From jimmy at nete.com Wed Dec 2 22:03:56 2015 From: jimmy at nete.com (Jimmy Griffin) Date: Thu, 3 Dec 2015 03:03:56 +0000 Subject: [Bio-Linux] Bio-Linux 8 Galaxy Server connectivity to SGE or Scheduler Message-ID: Hello All, I'm new to how to configure the galaxy server and how to connect it to a scheduler like SGE, Slurm, and/or Torque. Would someone be able to provide me some documentation on how to install and configure the Galaxy server to connect to a scheduler? Thanks -------------- next part -------------- An HTML attachment was scrubbed... URL: From avarus at fastmail.fm Tue Dec 15 05:44:15 2015 From: avarus at fastmail.fm (Tim Booth) Date: Tue, 15 Dec 2015 10:44:15 +0000 Subject: [Bio-linux-list] Merging of this list with bio-linux@nebclists.ac.uk Message-ID: <1450176255.23350.70.camel@balisaur> Dear Subscribers, You may have forgotten you were even on this list since the last message to go through it was back in 2010. However, I have just taken over management of the list and I am now about to shut down the active Bio-Linux users list (on nebclists.nerc.ac.uk) and move all subscribers to the Mailman server here on Bioinformatics.org. Therefore you will shortly start to see a bit of traffic. I hope you will stick around and join the discussion, but if you prefer not to then please unsubscribe using the link below. Main Bio-Linux site is currently: http://environmentalomics.org/bio-linux/ Cheers, TIM -- Hanlon's Razor: Never attribute to malice that which can be adequately explained by stupidity... but don't rule out malice. From tbooth at ceh.ac.uk Tue Dec 15 06:54:38 2015 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 15 Dec 2015 11:54:38 +0000 Subject: [Bio-linux-list] [Bio-Linux-list] Can't install Biolinux8 in DELL Precision T5810 In-Reply-To: References: Message-ID: <1450180478.23350.81.camel@balisaur> Hi Xavi, [Note - I've switched the discussion to the new mailing list server] I've seen similar issues where the driver tries to initialise the graphics card and the whole thing just locks up. It think you are on the right track booting the USB on a working machine and trying to tinker with the drivers, but I'd follow this guide and add the enablement drivers for X (I can't do this by default as it totally breaks VirtualBox support): https://wiki.ubuntu.com/Kernel/LTSEnablementStack On the working machine you should also do an integrity check on the USB to be sure. I'm surprised that removing "quiet splash" didn't at least give you some boot messages. If you replace "quiet splash" with the word "text" you should boot straight to a command prompt. Does that work? I'm also surprised by this bit: > it only boot in an Ubuntu 12.04 (instead of 14.04) GUI Bio-Linux 8 is 100% Ubuntu 14.04 so I'm not sure what this indicates. If you get to the text prompt as noted above run "lsb_release -a". This should confirm that you are on trusty/14.04 Cheers, TIM On Mon, 2015-12-14 at 20:09 +0100, Xavier Mart?nez Serrano wrote: > Hi all, > > > Recently we are trying to install Biolinux on a DELL Precision T5810 > machine, but despite lot of trials > we did not succeed. We burned Biolinux ISO into USB and DVD but none > of this works, we are only > able to reach the install menu ("Try Biolinux ", "Install Biolinux", > "Check files", ...), after that a black > screen appears and nothing else, no response from either USB or DVD. > > > We tried to boot with "nomodeset", "noacpl/nolapic" or > "vga=normal/vga=771" and removing > "quiet splash" options to see what is happening. None of the > combinations were successful. > > > We figured out that that could be related to the graphic card: AMD > Firepro W5100, therefore we > installed "flrgrx" driver in USB-Biolinux Live (we kept 5GB within it > for persistent files). But still > no luck, it only boot in an Ubuntu 12.04 (instead of 14.04) GUI and > when clicking to "Installl Biolinux" > the applications seem to start but then closes unexpectedly > complaining on "dbus". > > > We also tried to install original AMD Firepro drivers but no luck > either. > > > If someone could give us an idea of what is it happening or what could > we try ? > > > Thank you , > > > Xavi > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://environmentalomics.org/bio-linux +44 1491 69 2297 From xavier.depedro at vhir.org Tue Dec 15 07:01:38 2015 From: xavier.depedro at vhir.org (Xavier de Pedro) Date: Tue, 15 Dec 2015 13:01:38 +0100 Subject: [Bio-linux-list] [Bio-Linux-list] Can't install Biolinux8 in DELL Precision T5810 In-Reply-To: <1450180478.23350.81.camel@balisaur> References: <1450180478.23350.81.camel@balisaur> Message-ID: <56700122.1040705@vhir.org> Hi Xavi and all: And just in case, ensure that you keep your persistent file below 4Gb on a fat32 partition (otherwise, it won't use your changes). In addition, seeing "Ubuntu 12.04" might indicate that you didn't succeed at making the right LiveUSB disk out of current Biolinux8. My 2 cents Xavier El 15/12/15 a les 12:54, Tim Booth ha escrit: > Hi Xavi, > > [Note - I've switched the discussion to the new mailing list server] > > I've seen similar issues where the driver tries to initialise the > graphics card and the whole thing just locks up. It think you are on > the right track booting the USB on a working machine and trying to > tinker with the drivers, but I'd follow this guide and add the > enablement drivers for X (I can't do this by default as it totally > breaks VirtualBox support): > > https://wiki.ubuntu.com/Kernel/LTSEnablementStack > > On the working machine you should also do an integrity check on the USB > to be sure. > > I'm surprised that removing "quiet splash" didn't at least give you some > boot messages. If you replace "quiet splash" with the word "text" you > should boot straight to a command prompt. Does that work? > > I'm also surprised by this bit: > >> it only boot in an Ubuntu 12.04 (instead of 14.04) GUI > Bio-Linux 8 is 100% Ubuntu 14.04 so I'm not sure what this indicates. > If you get to the text prompt as noted above run "lsb_release -a". This > should confirm that you are on trusty/14.04 > > Cheers, > > TIM > > On Mon, 2015-12-14 at 20:09 +0100, Xavier Mart?nez Serrano wrote: >> Hi all, >> >> >> Recently we are trying to install Biolinux on a DELL Precision T5810 >> machine, but despite lot of trials >> we did not succeed. We burned Biolinux ISO into USB and DVD but none >> of this works, we are only >> able to reach the install menu ("Try Biolinux ", "Install Biolinux", >> "Check files", ...), after that a black >> screen appears and nothing else, no response from either USB or DVD. >> >> >> We tried to boot with "nomodeset", "noacpl/nolapic" or >> "vga=normal/vga=771" and removing >> "quiet splash" options to see what is happening. None of the >> combinations were successful. >> >> >> We figured out that that could be related to the graphic card: AMD >> Firepro W5100, therefore we >> installed "flrgrx" driver in USB-Biolinux Live (we kept 5GB within it >> for persistent files). But still >> no luck, it only boot in an Ubuntu 12.04 (instead of 14.04) GUI and >> when clicking to "Installl Biolinux" >> the applications seem to start but then closes unexpectedly >> complaining on "dbus". >> >> >> We also tried to install original AMD Firepro drivers but no luck >> either. >> >> >> If someone could give us an idea of what is it happening or what could >> we try ? >> >> >> Thank you , >> >> >> Xavi >> _______________________________________________ >> Bio-Linux mailing list >> Bio-Linux at nebclists.nerc.ac.uk >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Xavier de Pedro Puente, Ph.D. Statistics and Bioinformatics Unit (UEB) Vall d'Hebron Research Institute (VHIR) Passeig de la Vall d'Hebron, 119-129 08035 Barcelona. Catalonia. Spain Ph. +34 934894007 / Fax +34 934894015 xavier.depedro at vhir.org http://ueb.vhir.org Collaborate: http://www.yoinvestigo.org - http://www.faigrecerca.org From xmarti6 at xtec.cat Tue Dec 15 08:25:08 2015 From: xmarti6 at xtec.cat (=?UTF-8?Q?Xavier_Mart=C3=ADnez_Serrano?=) Date: Tue, 15 Dec 2015 13:25:08 +0000 Subject: [Bio-linux-list] [Bio-Linux-list] Can't install Biolinux8 in DELL Precision T5810 In-Reply-To: <56700122.1040705@vhir.org> References: <1450180478.23350.81.camel@balisaur> <56700122.1040705@vhir.org> Message-ID: Thanks for all your replies guys!! I finally managed to install it by booting to Biolinux-USB via text mode as you suggested and installing the specific graphic-card driver from there, using the last driver which is compatible with 14.04, previous one was not, only with 12.04, and this is the one that came in ubuntu repositories (fglrx package), probably due to that there was kind of mixture in GUI with 12.04. But the ISO I used was Biolinux 14.04, I'm sure of this, and I checked the ISO md5. Before solving it I also tried to install latest AMD Firepro W5100 drivers from that ISO-USB burn but probably the drivers or whatever messed up with fglrx package from Ubuntu repositories. So, to sum up, what I finally did to solve the problem was: 1) Boot Biolinux8-USB (from which I saved 5GB of free space in UnetBootin) in a computer with Internet access and download and extract there the latest graphic-card driver (for which I ensured it was compatible with 14.04) 2)Boot Biolinux8-USB in the computer of interest in text mode by replacing boot parameters "quiet splash" - > "text" 3)Go to the graphic-card driver and install the driver for distribution 14.04, in my case I did: sudo apt-get purge fglrx* sudo ./amd..... (driver binary file) --buildpkg Ubuntu/trusty Thanks again to all, and hope my experience can be helpful for others! Xavi (by the way Xavi de Pedro, best regards :) ) 2015-12-15 12:01 GMT+00:00 Xavier de Pedro : > Hi Xavi and all: > > And just in case, ensure that you keep your persistent file below 4Gb on > a fat32 partition (otherwise, it won't use your changes). > > In addition, seeing "Ubuntu 12.04" might indicate that you didn't > succeed at making the right LiveUSB disk out of current Biolinux8. > > My 2 cents > > Xavier > > > El 15/12/15 a les 12:54, Tim Booth ha escrit: > > Hi Xavi, > > > > [Note - I've switched the discussion to the new mailing list server] > > > > I've seen similar issues where the driver tries to initialise the > > graphics card and the whole thing just locks up. It think you are on > > the right track booting the USB on a working machine and trying to > > tinker with the drivers, but I'd follow this guide and add the > > enablement drivers for X (I can't do this by default as it totally > > breaks VirtualBox support): > > > > https://wiki.ubuntu.com/Kernel/LTSEnablementStack > > > > On the working machine you should also do an integrity check on the USB > > to be sure. > > > > I'm surprised that removing "quiet splash" didn't at least give you some > > boot messages. If you replace "quiet splash" with the word "text" you > > should boot straight to a command prompt. Does that work? > > > > I'm also surprised by this bit: > > > >> it only boot in an Ubuntu 12.04 (instead of 14.04) GUI > > Bio-Linux 8 is 100% Ubuntu 14.04 so I'm not sure what this indicates. > > If you get to the text prompt as noted above run "lsb_release -a". This > > should confirm that you are on trusty/14.04 > > > > Cheers, > > > > TIM > > > > On Mon, 2015-12-14 at 20:09 +0100, Xavier Mart?nez Serrano wrote: > >> Hi all, > >> > >> > >> Recently we are trying to install Biolinux on a DELL Precision T5810 > >> machine, but despite lot of trials > >> we did not succeed. We burned Biolinux ISO into USB and DVD but none > >> of this works, we are only > >> able to reach the install menu ("Try Biolinux ", "Install Biolinux", > >> "Check files", ...), after that a black > >> screen appears and nothing else, no response from either USB or DVD. > >> > >> > >> We tried to boot with "nomodeset", "noacpl/nolapic" or > >> "vga=normal/vga=771" and removing > >> "quiet splash" options to see what is happening. None of the > >> combinations were successful. > >> > >> > >> We figured out that that could be related to the graphic card: AMD > >> Firepro W5100, therefore we > >> installed "flrgrx" driver in USB-Biolinux Live (we kept 5GB within it > >> for persistent files). But still > >> no luck, it only boot in an Ubuntu 12.04 (instead of 14.04) GUI and > >> when clicking to "Installl Biolinux" > >> the applications seem to start but then closes unexpectedly > >> complaining on "dbus". > >> > >> > >> We also tried to install original AMD Firepro drivers but no luck > >> either. > >> > >> > >> If someone could give us an idea of what is it happening or what could > >> we try ? > >> > >> > >> Thank you , > >> > >> > >> Xavi > >> _______________________________________________ > >> Bio-Linux mailing list > >> Bio-Linux at nebclists.nerc.ac.uk > >> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > -- > Xavier de Pedro Puente, Ph.D. > Statistics and Bioinformatics Unit (UEB) > Vall d'Hebron Research Institute (VHIR) > Passeig de la Vall d'Hebron, 119-129 > 08035 Barcelona. Catalonia. Spain > > Ph. +34 934894007 / Fax +34 934894015 > xavier.depedro at vhir.org > http://ueb.vhir.org > > Collaborate: http://www.yoinvestigo.org - http://www.faigrecerca.org > > _______________________________________________ > Bio-linux-list mailing list > Bio-linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From avarus at fastmail.fm Tue Dec 15 10:21:11 2015 From: avarus at fastmail.fm (Tim Booth) Date: Tue, 15 Dec 2015 15:21:11 +0000 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics Message-ID: <1450192871.23350.116.camel@balisaur> Dear Bio-Linux users, For those who don't already know, I'm moving from my current job here in the Thames Valley to the fair city of Edinburgh, specifically to work for Edinburgh Genomics (https://genomics.ed.ac.uk/). In preparation I've been tidying up some things at this end and for example you'll have seen today the relocation of the mailing lists, and also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. The main website for Bio-Linux will remain at http://environmentalomics.org/bio-linux. In terms of the future development of Bio-Linux and the prospective Bio-Linux 9 I can't make any firm promises just yet but watch this space. If you want to get directly involved, join the -devel list (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The Ubuntu distribution and the Debian Med team, which provide 99% of Bio-Linux functionality, are still going strong, but I still see a need for a pre-configured bioinformatics distro and especially a platform to support teaching and e-learning. Therefore I'll do whatever I can within my new job to stay involved with and promote the Bio-Linux project. All the best, and Happy Christmas. TIM -- Hanlon's Razor: Never attribute to malice that which can be adequately explained by stupidity... but don't rule out malice. From morais at iq.usp.br Tue Dec 15 10:32:34 2015 From: morais at iq.usp.br (Carlos Morais) Date: Tue, 15 Dec 2015 13:32:34 -0200 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450192871.23350.116.camel@balisaur> References: <1450192871.23350.116.camel@balisaur> Message-ID: Hi Tim, Good luck on your new job. We'll miss you. Happy Christmas. Carlos On Tue, Dec 15, 2015 at 1:21 PM, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a need > for a pre-configured bioinformatics distro and especially a platform to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > > -- > Hanlon's Razor: Never attribute to malice that which can be adequately > explained by stupidity... but don't rule out malice. > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Tue Dec 15 17:02:16 2015 From: gawbul at gmail.com (Steve Moss) Date: Tue, 15 Dec 2015 22:02:16 +0000 Subject: [Bio-linux-list] [Bio-Linux-list] Can't install Biolinux8 in DELL Precision T5810 Message-ID: Dear Xavi, I've had issues installing Linux distros on Dell machines previously, particularly on the higher end desktop servers, which seem to have some annoying chipsets. For Ubuntu, I found that using the Dell specific Ubuntu release (with their built in kernel drivers) helped - http://linux.dell.com/files/ubuntu/precise/12.04-OSP1/dell-12.04.2_20130822_0809.iso . According to Ubuntu it should all be compatible http://www.ubuntu.com/certification/hardware/201405-15064/. Once thats installed you could then try upgrading to 14.04 and installing BioLinux 8 by following the guide "Upgrading Bio-Linux 7 (or Ubuntu) to Bio-Linux 8" guide here http://environmentalomics.org/bio-linux-installation/? Cheers, Steve --- *Dr. Stephen Moss* e: gawbul at gmail.com www: https://gawbul.github.io -------------- next part -------------- An HTML attachment was scrubbed... URL: From gawbul at gmail.com Tue Dec 15 17:10:12 2015 From: gawbul at gmail.com (Steve Moss) Date: Tue, 15 Dec 2015 22:10:12 +0000 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450192871.23350.116.camel@balisaur> References: <1450192871.23350.116.camel@balisaur> Message-ID: Dear Tim, Congrats on the new job, and thanks for all the awesome work you do and have done with Bio-Linux. Who will be taking over maintaining Bio-Linux? Will CEH continue supporting it? With 16.04 approaching a Bio-Linux 9 would be something to look forward to. Are all the scripts and code you use for building Bio-Linux publicly available? Is there a more in depth developers guide anywhere? I'd been keen to help as and when I can. Cheers, Steve --- *Dr. Stephen Moss* e: gawbul at gmail.com www: https://gawbul.github.io -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Tue Dec 15 17:36:26 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 15 Dec 2015 23:36:26 +0100 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: References: <1450192871.23350.116.camel@balisaur> Message-ID: <567095EA.7090807@minke-informatics.co.uk> On 15/12/15 23:10, Steve Moss wrote: > Dear Tim, > > Congrats on the new job, and thanks for all the awesome work you do and > have done with Bio-Linux. > > Who will be taking over maintaining Bio-Linux? Will CEH continue > supporting it? Hi, Steve. I'm going to continue helping Tim to maintain and support Bio-Linux but, as Tim said, future funding of the project is uncertain just now. > With 16.04 approaching a Bio-Linux 9 would be something to look forward > to. Are all the scripts and code you use for building Bio-Linux publicly > available? Is there a more in depth developers guide anywhere? I'd been > keen to help as and when I can. Me too - I hope lots of people will volunteer to continue the project that Tim has led so successfully - Bio-Linux will continue one way or another! Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From andorjkiss at gmail.com Tue Dec 15 17:37:04 2015 From: andorjkiss at gmail.com (Andor J Kiss) Date: Tue, 15 Dec 2015 17:37:04 -0500 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450192871.23350.116.camel@balisaur> References: <1450192871.23350.116.camel@balisaur> Message-ID: <1450219024.4925.1.camel@gmail.com> Hello, Thanks SO much for all the work you've done on Bio-Linux - it's truly an amazing distribution. Merry Christmas - Andor On Tue, 2015-12-15 at 15:21 +0000, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here > in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, > and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a > need > for a pre-configured bioinformatics distro and especially a platform > to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > From mmnashrullah at gmail.com Tue Dec 15 20:03:31 2015 From: mmnashrullah at gmail.com (Maulana Malik Nashrullah) Date: Wed, 16 Dec 2015 08:03:31 +0700 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450219024.4925.1.camel@gmail.com> References: <1450192871.23350.116.camel@balisaur> <1450219024.4925.1.camel@gmail.com> Message-ID: Dear Dr. Tim Booth, B.Eng Thanks so much for all the work you've done on Bio-Linux. We will miss you... Anyway, thanks for everything that you give to us. Sincerely, Maulana Malik Nashrullah Laboratory of Bioinformatics Biology Undergraduate Program Faculty of Mathematics and Natural Sciences Brawijaya University Malang, East Java, Indonesia 2015-12-16 5:37 GMT+07:00 Andor J Kiss : > Hello, > > Thanks SO much for all the work you've done on Bio-Linux - > it's truly an amazing distribution. > > Merry Christmas > > - Andor > > > On Tue, 2015-12-15 at 15:21 +0000, Tim Booth wrote: > > Dear Bio-Linux users, > > > > For those who don't already know, I'm moving from my current job here > > in > > the Thames Valley to the fair city of Edinburgh, specifically to work > > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > > > In preparation I've been tidying up some things at this end and for > > example you'll have seen today the relocation of the mailing lists, > > and > > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > > The main website for Bio-Linux will remain at > > http://environmentalomics.org/bio-linux. > > > > In terms of the future development of Bio-Linux and the prospective > > Bio-Linux 9 I can't make any firm promises just yet but watch this > > space. If you want to get directly involved, join the -devel list > > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > > Ubuntu distribution and the Debian Med team, which provide 99% of > > Bio-Linux functionality, are still going strong, but I still see a > > need > > for a pre-configured bioinformatics distro and especially a platform > > to > > support teaching and e-learning. Therefore I'll do whatever I can > > within my new job to stay involved with and promote the Bio-Linux > > project. > > > > All the best, and Happy Christmas. > > > > TIM > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From dksamuel2 at gmail.com Wed Dec 16 00:22:06 2015 From: dksamuel2 at gmail.com (Duleep Samuel) Date: Wed, 16 Dec 2015 10:52:06 +0530 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: References: <1450192871.23350.116.camel@balisaur> <1450219024.4925.1.camel@gmail.com> Message-ID: Hi Tim, Thanks for having done a great job, really BioLinux helped me to use Linux, Good luck on your new job. We'll miss you. Happy Christmas, Please do not forget BioLinux, regards, Dr.D.K.Samuel, Bangalore, India On Wed, Dec 16, 2015 at 6:33 AM, Maulana Malik Nashrullah < mmnashrullah at gmail.com> wrote: > Dear Dr. Tim Booth, B.Eng > > Thanks so much for all the work you've done on Bio-Linux. > We will miss you... > > Anyway, thanks for everything that you give to us. > > Sincerely, > > Maulana Malik Nashrullah > > Laboratory of Bioinformatics > Biology Undergraduate Program > Faculty of Mathematics and Natural Sciences > Brawijaya University > Malang, East Java, Indonesia > > 2015-12-16 5:37 GMT+07:00 Andor J Kiss : > >> Hello, >> >> Thanks SO much for all the work you've done on Bio-Linux - >> it's truly an amazing distribution. >> >> Merry Christmas >> >> - Andor >> >> >> On Tue, 2015-12-15 at 15:21 +0000, Tim Booth wrote: >> > Dear Bio-Linux users, >> > >> > For those who don't already know, I'm moving from my current job here >> > in >> > the Thames Valley to the fair city of Edinburgh, specifically to work >> > for Edinburgh Genomics (https://genomics.ed.ac.uk/). >> > >> > In preparation I've been tidying up some things at this end and for >> > example you'll have seen today the relocation of the mailing lists, >> > and >> > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. >> > The main website for Bio-Linux will remain at >> > http://environmentalomics.org/bio-linux. >> > >> > In terms of the future development of Bio-Linux and the prospective >> > Bio-Linux 9 I can't make any firm promises just yet but watch this >> > space. If you want to get directly involved, join the -devel list >> > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The >> > Ubuntu distribution and the Debian Med team, which provide 99% of >> > Bio-Linux functionality, are still going strong, but I still see a >> > need >> > for a pre-configured bioinformatics distro and especially a platform >> > to >> > support teaching and e-learning. Therefore I'll do whatever I can >> > within my new job to stay involved with and promote the Bio-Linux >> > project. >> > >> > All the best, and Happy Christmas. >> > >> > TIM >> > >> _______________________________________________ >> Bio-Linux-list mailing list >> Bio-Linux-list at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bio-linux-list >> > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From Christopher.Dubay at providence.org Wed Dec 16 12:28:55 2015 From: Christopher.Dubay at providence.org (Dubay, Christopher J) Date: Wed, 16 Dec 2015 17:28:55 +0000 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: References: <1450192871.23350.116.camel@balisaur> <1450219024.4925.1.camel@gmail.com> Message-ID: <3F9E65788480CD4282B12895264CC2143C33B63A@WN35105.or.providence.org> I want to pile-on here an add my sincere thanks to Tim and his good work on Biolinux. You have helped educate many, and moved science forward in an important way by helping provide empowering tools. All the best in your new endeavors! Cheers... Christopher Christopher Dubay, PhD Biomedical Informatics Program Manager Laboratory of Molecular and Tumor Immunology Earle A. Chiles Research Institute Providence Cancer Center 4805 NE Glisan St.- 2N57 Portland, OR 97213 USA T: (503) 215-7981 F: (503) 215-6841 christopher.dubay at providence.org From: bio-linux-list-bounces at bioinformatics.org [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Duleep Samuel Sent: Tuesday, December 15, 2015 9:22 PM To: Bio-Linux mailing list Subject: Re: [Bio-linux-list] Tim's move to Edinburgh Genomics Hi Tim, Thanks for having done a great job, really BioLinux helped me to use Linux, Good luck on your new job. We'll miss you. Happy Christmas, Please do not forget BioLinux, regards, Dr.D.K.Samuel, Bangalore, India On Wed, Dec 16, 2015 at 6:33 AM, Maulana Malik Nashrullah > wrote: Dear Dr. Tim Booth, B.Eng Thanks so much for all the work you've done on Bio-Linux. We will miss you... Anyway, thanks for everything that you give to us. Sincerely, Maulana Malik Nashrullah Laboratory of Bioinformatics Biology Undergraduate Program Faculty of Mathematics and Natural Sciences Brawijaya University Malang, East Java, Indonesia 2015-12-16 5:37 GMT+07:00 Andor J Kiss >: Hello, Thanks SO much for all the work you've done on Bio-Linux - it's truly an amazing distribution. Merry Christmas - Andor On Tue, 2015-12-15 at 15:21 +0000, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here > in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, > and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a > need > for a pre-configured bioinformatics distro and especially a platform > to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list ________________________________ This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From surojit0368 at yahoo.co.in Wed Dec 16 13:31:19 2015 From: surojit0368 at yahoo.co.in (Surojit Sen) Date: Wed, 16 Dec 2015 18:31:19 +0000 (UTC) Subject: [Bio-linux-list] hi References: <654408685.2088216.1450290679545.JavaMail.yahoo.ref@mail.yahoo.com> Message-ID: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> hi?SUROJIT SENAsstt. ProfessorDeptt.of Zoology.MARIANI College. P.O.MARIANI :JORHAT :ASSAM INDIAPin:785634+919435094183 -------------- next part -------------- An HTML attachment was scrubbed... URL: From zain.alvi at student.shu.edu Wed Dec 16 16:35:46 2015 From: zain.alvi at student.shu.edu (Zain A Alvi) Date: Wed, 16 Dec 2015 21:35:46 +0000 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <3F9E65788480CD4282B12895264CC2143C33B63A@WN35105.or.providence.org> References: <1450192871.23350.116.camel@balisaur> <1450219024.4925.1.camel@gmail.com> , <3F9E65788480CD4282B12895264CC2143C33B63A@WN35105.or.providence.org> Message-ID: Hi Tim, Thank you Tim for all the wonderful help and for providing such a great software Linux package for bioinformaticians and biologists. I hope you the best in all of your future endeavors at Edinburgh and beyond. Thank you again and I hope you have wonderful holidays. Kind regards, Zain ________________________________ From: bio-linux-list-bounces at bioinformatics.org on behalf of Dubay, Christopher J Sent: Wednesday, December 16, 2015 12:28 PM To: Bio-Linux mailing list Subject: Re: [Bio-linux-list] Tim's move to Edinburgh Genomics I want to pile-on here an add my sincere thanks to Tim and his good work on Biolinux. You have helped educate many, and moved science forward in an important way by helping provide empowering tools. All the best in your new endeavors! Cheers... Christopher Christopher Dubay, PhD Biomedical Informatics Program Manager Laboratory of Molecular and Tumor Immunology Earle A. Chiles Research Institute Providence Cancer Center 4805 NE Glisan St.- 2N57 Portland, OR 97213 USA T: (503) 215-7981 F: (503) 215-6841 christopher.dubay at providence.org From: bio-linux-list-bounces at bioinformatics.org [mailto:bio-linux-list-bounces at bioinformatics.org] On Behalf Of Duleep Samuel Sent: Tuesday, December 15, 2015 9:22 PM To: Bio-Linux mailing list Subject: Re: [Bio-linux-list] Tim's move to Edinburgh Genomics Hi Tim, Thanks for having done a great job, really BioLinux helped me to use Linux, Good luck on your new job. We'll miss you. Happy Christmas, Please do not forget BioLinux, regards, Dr.D.K.Samuel, Bangalore, India On Wed, Dec 16, 2015 at 6:33 AM, Maulana Malik Nashrullah > wrote: Dear Dr. Tim Booth, B.Eng Thanks so much for all the work you've done on Bio-Linux. We will miss you... Anyway, thanks for everything that you give to us. Sincerely, Maulana Malik Nashrullah Laboratory of Bioinformatics Biology Undergraduate Program Faculty of Mathematics and Natural Sciences Brawijaya University Malang, East Java, Indonesia 2015-12-16 5:37 GMT+07:00 Andor J Kiss >: Hello, Thanks SO much for all the work you've done on Bio-Linux - it's truly an amazing distribution. Merry Christmas - Andor On Tue, 2015-12-15 at 15:21 +0000, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here > in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, > and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a > need > for a pre-configured bioinformatics distro and especially a platform > to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list ________________________________ This message is intended for the sole use of the addressee, and may contain information that is privileged, confidential and exempt from disclosure under applicable law. If you are not the addressee you are hereby notified that you may not use, copy, disclose, or distribute to anyone the message or any information contained in the message. If you have received this message in error, please immediately advise the sender by reply email and delete this message. -------------- next part -------------- An HTML attachment was scrubbed... URL: From mkmodi at aau.ac.in Thu Dec 17 03:34:48 2015 From: mkmodi at aau.ac.in (Mahendra Modi) Date: Thu, 17 Dec 2015 14:04:48 +0530 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450192871.23350.116.camel@balisaur> References: <1450192871.23350.116.camel@balisaur> Message-ID: Dear Tim, Thank you very much for your wonderful work on Bio-Linux and best wishes for your new endeavour. We surely will miss you at Bio-Linux but we know that you will somehow remain attached to the project. Mahendra ________________________ *Prof. Mahendra K Modi* *Head, Agril Biotechnology & Coordinator, DIC* *Assam Agricultural University* *Jorhat 785013, India* On Tue, Dec 15, 2015 at 8:51 PM, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a need > for a pre-configured bioinformatics distro and especially a platform to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > > -- > Hanlon's Razor: Never attribute to malice that which can be adequately > explained by stupidity... but don't rule out malice. > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From xmarti6 at xtec.cat Thu Dec 17 11:00:42 2015 From: xmarti6 at xtec.cat (=?UTF-8?Q?Xavier_Mart=C3=ADnez_Serrano?=) Date: Thu, 17 Dec 2015 17:00:42 +0100 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: References: <1450192871.23350.116.camel@balisaur> Message-ID: All the best Tim! Thanks a lot for your help and your magnificient work! Xavi 2015-12-17 9:34 GMT+01:00 Mahendra Modi : > Dear Tim, > > Thank you very much for your wonderful work on Bio-Linux and best wishes > for your new endeavour. We surely will miss you at Bio-Linux but we know > that you will somehow remain attached to the project. > > Mahendra > > ________________________ > *Prof. Mahendra K Modi* > *Head, Agril Biotechnology & Coordinator, DIC* > *Assam Agricultural University* > *Jorhat 785013, India* > > > On Tue, Dec 15, 2015 at 8:51 PM, Tim Booth wrote: > >> Dear Bio-Linux users, >> >> For those who don't already know, I'm moving from my current job here in >> the Thames Valley to the fair city of Edinburgh, specifically to work >> for Edinburgh Genomics (https://genomics.ed.ac.uk/). >> >> In preparation I've been tidying up some things at this end and for >> example you'll have seen today the relocation of the mailing lists, and >> also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. >> The main website for Bio-Linux will remain at >> http://environmentalomics.org/bio-linux. >> >> In terms of the future development of Bio-Linux and the prospective >> Bio-Linux 9 I can't make any firm promises just yet but watch this >> space. If you want to get directly involved, join the -devel list >> (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The >> Ubuntu distribution and the Debian Med team, which provide 99% of >> Bio-Linux functionality, are still going strong, but I still see a need >> for a pre-configured bioinformatics distro and especially a platform to >> support teaching and e-learning. Therefore I'll do whatever I can >> within my new job to stay involved with and promote the Bio-Linux >> project. >> >> All the best, and Happy Christmas. >> >> TIM >> >> -- >> Hanlon's Razor: Never attribute to malice that which can be adequately >> explained by stupidity... but don't rule out malice. >> >> _______________________________________________ >> Bio-Linux-list mailing list >> Bio-Linux-list at bioinformatics.org >> http://www.bioinformatics.org/mailman/listinfo/bio-linux-list >> > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From karimse07 at yahoo.com Fri Dec 18 08:43:46 2015 From: karimse07 at yahoo.com (karim mah.) Date: Fri, 18 Dec 2015 13:43:46 +0000 (UTC) Subject: [Bio-linux-list] hi In-Reply-To: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> References: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> Message-ID: <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> hi need a bioinformatics partner . From: Surojit Sen To: "bio-linux-list at bioinformatics.org" Sent: Wednesday, December 16, 2015 8:31 PM Subject: [Bio-linux-list] hi hi?SUROJIT SENAsstt. ProfessorDeptt.of Zoology.MARIANI College. P.O.MARIANI :JORHAT :ASSAM INDIAPin:785634+919435094183 _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Fri Dec 18 09:27:29 2015 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Fri, 18 Dec 2015 14:27:29 +0000 Subject: [Bio-linux-list] hi In-Reply-To: <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> References: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> Message-ID: <567417D1.3040605@minke-informatics.co.uk> On 18/12/15 13:43, karim mah. wrote: > hi > > need a bioinformatics partner . Hi, Surojit. You need to explain a bit more what your project is about, your funding and how you plant to collaborate with a bioinformatics partner: If you just want your bioinformatics done for you then you are looking in the wrong place on this list... Bye, Tony. -- Minke Informatics Limited, Registered in Scotland - Company No. SC419028 Registered Office: 3 Donview, Bridge of Alford, AB33 8QJ, Scotland (UK) tel. +44(0)19755 63548 http://minke-informatics.co.uk mob. +44(0)7985 078324 mailto:tony.travis at minke-informatics.co.uk From amanjain at imtech.res.in Sat Dec 19 04:02:27 2015 From: amanjain at imtech.res.in (amanjain at imtech.res.in) Date: Sat, 19 Dec 2015 14:32:27 +0530 Subject: [Bio-linux-list] hi In-Reply-To: <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> References: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> Message-ID: <115bd041a0096af0f3bba6c0d6723034@imtech.res.in> What kind of bioinformatic work.. -------------- next part -------------- An HTML attachment was scrubbed... URL: From karimse07 at yahoo.com Sat Dec 19 14:24:49 2015 From: karimse07 at yahoo.com (karim mah.) Date: Sat, 19 Dec 2015 19:24:49 +0000 (UTC) Subject: [Bio-linux-list] hi In-Reply-To: <115bd041a0096af0f3bba6c0d6723034@imtech.res.in> References: <654408685.2088216.1450290679545.JavaMail.yahoo@mail.yahoo.com> <1412966659.675912.1450446226340.JavaMail.yahoo@mail.yahoo.com> <115bd041a0096af0f3bba6c0d6723034@imtech.res.in> Message-ID: <49951265.1187991.1450553089889.JavaMail.yahoo@mail.yahoo.com> For study and research " protein sequencing . From: "amanjain at imtech.res.in" To: Bio-Linux mailing list Sent: Saturday, December 19, 2015 11:02 AM Subject: Re: [Bio-linux-list] hi What kind of bioinformatic work..? _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: From kirannbishwa01 at gmail.com Tue Dec 29 19:36:22 2015 From: kirannbishwa01 at gmail.com (Bishwa Kiran) Date: Tue, 29 Dec 2015 19:36:22 -0500 Subject: [Bio-linux-list] Tim's move to Edinburgh Genomics In-Reply-To: <1450192871.23350.116.camel@balisaur> References: <1450192871.23350.116.camel@balisaur> Message-ID: Hi Tim, Good luck on your new job. Thanks for the help you have been !!! Happy new year, On Tue, Dec 15, 2015 at 10:21 AM, Tim Booth wrote: > Dear Bio-Linux users, > > For those who don't already know, I'm moving from my current job here in > the Thames Valley to the fair city of Edinburgh, specifically to work > for Edinburgh Genomics (https://genomics.ed.ac.uk/). > > In preparation I've been tidying up some things at this end and for > example you'll have seen today the relocation of the mailing lists, and > also the old group address of "helpdesk at nebc.nerc.ac.uk" is no more. > The main website for Bio-Linux will remain at > http://environmentalomics.org/bio-linux. > > In terms of the future development of Bio-Linux and the prospective > Bio-Linux 9 I can't make any firm promises just yet but watch this > space. If you want to get directly involved, join the -devel list > (http://www.bioinformatics.org/mailman/listinfo/bio-linux-devel). The > Ubuntu distribution and the Debian Med team, which provide 99% of > Bio-Linux functionality, are still going strong, but I still see a need > for a pre-configured bioinformatics distro and especially a platform to > support teaching and e-learning. Therefore I'll do whatever I can > within my new job to stay involved with and promote the Bio-Linux > project. > > All the best, and Happy Christmas. > > TIM > > -- > Hanlon's Razor: Never attribute to malice that which can be adequately > explained by stupidity... but don't rule out malice. > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mailman/listinfo/bio-linux-list > -- - Bish -------------- next part -------------- An HTML attachment was scrubbed... URL: