast, stats, or phylogenetics, etc? what about Partigene? genespring?) - you use the repository to build other systems - the documentation system - a built-in firewall, secure system - logging software - fact that things like partitioning and backups are built into the system - use of condor to build clusters (have you built a cluster?) - using Bio-Linux to build teaching labs, teach students, use in demonstrations - full-featured programming/database development environment - future access to the National Grid Service (NGS) - interactions with NEBC bioinformatics about analyses/projects you are running/developing on Bio-Linux - other... Any features that are not currently in Bio-Linux that you'd like to see can also be included! best, Dawn _______________________________________________ Bio-Linux mailing list Bio-Linux at envgen.nox.ac.uk http://envgen.nox.ac.uk/mailman/listinfo/bio-linux From btiwari at ceh.ac.uk Wed Jul 30 12:23:59 2008 From: btiwari at ceh.ac.uk (Bela Tiwari) Date: Wed, 30 Jul 2008 17:23:59 +0100 Subject: [Bio-Linux] work around script for extract_seq module via pregap4 Message-ID: Dear all, This message is for anyone who supports a machine with users that run the extract_seq module in Staden via pregap4. In the latest release of Staden (1.7.0) , the extract_seq module does not work properly via pregap4. We have reported this to the main Staden developer. In the meantime, for those who rely on extract_seq, we have put a script on the NEBC wiki that can be used in its stead. The script and instructions on how to use it can be found at: http://darwin.nerc-oxford.ac.uk/pgp-wiki/index.php/General_Bioinformatics_Scripts#Script:Extract_cleaned_sequences_from_.exp_files cheers, Bela ************************* Dr. Bela Tiwari Lead Bioinformatician NERC Environmental Bioinformatics Centre CEH Oxford Mansfield Road Oxford, OX1 3SR 01865 281975 ************************* -- This message (and any attachments) is for the recipient only. NERC is subject to the Freedom of Information Act 2000 and the contents of this email and any reply you make may be disclosed by NERC unless it is exempt from release under the Act. Any material supplied to NERC may be stored in an electronic records management system.