From pjotr.public14 at thebird.nl Tue Jan 1 07:19:07 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 1 Jan 2013 12:19:07 +0000 Subject: [BioRuby] t Message-ID: <20130101121907.GA15224@thebird.nl> Ten Simple Rules for the Open Development of Scientific Software by Andreas and James! http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002802 hear, hear! Pj. From ngoto at gen-info.osaka-u.ac.jp Thu Jan 3 09:21:37 2013 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 3 Jan 2013 23:21:37 +0900 Subject: [BioRuby] Removal of Bio::KEGG::API because the service discontinued Message-ID: <201301031428.r03ESJoU025001@portal.open-bio.org> Hi all, I'll remove Bio::KEGG::API in lib/bio/io/keggapi.rb and related contents. As already announced in the KEGG website (http://www.genome.jp/kegg/soap/), the SOAP API is discontinued in 2013/1/1 and the Bio::KEGG::API class no longer works. New version of KEGG API, which is based on REST, is already started. Users of old KEGG API should migrate to the new REST-based KEGG API. See http://www.kegg.jp/kegg/rest/ for more information. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From francesco.strozzi at gmail.com Sat Jan 12 17:33:48 2013 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 12 Jan 2013 14:33:48 -0800 Subject: [BioRuby] PAG 2013 Message-ID: Hi, I'm at PAG conference in San Diego. Is there some BioRubyst or open-bio developer here? It would be interesting to meet with other attendees. Just mail me if you are around. Cheers -- Francesco From pjotr.public14 at thebird.nl Tue Jan 29 03:40:11 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 29 Jan 2013 09:40:11 +0100 Subject: [BioRuby] Are the Bio* projects dying? Message-ID: <20130129084011.GA15860@thebird.nl> When I check the # of commits to BioRuby, BioPerl, BioPython, I notice the projects are not very active (to put it mildly). With BioRuby the # of downloads is still increasing - remember we hit 10K not that long ago, now we are at 35K. See http://biogems.info/ With Ruby/Biogems there is health, coming from some 10 regular committers. Ruby in Bioinformatics, going by downloads and citations, appears to be as healthy as ever. JRuby on the JVM may turn out to be a blessing for Ruby - especially if we can make our gems easily accessible to other JVM languages. But, what does this really mean for the Bio* projects as a whole? What happened to new blood? What should we do? Maybe it is merely my sense of disorientation and confusion in the face of an (apparently) meaningless and absurd world. Pj. From p.j.a.cock at googlemail.com Tue Jan 29 07:09:53 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 29 Jan 2013 12:09:53 +0000 Subject: [BioRuby] Are the Bio* projects dying? In-Reply-To: <20130129084011.GA15860@thebird.nl> References: <20130129084011.GA15860@thebird.nl> Message-ID: On Tue, Jan 29, 2013 at 8:40 AM, Pjotr Prins wrote: > When I check the # of commits to BioRuby, BioPerl, BioPython, I notice > the projects are not very active (to put it mildly). ... What is your benchmark? What are you comparing them against? For Biopython we're getting pull requests from new contributors fairly regularly - although the list of new contributors for the Biopython 1.61 is inflated as it is a bit overdue compared to our normal release schedule: https://github.com/biopython/biopython/blob/master/NEWS > But, what does this really mean for the Bio* projects as a whole? What > happened to new blood? What should we do? Make more effort for Google Summer of Code across the Bio* projects for 2013 (although I thought BioRuby and Biopython did quite well last year)? That seems to have been a good way to get new blood. Some of the more senior contributors may be in a position to encourage or direct PhD students to look at contributing to relevant Bio* projects (or other science OSS projects). That seems a good idea to me at least. Regards, Peter P.S. Did you mean to send this just to the BioRuby list? If you want a cross project discussion perhaps open-bio-l would be better? http://lists.open-bio.org/mailman/listinfo/open-bio-l From pjotr.public14 at thebird.nl Tue Jan 1 12:19:07 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 1 Jan 2013 12:19:07 +0000 Subject: [BioRuby] t Message-ID: <20130101121907.GA15224@thebird.nl> Ten Simple Rules for the Open Development of Scientific Software by Andreas and James! http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002802 hear, hear! Pj. From ngoto at gen-info.osaka-u.ac.jp Thu Jan 3 14:21:37 2013 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Thu, 3 Jan 2013 23:21:37 +0900 Subject: [BioRuby] Removal of Bio::KEGG::API because the service discontinued Message-ID: <201301031428.r03ESJoU025001@portal.open-bio.org> Hi all, I'll remove Bio::KEGG::API in lib/bio/io/keggapi.rb and related contents. As already announced in the KEGG website (http://www.genome.jp/kegg/soap/), the SOAP API is discontinued in 2013/1/1 and the Bio::KEGG::API class no longer works. New version of KEGG API, which is based on REST, is already started. Users of old KEGG API should migrate to the new REST-based KEGG API. See http://www.kegg.jp/kegg/rest/ for more information. Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org From francesco.strozzi at gmail.com Sat Jan 12 22:33:48 2013 From: francesco.strozzi at gmail.com (Francesco Strozzi) Date: Sat, 12 Jan 2013 14:33:48 -0800 Subject: [BioRuby] PAG 2013 Message-ID: Hi, I'm at PAG conference in San Diego. Is there some BioRubyst or open-bio developer here? It would be interesting to meet with other attendees. Just mail me if you are around. Cheers -- Francesco From pjotr.public14 at thebird.nl Tue Jan 29 08:40:11 2013 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Tue, 29 Jan 2013 09:40:11 +0100 Subject: [BioRuby] Are the Bio* projects dying? Message-ID: <20130129084011.GA15860@thebird.nl> When I check the # of commits to BioRuby, BioPerl, BioPython, I notice the projects are not very active (to put it mildly). With BioRuby the # of downloads is still increasing - remember we hit 10K not that long ago, now we are at 35K. See http://biogems.info/ With Ruby/Biogems there is health, coming from some 10 regular committers. Ruby in Bioinformatics, going by downloads and citations, appears to be as healthy as ever. JRuby on the JVM may turn out to be a blessing for Ruby - especially if we can make our gems easily accessible to other JVM languages. But, what does this really mean for the Bio* projects as a whole? What happened to new blood? What should we do? Maybe it is merely my sense of disorientation and confusion in the face of an (apparently) meaningless and absurd world. Pj. From p.j.a.cock at googlemail.com Tue Jan 29 12:09:53 2013 From: p.j.a.cock at googlemail.com (Peter Cock) Date: Tue, 29 Jan 2013 12:09:53 +0000 Subject: [BioRuby] Are the Bio* projects dying? In-Reply-To: <20130129084011.GA15860@thebird.nl> References: <20130129084011.GA15860@thebird.nl> Message-ID: On Tue, Jan 29, 2013 at 8:40 AM, Pjotr Prins wrote: > When I check the # of commits to BioRuby, BioPerl, BioPython, I notice > the projects are not very active (to put it mildly). ... What is your benchmark? What are you comparing them against? For Biopython we're getting pull requests from new contributors fairly regularly - although the list of new contributors for the Biopython 1.61 is inflated as it is a bit overdue compared to our normal release schedule: https://github.com/biopython/biopython/blob/master/NEWS > But, what does this really mean for the Bio* projects as a whole? What > happened to new blood? What should we do? Make more effort for Google Summer of Code across the Bio* projects for 2013 (although I thought BioRuby and Biopython did quite well last year)? That seems to have been a good way to get new blood. Some of the more senior contributors may be in a position to encourage or direct PhD students to look at contributing to relevant Bio* projects (or other science OSS projects). That seems a good idea to me at least. Regards, Peter P.S. Did you mean to send this just to the BioRuby list? If you want a cross project discussion perhaps open-bio-l would be better? http://lists.open-bio.org/mailman/listinfo/open-bio-l