From jan.aerts at bbsrc.ac.uk Thu May 4 10:04:26 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 15:04:26 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, I've added a new module map.rb to the cvs repository that describes markers and maps (such as linkage maps, radiation hybrid maps and the sort): * Bio::Map::SimpleMap * Bio::Map::Marker * Bio::Map::Mapping * Bio::Map::ActsLikeMap * Bio::Map::ActsLikeMarker Two important design decisions were taken in writing these modules: (1) relationship map-mapping-marker: ------------------------------------ In an early implementation, Map objects could have a list of Marker objects associated with them. However, a single Marker object can also be mapped to different Maps. As a result, to check which maps have a certain marker in common, all markers of all maps would have to be screened. Therefore, to facilitate this many-to-many relationship complication, I decided to put a Mapping object in between Map and Marker. Such a Mapping object has three things associated with it: Map, Marker and location (which is a Bio::Location object). If a marker A is added to a map B, a Mapping object is created and added to both the @mappings array in marker A, _and_ the @mappings array in map B. (2) mixins ActsLikeMap and ActsLikeMarker: ------------------------------------------ Different things can be mapped to different things, or in other words: different things can act as markers or as maps. * can act as markers: ** a microsatellite: when it's mapped on a linkage group ** a clone: when it's mapped to the cytogenetic map (using FISH), or if it's included in the physical map (FPC) ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone ** ... * can act as maps: ** a linkage group ** a radiation hybrid map ** a clone: when it has a BAC end sequence associated with it ** ... As it is nonsense to create a Marker class and have all these different types of markers inherit from it (would a clone inherit from Bio::Marker, or from Bio::Map?), I created two modules that can be mixed in with any class: Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker. As a result, a Clone class (which doesn't exist yet) can include both, and have properties of a map _and_ a marker. Give it a go. PS: Thinking about what can act like a map or a marker: a sequence can essentially also be considered a map (we actually talk about it that way in our department), with for example BLAST hits (or any other feature with a location) that act as markers. The unit of the map is 'bp'. Jan Aerts, PhD Bioinformatics Group Roslin Institute Roslin, Scotland, UK +44 131 527 4200 ---------The obligatory disclaimer-------- The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From jan.aerts at bbsrc.ac.uk Thu May 4 11:02:19 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 16:02:19 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACD9@rie2ksrv1.ri.bbsrc.ac.uk> Damn. No unit tests yet... I guess I'll have to learn what they are... For the mean time, you can run 'ruby map.rb' to see it working. It _should_... jan. > -----Original Message----- > From: Moses M. Hohman [mailto:mmhohman at northwestern.edu] > Sent: 04 May 2006 15:59 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] new module map.rb > > Hi Jan, > > Cool, I'll check it out. Do you have any unit tests for this? > > Moses > > On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > > > Hi all, > > > > I've added a new module map.rb to the cvs repository that describes > > markers and maps (such as linkage maps, radiation hybrid > maps and the > > sort): > > * Bio::Map::SimpleMap > > * Bio::Map::Marker > > * Bio::Map::Mapping > > * Bio::Map::ActsLikeMap > > * Bio::Map::ActsLikeMarker > > > > Two important design decisions were taken in writing these modules: > > (1) relationship map-mapping-marker: > > ------------------------------------ > > In an early implementation, Map objects could have a list of Marker > > objects associated with them. However, a single Marker > object can also > > be mapped to different Maps. As a result, to check which > maps have a > > certain marker in common, all markers of all maps would have to be > > screened. Therefore, to facilitate this many-to-many relationship > > complication, I decided to put a Mapping object in between Map and > > Marker. Such a Mapping object has three things associated with it: > > Map, > > Marker and location (which is a Bio::Location object). > > If a marker A is added to a map B, a Mapping object is created and > > added to both the @mappings array in marker A, _and_ the @mappings > > array in map B. > > > > (2) mixins ActsLikeMap and ActsLikeMarker: > > ------------------------------------------ > > Different things can be mapped to different things, or in > other words: > > different things can act as markers or as maps. > > * can act as markers: > > ** a microsatellite: when it's mapped on a linkage group > > ** a clone: when it's mapped to the cytogenetic map (using > FISH), or > > if it's included in the physical map (FPC) > > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > > ** ... > > * can act as maps: > > ** a linkage group > > ** a radiation hybrid map > > ** a clone: when it has a BAC end sequence associated with it > > ** ... > > > > As it is nonsense to create a Marker class and have all these > > different types of markers inherit from it (would a clone > inherit from > > Bio::Marker, or from Bio::Map?), I created two modules that can be > > mixed in with any class: Bio::Map::ActsLikeMap and > > Bio::Map::ActsLikeMarker. > > As a result, a Clone class (which doesn't exist yet) can > include both, > > and have properties of a map _and_ a marker. > > > > Give it a go. > > > > PS: Thinking about what can act like a map or a marker: a > sequence can > > essentially also be considered a map (we actually talk > about it that > > way in our department), with for example BLAST hits (or any other > > feature with a location) that act as markers. The unit of > the map is > > 'bp'. > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any > > attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From jan.aerts at bbsrc.ac.uk Thu May 4 12:27:28 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 17:27:28 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACDB@rie2ksrv1.ri.bbsrc.ac.uk> Done. (Except a test to check positions of markers relative to each other on the same map) > -----Original Message----- > From: Moses M. Hohman [mailto:mmhohman at northwestern.edu] > Sent: 04 May 2006 15:59 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] new module map.rb > > Hi Jan, > > Cool, I'll check it out. Do you have any unit tests for this? > > Moses > > On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > > > Hi all, > > > > I've added a new module map.rb to the cvs repository that describes > > markers and maps (such as linkage maps, radiation hybrid > maps and the > > sort): > > * Bio::Map::SimpleMap > > * Bio::Map::Marker > > * Bio::Map::Mapping > > * Bio::Map::ActsLikeMap > > * Bio::Map::ActsLikeMarker > > > > Two important design decisions were taken in writing these modules: > > (1) relationship map-mapping-marker: > > ------------------------------------ > > In an early implementation, Map objects could have a list of Marker > > objects associated with them. However, a single Marker > object can also > > be mapped to different Maps. As a result, to check which > maps have a > > certain marker in common, all markers of all maps would have to be > > screened. Therefore, to facilitate this many-to-many relationship > > complication, I decided to put a Mapping object in between Map and > > Marker. Such a Mapping object has three things associated with it: > > Map, > > Marker and location (which is a Bio::Location object). > > If a marker A is added to a map B, a Mapping object is created and > > added to both the @mappings array in marker A, _and_ the @mappings > > array in map B. > > > > (2) mixins ActsLikeMap and ActsLikeMarker: > > ------------------------------------------ > > Different things can be mapped to different things, or in > other words: > > different things can act as markers or as maps. > > * can act as markers: > > ** a microsatellite: when it's mapped on a linkage group > > ** a clone: when it's mapped to the cytogenetic map (using > FISH), or > > if it's included in the physical map (FPC) > > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > > ** ... > > * can act as maps: > > ** a linkage group > > ** a radiation hybrid map > > ** a clone: when it has a BAC end sequence associated with it > > ** ... > > > > As it is nonsense to create a Marker class and have all these > > different types of markers inherit from it (would a clone > inherit from > > Bio::Marker, or from Bio::Map?), I created two modules that can be > > mixed in with any class: Bio::Map::ActsLikeMap and > > Bio::Map::ActsLikeMarker. > > As a result, a Clone class (which doesn't exist yet) can > include both, > > and have properties of a map _and_ a marker. > > > > Give it a go. > > > > PS: Thinking about what can act like a map or a marker: a > sequence can > > essentially also be considered a map (we actually talk > about it that > > way in our department), with for example BLAST hits (or any other > > feature with a location) that act as markers. The unit of > the map is > > 'bp'. > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any > > attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From mmhohman at northwestern.edu Thu May 4 10:59:27 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Thu, 4 May 2006 10:59:27 -0400 Subject: [BioRuby] new module map.rb In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <2479663B-0D0D-4665-9561-7D16C7D22411@northwestern.edu> Hi Jan, Cool, I'll check it out. Do you have any unit tests for this? Moses On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > Hi all, > > I've added a new module map.rb to the cvs repository that describes > markers and maps (such as linkage maps, radiation hybrid maps and the > sort): > * Bio::Map::SimpleMap > * Bio::Map::Marker > * Bio::Map::Mapping > * Bio::Map::ActsLikeMap > * Bio::Map::ActsLikeMarker > > Two important design decisions were taken in writing these modules: > (1) relationship map-mapping-marker: > ------------------------------------ > In an early implementation, Map objects could have a list of Marker > objects associated with them. However, a single Marker object can also > be mapped to different Maps. As a result, to check which maps have a > certain marker in common, all markers of all maps would have to be > screened. Therefore, to facilitate this many-to-many relationship > complication, I decided to put a Mapping object in between Map and > Marker. Such a Mapping object has three things associated with it: > Map, > Marker and location (which is a Bio::Location object). > If a marker A is added to a map B, a Mapping object is created and > added > to both the @mappings array in marker A, _and_ the @mappings array in > map B. > > (2) mixins ActsLikeMap and ActsLikeMarker: > ------------------------------------------ > Different things can be mapped to different things, or in other words: > different things can act as markers or as maps. > * can act as markers: > ** a microsatellite: when it's mapped on a linkage group > ** a clone: when it's mapped to the cytogenetic map (using FISH), > or if > it's included in the physical map (FPC) > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > ** ... > * can act as maps: > ** a linkage group > ** a radiation hybrid map > ** a clone: when it has a BAC end sequence associated with it > ** ... > > As it is nonsense to create a Marker class and have all these > different > types of markers inherit from it (would a clone inherit from > Bio::Marker, or from Bio::Map?), I created two modules that can be > mixed > in with any class: Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker. > As a result, a Clone class (which doesn't exist yet) can include both, > and have properties of a map _and_ a marker. > > Give it a go. > > PS: Thinking about what can act like a map or a marker: a sequence can > essentially also be considered a map (we actually talk about it > that way > in our department), with for example BLAST hits (or any other feature > with a location) that act as markers. The unit of the map is 'bp'. > > Jan Aerts, PhD > Bioinformatics Group > Roslin Institute > Roslin, Scotland, UK > +44 131 527 4200 > > ---------The obligatory disclaimer-------- > The information contained in this e-mail (including any > attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at bbsrc.ac.uk Tue May 9 06:42:12 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Tue, 9 May 2006 11:42:12 +0100 Subject: [BioRuby] soap functional test fails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, The functional test soap_wsdl.rb fails here. Probably has something to do with our proxy. The environment variable HTTP_PROXY is set correctly. my_server>ruby ./test_soapwsdl.rb Loaded suite ./test_soapwsdl Started /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired (Timeout::Error) from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' from /usr/lib/ruby/1.8/net/http.rb:418:in `start' from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' ... 20 levels... from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' from /usr/lib/ruby/1.8/test/unit.rb:285 from /usr/lib/ruby/1.8/test/unit.rb:283 Many thanks, Jan Aerts, PhD Bioinformatics Group Roslin Institute Roslin, Scotland, UK +44 131 527 4200 ---------The obligatory disclaimer-------- The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From jan.aerts at bbsrc.ac.uk Tue May 9 14:22:18 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Tue, 9 May 2006 19:22:18 +0100 Subject: [BioRuby] combination bioruby and rails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. Anyone know of any bioruby/rails implementations? jan. From lavi.kfir at gmail.com Tue May 9 13:18:53 2006 From: lavi.kfir at gmail.com (Kfir Lavi) Date: Tue, 9 May 2006 19:18:53 +0200 Subject: [BioRuby] Best way to do homology search Message-ID: Hi, I have sql database with table of dna sequences. I would like to do homology search on the table. A user enter a sequence and the return is sequences with the percentage of similarity. Is there a simple function to use or I have to put some code together? I have read the Tutorial.rd but need more help. Thanks, Kfir From mmhohman at northwestern.edu Tue May 9 15:24:47 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Tue, 9 May 2006 14:24:47 -0500 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <8FA3D042-8C1F-41E2-B090-1C6370EAD140@northwestern.edu> So, I actually, for fun, took a look at this a couple months ago. I dropped it because I wasn't sure how well-maintained/in-use BioSQL was. Is it something actively used? If so, I'd be happy to help with this. Moses On May 9, 2006, at 1:22 PM, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that > there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based > database with a rails interface? A feature of the web-interface > could then be that sequences would be displayed graphically (with > features annotated; using SVG?), and that the user could run remote > BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue May 9 16:38:15 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 05:38:15 +0900 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> Hi Jan, There will be many possibilities if BioRuby is used with Rails (especially with ActiveRecord). The GFF database (which is used as a backend of GBrowse) loaded by the bp_load_gff.pl command in BioPerl is also a candidate in addition to the BioSQL. There are some related efforts have been made, as far as I know. * Nakao-san developed a Ensembl (Vega?) accessing module with ActiveRecord * Nikaido-san posted a short Japanese tutorial to build a gene expression database viewer with Rails in his weblog. * Ichinose-san created AJAX interface for BioRuby (and BioRuby shell) The point would be, what kind of integration (or how tightly) is ideal, if we integrate Rails *in* BioRuby. As for the Rails module in bio/shell, it is not finished but can be used in the following way for now: 1. start the bioruby shell in terminal1 and issue 'web' command terminal1% bioruby foo bioruby> web Copying web server files ... done DRb::DRbConnError: druby://localhost:81064 - # quit 2. open another terminal and start the server terminal2% cd foo terminal2% ruby script/server druby://localhost:81064 starting ... => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options the rails (webrick httpd) server will start. 3. Switch back to terminal1 and restart bioruby session. terminal1% bioruby foo bioruby> web Connected to server druby://localhost:81064 Open http://localhost:3000/shell/ 4. open http://localhost:3000/shell/ in your web browser the BioRuby logo and the message "Connected!" will be displayed. 5. then create some objects in the bioruby shell. bioruby> x = 123 bioruby> na = seq("atgcatgcatgc") bioruby> aa = na.translate then reload your browser and variables will be listed. By click on the variable, you may see the contents of the variable in Rails. This feature is a experimental implementation and I'm not clear what the goal would be. Do you want to call methods of the object in web interface? All objects should be stored by ActiveRecord? What kind of visualization is desired? Toshiaki On 2006/05/10, at 3:22, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue May 9 15:38:45 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 04:38:45 +0900 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <0EDE8435-EFA2-44EE-81B3-D33DE31E715B@hgc.jp> Hi Jan, There will be many possibilities if BioRuby is used with Rails (especially with ActiveRecord). The GFF database (which is used as a backend of GBrowse) loaded by the bp_load_gff.pl command in BioPerl is also a candidate in addition to the BioSQL. There are some related efforts have been made, as far as I know. * Nakao-san developed a Ensembl (Vega?) accessing module with ActiveRecord * Nikaido-san posted a short Japanese tutorial to build a gene expression database viewer with Rails in his weblog. * Ichinose-san created AJAX interface for BioRuby (and BioRuby shell) The point would be, what kind of integration (or how tightly) is ideal, if we integrate Rails *in* BioRuby. As for the Rails module in bio/shell, it is not finished but can be used in the following way for now: 1. start the bioruby shell in terminal1 and issue 'web' command terminal1% bioruby foo bioruby> web Copying web server files ... done DRb::DRbConnError: druby://localhost:81064 - # quit 2. open another terminal and start the server terminal2% cd foo terminal2% ruby script/server druby://localhost:81064 starting ... => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options the rails (webrick httpd) server will start. 3. Switch back to terminal1 and restart bioruby session. terminal1% bioruby foo bioruby> web Connected to server druby://localhost:81064 Open http://localhost:3000/shell/ 4. open http://localhost:3000/shell/ in your web browser the BioRuby logo and the message "Connected!" will be displayed. 5. then create some objects in the bioruby shell. bioruby> x = 123 bioruby> na = seq("atgcatgcatgc") bioruby> aa = na.translate then reload your browser and variables will be listed. By click on the variable, you may see the contents of the variable in Rails. This feature is a experimental implementation and I'm not clear what the goal would be. Do you want to call methods of the object in web interface? All objects should be stored by ActiveRecord? What kind of visualization is desired? Toshiaki On 2006/05/10, at 3:22, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Tue May 9 16:51:26 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Tue, 9 May 2006 15:51:26 -0500 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> Message-ID: <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> On May 9, 2006, at 3:38 PM, Toshiaki Katayama wrote: > The point would be, what kind of integration (or how tightly) is > ideal, if we integrate Rails *in* BioRuby. > My vote would be to keep any code that integrated both rails and bioruby as a separate module, so that bioruby won't depend on any rails components. Moses From k at bioruby.org Tue May 9 16:37:14 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Wed, 10 May 2006 05:37:14 +0900 Subject: [BioRuby] Best way to do homology search In-Reply-To: References: Message-ID: Hi, On 2006/05/10, at 2:18, Kfir Lavi wrote: > Hi, > I have sql database with table of dna sequences. > I would like to do homology search on the table. How do you plan to execute homology search against SQL database? BioRuby can parse the result of BLAST, FASTA etc. commands and these are usually performed for the FASTA formated sequence file. I think some of these programs support to run against SQL database directly, but I have never tried by myself. If the result formats are same in both way (flatfile DB and sql DB), you can use BioRuby parser to extract % similarity. Toshiaki > A user enter a sequence and the return is sequences with the > percentage of similarity. > Is there a simple function to use or I have to put some code together? > I have read the Tutorial.rd but need more help. > > Thanks, > Kfir > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue May 9 14:46:21 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 03:46:21 +0900 Subject: [BioRuby] soap functional test fails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Jan, Have you also set the environmental variable 'soap_use_proxy'? I think Ruby's SOAP library checks its value in addition to the HTTP_PROXY. Please see the RDoc documentation in bio/io/soapwsdl.rb file. Toshiaki On 2006/05/09, at 19:42, jan aerts (RI) wrote: > Hi all, > > The functional test soap_wsdl.rb fails here. Probably has something to > do with our proxy. The environment variable HTTP_PROXY is set correctly. > > my_server>ruby ./test_soapwsdl.rb > Loaded suite ./test_soapwsdl > Started > /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired > (Timeout::Error) > from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' > from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' > from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' > from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' > from /usr/lib/ruby/1.8/net/http.rb:418:in `start' > from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' > ... 20 levels... > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' > from /usr/lib/ruby/1.8/test/unit.rb:285 > from /usr/lib/ruby/1.8/test/unit.rb:283 > > Many thanks, > > Jan Aerts, PhD > Bioinformatics Group > Roslin Institute > Roslin, Scotland, UK > +44 131 527 4200 > > ---------The obligatory disclaimer-------- > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From k at bioruby.org Tue May 9 17:34:01 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Wed, 10 May 2006 06:34:01 +0900 Subject: [BioRuby] Fwd: O'Reilly UG Program News: DSUG Discount Changes References: Message-ID: <316D5374-AD88-4372-90EA-1FAFAC36487A@bioruby.org> We have the following offer from O'Reilly to the BioRuby user group. Toshiaki Begin forwarded message: > From: "Marsee Henon" > Date: 2006?5?4? 4:16:34:JST > To: k at bioruby.org > Subject: O'Reilly UG Program News: DSUG Discount Changes > > Hello, > > Can you please let your members know about the increase in our user > group discount? You can post this to your mailing list, web site, or in > your newsletter and please make sure you mention this at your next > meeting. > > Get 30% off a single book or 35% off two or more books from O'Reilly, No > Starch, Paraglyph, PC Publishing, Pragmatic Bookshelf, SitePoint, or > Syngress books you purchase directly from O'Reilly. Just use code DSUG > when ordering online or by phone 800-998-9938. Free ground shipping on > orders $29.95 or more in the US. > > > Other benefits you receive when you buy directly from O'Reilly include: > > *100% Satisfaction Guarantee* > If, for any reason, you're not completely satisfied with your purchase, > return it to us and get your money back. A return shipping label is > included with every direct purchase, and directions are posted online in > case you've misplaced it: > . > > *Safari Enabled* > Whenever possible, our books are "Safari Enabled." This means you can > access your book for free online for 45 days through the O'Reilly Safari > Bookshelf. How do you know if your book is Safari Enabled? Turn your > book over and look for the "Safari Enabled" logo on the bottom right of > the page. If it's there, flip through the last couple pages of your book > until you find directions for accessing your book online. > > *Booktech* > Have a question about your book? O'Reilly is the only publisher that > offers tech support for books. Send an email to > and we'll help you out. Be specific: Include > the book title and page number. It's also a good idea to include the > ISBN so we know what edition you have. > > *Reader Reviews* > Our reader reviews are read by most people at O'Reilly, including Tim > O'Reilly, all our editors, as well as sales, marketing, and PR. So if > you have praise, a gripe, or ideas for improvement, writing a reader > review on oreilly.com is a sure way for your voice to be heard. Just go > to your book's catalog page on oreilly.com and click the "Write a > Review" button. > > *Book Registration* > Register your book online and we'll notify you when the book has been > updated or a new edition is available. You can also win books and other > prizes. Haven't registered your books? Just go to > . > > *Newsletters* > Our newsletters keep you updated on the latest articles, books, news, > and events. A complete list of newsletters and lists can be found at > . > > We're working on a slew of additional benefits to serve you even better > so stay tuned. > > As always, thanks for your help spreading the word. > > Marsee Henon > > ================================================================ > O'Reilly > 1005 Gravenstein Highway North > Sebastopol, CA 95472 > http://ug.oreilly.com/ http://ug.oreilly.com/creativemedia/ > ================================================================ From jan.aerts at bbsrc.ac.uk Thu May 11 04:15:50 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 11 May 2006 09:15:50 +0100 Subject: [BioRuby] soap functional test fails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD0A@rie2ksrv1.ri.bbsrc.ac.uk> That did the trick. Thanks. > -----Original Message----- > From: Toshiaki Katayama [mailto:ktym at hgc.jp] > Sent: 09 May 2006 19:46 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] soap functional test fails > > Hi Jan, > > Have you also set the environmental variable 'soap_use_proxy'? > I think Ruby's SOAP library checks its value in addition to > the HTTP_PROXY. > Please see the RDoc documentation in bio/io/soapwsdl.rb file. > > Toshiaki > > On 2006/05/09, at 19:42, jan aerts (RI) wrote: > > > Hi all, > > > > The functional test soap_wsdl.rb fails here. Probably has > something to > > do with our proxy. The environment variable HTTP_PROXY is > set correctly. > > > > my_server>ruby ./test_soapwsdl.rb > > Loaded suite ./test_soapwsdl > > Started > > /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired > > (Timeout::Error) > > from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' > > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' > > from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' > > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' > > from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' > > from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' > > from /usr/lib/ruby/1.8/net/http.rb:418:in `start' > > from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' > > ... 20 levels... > > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' > > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' > > from /usr/lib/ruby/1.8/test/unit.rb:285 > > from /usr/lib/ruby/1.8/test/unit.rb:283 > > > > Many thanks, > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From lavi.kfir at gmail.com Thu May 11 04:16:12 2006 From: lavi.kfir at gmail.com (Kfir Lavi) Date: Thu, 11 May 2006 10:16:12 +0200 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> Message-ID: In other words, we need to write plugin for rails that make calls to the bioruby library. We first have to think of uses for the library on rails. This will make us understand the requierments for the plugin. I'm currently building web site with rubyonrails to disply reserch genomic data. And now I'm at a point of implementing searches on the internal database and on internet open databases. On the internal database I want to implement homology search. Any suggestions of building small interface will be appriciated. Regards, Kfir On 5/9/06, Moses M. Hohman wrote: > > On May 9, 2006, at 3:38 PM, Toshiaki Katayama wrote: > > > The point would be, what kind of integration (or how tightly) is > > ideal, if we integrate Rails *in* BioRuby. > > > > My vote would be to keep any code that integrated both rails and > bioruby as a separate module, so that bioruby won't depend on any > rails components. > > Moses > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at bbsrc.ac.uk Thu May 11 05:38:56 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 11 May 2006 10:38:56 +0100 Subject: [BioRuby] combination bioruby and rails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD0B@rie2ksrv1.ri.bbsrc.ac.uk> Hi Toshiaki, I've tried the approach you mentioned below yesterday, but still bump into that problem. Apparently, it has something to do with my setup of rails: when you run 'ruby script/server' in rails, the first line sent back to the screen is 'druby://localhost:81064'. When I do the same thing, the first line to screen is '=> Booting WEBrick...'. I haven't figured out yet how to solve that. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Toshiaki Katayama > Sent: 09 May 2006 21:38 > To: BioRuby ML Discussion List Project > Subject: Re: [BioRuby] combination bioruby and rails > <> > As for the Rails module in bio/shell, it is not finished but > can be used in the following way for now: > > 1. start the bioruby shell in terminal1 and issue 'web' command > > terminal1% bioruby foo > bioruby> web > Copying web server files ... done > DRb::DRbConnError: druby://localhost:81064 - > # > (my intention is to make this command will take care of > following steps automatically, however,) you may see the > DRb::DRbConnError message here, then quit. > > bioruby> quit > > 2. open another terminal and start the server > > terminal2% cd foo > terminal2% ruby script/server > druby://localhost:81064 > starting ... > => Booting WEBrick... > => Rails application started on http://0.0.0.0:3000 > => Ctrl-C to shutdown server; call with --help for options > > the rails (webrick httpd) server will start. > > 3. Switch back to terminal1 and restart bioruby session. > > terminal1% bioruby foo > bioruby> web > Connected to server druby://localhost:81064 > Open http://localhost:3000/shell/ > > 4. open http://localhost:3000/shell/ in your web browser > > the BioRuby logo and the message "Connected!" will be displayed. > <> From pjotr2006 at thebird.nl Tue May 23 15:50:44 2006 From: pjotr2006 at thebird.nl (Pjotr Prins) Date: Tue, 23 May 2006 21:50:44 +0200 Subject: [BioRuby] BOSC abstract due Message-ID: <20060523195044.GA29635@thebird.nl> Has anyone put in a paper for BOSC? http://www.open-bio.org/boscblog/ If not, we ought to do it. Jan are you interested? Otherwise I can give it a shot. Pj. From jan.aerts at bbsrc.ac.uk Wed May 24 11:25:12 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Wed, 24 May 2006 16:25:12 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> I'm afraid I'll have to pass on this. As someone who only started looking at ruby 5 months ago (let alone bioruby), I'm not familiar enough yet with the more advanced uses of ruby/bioruby. It's not difficult to explain the simple stuff ("It can read FASTA files", "It can run BLASTs"), but it would be interesting for the audience to give examples of advanced applications that are nevertheless (relatively) easy to do. I'm thinking integration with rails here, for example. Does anyone have other tools in mind that can be easily combined with bioruby? Something else that would be interesting: show how easy it is to add methods to existing bioruby objects, or alter them if you want them to behave differently. So back to you, Pjotr. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Pjotr Prins > Sent: 23 May 2006 20:51 > To: Toshiaki Katayama > Cc: BioRuby ML Discussion List Project > Subject: [BioRuby] BOSC abstract due > > Has anyone put in a paper for BOSC? > > http://www.open-bio.org/boscblog/ > > If not, we ought to do it. Jan are you interested? Otherwise > I can give it a shot. > > Pj. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr2006 at thebird.nl Wed May 24 13:13:28 2006 From: pjotr2006 at thebird.nl (Pjotr Prins) Date: Wed, 24 May 2006 19:13:28 +0200 Subject: [BioRuby] BOSC abstract due In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <20060524171328.GA5280@thebird.nl> Ah, there is that. Rails would be interesting for BOSC. Combination with BioRuby would be cool. I gather no one has put in an abstract? I suppose I can do it... Pj. On Wed, May 24, 2006 at 04:25:12PM +0100, jan aerts (RI) wrote: > I'm afraid I'll have to pass on this. As someone who only started > looking at ruby 5 months ago (let alone bioruby), I'm not familiar > enough yet with the more advanced uses of ruby/bioruby. > > It's not difficult to explain the simple stuff ("It can read FASTA > files", "It can run BLASTs"), but it would be interesting for the > audience to give examples of advanced applications that are nevertheless > (relatively) easy to do. I'm thinking integration with rails here, for > example. Does anyone have other tools in mind that can be easily > combined with bioruby? > Something else that would be interesting: show how easy it is to add > methods to existing bioruby objects, or alter them if you want them to > behave differently. > > So back to you, Pjotr. > > j. > > > -----Original Message----- > > From: bioruby-bounces at lists.open-bio.org > > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Pjotr Prins > > Sent: 23 May 2006 20:51 > > To: Toshiaki Katayama > > Cc: BioRuby ML Discussion List Project > > Subject: [BioRuby] BOSC abstract due > > > > Has anyone put in a paper for BOSC? > > > > http://www.open-bio.org/boscblog/ > > > > If not, we ought to do it. Jan are you interested? Otherwise > > I can give it a shot. > > > > Pj. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From isaacpei at gmail.com Wed May 24 22:13:49 2006 From: isaacpei at gmail.com (Isaac Xin Pei) Date: Wed, 24 May 2006 22:13:49 -0400 Subject: [BioRuby] bioruby development process / real life usage / visions? Message-ID: Dear All, I am very curious of the development process of bioruby, especially what the vision for bioruby project among the open bio projects? According to my understanding, - bioperl has the largest users community due to the history reason, rather than the languate itself - biopython solved the OOP issue in bioperl, and I like the language itself however, the biopython project in particular seems to have a rather loose developing process I am just not sure if I decide to pick it for everyday usage / long term programming project, it will help - bioruby: the library/class seems comprehensive the codes looks very clean first impression of programming using bioruby is that it does follow KISS principle : yet questions - the devloping process - does it have a large user community (or a large community/bioinformatics/biologists in Japan?) - the vision of the project? sorry for so many questions. in my research I have come to the point to using a programming language to investigage possible hypothesis in the genome, as well as a programming language to ease everyday bench work design ... hope to get some insights from you thanks! -- Best , Isaac - "A word fitly spoken Is like apples of gold in network of silver. " Proverbs 25:11 From k at bioruby.org Thu May 25 22:19:13 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Fri, 26 May 2006 11:19:13 +0900 Subject: [BioRuby] BOSC abstract due In-Reply-To: References: <20060523195044.GA29635@thebird.nl> Message-ID: <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> > If you could have another talk on integration of Rails or > some typical/impressive applications using BioRuby, > it would be very nice. and/or on your English documentation efforts - progress of the documentation is one of the most important point of our development in the past year, including launch of the bioruby-doc.org. Thanks, Toshiaki From k at bioruby.org Thu May 25 22:13:35 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Fri, 26 May 2006 11:13:35 +0900 Subject: [BioRuby] BOSC abstract due In-Reply-To: <20060523195044.GA29635@thebird.nl> References: <20060523195044.GA29635@thebird.nl> Message-ID: On 2006/05/24, at 4:50, Pjotr Prins wrote: > Has anyone put in a paper for BOSC? > > http://www.open-bio.org/boscblog/ Not yet, but I will. My topic would be focused on * release of BioRuby 1.1 - overview, updates and enhancements * BioRuby shell - as a CUI - as a 'Bio::Perl'-like module If you could have another talk on integration of Rails or some typical/impressive applications using BioRuby, it would be very nice. Other Bio* projects sometimes presented several talks in the past BOSC meeting, so if we could have two or more talks/lightnings this year, it may imply expansion of our community. Toshiaki > If not, we ought to do it. Jan are you interested? Otherwise I can > give it a shot. > > Pj. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From trevor at corevx.com Thu May 25 23:12:14 2006 From: trevor at corevx.com (Trevor Wennblom) Date: Thu, 25 May 2006 22:12:14 -0500 Subject: [BioRuby] BOSC abstract due In-Reply-To: <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> References: <20060523195044.GA29635@thebird.nl> <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> Message-ID: <4476720E.3010206@corevx.com> Toshiaki Katayama wrote: > of our development in the past year, > including launch of the bioruby-doc.org. > I suppose I should update that. ;) I'll get on that ASAP. Trevor From jan.aerts at bbsrc.ac.uk Fri May 26 03:37:16 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Fri, 26 May 2006 08:37:16 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> I _completely_ agree with Toshiaki's suggestion: bioruby would benefit most by having more people using it. That means that impressive but easy-to-do examples are key. Before the meeting and to be able to realize/demonstrate those examples, some things have to be done: * getting some bugs out (e.g. the proxy-problem for users behind proxy's...) * more documentation: ** of the classes themselves: I'm trying to do one or two every week, but start bumping into those that I have no idea about what they do or how they work. Therefore, we'll need people to document those as well (or have elaborate examples, so I can figure out what they do.) ** although bioruby in anger is very usefull, users would probably benefit from more elaborate examples as well (including the impressive ones). First thing I actually always do when using BioPerl, is check out the HOWTO's. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Toshiaki Katayama > Sent: 26 May 2006 03:14 > To: BioRuby ML Discussion List Project > Subject: Re: [BioRuby] BOSC abstract due > > If you could have another talk on integration of Rails or > some typical/impressive applications using BioRuby, it would > be very nice. > > Other Bio* projects sometimes presented several talks in the > past BOSC meeting, so if we could have two or more > talks/lightnings this year, it may imply expansion of our community. From jan.aerts at bbsrc.ac.uk Fri May 26 03:58:37 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Fri, 26 May 2006 08:58:37 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD80@rie2ksrv1.ri.bbsrc.ac.uk> All, Something I didn't mention in the other post: it might be important that users have a feeling of what lives within the bioruby group, i.e. what the developers and big users are musing about. That might help them to: * understand the history of how things are built * give them an idea of what might be coming up in bioruby * get and idea on ways that bioruby can be used * gives them the feeling that something is going on An example of the third point above: I just bumped into ActiveRDF, and am wondering if that could be used sensibly with bioruby. If that turns out to be true, it might be interesting for other people using bioruby as well. Even if no actual classes would have to be written (which would mean that there would be little documentation for this bioruby/activeRDF combination). Would a blog be too far-fetched or cumbersome? (Sorry: just thinking out loud. (Which actually might be a good thing.)) Jan, the-pondering-one > -----Original Message----- > From: jan aerts (RI) > Sent: 26 May 2006 08:37 > To: 'Toshiaki Katayama'; BioRuby ML Discussion List Project > Subject: RE: [BioRuby] BOSC abstract due > > I _completely_ agree with Toshiaki's suggestion: bioruby > would benefit most by having more people using it. That means > that impressive but easy-to-do examples are key. > > Before the meeting and to be able to realize/demonstrate > those examples, some things have to be done: > * getting some bugs out (e.g. the proxy-problem for users > behind proxy's...) > * more documentation: > ** of the classes themselves: I'm trying to do one or two > every week, but start bumping into those that I have no idea > about what they do or how they work. Therefore, we'll need > people to document those as well (or have elaborate examples, > so I can figure out what they do.) > ** although bioruby in anger is very usefull, users would > probably benefit from more elaborate examples as well > (including the impressive ones). First thing I actually > always do when using BioPerl, is check out the HOWTO's. > > j. > > > -----Original Message----- > > From: bioruby-bounces at lists.open-bio.org > > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Toshiaki > > Katayama > > Sent: 26 May 2006 03:14 > > To: BioRuby ML Discussion List Project > > Subject: Re: [BioRuby] BOSC abstract due > > > > If you could have another talk on integration of Rails or some > > typical/impressive applications using BioRuby, it would be > very nice. > > > > Other Bio* projects sometimes presented several talks in > the past BOSC > > meeting, so if we could have two or more talks/lightnings > this year, > > it may imply expansion of our community. > From ktym at hgc.jp Thu May 25 22:39:45 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 26 May 2006 11:39:45 +0900 Subject: [BioRuby] bioruby development process / real life usage / visions? In-Reply-To: References: Message-ID: <6551781B-CAEA-41C8-AE50-FE0F5F39D2F2@hgc.jp> On 2006/05/25, at 11:13, Isaac Xin Pei wrote: > Dear All, > > I am very curious of the development process of bioruby, especially what the > vision for bioruby project among the open bio projects? > According to my understanding, > > - bioperl has the largest users community due to the history reason, rather > than the languate itself > > - biopython solved the OOP issue in bioperl, and I like the language itself > however, the biopython project in particular seems to have a rather loose > developing process > I am just not sure if I decide to pick it for everyday usage / long term > programming project, it will help > > - bioruby: > the library/class seems comprehensive > the codes looks very clean > first impression of programming using bioruby is that it does follow KISS > principle > : yet questions > - the devloping process What do you mean? We have a CVS repository on open-bio.org as well as the other projects and contributions or enhancements discussed in this mailing list will be accepted to the repository by core developers. We also have a documentation on the development guideline: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/README.DEV?rev=1.10&cvsroot=bioruby&content-type=text/vnd.viewcvs-markup > - does it have a large user community (or a large > community/bioinformatics/biologists in Japan?) I suspect there are >300 users in the world from the download counts in apache's log. (maybe half of them are in Japan) and the number is steadily increasing even the actual number might still be smaller than other projects. We can't count users of Linux or BSD-like distribution having BioRuby bundled. The number of the developer is about 10, and the number of core developers are around 5. I had BioRuby tutorials and hands-on seminars in Japan for several years. > - the vision of the project? Now we are forcusing on - to expand user community - adding documentations and unit tests - to enhance ability of the BioRuby library - web services - post-genomic analysis - cheminformatics - integration with Rails > sorry for so many questions. > > in my research I have come to the point to using a programming language to > investigage possible hypothesis in the genome, as well as a programming > language to ease everyday bench work design ... If you are not sure, you should try some of the above libraries to choose your favorite. If you choose BioRuby after the consideration, could you let us know what point of the BioRuby you feel better or worse than other project. :) > hope to get some insights from you > > thanks! > > > > -- > > Best , Isaac > > - "A word fitly spoken Is like apples of gold in network of > silver. " Proverbs 25:11 > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Toshiaki Katayama -- Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan tel://+81-3-5449-5614, fax://+81-3-5449-5434 BioRuby project http://bioruby.org/ GenomeNet/KEGG http://www.genome.jp/ Human Genome Center http://www.hgc.jp/ From mmhohman at northwestern.edu Sat May 27 00:05:49 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Sat, 27 May 2006 00:05:49 -0400 Subject: [BioRuby] BOSC abstract due In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Jan, On May 26, 2006, at 3:37 AM, jan aerts (RI) wrote: > Before the meeting and to be able to realize/demonstrate those > examples, > some things have to be done: > * getting some bugs out (e.g. the proxy-problem for users behind > proxy's...) > * more documentation: > ** of the classes themselves: I'm trying to do one or two every week, > but start bumping into those that I have no idea about what they do or > how they work. Therefore, we'll need people to document those as well > (or have elaborate examples, so I can figure out what they do.) I'd be happy to help with the documentation effort if you'd like. Is there a way to let each other know which we're working on? Who's working on the proxy problem? Moses From trevor at corevx.com Sun May 28 23:15:33 2006 From: trevor at corevx.com (Trevor Wennblom) Date: Sun, 28 May 2006 22:15:33 -0500 Subject: [BioRuby] rcov - Test coverage Message-ID: <447A6755.9000400@corevx.com> Lately I've found rcov ( http://eigenclass.org/hiki.rb?rcov ) to be very useful in several of my other projects. In brief, rcov shows what parts of the code is actually tested. I went ahead and ran it on BioRuby and was pleased with the results. I've made them available here: http://bioruby-doc.org/coverage/ The command used to generate this report was "rcov runner.rb --replace-progname" from the test directory. On a related topic I've lately become fond of the project management software Trac ( http://www.edgewall.com/trac/ ). I think many of it's features would be incredibly useful to our project. I'm sure we could assist our friends at OpenBio with setting up a Trac installation if they don't already have this on their server. The only real complication involved would be upgrading our current CVSystem to Subversion. Does anyone have any strong feelings either way about this? Thanks, Trevor From jan.aerts at bbsrc.ac.uk Thu May 4 14:04:26 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 15:04:26 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, I've added a new module map.rb to the cvs repository that describes markers and maps (such as linkage maps, radiation hybrid maps and the sort): * Bio::Map::SimpleMap * Bio::Map::Marker * Bio::Map::Mapping * Bio::Map::ActsLikeMap * Bio::Map::ActsLikeMarker Two important design decisions were taken in writing these modules: (1) relationship map-mapping-marker: ------------------------------------ In an early implementation, Map objects could have a list of Marker objects associated with them. However, a single Marker object can also be mapped to different Maps. As a result, to check which maps have a certain marker in common, all markers of all maps would have to be screened. Therefore, to facilitate this many-to-many relationship complication, I decided to put a Mapping object in between Map and Marker. Such a Mapping object has three things associated with it: Map, Marker and location (which is a Bio::Location object). If a marker A is added to a map B, a Mapping object is created and added to both the @mappings array in marker A, _and_ the @mappings array in map B. (2) mixins ActsLikeMap and ActsLikeMarker: ------------------------------------------ Different things can be mapped to different things, or in other words: different things can act as markers or as maps. * can act as markers: ** a microsatellite: when it's mapped on a linkage group ** a clone: when it's mapped to the cytogenetic map (using FISH), or if it's included in the physical map (FPC) ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone ** ... * can act as maps: ** a linkage group ** a radiation hybrid map ** a clone: when it has a BAC end sequence associated with it ** ... As it is nonsense to create a Marker class and have all these different types of markers inherit from it (would a clone inherit from Bio::Marker, or from Bio::Map?), I created two modules that can be mixed in with any class: Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker. As a result, a Clone class (which doesn't exist yet) can include both, and have properties of a map _and_ a marker. Give it a go. PS: Thinking about what can act like a map or a marker: a sequence can essentially also be considered a map (we actually talk about it that way in our department), with for example BLAST hits (or any other feature with a location) that act as markers. The unit of the map is 'bp'. Jan Aerts, PhD Bioinformatics Group Roslin Institute Roslin, Scotland, UK +44 131 527 4200 ---------The obligatory disclaimer-------- The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From jan.aerts at bbsrc.ac.uk Thu May 4 15:02:19 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 16:02:19 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACD9@rie2ksrv1.ri.bbsrc.ac.uk> Damn. No unit tests yet... I guess I'll have to learn what they are... For the mean time, you can run 'ruby map.rb' to see it working. It _should_... jan. > -----Original Message----- > From: Moses M. Hohman [mailto:mmhohman at northwestern.edu] > Sent: 04 May 2006 15:59 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] new module map.rb > > Hi Jan, > > Cool, I'll check it out. Do you have any unit tests for this? > > Moses > > On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > > > Hi all, > > > > I've added a new module map.rb to the cvs repository that describes > > markers and maps (such as linkage maps, radiation hybrid > maps and the > > sort): > > * Bio::Map::SimpleMap > > * Bio::Map::Marker > > * Bio::Map::Mapping > > * Bio::Map::ActsLikeMap > > * Bio::Map::ActsLikeMarker > > > > Two important design decisions were taken in writing these modules: > > (1) relationship map-mapping-marker: > > ------------------------------------ > > In an early implementation, Map objects could have a list of Marker > > objects associated with them. However, a single Marker > object can also > > be mapped to different Maps. As a result, to check which > maps have a > > certain marker in common, all markers of all maps would have to be > > screened. Therefore, to facilitate this many-to-many relationship > > complication, I decided to put a Mapping object in between Map and > > Marker. Such a Mapping object has three things associated with it: > > Map, > > Marker and location (which is a Bio::Location object). > > If a marker A is added to a map B, a Mapping object is created and > > added to both the @mappings array in marker A, _and_ the @mappings > > array in map B. > > > > (2) mixins ActsLikeMap and ActsLikeMarker: > > ------------------------------------------ > > Different things can be mapped to different things, or in > other words: > > different things can act as markers or as maps. > > * can act as markers: > > ** a microsatellite: when it's mapped on a linkage group > > ** a clone: when it's mapped to the cytogenetic map (using > FISH), or > > if it's included in the physical map (FPC) > > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > > ** ... > > * can act as maps: > > ** a linkage group > > ** a radiation hybrid map > > ** a clone: when it has a BAC end sequence associated with it > > ** ... > > > > As it is nonsense to create a Marker class and have all these > > different types of markers inherit from it (would a clone > inherit from > > Bio::Marker, or from Bio::Map?), I created two modules that can be > > mixed in with any class: Bio::Map::ActsLikeMap and > > Bio::Map::ActsLikeMarker. > > As a result, a Clone class (which doesn't exist yet) can > include both, > > and have properties of a map _and_ a marker. > > > > Give it a go. > > > > PS: Thinking about what can act like a map or a marker: a > sequence can > > essentially also be considered a map (we actually talk > about it that > > way in our department), with for example BLAST hits (or any other > > feature with a location) that act as markers. The unit of > the map is > > 'bp'. > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any > > attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From jan.aerts at bbsrc.ac.uk Thu May 4 16:27:28 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 4 May 2006 17:27:28 +0100 Subject: [BioRuby] new module map.rb Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACDB@rie2ksrv1.ri.bbsrc.ac.uk> Done. (Except a test to check positions of markers relative to each other on the same map) > -----Original Message----- > From: Moses M. Hohman [mailto:mmhohman at northwestern.edu] > Sent: 04 May 2006 15:59 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] new module map.rb > > Hi Jan, > > Cool, I'll check it out. Do you have any unit tests for this? > > Moses > > On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > > > Hi all, > > > > I've added a new module map.rb to the cvs repository that describes > > markers and maps (such as linkage maps, radiation hybrid > maps and the > > sort): > > * Bio::Map::SimpleMap > > * Bio::Map::Marker > > * Bio::Map::Mapping > > * Bio::Map::ActsLikeMap > > * Bio::Map::ActsLikeMarker > > > > Two important design decisions were taken in writing these modules: > > (1) relationship map-mapping-marker: > > ------------------------------------ > > In an early implementation, Map objects could have a list of Marker > > objects associated with them. However, a single Marker > object can also > > be mapped to different Maps. As a result, to check which > maps have a > > certain marker in common, all markers of all maps would have to be > > screened. Therefore, to facilitate this many-to-many relationship > > complication, I decided to put a Mapping object in between Map and > > Marker. Such a Mapping object has three things associated with it: > > Map, > > Marker and location (which is a Bio::Location object). > > If a marker A is added to a map B, a Mapping object is created and > > added to both the @mappings array in marker A, _and_ the @mappings > > array in map B. > > > > (2) mixins ActsLikeMap and ActsLikeMarker: > > ------------------------------------------ > > Different things can be mapped to different things, or in > other words: > > different things can act as markers or as maps. > > * can act as markers: > > ** a microsatellite: when it's mapped on a linkage group > > ** a clone: when it's mapped to the cytogenetic map (using > FISH), or > > if it's included in the physical map (FPC) > > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > > ** ... > > * can act as maps: > > ** a linkage group > > ** a radiation hybrid map > > ** a clone: when it has a BAC end sequence associated with it > > ** ... > > > > As it is nonsense to create a Marker class and have all these > > different types of markers inherit from it (would a clone > inherit from > > Bio::Marker, or from Bio::Map?), I created two modules that can be > > mixed in with any class: Bio::Map::ActsLikeMap and > > Bio::Map::ActsLikeMarker. > > As a result, a Clone class (which doesn't exist yet) can > include both, > > and have properties of a map _and_ a marker. > > > > Give it a go. > > > > PS: Thinking about what can act like a map or a marker: a > sequence can > > essentially also be considered a map (we actually talk > about it that > > way in our department), with for example BLAST hits (or any other > > feature with a location) that act as markers. The unit of > the map is > > 'bp'. > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any > > attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > > > From mmhohman at northwestern.edu Thu May 4 14:59:27 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Thu, 4 May 2006 10:59:27 -0400 Subject: [BioRuby] new module map.rb In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DACD7@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <2479663B-0D0D-4665-9561-7D16C7D22411@northwestern.edu> Hi Jan, Cool, I'll check it out. Do you have any unit tests for this? Moses On May 4, 2006, at 10:04 AM, jan aerts (RI) wrote: > Hi all, > > I've added a new module map.rb to the cvs repository that describes > markers and maps (such as linkage maps, radiation hybrid maps and the > sort): > * Bio::Map::SimpleMap > * Bio::Map::Marker > * Bio::Map::Mapping > * Bio::Map::ActsLikeMap > * Bio::Map::ActsLikeMarker > > Two important design decisions were taken in writing these modules: > (1) relationship map-mapping-marker: > ------------------------------------ > In an early implementation, Map objects could have a list of Marker > objects associated with them. However, a single Marker object can also > be mapped to different Maps. As a result, to check which maps have a > certain marker in common, all markers of all maps would have to be > screened. Therefore, to facilitate this many-to-many relationship > complication, I decided to put a Mapping object in between Map and > Marker. Such a Mapping object has three things associated with it: > Map, > Marker and location (which is a Bio::Location object). > If a marker A is added to a map B, a Mapping object is created and > added > to both the @mappings array in marker A, _and_ the @mappings array in > map B. > > (2) mixins ActsLikeMap and ActsLikeMarker: > ------------------------------------------ > Different things can be mapped to different things, or in other words: > different things can act as markers or as maps. > * can act as markers: > ** a microsatellite: when it's mapped on a linkage group > ** a clone: when it's mapped to the cytogenetic map (using FISH), > or if > it's included in the physical map (FPC) > ** a piece of sequence: a BAC-end sequence is mapped to a BAC clone > ** ... > * can act as maps: > ** a linkage group > ** a radiation hybrid map > ** a clone: when it has a BAC end sequence associated with it > ** ... > > As it is nonsense to create a Marker class and have all these > different > types of markers inherit from it (would a clone inherit from > Bio::Marker, or from Bio::Map?), I created two modules that can be > mixed > in with any class: Bio::Map::ActsLikeMap and Bio::Map::ActsLikeMarker. > As a result, a Clone class (which doesn't exist yet) can include both, > and have properties of a map _and_ a marker. > > Give it a go. > > PS: Thinking about what can act like a map or a marker: a sequence can > essentially also be considered a map (we actually talk about it > that way > in our department), with for example BLAST hits (or any other feature > with a location) that act as markers. The unit of the map is 'bp'. > > Jan Aerts, PhD > Bioinformatics Group > Roslin Institute > Roslin, Scotland, UK > +44 131 527 4200 > > ---------The obligatory disclaimer-------- > The information contained in this e-mail (including any > attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at bbsrc.ac.uk Tue May 9 10:42:12 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Tue, 9 May 2006 11:42:12 +0100 Subject: [BioRuby] soap functional test fails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, The functional test soap_wsdl.rb fails here. Probably has something to do with our proxy. The environment variable HTTP_PROXY is set correctly. my_server>ruby ./test_soapwsdl.rb Loaded suite ./test_soapwsdl Started /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired (Timeout::Error) from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' from /usr/lib/ruby/1.8/net/http.rb:418:in `start' from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' ... 20 levels... from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' from /usr/lib/ruby/1.8/test/unit.rb:285 from /usr/lib/ruby/1.8/test/unit.rb:283 Many thanks, Jan Aerts, PhD Bioinformatics Group Roslin Institute Roslin, Scotland, UK +44 131 527 4200 ---------The obligatory disclaimer-------- The information contained in this e-mail (including any attachments) is confidential and is intended for the use of the addressee only. The opinions expressed within this e-mail (including any attachments) are the opinions of the sender and do not necessarily constitute those of Roslin Institute (Edinburgh) ("the Institute") unless specifically stated by a sender who is duly authorised to do so on behalf of the Institute. From jan.aerts at bbsrc.ac.uk Tue May 9 18:22:18 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Tue, 9 May 2006 19:22:18 +0100 Subject: [BioRuby] combination bioruby and rails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Hi all, Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. Anyone know of any bioruby/rails implementations? jan. From lavi.kfir at gmail.com Tue May 9 17:18:53 2006 From: lavi.kfir at gmail.com (Kfir Lavi) Date: Tue, 9 May 2006 19:18:53 +0200 Subject: [BioRuby] Best way to do homology search Message-ID: Hi, I have sql database with table of dna sequences. I would like to do homology search on the table. A user enter a sequence and the return is sequences with the percentage of similarity. Is there a simple function to use or I have to put some code together? I have read the Tutorial.rd but need more help. Thanks, Kfir From mmhohman at northwestern.edu Tue May 9 19:24:47 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Tue, 9 May 2006 14:24:47 -0500 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <8FA3D042-8C1F-41E2-B090-1C6370EAD140@northwestern.edu> So, I actually, for fun, took a look at this a couple months ago. I dropped it because I wasn't sure how well-maintained/in-use BioSQL was. Is it something actively used? If so, I'd be happy to help with this. Moses On May 9, 2006, at 1:22 PM, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that > there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based > database with a rails interface? A feature of the web-interface > could then be that sequences would be displayed graphically (with > features annotated; using SVG?), and that the user could run remote > BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Tue May 9 20:38:15 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 05:38:15 +0900 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> Hi Jan, There will be many possibilities if BioRuby is used with Rails (especially with ActiveRecord). The GFF database (which is used as a backend of GBrowse) loaded by the bp_load_gff.pl command in BioPerl is also a candidate in addition to the BioSQL. There are some related efforts have been made, as far as I know. * Nakao-san developed a Ensembl (Vega?) accessing module with ActiveRecord * Nikaido-san posted a short Japanese tutorial to build a gene expression database viewer with Rails in his weblog. * Ichinose-san created AJAX interface for BioRuby (and BioRuby shell) The point would be, what kind of integration (or how tightly) is ideal, if we integrate Rails *in* BioRuby. As for the Rails module in bio/shell, it is not finished but can be used in the following way for now: 1. start the bioruby shell in terminal1 and issue 'web' command terminal1% bioruby foo bioruby> web Copying web server files ... done DRb::DRbConnError: druby://localhost:81064 - # quit 2. open another terminal and start the server terminal2% cd foo terminal2% ruby script/server druby://localhost:81064 starting ... => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options the rails (webrick httpd) server will start. 3. Switch back to terminal1 and restart bioruby session. terminal1% bioruby foo bioruby> web Connected to server druby://localhost:81064 Open http://localhost:3000/shell/ 4. open http://localhost:3000/shell/ in your web browser the BioRuby logo and the message "Connected!" will be displayed. 5. then create some objects in the bioruby shell. bioruby> x = 123 bioruby> na = seq("atgcatgcatgc") bioruby> aa = na.translate then reload your browser and variables will be listed. By click on the variable, you may see the contents of the variable in Rails. This feature is a experimental implementation and I'm not clear what the goal would be. Do you want to call methods of the object in web interface? All objects should be stored by ActiveRecord? What kind of visualization is desired? Toshiaki On 2006/05/10, at 3:22, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue May 9 19:38:45 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 04:38:45 +0900 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <0EDE8435-EFA2-44EE-81B3-D33DE31E715B@hgc.jp> Hi Jan, There will be many possibilities if BioRuby is used with Rails (especially with ActiveRecord). The GFF database (which is used as a backend of GBrowse) loaded by the bp_load_gff.pl command in BioPerl is also a candidate in addition to the BioSQL. There are some related efforts have been made, as far as I know. * Nakao-san developed a Ensembl (Vega?) accessing module with ActiveRecord * Nikaido-san posted a short Japanese tutorial to build a gene expression database viewer with Rails in his weblog. * Ichinose-san created AJAX interface for BioRuby (and BioRuby shell) The point would be, what kind of integration (or how tightly) is ideal, if we integrate Rails *in* BioRuby. As for the Rails module in bio/shell, it is not finished but can be used in the following way for now: 1. start the bioruby shell in terminal1 and issue 'web' command terminal1% bioruby foo bioruby> web Copying web server files ... done DRb::DRbConnError: druby://localhost:81064 - # quit 2. open another terminal and start the server terminal2% cd foo terminal2% ruby script/server druby://localhost:81064 starting ... => Booting WEBrick... => Rails application started on http://0.0.0.0:3000 => Ctrl-C to shutdown server; call with --help for options the rails (webrick httpd) server will start. 3. Switch back to terminal1 and restart bioruby session. terminal1% bioruby foo bioruby> web Connected to server druby://localhost:81064 Open http://localhost:3000/shell/ 4. open http://localhost:3000/shell/ in your web browser the BioRuby logo and the message "Connected!" will be displayed. 5. then create some objects in the bioruby shell. bioruby> x = 123 bioruby> na = seq("atgcatgcatgc") bioruby> aa = na.translate then reload your browser and variables will be listed. By click on the variable, you may see the contents of the variable in Rails. This feature is a experimental implementation and I'm not clear what the goal would be. Do you want to call methods of the object in web interface? All objects should be stored by ActiveRecord? What kind of visualization is desired? Toshiaki On 2006/05/10, at 3:22, jan aerts (RI) wrote: > Hi all, > > Has anyone tried to integrate bioruby with rails? I noticed that there's a rails module in bio/shell, but couldn't get it working. > How straightforward would it be to implement a BioSQL-based database with a rails interface? A feature of the web-interface could then be that sequences would be displayed graphically (with features annotated; using SVG?), and that the user could run remote BLASTs right from within the sequence viewer... or something. > > Anyone know of any bioruby/rails implementations? > > jan. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Tue May 9 20:51:26 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Tue, 9 May 2006 15:51:26 -0500 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> Message-ID: <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> On May 9, 2006, at 3:38 PM, Toshiaki Katayama wrote: > The point would be, what kind of integration (or how tightly) is > ideal, if we integrate Rails *in* BioRuby. > My vote would be to keep any code that integrated both rails and bioruby as a separate module, so that bioruby won't depend on any rails components. Moses From k at bioruby.org Tue May 9 20:37:14 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Wed, 10 May 2006 05:37:14 +0900 Subject: [BioRuby] Best way to do homology search In-Reply-To: References: Message-ID: Hi, On 2006/05/10, at 2:18, Kfir Lavi wrote: > Hi, > I have sql database with table of dna sequences. > I would like to do homology search on the table. How do you plan to execute homology search against SQL database? BioRuby can parse the result of BLAST, FASTA etc. commands and these are usually performed for the FASTA formated sequence file. I think some of these programs support to run against SQL database directly, but I have never tried by myself. If the result formats are same in both way (flatfile DB and sql DB), you can use BioRuby parser to extract % similarity. Toshiaki > A user enter a sequence and the return is sequences with the > percentage of similarity. > Is there a simple function to use or I have to put some code together? > I have read the Tutorial.rd but need more help. > > Thanks, > Kfir > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ktym at hgc.jp Tue May 9 18:46:21 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Wed, 10 May 2006 03:46:21 +0900 Subject: [BioRuby] soap functional test fails In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DACF3@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Jan, Have you also set the environmental variable 'soap_use_proxy'? I think Ruby's SOAP library checks its value in addition to the HTTP_PROXY. Please see the RDoc documentation in bio/io/soapwsdl.rb file. Toshiaki On 2006/05/09, at 19:42, jan aerts (RI) wrote: > Hi all, > > The functional test soap_wsdl.rb fails here. Probably has something to > do with our proxy. The environment variable HTTP_PROXY is set correctly. > > my_server>ruby ./test_soapwsdl.rb > Loaded suite ./test_soapwsdl > Started > /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired > (Timeout::Error) > from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' > from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' > from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' > from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' > from /usr/lib/ruby/1.8/net/http.rb:418:in `start' > from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' > ... 20 levels... > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' > from /usr/lib/ruby/1.8/test/unit.rb:285 > from /usr/lib/ruby/1.8/test/unit.rb:283 > > Many thanks, > > Jan Aerts, PhD > Bioinformatics Group > Roslin Institute > Roslin, Scotland, UK > +44 131 527 4200 > > ---------The obligatory disclaimer-------- > The information contained in this e-mail (including any attachments) is > confidential and is intended for the use of the addressee only. The > opinions expressed within this e-mail (including any attachments) are > the opinions of the sender and do not necessarily constitute those of > Roslin Institute (Edinburgh) ("the Institute") unless specifically > stated by a sender who is duly authorised to do so on behalf of the > Institute. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From k at bioruby.org Tue May 9 21:34:01 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Wed, 10 May 2006 06:34:01 +0900 Subject: [BioRuby] Fwd: O'Reilly UG Program News: DSUG Discount Changes References: Message-ID: <316D5374-AD88-4372-90EA-1FAFAC36487A@bioruby.org> We have the following offer from O'Reilly to the BioRuby user group. Toshiaki Begin forwarded message: > From: "Marsee Henon" > Date: 2006?5?4? 4:16:34:JST > To: k at bioruby.org > Subject: O'Reilly UG Program News: DSUG Discount Changes > > Hello, > > Can you please let your members know about the increase in our user > group discount? You can post this to your mailing list, web site, or in > your newsletter and please make sure you mention this at your next > meeting. > > Get 30% off a single book or 35% off two or more books from O'Reilly, No > Starch, Paraglyph, PC Publishing, Pragmatic Bookshelf, SitePoint, or > Syngress books you purchase directly from O'Reilly. Just use code DSUG > when ordering online or by phone 800-998-9938. Free ground shipping on > orders $29.95 or more in the US. > > > Other benefits you receive when you buy directly from O'Reilly include: > > *100% Satisfaction Guarantee* > If, for any reason, you're not completely satisfied with your purchase, > return it to us and get your money back. A return shipping label is > included with every direct purchase, and directions are posted online in > case you've misplaced it: > . > > *Safari Enabled* > Whenever possible, our books are "Safari Enabled." This means you can > access your book for free online for 45 days through the O'Reilly Safari > Bookshelf. How do you know if your book is Safari Enabled? Turn your > book over and look for the "Safari Enabled" logo on the bottom right of > the page. If it's there, flip through the last couple pages of your book > until you find directions for accessing your book online. > > *Booktech* > Have a question about your book? O'Reilly is the only publisher that > offers tech support for books. Send an email to > and we'll help you out. Be specific: Include > the book title and page number. It's also a good idea to include the > ISBN so we know what edition you have. > > *Reader Reviews* > Our reader reviews are read by most people at O'Reilly, including Tim > O'Reilly, all our editors, as well as sales, marketing, and PR. So if > you have praise, a gripe, or ideas for improvement, writing a reader > review on oreilly.com is a sure way for your voice to be heard. Just go > to your book's catalog page on oreilly.com and click the "Write a > Review" button. > > *Book Registration* > Register your book online and we'll notify you when the book has been > updated or a new edition is available. You can also win books and other > prizes. Haven't registered your books? Just go to > . > > *Newsletters* > Our newsletters keep you updated on the latest articles, books, news, > and events. A complete list of newsletters and lists can be found at > . > > We're working on a slew of additional benefits to serve you even better > so stay tuned. > > As always, thanks for your help spreading the word. > > Marsee Henon > > ================================================================ > O'Reilly > 1005 Gravenstein Highway North > Sebastopol, CA 95472 > http://ug.oreilly.com/ http://ug.oreilly.com/creativemedia/ > ================================================================ From jan.aerts at bbsrc.ac.uk Thu May 11 08:15:50 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 11 May 2006 09:15:50 +0100 Subject: [BioRuby] soap functional test fails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD0A@rie2ksrv1.ri.bbsrc.ac.uk> That did the trick. Thanks. > -----Original Message----- > From: Toshiaki Katayama [mailto:ktym at hgc.jp] > Sent: 09 May 2006 19:46 > To: jan aerts (RI) > Cc: bioruby at open-bio.org > Subject: Re: [BioRuby] soap functional test fails > > Hi Jan, > > Have you also set the environmental variable 'soap_use_proxy'? > I think Ruby's SOAP library checks its value in addition to > the HTTP_PROXY. > Please see the RDoc documentation in bio/io/soapwsdl.rb file. > > Toshiaki > > On 2006/05/09, at 19:42, jan aerts (RI) wrote: > > > Hi all, > > > > The functional test soap_wsdl.rb fails here. Probably has > something to > > do with our proxy. The environment variable HTTP_PROXY is > set correctly. > > > > my_server>ruby ./test_soapwsdl.rb > > Loaded suite ./test_soapwsdl > > Started > > /usr/lib/ruby/1.8/timeout.rb:43:in `new': execution expired > > (Timeout::Error) > > from /usr/lib/ruby/1.8/net/protocol.rb:83:in `connect' > > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `timeout' > > from /usr/lib/ruby/1.8/timeout.rb:62:in `timeout' > > from /usr/lib/ruby/1.8/net/protocol.rb:82:in `connect' > > from /usr/lib/ruby/1.8/net/protocol.rb:64:in `initialize' > > from /usr/lib/ruby/1.8/net/http.rb:429:in `do_start' > > from /usr/lib/ruby/1.8/net/http.rb:418:in `start' > > from /usr/lib/ruby/1.8/soap/netHttpClient.rb:115:in `start' > > ... 20 levels... > > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:200:in `run' > > from /usr/lib/ruby/1.8/test/unit/autorunner.rb:13:in `run' > > from /usr/lib/ruby/1.8/test/unit.rb:285 > > from /usr/lib/ruby/1.8/test/unit.rb:283 > > > > Many thanks, > > > > Jan Aerts, PhD > > Bioinformatics Group > > Roslin Institute > > Roslin, Scotland, UK > > +44 131 527 4200 > > > > ---------The obligatory disclaimer-------- The information > contained > > in this e-mail (including any attachments) is > > confidential and is intended for the use of the addressee > only. The > > opinions expressed within this e-mail (including any > attachments) are > > the opinions of the sender and do not necessarily > constitute those of > > Roslin Institute (Edinburgh) ("the Institute") unless specifically > > stated by a sender who is duly authorised to do so on behalf of the > > Institute. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From lavi.kfir at gmail.com Thu May 11 08:16:12 2006 From: lavi.kfir at gmail.com (Kfir Lavi) Date: Thu, 11 May 2006 10:16:12 +0200 Subject: [BioRuby] combination bioruby and rails In-Reply-To: <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> References: <84DA9D8AC9B05F4B889E7C70238CB45103CA504B@rie2ksrv1.ri.bbsrc.ac.uk> <2FE153AF-B739-46AD-A51A-5A845629E52D@hgc.jp> <8D182845-7DC7-439C-8398-0A8223DB6960@northwestern.edu> Message-ID: In other words, we need to write plugin for rails that make calls to the bioruby library. We first have to think of uses for the library on rails. This will make us understand the requierments for the plugin. I'm currently building web site with rubyonrails to disply reserch genomic data. And now I'm at a point of implementing searches on the internal database and on internet open databases. On the internal database I want to implement homology search. Any suggestions of building small interface will be appriciated. Regards, Kfir On 5/9/06, Moses M. Hohman wrote: > > On May 9, 2006, at 3:38 PM, Toshiaki Katayama wrote: > > > The point would be, what kind of integration (or how tightly) is > > ideal, if we integrate Rails *in* BioRuby. > > > > My vote would be to keep any code that integrated both rails and > bioruby as a separate module, so that bioruby won't depend on any > rails components. > > Moses > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From jan.aerts at bbsrc.ac.uk Thu May 11 09:38:56 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Thu, 11 May 2006 10:38:56 +0100 Subject: [BioRuby] combination bioruby and rails Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD0B@rie2ksrv1.ri.bbsrc.ac.uk> Hi Toshiaki, I've tried the approach you mentioned below yesterday, but still bump into that problem. Apparently, it has something to do with my setup of rails: when you run 'ruby script/server' in rails, the first line sent back to the screen is 'druby://localhost:81064'. When I do the same thing, the first line to screen is '=> Booting WEBrick...'. I haven't figured out yet how to solve that. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Toshiaki Katayama > Sent: 09 May 2006 21:38 > To: BioRuby ML Discussion List Project > Subject: Re: [BioRuby] combination bioruby and rails > <> > As for the Rails module in bio/shell, it is not finished but > can be used in the following way for now: > > 1. start the bioruby shell in terminal1 and issue 'web' command > > terminal1% bioruby foo > bioruby> web > Copying web server files ... done > DRb::DRbConnError: druby://localhost:81064 - > # > (my intention is to make this command will take care of > following steps automatically, however,) you may see the > DRb::DRbConnError message here, then quit. > > bioruby> quit > > 2. open another terminal and start the server > > terminal2% cd foo > terminal2% ruby script/server > druby://localhost:81064 > starting ... > => Booting WEBrick... > => Rails application started on http://0.0.0.0:3000 > => Ctrl-C to shutdown server; call with --help for options > > the rails (webrick httpd) server will start. > > 3. Switch back to terminal1 and restart bioruby session. > > terminal1% bioruby foo > bioruby> web > Connected to server druby://localhost:81064 > Open http://localhost:3000/shell/ > > 4. open http://localhost:3000/shell/ in your web browser > > the BioRuby logo and the message "Connected!" will be displayed. > <> From pjotr2006 at thebird.nl Tue May 23 19:50:44 2006 From: pjotr2006 at thebird.nl (Pjotr Prins) Date: Tue, 23 May 2006 21:50:44 +0200 Subject: [BioRuby] BOSC abstract due Message-ID: <20060523195044.GA29635@thebird.nl> Has anyone put in a paper for BOSC? http://www.open-bio.org/boscblog/ If not, we ought to do it. Jan are you interested? Otherwise I can give it a shot. Pj. From jan.aerts at bbsrc.ac.uk Wed May 24 15:25:12 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Wed, 24 May 2006 16:25:12 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> I'm afraid I'll have to pass on this. As someone who only started looking at ruby 5 months ago (let alone bioruby), I'm not familiar enough yet with the more advanced uses of ruby/bioruby. It's not difficult to explain the simple stuff ("It can read FASTA files", "It can run BLASTs"), but it would be interesting for the audience to give examples of advanced applications that are nevertheless (relatively) easy to do. I'm thinking integration with rails here, for example. Does anyone have other tools in mind that can be easily combined with bioruby? Something else that would be interesting: show how easy it is to add methods to existing bioruby objects, or alter them if you want them to behave differently. So back to you, Pjotr. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Pjotr Prins > Sent: 23 May 2006 20:51 > To: Toshiaki Katayama > Cc: BioRuby ML Discussion List Project > Subject: [BioRuby] BOSC abstract due > > Has anyone put in a paper for BOSC? > > http://www.open-bio.org/boscblog/ > > If not, we ought to do it. Jan are you interested? Otherwise > I can give it a shot. > > Pj. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby > From pjotr2006 at thebird.nl Wed May 24 17:13:28 2006 From: pjotr2006 at thebird.nl (Pjotr Prins) Date: Wed, 24 May 2006 19:13:28 +0200 Subject: [BioRuby] BOSC abstract due In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DAD6E@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: <20060524171328.GA5280@thebird.nl> Ah, there is that. Rails would be interesting for BOSC. Combination with BioRuby would be cool. I gather no one has put in an abstract? I suppose I can do it... Pj. On Wed, May 24, 2006 at 04:25:12PM +0100, jan aerts (RI) wrote: > I'm afraid I'll have to pass on this. As someone who only started > looking at ruby 5 months ago (let alone bioruby), I'm not familiar > enough yet with the more advanced uses of ruby/bioruby. > > It's not difficult to explain the simple stuff ("It can read FASTA > files", "It can run BLASTs"), but it would be interesting for the > audience to give examples of advanced applications that are nevertheless > (relatively) easy to do. I'm thinking integration with rails here, for > example. Does anyone have other tools in mind that can be easily > combined with bioruby? > Something else that would be interesting: show how easy it is to add > methods to existing bioruby objects, or alter them if you want them to > behave differently. > > So back to you, Pjotr. > > j. > > > -----Original Message----- > > From: bioruby-bounces at lists.open-bio.org > > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Pjotr Prins > > Sent: 23 May 2006 20:51 > > To: Toshiaki Katayama > > Cc: BioRuby ML Discussion List Project > > Subject: [BioRuby] BOSC abstract due > > > > Has anyone put in a paper for BOSC? > > > > http://www.open-bio.org/boscblog/ > > > > If not, we ought to do it. Jan are you interested? Otherwise > > I can give it a shot. > > > > Pj. > > > > _______________________________________________ > > BioRuby mailing list > > BioRuby at lists.open-bio.org > > http://lists.open-bio.org/mailman/listinfo/bioruby > > From isaacpei at gmail.com Thu May 25 02:13:49 2006 From: isaacpei at gmail.com (Isaac Xin Pei) Date: Wed, 24 May 2006 22:13:49 -0400 Subject: [BioRuby] bioruby development process / real life usage / visions? Message-ID: Dear All, I am very curious of the development process of bioruby, especially what the vision for bioruby project among the open bio projects? According to my understanding, - bioperl has the largest users community due to the history reason, rather than the languate itself - biopython solved the OOP issue in bioperl, and I like the language itself however, the biopython project in particular seems to have a rather loose developing process I am just not sure if I decide to pick it for everyday usage / long term programming project, it will help - bioruby: the library/class seems comprehensive the codes looks very clean first impression of programming using bioruby is that it does follow KISS principle : yet questions - the devloping process - does it have a large user community (or a large community/bioinformatics/biologists in Japan?) - the vision of the project? sorry for so many questions. in my research I have come to the point to using a programming language to investigage possible hypothesis in the genome, as well as a programming language to ease everyday bench work design ... hope to get some insights from you thanks! -- Best , Isaac - "A word fitly spoken Is like apples of gold in network of silver. " Proverbs 25:11 From k at bioruby.org Fri May 26 02:19:13 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Fri, 26 May 2006 11:19:13 +0900 Subject: [BioRuby] BOSC abstract due In-Reply-To: References: <20060523195044.GA29635@thebird.nl> Message-ID: <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> > If you could have another talk on integration of Rails or > some typical/impressive applications using BioRuby, > it would be very nice. and/or on your English documentation efforts - progress of the documentation is one of the most important point of our development in the past year, including launch of the bioruby-doc.org. Thanks, Toshiaki From k at bioruby.org Fri May 26 02:13:35 2006 From: k at bioruby.org (Toshiaki Katayama) Date: Fri, 26 May 2006 11:13:35 +0900 Subject: [BioRuby] BOSC abstract due In-Reply-To: <20060523195044.GA29635@thebird.nl> References: <20060523195044.GA29635@thebird.nl> Message-ID: On 2006/05/24, at 4:50, Pjotr Prins wrote: > Has anyone put in a paper for BOSC? > > http://www.open-bio.org/boscblog/ Not yet, but I will. My topic would be focused on * release of BioRuby 1.1 - overview, updates and enhancements * BioRuby shell - as a CUI - as a 'Bio::Perl'-like module If you could have another talk on integration of Rails or some typical/impressive applications using BioRuby, it would be very nice. Other Bio* projects sometimes presented several talks in the past BOSC meeting, so if we could have two or more talks/lightnings this year, it may imply expansion of our community. Toshiaki > If not, we ought to do it. Jan are you interested? Otherwise I can > give it a shot. > > Pj. > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From trevor at corevx.com Fri May 26 03:12:14 2006 From: trevor at corevx.com (Trevor Wennblom) Date: Thu, 25 May 2006 22:12:14 -0500 Subject: [BioRuby] BOSC abstract due In-Reply-To: <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> References: <20060523195044.GA29635@thebird.nl> <7C374AA6-D341-4263-95CA-3C5C807E056B@bioruby.org> Message-ID: <4476720E.3010206@corevx.com> Toshiaki Katayama wrote: > of our development in the past year, > including launch of the bioruby-doc.org. > I suppose I should update that. ;) I'll get on that ASAP. Trevor From jan.aerts at bbsrc.ac.uk Fri May 26 07:37:16 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Fri, 26 May 2006 08:37:16 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> I _completely_ agree with Toshiaki's suggestion: bioruby would benefit most by having more people using it. That means that impressive but easy-to-do examples are key. Before the meeting and to be able to realize/demonstrate those examples, some things have to be done: * getting some bugs out (e.g. the proxy-problem for users behind proxy's...) * more documentation: ** of the classes themselves: I'm trying to do one or two every week, but start bumping into those that I have no idea about what they do or how they work. Therefore, we'll need people to document those as well (or have elaborate examples, so I can figure out what they do.) ** although bioruby in anger is very usefull, users would probably benefit from more elaborate examples as well (including the impressive ones). First thing I actually always do when using BioPerl, is check out the HOWTO's. j. > -----Original Message----- > From: bioruby-bounces at lists.open-bio.org > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of > Toshiaki Katayama > Sent: 26 May 2006 03:14 > To: BioRuby ML Discussion List Project > Subject: Re: [BioRuby] BOSC abstract due > > If you could have another talk on integration of Rails or > some typical/impressive applications using BioRuby, it would > be very nice. > > Other Bio* projects sometimes presented several talks in the > past BOSC meeting, so if we could have two or more > talks/lightnings this year, it may imply expansion of our community. From jan.aerts at bbsrc.ac.uk Fri May 26 07:58:37 2006 From: jan.aerts at bbsrc.ac.uk (jan aerts (RI)) Date: Fri, 26 May 2006 08:58:37 +0100 Subject: [BioRuby] BOSC abstract due Message-ID: <84DA9D8AC9B05F4B889E7C70238CB451030DAD80@rie2ksrv1.ri.bbsrc.ac.uk> All, Something I didn't mention in the other post: it might be important that users have a feeling of what lives within the bioruby group, i.e. what the developers and big users are musing about. That might help them to: * understand the history of how things are built * give them an idea of what might be coming up in bioruby * get and idea on ways that bioruby can be used * gives them the feeling that something is going on An example of the third point above: I just bumped into ActiveRDF, and am wondering if that could be used sensibly with bioruby. If that turns out to be true, it might be interesting for other people using bioruby as well. Even if no actual classes would have to be written (which would mean that there would be little documentation for this bioruby/activeRDF combination). Would a blog be too far-fetched or cumbersome? (Sorry: just thinking out loud. (Which actually might be a good thing.)) Jan, the-pondering-one > -----Original Message----- > From: jan aerts (RI) > Sent: 26 May 2006 08:37 > To: 'Toshiaki Katayama'; BioRuby ML Discussion List Project > Subject: RE: [BioRuby] BOSC abstract due > > I _completely_ agree with Toshiaki's suggestion: bioruby > would benefit most by having more people using it. That means > that impressive but easy-to-do examples are key. > > Before the meeting and to be able to realize/demonstrate > those examples, some things have to be done: > * getting some bugs out (e.g. the proxy-problem for users > behind proxy's...) > * more documentation: > ** of the classes themselves: I'm trying to do one or two > every week, but start bumping into those that I have no idea > about what they do or how they work. Therefore, we'll need > people to document those as well (or have elaborate examples, > so I can figure out what they do.) > ** although bioruby in anger is very usefull, users would > probably benefit from more elaborate examples as well > (including the impressive ones). First thing I actually > always do when using BioPerl, is check out the HOWTO's. > > j. > > > -----Original Message----- > > From: bioruby-bounces at lists.open-bio.org > > [mailto:bioruby-bounces at lists.open-bio.org] On Behalf Of Toshiaki > > Katayama > > Sent: 26 May 2006 03:14 > > To: BioRuby ML Discussion List Project > > Subject: Re: [BioRuby] BOSC abstract due > > > > If you could have another talk on integration of Rails or some > > typical/impressive applications using BioRuby, it would be > very nice. > > > > Other Bio* projects sometimes presented several talks in > the past BOSC > > meeting, so if we could have two or more talks/lightnings > this year, > > it may imply expansion of our community. > From ktym at hgc.jp Fri May 26 02:39:45 2006 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri, 26 May 2006 11:39:45 +0900 Subject: [BioRuby] bioruby development process / real life usage / visions? In-Reply-To: References: Message-ID: <6551781B-CAEA-41C8-AE50-FE0F5F39D2F2@hgc.jp> On 2006/05/25, at 11:13, Isaac Xin Pei wrote: > Dear All, > > I am very curious of the development process of bioruby, especially what the > vision for bioruby project among the open bio projects? > According to my understanding, > > - bioperl has the largest users community due to the history reason, rather > than the languate itself > > - biopython solved the OOP issue in bioperl, and I like the language itself > however, the biopython project in particular seems to have a rather loose > developing process > I am just not sure if I decide to pick it for everyday usage / long term > programming project, it will help > > - bioruby: > the library/class seems comprehensive > the codes looks very clean > first impression of programming using bioruby is that it does follow KISS > principle > : yet questions > - the devloping process What do you mean? We have a CVS repository on open-bio.org as well as the other projects and contributions or enhancements discussed in this mailing list will be accepted to the repository by core developers. We also have a documentation on the development guideline: http://code.open-bio.org/cgi-bin/viewcvs/viewcvs.cgi/bioruby/README.DEV?rev=1.10&cvsroot=bioruby&content-type=text/vnd.viewcvs-markup > - does it have a large user community (or a large > community/bioinformatics/biologists in Japan?) I suspect there are >300 users in the world from the download counts in apache's log. (maybe half of them are in Japan) and the number is steadily increasing even the actual number might still be smaller than other projects. We can't count users of Linux or BSD-like distribution having BioRuby bundled. The number of the developer is about 10, and the number of core developers are around 5. I had BioRuby tutorials and hands-on seminars in Japan for several years. > - the vision of the project? Now we are forcusing on - to expand user community - adding documentations and unit tests - to enhance ability of the BioRuby library - web services - post-genomic analysis - cheminformatics - integration with Rails > sorry for so many questions. > > in my research I have come to the point to using a programming language to > investigage possible hypothesis in the genome, as well as a programming > language to ease everyday bench work design ... If you are not sure, you should try some of the above libraries to choose your favorite. If you choose BioRuby after the consideration, could you let us know what point of the BioRuby you feel better or worse than other project. :) > hope to get some insights from you > > thanks! > > > > -- > > Best , Isaac > > - "A word fitly spoken Is like apples of gold in network of > silver. " Proverbs 25:11 > > _______________________________________________ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby Toshiaki Katayama -- Human Genome Center, Institute of Medical Science, University of Tokyo 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-0071, Japan tel://+81-3-5449-5614, fax://+81-3-5449-5434 BioRuby project http://bioruby.org/ GenomeNet/KEGG http://www.genome.jp/ Human Genome Center http://www.hgc.jp/ From mmhohman at northwestern.edu Sat May 27 04:05:49 2006 From: mmhohman at northwestern.edu (Moses M. Hohman) Date: Sat, 27 May 2006 00:05:49 -0400 Subject: [BioRuby] BOSC abstract due In-Reply-To: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> References: <84DA9D8AC9B05F4B889E7C70238CB451030DAD7F@rie2ksrv1.ri.bbsrc.ac.uk> Message-ID: Hi Jan, On May 26, 2006, at 3:37 AM, jan aerts (RI) wrote: > Before the meeting and to be able to realize/demonstrate those > examples, > some things have to be done: > * getting some bugs out (e.g. the proxy-problem for users behind > proxy's...) > * more documentation: > ** of the classes themselves: I'm trying to do one or two every week, > but start bumping into those that I have no idea about what they do or > how they work. Therefore, we'll need people to document those as well > (or have elaborate examples, so I can figure out what they do.) I'd be happy to help with the documentation effort if you'd like. Is there a way to let each other know which we're working on? Who's working on the proxy problem? Moses From trevor at corevx.com Mon May 29 03:15:33 2006 From: trevor at corevx.com (Trevor Wennblom) Date: Sun, 28 May 2006 22:15:33 -0500 Subject: [BioRuby] rcov - Test coverage Message-ID: <447A6755.9000400@corevx.com> Lately I've found rcov ( http://eigenclass.org/hiki.rb?rcov ) to be very useful in several of my other projects. In brief, rcov shows what parts of the code is actually tested. I went ahead and ran it on BioRuby and was pleased with the results. I've made them available here: http://bioruby-doc.org/coverage/ The command used to generate this report was "rcov runner.rb --replace-progname" from the test directory. On a related topic I've lately become fond of the project management software Trac ( http://www.edgewall.com/trac/ ). I think many of it's features would be incredibly useful to our project. I'm sure we could assist our friends at OpenBio with setting up a Trac installation if they don't already have this on their server. The only real complication involved would be upgrading our current CVSystem to Subversion. Does anyone have any strong feelings either way about this? Thanks, Trevor