From thorne at cs.man.ac.uk Wed Jun 6 18:18:13 2007 From: thorne at cs.man.ac.uk (Dave Thorne) Date: Wed, 06 Jun 2007 23:18:13 +0100 Subject: [BioRuby] A couple of changes to DAS... Message-ID: <466732A5.3060802@cs.man.ac.uk> Good evening, I have just spent a successful couple of hours porting the latest bio/io/das.rb file to Python (their DAS support is rather meagre). During the process I found a couple of lines in the original ruby module that I think contain mistakes. I have attached an appropriate diff file. The two small changes are as follows: line 71: dsn.mapmaster = e.name should be (?): dsn.mapmaster = e.text line 97: segment.stop = e.attributes['orientation'] should be: segment.orientation = e.attributes['orientation'] I will leave it up to whomever has CVS/SVN access to commit these changes to the codebase. Also, for completeness (and in case anyone is interested) I've attached my python module file. Yours, Dave Thorne -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: das.rb.diff Url: http://lists.open-bio.org/pipermail/bioruby/attachments/20070606/7269ed24/attachment.pl From email2ants at gmail.com Thu Jun 7 05:18:56 2007 From: email2ants at gmail.com (Anthony Underwood) Date: Thu, 7 Jun 2007 10:18:56 +0100 Subject: [BioRuby] Neighbour Joining alogorithm Message-ID: Hi All, I have been using the ruby-cluster contribution (http://bioruby.org/ archive/contrib/ruby-cluster/) with some success. Does anybody know if there is a similar implementation for the neighbour-joining algorithm? Many thanks Anthony From email2ants at gmail.com Fri Jun 22 07:12:41 2007 From: email2ants at gmail.com (Anthony Underwood) Date: Fri, 22 Jun 2007 12:12:41 +0100 Subject: [BioRuby] ISMB and Bioinformatics Open Source Conference Message-ID: Hi BioRuby people. Just a quick message to ask if anyone is going to ISMB and particularly the Bioinformatics Open Source Conference. I would love to see BioRuby take off in a bigger way especially its integration with Ruby on Rails. I'm hoping to meet some of you and chat about it in Vienna. Please get in touch if you are heading over to ISMB next month. Anthony Dr Anthony Underwood Bioinformatics Unit | Statistics, Modelling and Bioinformatics Department Centre for Infections Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 3276466 f: 0208 3276738 e:anthony.underwood at hpa.org.uk From ktym at hgc.jp Wed Jun 27 01:42:16 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 27 Jun 2007 14:42:16 +0900 Subject: [BioRuby] ISMB and Bioinformatics Open Source Conference In-Reply-To: References: Message-ID: <4C93063A-395A-4250-87EA-133C54B46E76@hgc.jp> Hi Anthony, I'll have a presentation on "BioRuby project update" at BOSC2007 and will include how to use BioRuby with Rails. http://www.open-bio.org/wiki/BOSC_2007_Schedule I only stay during the BOSC in Vienna, so please contact me there. Regards, Toshiaki Katayama On 2007/06/22, at 20:12, Anthony Underwood wrote: > Hi BioRuby people. > > Just a quick message to ask if anyone is going to ISMB and > particularly the Bioinformatics Open Source Conference. I would love > to see BioRuby take off in a bigger way especially its integration > with Ruby on Rails. I'm hoping to meet some of you and chat about it > in Vienna. > > Please get in touch if you are heading over to ISMB next month. > > Anthony > > > > Dr Anthony Underwood > Bioinformatics Unit | Statistics, Modelling and Bioinformatics > Department > Centre for Infections > Health Protection Agency > 61 Colindale Avenue > London > NW9 5HT > t: 0208 3276466 f: 0208 3276738 e:anthony.underwood at hpa.org.uk > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From thorne at cs.man.ac.uk Wed Jun 6 22:18:13 2007 From: thorne at cs.man.ac.uk (Dave Thorne) Date: Wed, 06 Jun 2007 23:18:13 +0100 Subject: [BioRuby] A couple of changes to DAS... Message-ID: <466732A5.3060802@cs.man.ac.uk> Good evening, I have just spent a successful couple of hours porting the latest bio/io/das.rb file to Python (their DAS support is rather meagre). During the process I found a couple of lines in the original ruby module that I think contain mistakes. I have attached an appropriate diff file. The two small changes are as follows: line 71: dsn.mapmaster = e.name should be (?): dsn.mapmaster = e.text line 97: segment.stop = e.attributes['orientation'] should be: segment.orientation = e.attributes['orientation'] I will leave it up to whomever has CVS/SVN access to commit these changes to the codebase. Also, for completeness (and in case anyone is interested) I've attached my python module file. Yours, Dave Thorne -------------- next part -------------- An embedded and charset-unspecified text was scrubbed... Name: das.rb.diff URL: From email2ants at gmail.com Thu Jun 7 09:18:56 2007 From: email2ants at gmail.com (Anthony Underwood) Date: Thu, 7 Jun 2007 10:18:56 +0100 Subject: [BioRuby] Neighbour Joining alogorithm Message-ID: Hi All, I have been using the ruby-cluster contribution (http://bioruby.org/ archive/contrib/ruby-cluster/) with some success. Does anybody know if there is a similar implementation for the neighbour-joining algorithm? Many thanks Anthony From email2ants at gmail.com Fri Jun 22 11:12:41 2007 From: email2ants at gmail.com (Anthony Underwood) Date: Fri, 22 Jun 2007 12:12:41 +0100 Subject: [BioRuby] ISMB and Bioinformatics Open Source Conference Message-ID: Hi BioRuby people. Just a quick message to ask if anyone is going to ISMB and particularly the Bioinformatics Open Source Conference. I would love to see BioRuby take off in a bigger way especially its integration with Ruby on Rails. I'm hoping to meet some of you and chat about it in Vienna. Please get in touch if you are heading over to ISMB next month. Anthony Dr Anthony Underwood Bioinformatics Unit | Statistics, Modelling and Bioinformatics Department Centre for Infections Health Protection Agency 61 Colindale Avenue London NW9 5HT t: 0208 3276466 f: 0208 3276738 e:anthony.underwood at hpa.org.uk From ktym at hgc.jp Wed Jun 27 05:42:16 2007 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 27 Jun 2007 14:42:16 +0900 Subject: [BioRuby] ISMB and Bioinformatics Open Source Conference In-Reply-To: References: Message-ID: <4C93063A-395A-4250-87EA-133C54B46E76@hgc.jp> Hi Anthony, I'll have a presentation on "BioRuby project update" at BOSC2007 and will include how to use BioRuby with Rails. http://www.open-bio.org/wiki/BOSC_2007_Schedule I only stay during the BOSC in Vienna, so please contact me there. Regards, Toshiaki Katayama On 2007/06/22, at 20:12, Anthony Underwood wrote: > Hi BioRuby people. > > Just a quick message to ask if anyone is going to ISMB and > particularly the Bioinformatics Open Source Conference. I would love > to see BioRuby take off in a bigger way especially its integration > with Ruby on Rails. I'm hoping to meet some of you and chat about it > in Vienna. > > Please get in touch if you are heading over to ISMB next month. > > Anthony > > > > Dr Anthony Underwood > Bioinformatics Unit | Statistics, Modelling and Bioinformatics > Department > Centre for Infections > Health Protection Agency > 61 Colindale Avenue > London > NW9 5HT > t: 0208 3276466 f: 0208 3276738 e:anthony.underwood at hpa.org.uk > > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby