From tbooth at ceh.ac.uk Wed Jan 2 06:52:17 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 2 Jan 2013 11:52:17 +0000 Subject: [Bio-Linux] A Unity Lens (ie. a better applications menu) for Bio-Linux In-Reply-To: <27940_1356531901_ZZi0b7Gm8gJMH.00_fbfdd46e6222.50db16cd@fh-bielefeld.de> References: <1356111166.7339.14.camel@balisaur> <27940_1356531901_ZZi0b7Gm8gJMH.00_fbfdd46e6222.50db16cd@fh-bielefeld.de> Message-ID: <1357127537.2977.33.camel@balisaur> Hi, Sasa is right that this controversial feature (unity-lens-shopping) is not in Ubuntu 12.04 and therefore has no relevance to Bio-Linux 7. When releasing Bio-Linux, I know that the system is used in both corporate and government environments where data protection is a legal requirement, and so it's imperative that the system doesn't leak data to third parties. It's probably worth noting that I already remove things like the Ubuntu One client and automated crash reporting from Bio-Linux as these can send data to third parties and I don't think they are services most Bio-Linux users will want. I'd almost certainly remove things like the shopping lens for the same reason. My personal opinion, as an Ubuntu user, is that Canonical should be able to achieve their aims for Ubuntu, and make themselves some cash, in a way that leaves the user in control and does not compromise privacy. I hope we'll see these changes in forthcoming releases, and if so I'll probably use the features happily at home but I'll also remove them from Bio-Linux. (BTW - I can assure you, the new Bioinformatics lens for Bio-Linux doesn't do any web searching at all) Cheers, TIM On Wed, 2012-12-26 at 14:25 +0000, Sasa Paporovic wrote: > The switch to Debian is one possibility, but you can also do on a > terminal > > sudo apt-get remove unity-lens-shopping > > This deletes the component(unity shopping lens) of the unity desktop > that causes the information traffic to amazon and canonical. > > BTW: AFAIK Biolinux 7 is based on Ubuntu12.04(Precise). In this > version is no unity shopping lens. It was first introduced at the end > of the development phase of Ubuntu12.10(Quantal). With this it has > never reached Biolinux. > > ----- Original Message ----- > From: Damien Zammit > Date: Wednesday, December 26, 2012 9:12 > Subject: Re: [Bio-Linux] A Unity Lens (ie. a better applications menu) > for Bio-Linux > To: Bio-Linux help and discussion > > > On 22 December 2012 04:32, Tim Booth wrote: > > > taken a few days while things are quiet before Christmas and > > I've made a > > > package that adds a bioinformatics section (or a lens, as they are > > > called) into the main menu panel. It looks like this: > > > > Hi there, > > I realise I am just a single user and my opinion doesn't count for > > much in terms of a survey of user opinions. However, for > > what it's > > worth, it has come to my attention that Canonical have been > collecting > > information about what people search for in the Unity search bar and > > your Ubuntu computer sends this information to Amazon for marketing > > purposes automatically. > > I'm so disappointed by this feature that I made the switch to > Debian, > > since the presence of this feature circumvents the freedom of a user > > to their privacy. > > > > Regards, > > Damien > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From ericstout at gmail.com Thu Jan 10 02:15:13 2013 From: ericstout at gmail.com (Eric Stout) Date: Thu, 10 Jan 2013 07:15:13 +0000 Subject: [Bio-Linux] What is the user-name and password when running live from the DVD? Message-ID: I recently started using Bio-Linux 7 live from the DVD. What is the user and password? I've logged off, but cannot shut down or restart. I have an NTFS formatted USB stick loaded with data which I'm afraid is still mounted. I tried the default from Ubuntu 12.04 which is user: ubuntu, password left blank. Bio-Linux 7 (live) is saying invalid password, please try again. -------------- next part -------------- An HTML attachment was scrubbed... URL: From tbooth at ceh.ac.uk Thu Jan 10 05:11:13 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Thu, 10 Jan 2013 10:11:13 +0000 Subject: [Bio-Linux] What is the user-name and password when running live from the DVD? In-Reply-To: References: Message-ID: <1357812673.18146.131.camel@balisaur> Hi Eric, The user name is 'live', with a blank password. If you just want to ensure a clean shutdown, you can do this without needing to log in at all: Hit Ctrl+Alt+F1 to get the text console Hit Ctrl+Alt+Del to force a shutdown/restart Cheers, TIM On Thu, 2013-01-10 at 07:15 +0000, Eric Stout wrote: > I recently started using Bio-Linux 7 live from the DVD. What is the > user and password? > > I've logged off, but cannot shut down or restart. I have an NTFS > formatted USB stick loaded with data which I'm afraid is still > mounted. > > I tried the default from Ubuntu 12.04 which is user: ubuntu, password > left blank. Bio-Linux 7 (live) is saying invalid password, please try > again. -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From tbooth at ceh.ac.uk Tue Jan 22 06:11:33 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Tue, 22 Jan 2013 11:11:33 +0000 Subject: [Bio-Linux] Places available on introductory Bio-Linux 7 course this Friday Message-ID: <1358853093.18146.582.camel@balisaur> Dear All, We have some spaces left on the 1-day Bio-Linux course in Sheffield this Friday, 25th Jan. At this point, registration is open to all so please sign up if you are interested, and please pass this on to anyone who might be interested, particularly PhD students. Details: This NBAF course is an updated version of our popular Introduction to Bio-Linux course, now based on the latest version 7 release of Bio-Linux and featuring some of the latest tools for environmental sequence analysis. The one-day course introduces the new user to the Bio-Linux 7 system. It includes a tour of the desktop, information on finding programs and documentation, and provides experience running graphical and command line tools. The course is made up of two parts: Part 1 introduces you to the Linux desktop environment and command shell. Part 2 focuses on running bioinformatics programs and providing the information you need to make intelligent choices about the programs and interfaces you use for your bioinformatics analyses. The cost of the course (?30) is to cover the included lunch and refreshments etc. Attendees will also receive a course book and USB stick. The course will run from 9:45am until 5pm - a draft schedule is here: https://docs.google.com/document/d/12pwdzeEfti4gBSZLmsIRlcAYumby6_YT_fCPcBlVJ0I/edit Sign up here: http://onlineshop.shef.ac.uk/browse/extra_info.asp?modid=1&prodid=2441&deptid=7&catid=137&prodvarid=0 Cheers, TIM -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From kellert at ohsu.edu Tue Jan 22 12:41:34 2013 From: kellert at ohsu.edu (Tom Keller) Date: Tue, 22 Jan 2013 09:41:34 -0800 Subject: [Bio-Linux] Bio-Linux Digest, Vol 53, Issue 3 In-Reply-To: References: Message-ID: <53E6CBBB-AECF-4C23-A9CA-CCF09BE8FC6A@ohsu.edu> Perhaps the book and notes from the course could be sold as a way to support the project. ... for those of us too far away to attend the course. Thanks, Tom MMI DNA Services Core Facility; 503-494-2442; Office: 5333 RJH; member of OHSU Shared Resources On Jan 22, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote: > Send Bio-Linux mailing list submissions to > bio-linux at nebclists.nerc.ac.uk > > To subscribe or unsubscribe via the World Wide Web, visit > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > or, via email, send a message with subject or body 'help' to > bio-linux-request at nebclists.nerc.ac.uk > > You can reach the person managing the list at > bio-linux-owner at nebclists.nerc.ac.uk > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-Linux digest..." > > > Today's Topics: > > 1. Places available on introductory Bio-Linux 7 course this > Friday (Tim Booth) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 22 Jan 2013 11:11:33 +0000 > From: Tim Booth > Subject: [Bio-Linux] Places available on introductory Bio-Linux 7 > course this Friday > To: Bio-Linux mailing list > Message-ID: <1358853093.18146.582.camel at balisaur> > Content-Type: text/plain; charset="UTF-8" > > Dear All, > > We have some spaces left on the 1-day Bio-Linux course in Sheffield this > Friday, 25th Jan. At this point, registration is open to all so please > sign up if you are interested, and please pass this on to anyone who > might be interested, particularly PhD students. > > Details: > > > This NBAF course is an updated version of our popular Introduction to > Bio-Linux course, now based on the latest version 7 release of Bio-Linux > and featuring some of the latest tools for environmental sequence > analysis. > > The one-day course introduces the new user to the Bio-Linux 7 system. It > includes a tour of the desktop, information on finding programs and > documentation, and provides experience running graphical and command > line tools. > > The course is made up of two parts: Part 1 introduces you to the Linux > desktop environment and command shell. Part 2 focuses on running > bioinformatics programs and providing the information you need to make > intelligent choices about the programs and interfaces you use for your > bioinformatics analyses. > > The cost of the course (?30) is to cover the included lunch and > refreshments etc. Attendees will also receive a course book and USB > stick. > > The course will run from 9:45am until 5pm - a draft schedule is here: > https://docs.google.com/document/d/12pwdzeEfti4gBSZLmsIRlcAYumby6_YT_fCPcBlVJ0I/edit > > Sign up here: > http://onlineshop.shef.ac.uk/browse/extra_info.asp?modid=1&prodid=2441&deptid=7&catid=137&prodvarid=0 > > Cheers, > > TIM > > > -- > Tim Booth > NERC Environmental Bioinformatics Centre > > Centre for Ecology and Hydrology > Maclean Bldg, Benson Lane > Crowmarsh Gifford > Wallingford, England > OX10 8BB > > http://nebc.nerc.ac.uk > +44 1491 69 2705 > > > ------------------------------ > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > End of Bio-Linux Digest, Vol 53, Issue 3 > **************************************** From tbooth at ceh.ac.uk Wed Jan 23 11:47:39 2013 From: tbooth at ceh.ac.uk (Tim Booth) Date: Wed, 23 Jan 2013 16:47:39 +0000 Subject: [Bio-Linux] Introductory Bio-Linux course In-Reply-To: <53E6CBBB-AECF-4C23-A9CA-CCF09BE8FC6A@ohsu.edu> References: <53E6CBBB-AECF-4C23-A9CA-CCF09BE8FC6A@ohsu.edu> Message-ID: <1358959659.18146.646.camel@balisaur> Hi Tom, We're considering an "enhanced" USB distribution with extra material including video tutorials that people would be able to purchase. In the meantime, we're continuing to give the course book away for free as PDF. http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7 Aside from the practicalities of publishing it, there is a lot of material in there that we've borrowed from sources who may well object to it being sold on for a charge. Cheers, TIM On Tue, 2013-01-22 at 17:41 +0000, Tom Keller wrote: > Perhaps the book and notes from the course could be sold as a way to > support the project. ... for those of us too far away to attend the > course. > Thanks, > Tom > > MMI DNA Services Core Facility; 503-494-2442; Office: 5333 RJH; member of OHSU Shared Resources > > > > > > > On Jan 22, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote: > > > Send Bio-Linux mailing list submissions to > > bio-linux at nebclists.nerc.ac.uk > > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > or, via email, send a message with subject or body 'help' to > > bio-linux-request at nebclists.nerc.ac.uk > > > > You can reach the person managing the list at > > bio-linux-owner at nebclists.nerc.ac.uk > > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Bio-Linux digest..." > > > > > > Today's Topics: > > > > 1. Places available on introductory Bio-Linux 7 course this > > Friday (Tim Booth) > > > > > > ---------------------------------------------------------------------- > > > > Message: 1 > > Date: Tue, 22 Jan 2013 11:11:33 +0000 > > From: Tim Booth > > Subject: [Bio-Linux] Places available on introductory Bio-Linux 7 > > course this Friday > > To: Bio-Linux mailing list > > Message-ID: <1358853093.18146.582.camel at balisaur> > > Content-Type: text/plain; charset="UTF-8" > > > > Dear All, > > > > We have some spaces left on the 1-day Bio-Linux course in Sheffield this > > Friday, 25th Jan. At this point, registration is open to all so please > > sign up if you are interested, and please pass this on to anyone who > > might be interested, particularly PhD students. > > > > Details: > > > > > > This NBAF course is an updated version of our popular Introduction to > > Bio-Linux course, now based on the latest version 7 release of Bio-Linux > > and featuring some of the latest tools for environmental sequence > > analysis. > > > > The one-day course introduces the new user to the Bio-Linux 7 system. It > > includes a tour of the desktop, information on finding programs and > > documentation, and provides experience running graphical and command > > line tools. > > > > The course is made up of two parts: Part 1 introduces you to the Linux > > desktop environment and command shell. Part 2 focuses on running > > bioinformatics programs and providing the information you need to make > > intelligent choices about the programs and interfaces you use for your > > bioinformatics analyses. > > > > The cost of the course (?30) is to cover the included lunch and > > refreshments etc. Attendees will also receive a course book and USB > > stick. > > > > The course will run from 9:45am until 5pm - a draft schedule is here: > > https://docs.google.com/document/d/12pwdzeEfti4gBSZLmsIRlcAYumby6_YT_fCPcBlVJ0I/edit > > > > Sign up here: > > http://onlineshop.shef.ac.uk/browse/extra_info.asp?modid=1&prodid=2441&deptid=7&catid=137&prodvarid=0 > > > > Cheers, > > > > TIM > > > > > > -- > > Tim Booth > > NERC Environmental Bioinformatics Centre > > > > Centre for Ecology and Hydrology > > Maclean Bldg, Benson Lane > > Crowmarsh Gifford > > Wallingford, England > > OX10 8BB > > > > http://nebc.nerc.ac.uk > > +44 1491 69 2705 > > > > > > ------------------------------ > > > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > End of Bio-Linux Digest, Vol 53, Issue 3 > > **************************************** > > _______________________________________________ > Bio-Linux mailing list > Bio-Linux at nebclists.nerc.ac.uk > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux -- Tim Booth NERC Environmental Bioinformatics Centre Centre for Ecology and Hydrology Maclean Bldg, Benson Lane Crowmarsh Gifford Wallingford, England OX10 8BB http://nebc.nerc.ac.uk +44 1491 69 2705 From andorjkiss at gmail.com Thu Jan 24 08:16:54 2013 From: andorjkiss at gmail.com (Andor J Kiss) Date: Thu, 24 Jan 2013 08:16:54 -0500 Subject: [Bio-Linux] Introductory Bio-Linux course In-Reply-To: <1358959659.18146.646.camel@balisaur> References: <53E6CBBB-AECF-4C23-A9CA-CCF09BE8FC6A@ohsu.edu> <1358959659.18146.646.camel@balisaur> Message-ID: <1359033414.3312.85.camel@methy1> Hi Tim, This is REALLY useful guide to BioLinux, and I really like how it has the introduction to Linux at the beginning - always a big barrier to first time users that have been "trained" with only GUIs. Thanks for making this available for download. Just a thought: Maybe you could make the USBs/Images and "ask" for donations - as opposed to "selling" them? Regards, -- __________________________________________________________________ Andor J Kiss, Supervisor Center for Bioinformatics and Functional Genomics 086 Pearson Hall ~ Miami University 700 East High Street Oxford, Ohio 45056 USA eMAIL: kissaj at MiamiOH.edu Telephone: +1 (513) 529-4280 Fax: +1 (513) 529-2431 URL (CBFG): http://www.cas.muohio.edu/cbfg URL (Research): http://openwetware.org/wiki/User:Andor_J_Kiss On Wed, 2013-01-23 at 16:47 +0000, Tim Booth wrote: > Hi Tom, > > We're considering an "enhanced" USB distribution with extra material > including video tutorials that people would be able to purchase. In the > meantime, we're continuing to give the course book away for free as PDF. > > http://nebc.nerc.ac.uk/support/training/course-notes/past-notes/intro-bl7 > > Aside from the practicalities of publishing it, there is a lot of > material in there that we've borrowed from sources who may well object > to it being sold on for a charge. > > Cheers, > > TIM > > On Tue, 2013-01-22 at 17:41 +0000, Tom Keller wrote: > > Perhaps the book and notes from the course could be sold as a way to > > support the project. ... for those of us too far away to attend the > > course. > > Thanks, > > Tom > > > > MMI DNA Services Core Facility; 503-494-2442; Office: 5333 RJH; member of OHSU Shared Resources > > > > > > > > > > > > > > On Jan 22, 2013, at 4:00 AM, bio-linux-request at nebclists.nerc.ac.uk wrote: > > > > > Send Bio-Linux mailing list submissions to > > > bio-linux at nebclists.nerc.ac.uk > > > > > > To subscribe or unsubscribe via the World Wide Web, visit > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > or, via email, send a message with subject or body 'help' to > > > bio-linux-request at nebclists.nerc.ac.uk > > > > > > You can reach the person managing the list at > > > bio-linux-owner at nebclists.nerc.ac.uk > > > > > > When replying, please edit your Subject line so it is more specific > > > than "Re: Contents of Bio-Linux digest..." > > > > > > > > > Today's Topics: > > > > > > 1. Places available on introductory Bio-Linux 7 course this > > > Friday (Tim Booth) > > > > > > > > > ---------------------------------------------------------------------- > > > > > > Message: 1 > > > Date: Tue, 22 Jan 2013 11:11:33 +0000 > > > From: Tim Booth > > > Subject: [Bio-Linux] Places available on introductory Bio-Linux 7 > > > course this Friday > > > To: Bio-Linux mailing list > > > Message-ID: <1358853093.18146.582.camel at balisaur> > > > Content-Type: text/plain; charset="UTF-8" > > > > > > Dear All, > > > > > > We have some spaces left on the 1-day Bio-Linux course in Sheffield this > > > Friday, 25th Jan. At this point, registration is open to all so please > > > sign up if you are interested, and please pass this on to anyone who > > > might be interested, particularly PhD students. > > > > > > Details: > > > > > > > > > This NBAF course is an updated version of our popular Introduction to > > > Bio-Linux course, now based on the latest version 7 release of Bio-Linux > > > and featuring some of the latest tools for environmental sequence > > > analysis. > > > > > > The one-day course introduces the new user to the Bio-Linux 7 system. It > > > includes a tour of the desktop, information on finding programs and > > > documentation, and provides experience running graphical and command > > > line tools. > > > > > > The course is made up of two parts: Part 1 introduces you to the Linux > > > desktop environment and command shell. Part 2 focuses on running > > > bioinformatics programs and providing the information you need to make > > > intelligent choices about the programs and interfaces you use for your > > > bioinformatics analyses. > > > > > > The cost of the course (?30) is to cover the included lunch and > > > refreshments etc. Attendees will also receive a course book and USB > > > stick. > > > > > > The course will run from 9:45am until 5pm - a draft schedule is here: > > > https://docs.google.com/document/d/12pwdzeEfti4gBSZLmsIRlcAYumby6_YT_fCPcBlVJ0I/edit > > > > > > Sign up here: > > > http://onlineshop.shef.ac.uk/browse/extra_info.asp?modid=1&prodid=2441&deptid=7&catid=137&prodvarid=0 > > > > > > Cheers, > > > > > > TIM > > > > > > > > > -- > > > Tim Booth > > > NERC Environmental Bioinformatics Centre > > > > > > Centre for Ecology and Hydrology > > > Maclean Bldg, Benson Lane > > > Crowmarsh Gifford > > > Wallingford, England > > > OX10 8BB > > > > > > http://nebc.nerc.ac.uk > > > +44 1491 69 2705 > > > > > > > > > ------------------------------ > > > > > > _______________________________________________ > > > Bio-Linux mailing list > > > Bio-Linux at nebclists.nerc.ac.uk > > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > > > > > > > > > End of Bio-Linux Digest, Vol 53, Issue 3 > > > **************************************** > > > > _______________________________________________ > > Bio-Linux mailing list > > Bio-Linux at nebclists.nerc.ac.uk > > http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux > -------------- next part -------------- An HTML attachment was scrubbed... URL: