From pjotr.public14 at thebird.nl Wed Oct 3 09:02:18 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 3 Oct 2012 15:02:18 +0200 Subject: [BioRuby] Removing copyright statements from BioRuby sources Message-ID: <20121003130218.GA32334@thebird.nl> A few weeks ago all BioRuby panel members were together in Japan. We used this time to discuss the future of BioRuby, and we took some decisions. An important decision was to remove all personal copyright statements from the BioRuby source code, and replace it with a single copyright by the BioRuby project, before the next BioRuby release. The reason is that commits are all stored in version control. Copyright statements do not always reflect the work that has gone into a file: some people contribute a lot, others much less, and shared copyright statements do not reflect the work gone in. The commit history, however, does reflect history, and acts like a copyright, subject to the LICENSE that goes with BioRuby. So, the removal of copyright statements does not mean the loss of "your" copyright written by "you". If any existing copyright holders take issue with this decision, we will study the implications of either removing the submitted code, move the code out to a biogem, or retaining the copyright for special cases. We invite all copyright holders to send complaints to us now. If no complaint is received before November 1st, 2012, we'll assume the copyright holder to agree. Naohisa, Pjotr, Raoul, Francesco and Toshiaki From pjotr.public14 at thebird.nl Wed Oct 3 09:08:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 3 Oct 2012 15:08:27 +0200 Subject: [BioRuby] Changing the BioRuby license Message-ID: <20121003130827.GB32334@thebird.nl> Separately, we want to align BioRuby's license with the new license of Ruby: http://svn.ruby-lang.org/repos/ruby/tags/v1_9_3_0/NEWS Ruby's License is changed from a dual license with GPLv2 to a dual license with 2-clause BSDL. Complicated, huh ;). Essentially it is a more free license: 'do with the source what you want, as long as you maintain the copyright notice, but don't blame us if something goes wrong'. BioRuby's license is "The Ruby's License" without specifying versions, therefore BioRuby's license will be updated to the new Ruby License. Naohisa, Pjotr, Raoul, Francesco and Toshiaki From pjotr.public14 at thebird.nl Sun Oct 14 11:30:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 14 Oct 2012 17:30:35 +0200 Subject: [BioRuby] Ruby on Android Message-ID: <20121014153035.GA31719@thebird.nl> Better than playing with birds https://play.google.com/store/apps/details?id=org.ruboto.irb From john.woods at marcottelab.org Mon Oct 15 14:05:27 2012 From: john.woods at marcottelab.org (John Woods) Date: Mon, 15 Oct 2012 13:05:27 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) Message-ID: BioRubyists, I would be immensely grateful if you could help me distribute this to interested students. While it's targeted at graduate students, we will accept any student researchers, and even post-docs potentially. http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ We are incredibly pleased to announce that the Ruby Association has awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to work on NMatrix, our Ruby matrix library. We plan to provide each fellow with a monthly stipend competitive with her or his home institution (e.g., if research assistants in your graduate program typically receive $1,500 per month, your stipend with us would be $1,500 per month). Tenure length is typically a semester or a quarter, depending on the system used at your home institution. Fluency in Ruby and C/C++ is highly recommended. Please write me back if you have any questions. Cheers, John Woods Director, SciRuby Project From john.woods at marcottelab.org Tue Oct 16 16:19:21 2012 From: john.woods at marcottelab.org (John Woods) Date: Tue, 16 Oct 2012 15:19:21 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: As a side note, I would greatly appreciate it if you could write me back and let me know that you've forwarded this. I'm getting a tad worried that we're not going to see many applications. Cheers, John On Mon, Oct 15, 2012 at 1:05 PM, John Woods wrote: > BioRubyists, I would be immensely grateful if you could help me distribute > this to interested students. While it's targeted at graduate students, we > will accept any student researchers, and even post-docs potentially. > > > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ > > We are incredibly pleased to announce that the Ruby Association has > awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to > work on NMatrix, our Ruby matrix library. > > We plan to provide each fellow with a monthly stipend competitive with her > or his home institution (e.g., if research assistants in your graduate > program typically receive $1,500 per month, your stipend with us would be > $1,500 per month). > > Tenure length is typically a semester or a quarter, depending on the > system used at your home institution. > > Fluency in Ruby and C/C++ is highly recommended. > > > Please write me back if you have any questions. > > Cheers, > John Woods > Director, SciRuby Project > From russell.whitaker at gmail.com Tue Oct 16 17:30:38 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Tue, 16 Oct 2012 14:30:38 -0700 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: Would you mind if I distributed this to my Columbia University alumni network then? Russell Sent from my iPad On Oct 16, 2012, at 1:19 PM, John Woods wrote: > As a side note, I would greatly appreciate it if you could write me back > and let me know that you've forwarded this. I'm getting a tad worried that > we're not going to see many applications. > > Cheers, > John > > > On Mon, Oct 15, 2012 at 1:05 PM, John Woods wrote: > >> BioRubyists, I would be immensely grateful if you could help me distribute >> this to interested students. While it's targeted at graduate students, we >> will accept any student researchers, and even post-docs potentially. >> >> >> http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ >> >> We are incredibly pleased to announce that the Ruby Association has >> awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to >> work on NMatrix, our Ruby matrix library. >> >> We plan to provide each fellow with a monthly stipend competitive with her >> or his home institution (e.g., if research assistants in your graduate >> program typically receive $1,500 per month, your stipend with us would be >> $1,500 per month). >> >> Tenure length is typically a semester or a quarter, depending on the >> system used at your home institution. >> >> Fluency in Ruby and C/C++ is highly recommended. >> >> >> Please write me back if you have any questions. >> >> Cheers, >> John Woods >> Director, SciRuby Project >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From john.woods at marcottelab.org Tue Oct 16 17:35:06 2012 From: john.woods at marcottelab.org (John Woods) Date: Tue, 16 Oct 2012 16:35:06 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: By all means, please distribute extensively! Cheers, John On Tue, Oct 16, 2012 at 4:30 PM, Russell Whitaker < russell.whitaker at gmail.com> wrote: > Would you mind if I distributed this to my Columbia University alumni > network then? > > Russell > > Sent from my iPad > > On Oct 16, 2012, at 1:19 PM, John Woods > wrote: > > > As a side note, I would greatly appreciate it if you could write me back > > and let me know that you've forwarded this. I'm getting a tad worried > that > > we're not going to see many applications. > > > > Cheers, > > John > > > > > > On Mon, Oct 15, 2012 at 1:05 PM, John Woods >wrote: > > > >> BioRubyists, I would be immensely grateful if you could help me > distribute > >> this to interested students. While it's targeted at graduate students, > we > >> will accept any student researchers, and even post-docs potentially. > >> > >> > >> > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ > >> > >> We are incredibly pleased to announce that the Ruby Association has > >> awarded us a 1,000,000 JPY grant, which we want to use to hire fellows > to > >> work on NMatrix, our Ruby matrix library. > >> > >> We plan to provide each fellow with a monthly stipend competitive with > her > >> or his home institution (e.g., if research assistants in your graduate > >> program typically receive $1,500 per month, your stipend with us would > be > >> $1,500 per month). > >> > >> Tenure length is typically a semester or a quarter, depending on the > >> system used at your home institution. > >> > >> Fluency in Ruby and C/C++ is highly recommended. > >> > >> > >> Please write me back if you have any questions. > >> > >> Cheers, > >> John Woods > >> Director, SciRuby Project > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From john.woods at marcottelab.org Mon Oct 22 15:26:22 2012 From: john.woods at marcottelab.org (John Woods) Date: Mon, 22 Oct 2012 14:26:22 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: Hey folks, Could someone please forward this to the Japanese BioRuby listserv for me? The subject is written just below. Please write back and let me know if you've forwarded. *Subject:* SciRuby ????????????????? BioRubyist ?? ?? SciRuby ???????????????????????????????????????? ????????????????????????????????????????????? ??????????????????????? ? Ruby ??????????100??????????????????????????????? ????????? Ruby ???????????????NMatrix??????????????? ?????????? ?????????????????????????????(?????????????? ????????1500???????????????????1500???????) ???????????????????????????? ????Ruby ?? C++?????????????????????????????????? ????? ?????:2012?10?31? ??????????????????URL: (??????) http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships- available/ ????????????????????????????? John Woods (??? ????) SciRuby ?????? ?? sciruby.project at gmail.com ?????????????? From ngoto at gen-info.osaka-u.ac.jp Thu Oct 25 05:15:12 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 25 Oct 2012 18:15:12 +0900 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: <201210250922.q9P9MbYA024099@portal.open-bio.org> Hi John, I forwarded the announcement to bioruby-ja at lists.open-bio.org, but I haven't received the mail form the list. It seems there are some troubles in the bioruby-ja list. I also forwarded it to the mailing list of Dennou Ruby Project (http://ruby.gfd-dennou.org/), Rubyist community in the field of geophysics in Japan. ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 22 Oct 2012 14:26:22 -0500 John Woods wrote: > Hey folks, > > Could someone please forward this to the Japanese BioRuby listserv for me? > The subject is written just below. Please write back and let me know if > you've forwarded. > > *Subject:* SciRuby ????????????????? > > BioRubyist ?? > > ?? SciRuby ???????????????????????????????????????? > ????????????????????????????????????????????? > ??????????????????????? > > ? > > Ruby ??????????100??????????????????????????????? > ????????? Ruby ???????????????NMatrix??????????????? > ?????????? > > ?????????????????????????????(?????????????? > ????????1500???????????????????1500???????) > > ???????????????????????????? > > ????Ruby ?? C++?????????????????????????????????? > ????? > > ?????:2012?10?31? > > ??????????????????URL: (??????) > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships- > available/ > > ????????????????????????????? > > John Woods (??? ????) > SciRuby ?????? ?? > sciruby.project at gmail.com > > ?????????????? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From pjotr.public14 at thebird.nl Wed Oct 3 13:02:18 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 3 Oct 2012 15:02:18 +0200 Subject: [BioRuby] Removing copyright statements from BioRuby sources Message-ID: <20121003130218.GA32334@thebird.nl> A few weeks ago all BioRuby panel members were together in Japan. We used this time to discuss the future of BioRuby, and we took some decisions. An important decision was to remove all personal copyright statements from the BioRuby source code, and replace it with a single copyright by the BioRuby project, before the next BioRuby release. The reason is that commits are all stored in version control. Copyright statements do not always reflect the work that has gone into a file: some people contribute a lot, others much less, and shared copyright statements do not reflect the work gone in. The commit history, however, does reflect history, and acts like a copyright, subject to the LICENSE that goes with BioRuby. So, the removal of copyright statements does not mean the loss of "your" copyright written by "you". If any existing copyright holders take issue with this decision, we will study the implications of either removing the submitted code, move the code out to a biogem, or retaining the copyright for special cases. We invite all copyright holders to send complaints to us now. If no complaint is received before November 1st, 2012, we'll assume the copyright holder to agree. Naohisa, Pjotr, Raoul, Francesco and Toshiaki From pjotr.public14 at thebird.nl Wed Oct 3 13:08:27 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Wed, 3 Oct 2012 15:08:27 +0200 Subject: [BioRuby] Changing the BioRuby license Message-ID: <20121003130827.GB32334@thebird.nl> Separately, we want to align BioRuby's license with the new license of Ruby: http://svn.ruby-lang.org/repos/ruby/tags/v1_9_3_0/NEWS Ruby's License is changed from a dual license with GPLv2 to a dual license with 2-clause BSDL. Complicated, huh ;). Essentially it is a more free license: 'do with the source what you want, as long as you maintain the copyright notice, but don't blame us if something goes wrong'. BioRuby's license is "The Ruby's License" without specifying versions, therefore BioRuby's license will be updated to the new Ruby License. Naohisa, Pjotr, Raoul, Francesco and Toshiaki From pjotr.public14 at thebird.nl Sun Oct 14 15:30:35 2012 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sun, 14 Oct 2012 17:30:35 +0200 Subject: [BioRuby] Ruby on Android Message-ID: <20121014153035.GA31719@thebird.nl> Better than playing with birds https://play.google.com/store/apps/details?id=org.ruboto.irb From john.woods at marcottelab.org Mon Oct 15 18:05:27 2012 From: john.woods at marcottelab.org (John Woods) Date: Mon, 15 Oct 2012 13:05:27 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) Message-ID: BioRubyists, I would be immensely grateful if you could help me distribute this to interested students. While it's targeted at graduate students, we will accept any student researchers, and even post-docs potentially. http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ We are incredibly pleased to announce that the Ruby Association has awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to work on NMatrix, our Ruby matrix library. We plan to provide each fellow with a monthly stipend competitive with her or his home institution (e.g., if research assistants in your graduate program typically receive $1,500 per month, your stipend with us would be $1,500 per month). Tenure length is typically a semester or a quarter, depending on the system used at your home institution. Fluency in Ruby and C/C++ is highly recommended. Please write me back if you have any questions. Cheers, John Woods Director, SciRuby Project From john.woods at marcottelab.org Tue Oct 16 20:19:21 2012 From: john.woods at marcottelab.org (John Woods) Date: Tue, 16 Oct 2012 15:19:21 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: As a side note, I would greatly appreciate it if you could write me back and let me know that you've forwarded this. I'm getting a tad worried that we're not going to see many applications. Cheers, John On Mon, Oct 15, 2012 at 1:05 PM, John Woods wrote: > BioRubyists, I would be immensely grateful if you could help me distribute > this to interested students. While it's targeted at graduate students, we > will accept any student researchers, and even post-docs potentially. > > > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ > > We are incredibly pleased to announce that the Ruby Association has > awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to > work on NMatrix, our Ruby matrix library. > > We plan to provide each fellow with a monthly stipend competitive with her > or his home institution (e.g., if research assistants in your graduate > program typically receive $1,500 per month, your stipend with us would be > $1,500 per month). > > Tenure length is typically a semester or a quarter, depending on the > system used at your home institution. > > Fluency in Ruby and C/C++ is highly recommended. > > > Please write me back if you have any questions. > > Cheers, > John Woods > Director, SciRuby Project > From russell.whitaker at gmail.com Tue Oct 16 21:30:38 2012 From: russell.whitaker at gmail.com (Russell Whitaker) Date: Tue, 16 Oct 2012 14:30:38 -0700 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: Would you mind if I distributed this to my Columbia University alumni network then? Russell Sent from my iPad On Oct 16, 2012, at 1:19 PM, John Woods wrote: > As a side note, I would greatly appreciate it if you could write me back > and let me know that you've forwarded this. I'm getting a tad worried that > we're not going to see many applications. > > Cheers, > John > > > On Mon, Oct 15, 2012 at 1:05 PM, John Woods wrote: > >> BioRubyists, I would be immensely grateful if you could help me distribute >> this to interested students. While it's targeted at graduate students, we >> will accept any student researchers, and even post-docs potentially. >> >> >> http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ >> >> We are incredibly pleased to announce that the Ruby Association has >> awarded us a 1,000,000 JPY grant, which we want to use to hire fellows to >> work on NMatrix, our Ruby matrix library. >> >> We plan to provide each fellow with a monthly stipend competitive with her >> or his home institution (e.g., if research assistants in your graduate >> program typically receive $1,500 per month, your stipend with us would be >> $1,500 per month). >> >> Tenure length is typically a semester or a quarter, depending on the >> system used at your home institution. >> >> Fluency in Ruby and C/C++ is highly recommended. >> >> >> Please write me back if you have any questions. >> >> Cheers, >> John Woods >> Director, SciRuby Project >> > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From john.woods at marcottelab.org Tue Oct 16 21:35:06 2012 From: john.woods at marcottelab.org (John Woods) Date: Tue, 16 Oct 2012 16:35:06 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: By all means, please distribute extensively! Cheers, John On Tue, Oct 16, 2012 at 4:30 PM, Russell Whitaker < russell.whitaker at gmail.com> wrote: > Would you mind if I distributed this to my Columbia University alumni > network then? > > Russell > > Sent from my iPad > > On Oct 16, 2012, at 1:19 PM, John Woods > wrote: > > > As a side note, I would greatly appreciate it if you could write me back > > and let me know that you've forwarded this. I'm getting a tad worried > that > > we're not going to see many applications. > > > > Cheers, > > John > > > > > > On Mon, Oct 15, 2012 at 1:05 PM, John Woods >wrote: > > > >> BioRubyists, I would be immensely grateful if you could help me > distribute > >> this to interested students. While it's targeted at graduate students, > we > >> will accept any student researchers, and even post-docs potentially. > >> > >> > >> > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships-available/ > >> > >> We are incredibly pleased to announce that the Ruby Association has > >> awarded us a 1,000,000 JPY grant, which we want to use to hire fellows > to > >> work on NMatrix, our Ruby matrix library. > >> > >> We plan to provide each fellow with a monthly stipend competitive with > her > >> or his home institution (e.g., if research assistants in your graduate > >> program typically receive $1,500 per month, your stipend with us would > be > >> $1,500 per month). > >> > >> Tenure length is typically a semester or a quarter, depending on the > >> system used at your home institution. > >> > >> Fluency in Ruby and C/C++ is highly recommended. > >> > >> > >> Please write me back if you have any questions. > >> > >> Cheers, > >> John Woods > >> Director, SciRuby Project > >> > > _______________________________________________ > > BioRuby Project - http://www.bioruby.org/ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > From john.woods at marcottelab.org Mon Oct 22 19:26:22 2012 From: john.woods at marcottelab.org (John Woods) Date: Mon, 22 Oct 2012 14:26:22 -0500 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: Hey folks, Could someone please forward this to the Japanese BioRuby listserv for me? The subject is written just below. Please write back and let me know if you've forwarded. *Subject:* SciRuby ????????????????? BioRubyist ?? ?? SciRuby ???????????????????????????????????????? ????????????????????????????????????????????? ??????????????????????? ? Ruby ??????????100??????????????????????????????? ????????? Ruby ???????????????NMatrix??????????????? ?????????? ?????????????????????????????(?????????????? ????????1500???????????????????1500???????) ???????????????????????????? ????Ruby ?? C++?????????????????????????????????? ????? ?????:2012?10?31? ??????????????????URL: (??????) http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships- available/ ????????????????????????????? John Woods (??? ????) SciRuby ?????? ?? sciruby.project at gmail.com ?????????????? From ngoto at gen-info.osaka-u.ac.jp Thu Oct 25 09:15:12 2012 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 25 Oct 2012 18:15:12 +0900 Subject: [BioRuby] SciRuby Fellowship Applications due October 31st (please forward widely) In-Reply-To: References: Message-ID: <201210250922.q9P9MbYA024099@portal.open-bio.org> Hi John, I forwarded the announcement to bioruby-ja at lists.open-bio.org, but I haven't received the mail form the list. It seems there are some troubles in the bioruby-ja list. I also forwarded it to the mailing list of Dennou Ruby Project (http://ruby.gfd-dennou.org/), Rubyist community in the field of geophysics in Japan. ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Mon, 22 Oct 2012 14:26:22 -0500 John Woods wrote: > Hey folks, > > Could someone please forward this to the Japanese BioRuby listserv for me? > The subject is written just below. Please write back and let me know if > you've forwarded. > > *Subject:* SciRuby ????????????????? > > BioRubyist ?? > > ?? SciRuby ???????????????????????????????????????? > ????????????????????????????????????????????? > ??????????????????????? > > ? > > Ruby ??????????100??????????????????????????????? > ????????? Ruby ???????????????NMatrix??????????????? > ?????????? > > ?????????????????????????????(?????????????? > ????????1500???????????????????1500???????) > > ???????????????????????????? > > ????Ruby ?? C++?????????????????????????????????? > ????? > > ?????:2012?10?31? > > ??????????????????URL: (??????) > http://sciruby.com/blog/2012/09/24/sciruby-receives-ruby-association-grant--fellowships- > available/ > > ????????????????????????????? > > John Woods (??? ????) > SciRuby ?????? ?? > sciruby.project at gmail.com > > ?????????????? > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby