From tony.travis at minke-informatics.co.uk Mon Feb 13 07:35:50 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 13 Feb 2017 12:35:50 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated Message-ID: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> Hi, [apologies to Mark Twain] I've seen a comments on SeqAnswers that Bio-Linux is 'dead' and people are concerned that Bio-Linux is no longer being maintained because the lead developer Tim Booth has now left the Bio-Linux project for a new job. Let me assure you that Bio-Linux is not dead, the PPA's are working and so are the mailing lists, like this one. It's a testament to the great work that Tim did that we can still keep our Bio-Linux 8 systems up-to-date simply using: apt update apt full-upgrade Bear in mind that Ubuntu 14.04 LTS will be supported until April 2019: > https://wiki.ubuntu.com/LTS Please spread the word that we are seeking funding to develop Bio-Linux 9 based on Ubuntu 16.04 LTS, and post your experiences of upgrading Bio-Linux 8 to Ubuntu 16.04 LTS here so we can make a community effort to fix the problems. Bio-Linux is supported by its user community but it also depends on contributions from the Debian-Med team, who are making their bioinformatics packages available to Ubuntu users before they are available via the Debian repositories. Thanks, 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 briancady101 at yahoo.com Mon Feb 13 12:56:25 2017 From: briancady101 at yahoo.com (Brian Cady) Date: Mon, 13 Feb 2017 17:56:25 +0000 (UTC) Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> Message-ID: <1385100018.3504856.1487008585221@mail.yahoo.com> Tony and all, Could we crowdfund, at $25 each, the building of BioLinux 9? How many are on this listserv? Brian On Monday, February 13, 2017 7:36 AM, Tony Travis wrote: Hi, [apologies to Mark Twain] I've seen a comments on SeqAnswers that Bio-Linux is 'dead' and people are concerned that Bio-Linux is no longer being maintained because the lead developer Tim Booth has now left the Bio-Linux project for a new job. Let me assure you that Bio-Linux is not dead, the PPA's are working and so are the mailing lists, like this one. It's a testament to the great work that Tim did that we can still keep our Bio-Linux 8 systems up-to-date simply using: ? apt update ? apt full-upgrade Bear in mind that Ubuntu 14.04 LTS will be supported until April 2019: > https://wiki.ubuntu.com/LTS Please spread the word that we are seeking funding to develop Bio-Linux 9 based on Ubuntu 16.04 LTS, and post your experiences of upgrading Bio-Linux 8 to Ubuntu 16.04 LTS here so we can make a community effort to fix the problems. Bio-Linux is supported by its user community but it also depends on contributions from the Debian-Med team, who are making their bioinformatics packages available to Ubuntu users before they are available via the Debian repositories. Thanks, ? 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 _______________________________________________ Bio-Linux-list mailing list Bio-Linux-list at bioinformatics.org http://www.bioinformatics.org/mm/listinfo/bio-linux-list -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Tue Feb 14 08:08:01 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Tue, 14 Feb 2017 13:08:01 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <1385100018.3504856.1487008585221@mail.yahoo.com> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> Message-ID: <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> On 13/02/17 17:56, Brian Cady wrote: > Tony and all, > > Could we crowdfund, at $25 each, the building of BioLinux 9? How many > are on this listserv? Hi, Brian. I've thought about crowdfunding e.g. on Kickstarter as a way of funding the development of Bio-Linux, but I think this is method a last resort. I'm actively seeking funding through more conventional routes at the moment and I'll post to the list when I have more information. 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 raonyguimaraes at gmail.com Tue Feb 14 20:25:06 2017 From: raonyguimaraes at gmail.com (=?UTF-8?Q?Raony_Guimaraes_Corr=C3=AAa_Do_Carmo_Lisboa_Cardenas?=) Date: Wed, 15 Feb 2017 01:25:06 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: Hi Tony, Just would like to say a few words here. I sadly saw the development of Biolinux packages stalling on Launchpad . I still believe there is a place for a Bioinformatics targeted linux distro. After speaking with Tim, I kind of felt he would like to see some of the effort that was put on Biolinux going to DebianMed. What's your position in terms of that ? Do you have any estimate for the amount of money you would need to raise to keep the development of Biolinux ? Have you considered using Patreon ? Please don't let this project die! What's the plan and timeline to start upgrading the packages to Xenial ? My biggest suggestion would be to try to base the next release of Biolinux on Ubuntu Mate 16.04, the lead developer also lives in the UK (Martin Wimpress ). Maybe we should even consider targeting the next 18.04 LTS release ... This branch will effectively be created in October of this year. What about snaps ? Have you considered packaging the current and future bioinformatic tools we have using that ? What's the road map for the project ? What are the most important packages you guys are planning to start upgrading? I'm currently living in Ireland, so I would love to visit you guys anytime to have a more profound conversation about this things. Kind Regards. _____________________________________________ Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas PhD in Bioinformatics email: raonyguimaraes at gmail.com skype/hangouts: raonyguimaraes phone: +353 83 8389 337 _____________________________________________ On Tue, Feb 14, 2017 at 1:08 PM, Tony Travis < tony.travis at minke-informatics.co.uk> wrote: > On 13/02/17 17:56, Brian Cady wrote: > > Tony and all, > > > > Could we crowdfund, at $25 each, the building of BioLinux 9? How many > > are on this listserv? > > Hi, Brian. > > I've thought about crowdfunding e.g. on Kickstarter as a way of funding > the development of Bio-Linux, but I think this is method a last resort. > > I'm actively seeking funding through more conventional routes at the > moment and I'll post to the list when I have more information. > > 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 > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -------------- next part -------------- An HTML attachment was scrubbed... URL: From prash at bioclues.org Wed Feb 15 02:16:58 2017 From: prash at bioclues.org (Prash) Date: Wed, 15 Feb 2017 12:46:58 +0530 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: Dear All esp Tony Sad to see this e mail. I have been a great fan of Bio-linux. The support page at Bioinformatics.Org could be linked with Bio-Linux. It would be nice if you could put a word to Jeff. Second, as a regional affiliate of India, we at Bioclues.org would be glad to donate an iota of monies from members' registration. We have inbix.bioclues.org coming up in November '17 and we might consider donating a part of sponsors' money. Please allow us to get back to you. That said, crowdfunding should be on the anvil. Long live Bio-linux! Regards Prash On Wed, Feb 15, 2017 at 6:55 AM, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote: > Hi Tony, > > Just would like to say a few words here. I sadly saw the development of > Biolinux packages stalling on Launchpad . > > I still believe there is a place for a Bioinformatics targeted linux > distro. > > After speaking with Tim, I kind of felt he would like to see some of the > effort that was put on Biolinux going to DebianMed. What's your position in > terms of that ? > > Do you have any estimate for the amount of money you would need to raise > to keep the development of Biolinux ? Have you considered using Patreon ? > > Please don't let this project die! What's the plan and timeline to start > upgrading the packages to Xenial ? > > My biggest suggestion would be to try to base the next release of Biolinux > on Ubuntu Mate 16.04, the lead developer also > lives in the UK (Martin Wimpress ). > Maybe we should even consider targeting the next 18.04 LTS release ... This > branch will effectively be created in October of this year. > > What about snaps ? Have you considered packaging the current and future > bioinformatic tools we have using that ? > > What's the road map for the project ? What are the most important packages > you guys are planning to start upgrading? > > I'm currently living in Ireland, so I would love to visit you guys anytime > to have a more profound conversation about this things. > > Kind Regards. > > _____________________________________________ > > Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas > PhD in Bioinformatics > > email: raonyguimaraes at gmail.com > skype/hangouts: raonyguimaraes > phone: +353 83 8389 337 > _____________________________________________ > > On Tue, Feb 14, 2017 at 1:08 PM, Tony Travis informatics.co.uk> wrote: > >> On 13/02/17 17:56, Brian Cady wrote: >> > Tony and all, >> > >> > Could we crowdfund, at $25 each, the building of BioLinux 9? How many >> > are on this listserv? >> >> Hi, Brian. >> >> I've thought about crowdfunding e.g. on Kickstarter as a way of funding >> the development of Bio-Linux, but I think this is method a last resort. >> >> I'm actively seeking funding through more conventional routes at the >> moment and I'll post to the list when I have more information. >> >> 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 >> _______________________________________________ >> Bio-Linux-list mailing list >> Bio-Linux-list at bioinformatics.org >> http://www.bioinformatics.org/mm/listinfo/bio-linux-list >> > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From 3nrique.0 at gmail.com Wed Feb 15 05:03:39 2017 From: 3nrique.0 at gmail.com (Enrique Ortega) Date: Wed, 15 Feb 2017 11:03:39 +0100 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: Hello all, I do agree with Raony in maybe skyping 16.04 and going straight for 18.04 LTS. Mate is a very good option, It's compatible with X2Go (as well as this other window managers ) so for learning purposes it's makes biologists more comfortable than a terminal through ssh. It's true that through Patreon the project can be financed, even partially. I hadn't heard about DebianMed, it looks amazing. The only downside I see is that a boot key on debian doesn't allow to have a persistent space for the user (updating/installing packages, adding/modifying files). I'm a group person, so i'll go with the choice of the group. In my previous position the SysAdmin used modules to keep a tidy $PATH and a responsive terminal. It allows also to install different versions of softwares (like compilers or java versions required to use a software). I'm very optimistic in the future of bio-linux (of debianMed). It's an amazing time saving tool when you need to deploy tools and are too noob (like me) or too busy to install and configure each tool one by one. And the tutorials included are great ! Best Regards Enrique On 15 February 2017 at 08:16, Prash wrote: > Dear All esp Tony > > Sad to see this e mail. I have been a great fan of Bio-linux. The support > page at Bioinformatics.Org could be linked with Bio-Linux. It would be > nice if you could put a word to Jeff. > > Second, as a regional affiliate of India, we at Bioclues.org would be glad > to donate an iota of monies from members' registration. We have > inbix.bioclues.org coming up in November '17 and we might consider > donating a part of sponsors' money. Please allow us to get back to you. > > That said, crowdfunding should be on the anvil. Long live Bio-linux! > > Regards > Prash > > > > On Wed, Feb 15, 2017 at 6:55 AM, Raony Guimaraes Corr?a Do Carmo Lisboa > Cardenas wrote: > >> Hi Tony, >> >> Just would like to say a few words here. I sadly saw the development of >> Biolinux packages stalling on Launchpad >> . >> >> I still believe there is a place for a Bioinformatics targeted linux >> distro. >> >> After speaking with Tim, I kind of felt he would like to see some of the >> effort that was put on Biolinux going to DebianMed. What's your position in >> terms of that ? >> >> Do you have any estimate for the amount of money you would need to raise >> to keep the development of Biolinux ? Have you considered using Patreon ? >> >> Please don't let this project die! What's the plan and timeline to start >> upgrading the packages to Xenial ? >> >> My biggest suggestion would be to try to base the next release of >> Biolinux on Ubuntu Mate 16.04, the lead >> developer also lives in the UK (Martin Wimpress >> ). Maybe we should even >> consider targeting the next 18.04 LTS release ... This branch will >> effectively be created in October of this year. >> >> What about snaps ? Have you considered packaging the current and future >> bioinformatic tools we have using that ? >> >> What's the road map for the project ? What are the most important >> packages you guys are planning to start upgrading? >> >> I'm currently living in Ireland, so I would love to visit you guys >> anytime to have a more profound conversation about this things. >> >> Kind Regards. >> >> _____________________________________________ >> >> Raony Guimar?es Corr?a Do Carmo Lisboa Cardenas >> PhD in Bioinformatics >> >> email: raonyguimaraes at gmail.com >> skype/hangouts: raonyguimaraes >> phone: +353 83 8389 337 >> _____________________________________________ >> >> On Tue, Feb 14, 2017 at 1:08 PM, Tony Travis < >> tony.travis at minke-informatics.co.uk> wrote: >> >>> On 13/02/17 17:56, Brian Cady wrote: >>> > Tony and all, >>> > >>> > Could we crowdfund, at $25 each, the building of BioLinux 9? How many >>> > are on this listserv? >>> >>> Hi, Brian. >>> >>> I've thought about crowdfunding e.g. on Kickstarter as a way of funding >>> the development of Bio-Linux, but I think this is method a last resort. >>> >>> I'm actively seeking funding through more conventional routes at the >>> moment and I'll post to the list when I have more information. >>> >>> 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 >>> _______________________________________________ >>> Bio-Linux-list mailing list >>> Bio-Linux-list at bioinformatics.org >>> http://www.bioinformatics.org/mm/listinfo/bio-linux-list >>> >> >> >> _______________________________________________ >> Bio-Linux-list mailing list >> Bio-Linux-list at bioinformatics.org >> http://www.bioinformatics.org/mm/listinfo/bio-linux-list >> >> > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Sat Feb 18 10:55:08 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sat, 18 Feb 2017 15:55:08 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <1385100018.3504856.1487008585221@mail.yahoo.com> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> Message-ID: <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> On 13/02/17 17:56, Brian Cady wrote: > Tony and all, > > Could we crowdfund, at $25 each, the building of BioLinux 9? Hi, Brian. I have thought about crowd-funding, but I think this should be a method of last resort if we can't get funding any other way because one of the founding principles of Bio-Linux is that it can be distributed freely. > How many are on this listserv? You can see the membership list here: > http://www.bioinformatics.org/mm/roster/bio-linux-list There are 307 list subscribers at present... One idea that might make a small amount of money would be for me to sell the "Minke-Informatics" branded 8GB Bio-Linux 8 USB-sticks that I use for Bio-Linux courses (see image attached) for $25 (?20) + postage. If anyone wants to buy one or more of these Bio-Linux 8 USB-sticks to help support the development of Bio-Linux, then please send a Stamped Addressed Envelope to the address in my signature below and payment of ?20 or $25 (plus postage if the envelope is not stamped) by PayPal to my email address below. I'll post a tutorial about how to upgrade these Bio-Linux 8 USB-sticks to Bio-Linux 9 in due course. 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 -------------- next part -------------- A non-text attachment was scrubbed... Name: Minke Informatics USB-stick.jpg Type: image/jpeg Size: 53677 bytes Desc: not available URL: From kirannbishwa01 at gmail.com Sat Feb 18 11:41:09 2017 From: kirannbishwa01 at gmail.com (Bishwa Kiran) Date: Sat, 18 Feb 2017 11:41:09 -0500 Subject: [Bio-linux-list] Is biolinux still on Ubuntu 14? Message-ID: <9D5BF79A-AE47-410D-809A-5ECD94CF96A4@gmail.com> I begun with bio Linux and liked it a lot. But, I think the latest biolinux is still using Ubuntu 14 as it's base. So, had to go with Ubuntu 16 and add the required softwares. Has there been any momentum to take this the latest Ubuntu base. Thanks, > On Feb 18, 2017, at 10:55 AM, Tony Travis wrote: > >> On 13/02/17 17:56, Brian Cady wrote: >> Tony and all, >> >> Could we crowdfund, at $25 each, the building of BioLinux 9? > > Hi, Brian. > > I have thought about crowd-funding, but I think this should be a method > of last resort if we can't get funding any other way because one of the > founding principles of Bio-Linux is that it can be distributed freely. > >> How many are on this listserv? > > You can see the membership list here: > >> http://www.bioinformatics.org/mm/roster/bio-linux-list > > There are 307 list subscribers at present... > > One idea that might make a small amount of money would be for me to sell > the "Minke-Informatics" branded 8GB Bio-Linux 8 USB-sticks that I use > for Bio-Linux courses (see image attached) for $25 (?20) + postage. > > If anyone wants to buy one or more of these Bio-Linux 8 USB-sticks to > help support the development of Bio-Linux, then please send a Stamped > Addressed Envelope to the address in my signature below and payment of > ?20 or $25 (plus postage if the envelope is not stamped) by PayPal to my > email address below. > > I'll post a tutorial about how to upgrade these Bio-Linux 8 USB-sticks > to Bio-Linux 9 in due course. > > 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 > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list From aleimba at gwdg.de Sat Feb 18 12:11:30 2017 From: aleimba at gwdg.de (Andreas Leimbach) Date: Sat, 18 Feb 2017 18:11:30 +0100 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> Message-ID: <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> Hi Tony, thanks a lot for your efforts for keeping BioLinux alive! It's a fantastic project, although Bioconda, linuxbrew etc. are becoming more and more interesting alternatives for certain applications. Sadly, I'm not that knowledgeable in funding, but for me BioLinux definitely falls under the topic Open Science (OS). Thus, there might be money to support dev in the current OS environment of funding agencies. What about EU projects like Horizon 2020 that support OS? https://ec.europa.eu/research/openscience/index.cfm How is Debian Med funded? Maybe the OKFN (https://science.okfn.org/) or Mozilla Science Lab (https://science.mozilla.org/) have ideas how to tap funding agencies? They should have mailing lists for asking such a question. After all BioLinux is definitely mostly used by university affiliated researchers. Just my 2 cents ... Best, Andreas On 02/18/2017 04:55 PM, Tony Travis wrote: > On 13/02/17 17:56, Brian Cady wrote: >> Tony and all, >> >> Could we crowdfund, at $25 each, the building of BioLinux 9? > > Hi, Brian. > > I have thought about crowd-funding, but I think this should be a method > of last resort if we can't get funding any other way because one of the > founding principles of Bio-Linux is that it can be distributed freely. > >> How many are on this listserv? > > You can see the membership list here: > >> http://www.bioinformatics.org/mm/roster/bio-linux-list > > There are 307 list subscribers at present... > > One idea that might make a small amount of money would be for me to sell > the "Minke-Informatics" branded 8GB Bio-Linux 8 USB-sticks that I use > for Bio-Linux courses (see image attached) for $25 (?20) + postage. > > If anyone wants to buy one or more of these Bio-Linux 8 USB-sticks to > help support the development of Bio-Linux, then please send a Stamped > Addressed Envelope to the address in my signature below and payment of > ?20 or $25 (plus postage if the envelope is not stamped) by PayPal to my > email address below. > > I'll post a tutorial about how to upgrade these Bio-Linux 8 USB-sticks > to Bio-Linux 9 in due course. > > Bye, > > Tony. > > > > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list > -- Andreas Leimbach Universit?t M?nster Institut f?r Hygiene Mendelstr. 7 D-48149 M?nster Germany Tel.: +49 (0)551 39 33843 E-Mail: aleimba at gwdg.de From tony.travis at minke-informatics.co.uk Sat Feb 18 12:32:03 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sat, 18 Feb 2017 17:32:03 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: <59b3664b-0d1f-7d08-2166-202704499a8c@minke-informatics.co.uk> On 15/02/17 01:25, Raony Guimaraes Corr?a Do Carmo Lisboa Cardenas wrote: > Hi Tony, > > Just would like to say a few words here. I sadly saw the development of > Biolinux packages stalling on Launchpad . Hi, Raony. That link is to a bug-tracking page that Tim created during the development of Bio-Linux 7, but few people actually used it because most reported bugs on the mailing lists. Please take a look at the PPA: > https://launchpad.net/~nebc/+archive/ubuntu/bio-linux?field.series_filter=trusty It is true that no packages have been updated in over a year, but Tim was leading the development work and he has now left. Until recently, I was too busy to take over and that is why development has stalled. > I still believe there is a place for a Bioinformatics targeted linux distro. Actually, there are already quite a few - Notable amongst which is Debain-Med: > https://alioth.debian.org/projects/debian-med As you see there are quite a few project members and the Debian-Med team have contributed significantly to the success of Bio-Linux. > After speaking with Tim, I kind of felt he would like to see some of the > effort that was put on Biolinux going to DebianMed. What's your position > in terms of that ? I agree with Tim, but that does not mean abandoning Bio-Linux! What is important about Bio-Linux, in my view, is that it gives the biologist a complete and fully-configured bioinformatics workstation platform ready to run that requires little or no system administration knowledge to use for bioinformatics work along with teaching materials and supporting documentation. Bio-Linux is, also, a platform on which you can run software packaged by the Debian-Med team before it becomes available in the Ubuntu repositories automatically from the Debian 'unstable' release: > https://launchpad.net/ubuntu/+source/debian-med Debian-Med have been extremely helpful and supportive towards Bio-Linux and we have jointly organised Debian-Med 'Sprints'. See 'Meetings' at: > https://wiki.debian.org/DebianMed [I organised the 4th one in Scotland in 2014] > Do you have any estimate for the amount of money you would need to raise > to keep the development of Biolinux ? I discussed this with Tim and we think it would take a full-time post-doc about six months to create Bio-Linux 9 and update all the teaching materials and documentation. > Have you considered using Patreon ? No, not heard of that? > Please don't let this project die! What's the plan and timeline to start > upgrading the packages to Xenial ? I'm doing it already, privately, on a small scale. I'm waiting to see the outcome of funding requests before taking the project any further. Please note that Steve Moss has forked Tim's "build-bio-linux" GitHub repository as a starting point for community development of Bio-Linux: > https://github.com/Bio-Linux @Steve - Please let the list know what your plans are on GitHub? > My biggest suggestion would be to try to base the next release of > Biolinux on Ubuntu Mate 16.04, the lead > developer also lives in the UK (Martin Wimpress > ). You don't need to do that because the present version can be used with either a Unity or MATE local desktop. However, the only remote desktop supported is MATE because Unity requires hardware acceleration that is not available on a remote "x2go" session and MATE does not require it. > Maybe we should even > consider targeting the next 18.04 LTS release ... This branch will > effectively be created in October of this year. I don't see the point - The current 14.04 LTS will be supported until April 2019 and no End-of-Life date has been announced for 16.04 LTS. > https://wiki.ubuntu.com/Releases I'm only considering development of Bio-Linux 9 on Ubuntu 16.04 LTS. > What about snaps ? Have you considered packaging the current and future > bioinformatic tools we have using that ? One of the reasons that NERC/EOS supported the development of Bio-Linux was to promote "Reproducible Research". From that point of view, I think that lightweight containers like "Docker" and "SNAP" are a good idea. However, The isolation of dependencies comes at a cost: Like the difference between static and dynamic linking of executable binaries. it is always a compromise between requiring libraries to be present, but being able to share them between executables, and having statically linked executables with no external dependencies but unable to share. To me, this is a microcosm of hiding application dependencies in 'lightweight' containers... I'm not against it, but I am sceptical that it will help in our use-case :-) > What's the road map for the project ? What are the most important > packages you guys are planning to start upgrading? For me, it's QIIME, which has been a problem for some of my friends and colleagues who want to use it under Bio-Linux 8 upgraded to Ubuntu 16.04 LTS. The other major disaster area is Galaxy, but I've not looked at it yet. Otherwise, I want to weed out any use of /usr/local by any Bio-Linux packages (which is bad practice, but was a pragmatic way of building the original binary packages before advice from Debian-Med). Best practice is to reserve /usr/local for manually installed software. > I'm currently living in Ireland, so I would love to visit you guys > anytime to have a more profound conversation about this things. OK, my address is in my signature below and I live next to a pub! 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 tony.travis at minke-informatics.co.uk Sat Feb 18 13:10:15 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sat, 18 Feb 2017 18:10:15 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: On 15/02/17 07:16, Prash wrote: > Dear All esp Tony > > Sad to see this e mail. I have been a great fan of Bio-linux. The > support page at Bioinformatics.Org could be linked with Bio-Linux. It > would be nice if you could put a word to Jeff. Hi, Prash. There is already a Bio-Linux group on bioinformatics.org: > http://www.bioinformatics.org/groups/?group_id=341 It's quite old, but I'm trying to bring it back to life. > Second, as a regional affiliate of India, we at Bioclues.org would be > glad to donate an iota of monies from members' registration. We have > inbix.bioclues.org coming up in November '17 > and we might consider donating a part of sponsors' money. Please allow > us to get back to you. Thanks, but something might have been lost in translation: iota - an extremely small amount I posted an email earlier today about one possible way of raising a small amount of funding for Bio-Linux development by selling Minke Informatics branded USB-sticks with Bio-Linux 8 on them: See my reply to a message from Brian Cady > That said, crowdfunding should be on the anvil. Long live Bio-linux! Thanks for your enthusiastic support! 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 tony.travis at minke-informatics.co.uk Sun Feb 19 07:01:20 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 19 Feb 2017 12:01:20 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <447d207c-e506-7d18-9250-056d4e01f0f7@minke-informatics.co.uk> Message-ID: <2bf5651b-6190-94c9-65ac-69154041fea5@minke-informatics.co.uk> On 15/02/17 10:03, Enrique Ortega wrote: > Hello all, > > I do agree with Raony in maybe skyping 16.04 and going straight for > 18.04 LTS. Mate is a very good option, It's compatible with X2Go (as > well as this other window managers > ) > so for learning purposes it's makes biologists more comfortable than a > terminal through ssh. Hi, Enrique. As I said in my reply to Raony, I don't see the point of developing for 18.04 LTS because and End-of-Life hasn't been announced for 16.04 LTS and even 14.04 LTS is supported until April 2019... > It's true that through Patreon the project can be financed, even partially. I'd not heard about Patreon before, but after looking just now it seems more about supporting 'content' creators than software developers... > I hadn't heard about DebianMed, it looks amazing. The only downside I > see is that a boot key on debian doesn't allow to have a persistent > space for the user (updating/installing packages, adding/modifying > files). I'm a group person, so i'll go with the choice of the group. You can create a 'persistent' USB 'live' system with persistence for any distribution: The 'persistence' is a kernel option and the casper FS automatically looks for "casper-rw" to use as a COW (Copy On Write) partition. Take a look at these tools: > https://unetbootin.github.io/ > https://www.pendrivelinux.com/ > In my previous position the SysAdmin used modules > to keep a tidy $PATH and a responsive > terminal. It allows also to install different versions of softwares > (like compilers or java versions required to use a software). Debian/Ubuntu uses profile 'fragments' to allow the package manager to add and remove components to PATH and other environmental variables in: /etc/profile.d This is where changes should be made, and there is also a mechanism to select 'alternatives' e.g.: > ajt at beluga:~$ sudo update-alternatives --list java > /usr/lib/jvm/java-8-openjdk-amd64/jre/bin/java > /usr/lib/jvm/java-8-oracle/jre/bin/java Although, in the case of Java, this is better done using: > ajt at beluga:~$ sudo update-java-alternatives --list > java-1.8.0-openjdk-amd64 1081 /usr/lib/jvm/java-1.8.0-openjdk-amd64 > java-8-oracle 1081 /usr/lib/jvm/java-8-oracle [for more details use: man update-alternatives] > I'm very optimistic in the future of bio-linux (of debianMed). It's an > amazing time saving tool when you need to deploy tools and are too noob > (like me) or too busy to install and configure each tool one by one. And > the tutorials included are great ! Glad you find Bio-Linux useful and thanks for your support! 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 tony.travis at minke-informatics.co.uk Sun Feb 19 07:04:25 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 19 Feb 2017 12:04:25 +0000 Subject: [Bio-linux-list] Is biolinux still on Ubuntu 14? In-Reply-To: <9D5BF79A-AE47-410D-809A-5ECD94CF96A4@gmail.com> References: <9D5BF79A-AE47-410D-809A-5ECD94CF96A4@gmail.com> Message-ID: <83128ecc-7052-3022-ecf7-3c374c49a014@minke-informatics.co.uk> On 18/02/17 16:41, Bishwa Kiran wrote: > I begun with bio Linux and liked it a lot. But, I think the latest > biolinux is still using Ubuntu 14 as it's base. So, had to go with > Ubuntu 16 and add the required softwares. Has there been any momentum > to take this the latest Ubuntu base. Hi, Bishwa. Is there any particular reason why you need to use Ubuntu 16.04 LTS? Ubuntu 14.04 LTS will be supported until April 2019: > https://wiki.ubuntu.com/Releases Glad you like Bio-Linux :-) 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 tony.travis at minke-informatics.co.uk Sun Feb 19 07:29:45 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 19 Feb 2017 12:29:45 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> Message-ID: On 18/02/17 17:11, Andreas Leimbach wrote: > Hi Tony, > > thanks a lot for your efforts for keeping BioLinux alive! It's a > fantastic project, although Bioconda, linuxbrew etc. are becoming more > and more interesting alternatives for certain applications. Hi, Andreas. For anyone who doesn't already know, "Bioconda" is a meta-package manager for bioinformatics applications: > https://bioconda.github.io/ Similarly, "LinuxBrew" is a port of the Mac OS "Homebrew" non-Apple crowd-funded package manager that is also supported by "Bioconda". > http://linuxbrew.sh/ I've looked at both of these and what bothers me most is the extra responsibility placed on biologists to make use of these systems. The USP of Bio-Linux is that it's a complete bioinformatics workstation platform that biologists with little or no prior experience of system administration can make use of to learn how to do bioinformatics. > Sadly, I'm not that knowledgeable in funding, but for me BioLinux > definitely falls under the topic Open Science (OS). Thus, there might be > money to support dev in the current OS environment of funding agencies. > What about EU projects like Horizon 2020 that support OS? > > https://ec.europa.eu/research/openscience/index.cfm Brexit has put an end to all that... :-( > How is Debian Med funded? It's part of Debian - A Debian 'blend' supported by volunteers. > Maybe the OKFN (https://science.okfn.org/) or Mozilla Science Lab > (https://science.mozilla.org/) have ideas how to tap funding agencies? > They should have mailing lists for asking such a question. After all > BioLinux is definitely mostly used by university affiliated researchers. In fact, Bio-Linux was funded specifically by EOS/NERC to support NERC grant awardees but made publically available because NERC funding comes from the UK taxpayer and anything it does is made publically available. > Just my 2 cents ... Every cent counts :-) Thanks for all your suggestions, 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 aleimba at gwdg.de Sun Feb 19 08:24:36 2017 From: aleimba at gwdg.de (Andreas Leimbach) Date: Sun, 19 Feb 2017 14:24:36 +0100 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> Message-ID: <2897b6a6-1ccf-2720-d75f-371fde8953cb@gwdg.de> Hi Tony, crap, I didn't think of Brexit ... One more thing I remembered is the Software Sustainability Institute (https://www.software.ac.uk/). They have a small scale fellowship program (but already closed for 2017): https://www.software.ac.uk/fellowship-programme But you're probably familiar with that already ... Best, Andreas P.S.: There's a grass-root movement in Germany trying to copy the SSI's goals (http://www.de-rse.org/en/index.html), but naturally no funding available (yet) ... On 02/19/2017 01:29 PM, Tony Travis wrote: > On 18/02/17 17:11, Andreas Leimbach wrote: >> Hi Tony, >> >> thanks a lot for your efforts for keeping BioLinux alive! It's a >> fantastic project, although Bioconda, linuxbrew etc. are becoming more >> and more interesting alternatives for certain applications. > > Hi, Andreas. > > For anyone who doesn't already know, "Bioconda" is a meta-package > manager for bioinformatics applications: > >> https://bioconda.github.io/ > > Similarly, "LinuxBrew" is a port of the Mac OS "Homebrew" non-Apple > crowd-funded package manager that is also supported by "Bioconda". > >> http://linuxbrew.sh/ > > I've looked at both of these and what bothers me most is the extra > responsibility placed on biologists to make use of these systems. > > The USP of Bio-Linux is that it's a complete bioinformatics workstation > platform that biologists with little or no prior experience of system > administration can make use of to learn how to do bioinformatics. > >> Sadly, I'm not that knowledgeable in funding, but for me BioLinux >> definitely falls under the topic Open Science (OS). Thus, there might be >> money to support dev in the current OS environment of funding agencies. >> What about EU projects like Horizon 2020 that support OS? >> >> https://ec.europa.eu/research/openscience/index.cfm > > Brexit has put an end to all that... :-( > >> How is Debian Med funded? > > It's part of Debian - A Debian 'blend' supported by volunteers. > >> Maybe the OKFN (https://science.okfn.org/) or Mozilla Science Lab >> (https://science.mozilla.org/) have ideas how to tap funding agencies? >> They should have mailing lists for asking such a question. After all >> BioLinux is definitely mostly used by university affiliated researchers. > > In fact, Bio-Linux was funded specifically by EOS/NERC to support NERC > grant awardees but made publically available because NERC funding comes > from the UK taxpayer and anything it does is made publically available. > >> Just my 2 cents ... > > Every cent counts :-) > > Thanks for all your suggestions, > > Tony. > -- Andreas Leimbach Universit?t M?nster Institut f?r Hygiene Mendelstr. 7 D-48149 M?nster Germany Tel.: +49 (0)551 39 33843 E-Mail: aleimba at gwdg.de From tony.travis at minke-informatics.co.uk Sun Feb 19 12:00:28 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Sun, 19 Feb 2017 17:00:28 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <2897b6a6-1ccf-2720-d75f-371fde8953cb@gwdg.de> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> <2897b6a6-1ccf-2720-d75f-371fde8953cb@gwdg.de> Message-ID: <4fed950e-f8f6-6676-c5d1-124a4d4bf546@minke-informatics.co.uk> On 19/02/17 13:24, Andreas Leimbach wrote: > Hi Tony, > > crap, I didn't think of Brexit ... Hi, Andreas. I believe in democracy, but ALL regions of Scotland voted to remain! > One more thing I remembered is the Software Sustainability Institute > (https://www.software.ac.uk/). They have a small scale fellowship > program (but already closed for 2017): > https://www.software.ac.uk/fellowship-programme > > But you're probably familiar with that already ... Yes, I applied in 2016 but my Bio-Linux project wasn't shortlisted. 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 kirannbishwa01 at gmail.com Sun Feb 19 23:43:41 2017 From: kirannbishwa01 at gmail.com (Bishwa Kiran) Date: Sun, 19 Feb 2017 23:43:41 -0500 Subject: [Bio-linux-list] Is biolinux still on Ubuntu 14? In-Reply-To: <83128ecc-7052-3022-ecf7-3c374c49a014@minke-informatics.co.uk> References: <9D5BF79A-AE47-410D-809A-5ECD94CF96A4@gmail.com> <83128ecc-7052-3022-ecf7-3c374c49a014@minke-informatics.co.uk> Message-ID: <76EAAE32-ABC4-4FB3-AF1A-7EF5247437B4@gmail.com> I have personally found ubuntu 16 to be more stable and able to manage memory more efficiently. Also, several required add-on are really handy - like being able to run terminal from any folder in ubuntu 16, but in ubuntu 14 i had to add some updates to get this functionality. Most importantly I was not able to put biolinux in sleep/suspend mode when I wanted. I have to do this because sometimes I have to pause my work and resume after couple hours and days without rebooting the whole system. This issue made me switch to ubuntu 16. - Bishwa K. > On Feb 19, 2017, at 7:04 AM, Tony Travis wrote: > >> On 18/02/17 16:41, Bishwa Kiran wrote: >> I begun with bio Linux and liked it a lot. But, I think the latest >> biolinux is still using Ubuntu 14 as it's base. So, had to go with >> Ubuntu 16 and add the required softwares. Has there been any momentum >> to take this the latest Ubuntu base. > > Hi, Bishwa. > > Is there any particular reason why you need to use Ubuntu 16.04 LTS? > > Ubuntu 14.04 LTS will be supported until April 2019: > >> https://wiki.ubuntu.com/Releases > > Glad you like Bio-Linux :-) > > 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 > _______________________________________________ > Bio-Linux-list mailing list > Bio-Linux-list at bioinformatics.org > http://www.bioinformatics.org/mm/listinfo/bio-linux-list From kissaj at miamioh.edu Mon Feb 20 06:31:35 2017 From: kissaj at miamioh.edu (Andor J Kiss) Date: Mon, 20 Feb 2017 06:31:35 -0500 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> Message-ID: <1487590295.7094.11.camel@miamioh.edu> Hi Tony (& All). There are some US-UK funding opportunities for NSF (US) and BIO-UK BBSRC (UK) specifically for bioinformatics. ?We might check into these and maybe generate a large project grant between several PIs to hire programmers/maintainers? URL:?https://www.nsf.gov/news/news_summ.jsp?cntn_id=130555 What does everyone think? Regards, -- _________________________________________________________________________________________________________________________ Andor J Kiss, PhD Director - Center for Bioinformatics & 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://miamioh.edu/cas/academics/centers/cbfg/? URL (CBFG Services):?https://www.scienceexchange.com/labs/center-for-bioinformatics-functional-genomics URL (Research):?http://openwetware.org/wiki/User:Andor_J_Kiss? On Sun, 2017-02-19 at 12:29 +0000, Tony Travis wrote: > On 18/02/17 17:11, Andreas Leimbach wrote: > > > > Hi Tony, > > > > thanks a lot for your efforts for keeping BioLinux alive! It's a > > fantastic project, although Bioconda, linuxbrew etc. are becoming > > more > > and more interesting alternatives for certain applications. > Hi, Andreas. > > For anyone who doesn't already know, "Bioconda" is a meta-package > manager for bioinformatics applications: > > > > > https://bioconda.github.io/ > Similarly, "LinuxBrew" is a port of the Mac OS "Homebrew" non-Apple > crowd-funded package manager that is also supported by "Bioconda". > > > > > http://linuxbrew.sh/ > I've looked at both of these and what bothers me most is the extra > responsibility placed on biologists to make use of these systems. > > The USP of Bio-Linux is that it's a complete bioinformatics > workstation > platform that biologists with little or no prior experience of system > administration can make use of to learn how to do bioinformatics. > > > > > Sadly, I'm not that knowledgeable in funding, but for me BioLinux > > definitely falls under the topic Open Science (OS). Thus, there > > might be > > money to support dev in the current OS environment of funding > > agencies. > > What about EU projects like Horizon 2020 that support OS? > > > > https://ec.europa.eu/research/openscience/index.cfm > Brexit has put an end to all that... :-( > > > > > How is Debian Med funded? > It's part of Debian - A Debian 'blend' supported by volunteers. > > > > > Maybe the OKFN (https://science.okfn.org/) or Mozilla Science Lab > > (https://science.mozilla.org/) have ideas how to tap funding > > agencies? > > They should have mailing lists for asking such a question. After > > all > > BioLinux is definitely mostly used by university affiliated > > researchers. > In fact, Bio-Linux was funded specifically by EOS/NERC to support > NERC > grant awardees but made publically available because NERC funding > comes > from the UK taxpayer and anything it does is made publically > available. > > > > > Just my 2 cents ... > Every cent counts :-) > > Thanks for all your suggestions, > > ? Tony. > -------------- next part -------------- An HTML attachment was scrubbed... URL: From tony.travis at minke-informatics.co.uk Mon Feb 20 07:06:13 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 20 Feb 2017 12:06:13 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <1487590295.7094.11.camel@miamioh.edu> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> <1487590295.7094.11.camel@miamioh.edu> Message-ID: On 20/02/17 11:31, Andor J Kiss wrote: > Hi Tony (& All). > > There are some US-UK funding opportunities for NSF (US) and BIO-UK BBSRC > (UK) specifically for bioinformatics. We might check into these and > maybe generate a large project grant between several PIs to hire > programmers/maintainers? > > URL: https://www.nsf.gov/news/news_summ.jsp?cntn_id=130555 > > What does everyone think? Hi, Andor. That would fit in well with my use of the fantastic NFS-funded CyVerse "Atmosphere" training cluster at the University of Arizona, which I've used several times now to run my "Introduction to Bio-Linux" courses. > https://atmo.cyverse.org/application/images?q=bio-linux I'm also looking into ways that we might fund running an "Atmosphere" instance on our local OpenStack HPC service here at the University of Aberdeen. There is a CyVerse UK project, but they did NOT get funding to run "Atmosphere". We tried to get BBSRC funding in the past, but we were unsuccessful. Bye, Tony. Dr. A.J.Travis, University of Aberdeen, Institute of Biological and Environmental Sciences, Cruickshank Building, St. Machar Drive, Aberdeen AB24 3UU, Scotland, UK. tel +44(0)1224 272700, fax +44 (0)1224 272 396 http://www.abdn.ac.uk, mailto:tony.travis at abdn.ac.uk, skype:ajtravis -- 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 tony.travis at minke-informatics.co.uk Mon Feb 20 07:10:04 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 20 Feb 2017 12:10:04 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> <1487590295.7094.11.camel@miamioh.edu> Message-ID: <36cf57ac-7952-8c6e-5ec6-00bc32ef4dcb@minke-informatics.co.uk> On 20/02/17 12:06, Tony Travis wrote: > [...] > That would fit in well with my use of the fantastic NFS-funded CyVerse > "Atmosphere" training cluster at the University of Arizona, which I've > used several times now to run my "Introduction to Bio-Linux" courses. Sorry, I mean "NSF-funded"... I've got NFS on the brain just now :-) 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 tony.travis at minke-informatics.co.uk Mon Feb 20 07:24:08 2017 From: tony.travis at minke-informatics.co.uk (Tony Travis) Date: Mon, 20 Feb 2017 12:24:08 +0000 Subject: [Bio-linux-list] The reports of Bio-Linux's death are greatly exaggerated In-Reply-To: <1487590295.7094.11.camel@miamioh.edu> References: <7b868c97-1022-0db1-ddd0-3bb370e796a2@minke-informatics.co.uk> <1385100018.3504856.1487008585221@mail.yahoo.com> <3a62e226-0926-be3b-d797-3897cdbe1c3d@minke-informatics.co.uk> <68ee5337-ebe4-8f5a-3b86-8e6b8f351a78@gwdg.de> <1487590295.7094.11.camel@miamioh.edu> Message-ID: <1b870bd8-e4c9-6f3b-bd25-1799db3fb166@minke-informatics.co.uk> On 20/02/17 11:31, Andor J Kiss wrote: > Hi Tony (& All). > > There are some US-UK funding opportunities for NSF (US) and BIO-UK BBSRC > (UK) specifically for bioinformatics. We might check into these and > maybe generate a large project grant between several PIs to hire > programmers/maintainers? > > URL: https://www.nsf.gov/news/news_summ.jsp?cntn_id=130555 > > What does everyone think? Hi, Andor. That call is now closed: > http://www.bbsrc.ac.uk/funding/filter/nsfbio-lead-agency-pilot/ Let's keep an eye open for other, similar calls. 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