From ngoto at gen-info.osaka-u.ac.jp Fri Oct 1 06:01:51 2010 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 1 Oct 2010 19:01:51 +0900 Subject: [BioRuby] May I contribute a 23andMe flatfile parser? In-Reply-To: References: Message-ID: <20101001100152.495F81CBC3D4@idnmail.gen-info.osaka-u.ac.jp> Hi Russell, Please do so. No one has right to prohibit development. No response from anyone for a week suggest that it does not exist. In BioRuby, no data class for a SNP. Writing general SNP class, not specific to 23andMe, may also be needed during the development of the parser. I found the data format description and sample data in SNPedia. It seems it is a simple tab-separated text. Is it the "23andMe SNP/genotype flatfile" you wrote? http://www.snpedia.com/index.php/23andMe Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Fri, 24 Sep 2010 03:34:06 -0400 Russell Whitaker wrote: > Hi all / ??????????????? > > [Please let me know if my Japanese is mojibake / ????] > > I'm a former professional software engineer who left Google 3 years > ago to pursue a degree in biochemistry from Columbia University (which > I did in fact complete, 4 months ago). After having programmed other languages > over a nearly 20 year career - one in Japan, by the way - I switched from > Python to Ruby/Rails at Google, and have committed to continue with that > as primary platform (except for statistical applications, for which I'm doing R > when needed). > > I've been researching best platforms for going general bioinformatics > work, and of course discovered BioRuby, which is why I'm here on this list. > > A few hours of digging have convinced me that a 23andMe SNP/genotype > flatfile parser does not yet exist in BioRuby. However, I may be wrong, so I'll > ask: does one exist? No mention of "23andMe" exists in the list archives. > > Would anyone object to my writing one? I've been familiarizing myself with > the development process for this group, e.g.: > > http://lists.open-bio.org/pipermail/bioruby/2010-June/001319.html > > I already have a GitHub account, of course. > > Thanks in advance for your help, and I look forward to contributing to this > project. > > ????????????? > ???? > > -- > Russell Whitaker > http://twitter.com/OrthoNormalRuss > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From georgkam at gmail.com Fri Oct 8 14:21:29 2010 From: georgkam at gmail.com (George Githinji) Date: Fri, 8 Oct 2010 21:21:29 +0300 Subject: [BioRuby] Guidelines for writing bioruby plugins Message-ID: Hi Bioruby developers, I have heard of bioruby plugins and also seen two such plugins from github http://github.com/pjotrp/bioruby-gff3-plugin and http://github.com/helios/bioruby-plugin-graphics 1. Is the plugin system supposed to open development methods? (helios uses unit testing while pjotrp uses r-spec for testing) 2. Will the core developers concentrate on making bioruby core more stable? 3. What constitutes Bioruby core? 4. Are there plugin development guidelines? 5. How is the plugin system supposed to work? More practically I have created a library for calculating the isoelectric point of a protein using Ruby (http://github.com/georgeG/isoelectric_point_4_R). Using shoulda as the testing framework. I would like to turn it to a bioruby plugin while adhering to a 'bioruby plugin development standard' if it exists. Please advise Thank you -- --------------- Sincerely George KEMRI/Wellcome-Trust Research Program Skype: george_g2 Blog: http://biorelated.wordpress.com/ From pjotr.public14 at thebird.nl Sat Oct 9 05:05:26 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 9 Oct 2010 11:05:26 +0200 Subject: [BioRuby] Guidelines for writing bioruby plugins In-Reply-To: References: Message-ID: <20101009090526.GA510@thebird.nl> Hi George, The plugin system is in a conceptual stage. I intend to write an 'Anatomy of a BioRuby plugin' soon. Some quick responses On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote: > Hi Bioruby developers, > > I have heard of bioruby plugins and also seen two such plugins from github > http://github.com/pjotrp/bioruby-gff3-plugin and > http://github.com/helios/bioruby-plugin-graphics > > 1. Is the plugin system supposed to open development methods? (helios > uses unit testing while pjotrp uses r-spec for testing) You are free to choose > 2. Will the core developers concentrate on making bioruby core more stable? That is the goal > 3. What constitutes Bioruby core? Anything we agree on that belongs in core and can be stable and maintained. > 4. Are there plugin development guidelines? Planned > 5. How is the plugin system supposed to work? The first stage is by simply adding a search path. We can make it more sophisticated in time - i.e. plugins that can get loaded by BioRuby core, etc. Some of it has already been done by us, but needs to solidify. > More practically I have created a library for calculating the > isoelectric point of a protein using Ruby > (http://github.com/georgeG/isoelectric_point_4_R). > Using shoulda as the testing framework. I would like to turn it to a > bioruby plugin while adhering to a 'bioruby plugin development > standard' if it exists. Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module naming conventions and name your project like bioruby-xxxx-plugin, so it is clear it can work that way. > Please advise Pj. From georgkam at gmail.com Sat Oct 9 08:46:11 2010 From: georgkam at gmail.com (George Githinji) Date: Sat, 9 Oct 2010 15:46:11 +0300 Subject: [BioRuby] Guidelines for writing bioruby plugins In-Reply-To: <20101009090526.GA510@thebird.nl> References: <20101009090526.GA510@thebird.nl> Message-ID: Hi Pjotr Thank you very much for the explanation. On Sat, Oct 9, 2010 at 12:05 PM, Pjotr Prins wrote: > Hi George, > > The plugin system is in a conceptual stage. I intend to write an > 'Anatomy of a BioRuby plugin' soon. ?Some quick responses > > On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote: >> Hi Bioruby developers, >> >> I have heard of bioruby plugins and also seen two such plugins from github >> http://github.com/pjotrp/bioruby-gff3-plugin and >> http://github.com/helios/bioruby-plugin-graphics >> >> 1. Is ?the plugin system supposed to open development methods? (helios >> uses unit testing while pjotrp uses r-spec for testing) > > You are free to choose > >> 2. Will the core developers concentrate on making bioruby core more stable? > > That is the goal > >> 3. What constitutes Bioruby core? > > Anything we agree on that belongs in core and can be stable and > maintained. > >> 4. Are there plugin development guidelines? > > Planned > >> 5. How is the plugin system supposed to work? > > The first stage is by simply adding a search path. We can make it > more sophisticated in time - i.e. plugins that can get loaded by > BioRuby core, etc. Some of it has already been done by us, but needs to > solidify. > >> More practically I have created a library for calculating the >> isoelectric point of a protein using Ruby >> (http://github.com/georgeG/isoelectric_point_4_R). >> Using shoulda as the testing framework. I would like to turn it to a >> bioruby plugin while adhering to a 'bioruby plugin development >> standard' if it exists. > > Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module > naming conventions and name your project like bioruby-xxxx-plugin, so > it is clear it can work that way. > >> Please advise > > Pj. > -- --------------- Sincerely George KEMRI/Wellcome-Trust Research Program Skype: george_g2 Blog: http://biorelated.wordpress.com/ From ngoto at gen-info.osaka-u.ac.jp Fri Oct 22 02:44:05 2010 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 22 Oct 2010 15:44:05 +0900 Subject: [BioRuby] BioRuby 1.4.1 released Message-ID: <20101022154404.5A5B.EEF6E030@gen-info.osaka-u.ac.jp> We are pleased to announce the release of BioRuby 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added. Here is a brief summary of changes. PAML Codeml support is significantly improved: PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins. KEGG PATHWAY and KEGG MODULE parsers are added: The code is developed by Kozo Nishida and Toshiaki Katayama. Bio::KEGG::GENES and Bio::KEGG::GENOME bug fixes and new methods: Some of them are due to the file format changes. Test codes are added and improved: They are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto. Bug fixes in Bio::Tree: some methods did not work correctly. Platform-dependent bug when calling external programs: Detection of platform is improved not to call fork(2) on platforms that do not support it (e.g. JRuby). In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog. The archive is available at: http://bioruby.org/archive/bioruby-1.4.1.tar.gz Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.1.gem We also put RubyGems package at RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command: % gem search ?remote bio and find ?bio (1.4.1)? in the list. Then, % sudo gem install bio Finally, we are sorry that many new features are waiting to be merged to BioRuby, including HMMER3 support. These will be included in the next major release version. Hope you enjoy. -- Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp From yannick.wurm at unil.ch Wed Oct 27 03:19:58 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Wed, 27 Oct 2010 14:19:58 +0700 Subject: [BioRuby] logo & mailing list Message-ID: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Hello, I've just moved to Jakarta (the city, not the framework!), and have been asked to give a small overview of bioinformatics & bioruby at the Jakarta.rb ruby user group meeting on Sunday. I have two questions: - is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png is very petite. - I could not find a searchable mailing list archive? Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) Thanks & all the best, Yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html From tomoakin at kenroku.kanazawa-u.ac.jp Wed Oct 27 07:50:46 2010 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Wed, 27 Oct 2010 20:50:46 +0900 Subject: [BioRuby] logo & mailing list In-Reply-To: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Hi, > - I could not find a searchable mailing list archive? > Is there a reason to not mirror the mailing list on Gmane or > another service? (it can be read-only) Perhaps just short of human resource to do that. Current list archive is in fact indexed by google and perhaps other search engines. If you want to search the list, for example, "HMMER" you can ask google like: HMMER site:http://lists.open-bio.org/pipermail/bioruby So, there is little incentive to setup a dedicated search system. If you are not decided to search only that mailing list, a simpler query like: HMMER bioruby works to search a broader information and usually returns some good information if present. Best wishes, -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From biopython at maubp.freeserve.co.uk Wed Oct 27 08:44:53 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 27 Oct 2010 13:44:53 +0100 Subject: [BioRuby] logo & mailing list In-Reply-To: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: On Wed, Oct 27, 2010 at 8:19 AM, Yannick Wurm wrote: > > Hello, > > I've just moved to Jakarta (the city, not the framework!), and have been > asked to give a small overview of bioinformatics & bioruby at the > Jakarta.rb ruby user group meeting on Sunday. > I have two questions: > ? ? ? ?- is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png ?is very petite. This is 150 by 150 pixels, and might be more suitable: http://www.open-bio.org/w/images/5/5a/BioRuby_logo_tiny.png But I agree, a large version would be nicer. Peter From yannick.wurm at unil.ch Sat Oct 30 02:03:56 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Sat, 30 Oct 2010 13:03:56 +0700 Subject: [BioRuby] logo & mailing list In-Reply-To: <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Message-ID: Dear Tomoaki-san, thank you for your reply. I think the problem with the google search is first that novice users (biologists that have never programmed before) are unlikely to know about google's "site:" feature. Second, navigating the thread hierarchy is not as user-friendly in the pipermail archives as on a dedicated service. This is why when I need something about bioconductor, I systematically go to the gmane bioconductor mirror (http://news.gmane.org/gmane.science.biology.informatics.conductor ). Having bioruby archived on GMANE would only require filling out the following form: http://gmane.org/subscribe.php . I am happy to set it up if nobody is opposed. (FYI, all email addresses remain hidden in obfuscated images) Thanks & all the best, yannick On 27 Oct 2010, at 18:50, Tomoaki NISHIYAMA wrote: > Hi, > >> - I could not find a searchable mailing list archive? >> Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) > > > Perhaps just short of human resource to do that. > Current list archive is in fact indexed by google > and perhaps other search engines. > If you want to search the list, for example, "HMMER" > you can ask google like: > HMMER site:http://lists.open-bio.org/pipermail/bioruby > > So, there is little incentive to setup a dedicated search system. > If you are not decided to search only that mailing list, > a simpler query like: > HMMER bioruby > works to search a broader information and usually returns > some good information if present. > > Best wishes, > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html From yannick.wurm at unil.ch Sat Oct 30 02:06:00 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Sat, 30 Oct 2010 13:06:00 +0700 Subject: [BioRuby] logo & mailing list In-Reply-To: References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: <3B781E5A-0925-42D4-A631-24CE2011B3C8@unil.ch> Thanks Peter, I'm not sure all of that is the logo? I think only the guitarpick is the logo :) http://bioruby.org/images/bioruby-gem.png Best, yannick On 27 Oct 2010, at 19:44, Peter wrote: > On Wed, Oct 27, 2010 at 8:19 AM, Yannick Wurm wrote: >> >> Hello, >> >> I've just moved to Jakarta (the city, not the framework!), and have been >> asked to give a small overview of bioinformatics & bioruby at the >> Jakarta.rb ruby user group meeting on Sunday. >> I have two questions: >> - is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png is very petite. > > This is 150 by 150 pixels, and might be more suitable: > > http://www.open-bio.org/w/images/5/5a/BioRuby_logo_tiny.png > > But I agree, a large version would be nicer. > > Peter From pjotr.public14 at thebird.nl Sat Oct 30 02:48:40 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Oct 2010 08:48:40 +0200 Subject: [BioRuby] logo & mailing list In-Reply-To: References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Message-ID: <20101030064840.GA24484@thebird.nl> Maybe we could add a specialised google search box on the site, or somewhere, which does the site search? If it would list, or log, last searches it may even be informative for what people are looking for. Ignoring privacy concerns ;) Any Ajax gurus out there? Pj. On Sat, Oct 30, 2010 at 01:03:56PM +0700, Yannick Wurm wrote: > Dear Tomoaki-san, > > thank you for your reply. > I think the problem with the google search is first that novice users (biologists that have never programmed before) are unlikely to know about google's "site:" feature. Second, navigating the thread hierarchy is not as user-friendly in the pipermail archives as on a dedicated service. > > This is why when I need something about bioconductor, I systematically go to the gmane bioconductor mirror (http://news.gmane.org/gmane.science.biology.informatics.conductor ). > > > Having bioruby archived on GMANE would only require filling out the following form: http://gmane.org/subscribe.php . > I am happy to set it up if nobody is opposed. (FYI, all email addresses remain hidden in obfuscated images) > > Thanks & all the best, > yannick > > > > > On 27 Oct 2010, at 18:50, Tomoaki NISHIYAMA wrote: > > > Hi, > > > >> - I could not find a searchable mailing list archive? > >> Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) > > > > > > Perhaps just short of human resource to do that. > > Current list archive is in fact indexed by google > > and perhaps other search engines. > > If you want to search the list, for example, "HMMER" > > you can ask google like: > > HMMER site:http://lists.open-bio.org/pipermail/bioruby > > > > So, there is little incentive to setup a dedicated search system. > > If you are not decided to search only that mailing list, > > a simpler query like: > > HMMER bioruby > > works to search a broader information and usually returns > > some good information if present. > > > > Best wishes, > > -- > > Tomoaki NISHIYAMA > > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > > > > > -------------------------------------------- > yannick . wurm @ unil . ch > Ant Genomics, Ecology & Evolution @ Lausanne > http://www.unil.ch/dee/page28685_fr.html > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From ngoto at gen-info.osaka-u.ac.jp Fri Oct 1 10:01:51 2010 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa GOTO) Date: Fri, 1 Oct 2010 19:01:51 +0900 Subject: [BioRuby] May I contribute a 23andMe flatfile parser? In-Reply-To: References: Message-ID: <20101001100152.495F81CBC3D4@idnmail.gen-info.osaka-u.ac.jp> Hi Russell, Please do so. No one has right to prohibit development. No response from anyone for a week suggest that it does not exist. In BioRuby, no data class for a SNP. Writing general SNP class, not specific to 23andMe, may also be needed during the development of the parser. I found the data format description and sample data in SNPedia. It seems it is a simple tab-separated text. Is it the "23andMe SNP/genotype flatfile" you wrote? http://www.snpedia.com/index.php/23andMe Naohisa Goto ngoto at gen-info.osaka-u.ac.jp / ng at bioruby.org On Fri, 24 Sep 2010 03:34:06 -0400 Russell Whitaker wrote: > Hi all / ??????????????? > > [Please let me know if my Japanese is mojibake / ????] > > I'm a former professional software engineer who left Google 3 years > ago to pursue a degree in biochemistry from Columbia University (which > I did in fact complete, 4 months ago). After having programmed other languages > over a nearly 20 year career - one in Japan, by the way - I switched from > Python to Ruby/Rails at Google, and have committed to continue with that > as primary platform (except for statistical applications, for which I'm doing R > when needed). > > I've been researching best platforms for going general bioinformatics > work, and of course discovered BioRuby, which is why I'm here on this list. > > A few hours of digging have convinced me that a 23andMe SNP/genotype > flatfile parser does not yet exist in BioRuby. However, I may be wrong, so I'll > ask: does one exist? No mention of "23andMe" exists in the list archives. > > Would anyone object to my writing one? I've been familiarizing myself with > the development process for this group, e.g.: > > http://lists.open-bio.org/pipermail/bioruby/2010-June/001319.html > > I already have a GitHub account, of course. > > Thanks in advance for your help, and I look forward to contributing to this > project. > > ????????????? > ???? > > -- > Russell Whitaker > http://twitter.com/OrthoNormalRuss > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby From georgkam at gmail.com Fri Oct 8 18:21:29 2010 From: georgkam at gmail.com (George Githinji) Date: Fri, 8 Oct 2010 21:21:29 +0300 Subject: [BioRuby] Guidelines for writing bioruby plugins Message-ID: Hi Bioruby developers, I have heard of bioruby plugins and also seen two such plugins from github http://github.com/pjotrp/bioruby-gff3-plugin and http://github.com/helios/bioruby-plugin-graphics 1. Is the plugin system supposed to open development methods? (helios uses unit testing while pjotrp uses r-spec for testing) 2. Will the core developers concentrate on making bioruby core more stable? 3. What constitutes Bioruby core? 4. Are there plugin development guidelines? 5. How is the plugin system supposed to work? More practically I have created a library for calculating the isoelectric point of a protein using Ruby (http://github.com/georgeG/isoelectric_point_4_R). Using shoulda as the testing framework. I would like to turn it to a bioruby plugin while adhering to a 'bioruby plugin development standard' if it exists. Please advise Thank you -- --------------- Sincerely George KEMRI/Wellcome-Trust Research Program Skype: george_g2 Blog: http://biorelated.wordpress.com/ From pjotr.public14 at thebird.nl Sat Oct 9 09:05:26 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 9 Oct 2010 11:05:26 +0200 Subject: [BioRuby] Guidelines for writing bioruby plugins In-Reply-To: References: Message-ID: <20101009090526.GA510@thebird.nl> Hi George, The plugin system is in a conceptual stage. I intend to write an 'Anatomy of a BioRuby plugin' soon. Some quick responses On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote: > Hi Bioruby developers, > > I have heard of bioruby plugins and also seen two such plugins from github > http://github.com/pjotrp/bioruby-gff3-plugin and > http://github.com/helios/bioruby-plugin-graphics > > 1. Is the plugin system supposed to open development methods? (helios > uses unit testing while pjotrp uses r-spec for testing) You are free to choose > 2. Will the core developers concentrate on making bioruby core more stable? That is the goal > 3. What constitutes Bioruby core? Anything we agree on that belongs in core and can be stable and maintained. > 4. Are there plugin development guidelines? Planned > 5. How is the plugin system supposed to work? The first stage is by simply adding a search path. We can make it more sophisticated in time - i.e. plugins that can get loaded by BioRuby core, etc. Some of it has already been done by us, but needs to solidify. > More practically I have created a library for calculating the > isoelectric point of a protein using Ruby > (http://github.com/georgeG/isoelectric_point_4_R). > Using shoulda as the testing framework. I would like to turn it to a > bioruby plugin while adhering to a 'bioruby plugin development > standard' if it exists. Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module naming conventions and name your project like bioruby-xxxx-plugin, so it is clear it can work that way. > Please advise Pj. From georgkam at gmail.com Sat Oct 9 12:46:11 2010 From: georgkam at gmail.com (George Githinji) Date: Sat, 9 Oct 2010 15:46:11 +0300 Subject: [BioRuby] Guidelines for writing bioruby plugins In-Reply-To: <20101009090526.GA510@thebird.nl> References: <20101009090526.GA510@thebird.nl> Message-ID: Hi Pjotr Thank you very much for the explanation. On Sat, Oct 9, 2010 at 12:05 PM, Pjotr Prins wrote: > Hi George, > > The plugin system is in a conceptual stage. I intend to write an > 'Anatomy of a BioRuby plugin' soon. ?Some quick responses > > On Fri, Oct 08, 2010 at 09:21:29PM +0300, George Githinji wrote: >> Hi Bioruby developers, >> >> I have heard of bioruby plugins and also seen two such plugins from github >> http://github.com/pjotrp/bioruby-gff3-plugin and >> http://github.com/helios/bioruby-plugin-graphics >> >> 1. Is ?the plugin system supposed to open development methods? (helios >> uses unit testing while pjotrp uses r-spec for testing) > > You are free to choose > >> 2. Will the core developers concentrate on making bioruby core more stable? > > That is the goal > >> 3. What constitutes Bioruby core? > > Anything we agree on that belongs in core and can be stable and > maintained. > >> 4. Are there plugin development guidelines? > > Planned > >> 5. How is the plugin system supposed to work? > > The first stage is by simply adding a search path. We can make it > more sophisticated in time - i.e. plugins that can get loaded by > BioRuby core, etc. Some of it has already been done by us, but needs to > solidify. > >> More practically I have created a library for calculating the >> isoelectric point of a protein using Ruby >> (http://github.com/georgeG/isoelectric_point_4_R). >> Using shoulda as the testing framework. I would like to turn it to a >> bioruby plugin while adhering to a 'bioruby plugin development >> standard' if it exists. > > Cool. For now, make sure it has ./lib/bio/xxx, use BioRuby module > naming conventions and name your project like bioruby-xxxx-plugin, so > it is clear it can work that way. > >> Please advise > > Pj. > -- --------------- Sincerely George KEMRI/Wellcome-Trust Research Program Skype: george_g2 Blog: http://biorelated.wordpress.com/ From ngoto at gen-info.osaka-u.ac.jp Fri Oct 22 06:44:05 2010 From: ngoto at gen-info.osaka-u.ac.jp (Naohisa Goto) Date: Fri, 22 Oct 2010 15:44:05 +0900 Subject: [BioRuby] BioRuby 1.4.1 released Message-ID: <20101022154404.5A5B.EEF6E030@gen-info.osaka-u.ac.jp> We are pleased to announce the release of BioRuby 1.4.1. This new release fixes bugs existed in 1.4.0 and new features are added. Here is a brief summary of changes. PAML Codeml support is significantly improved: PAML Codeml result parser is completely rewritten and is significantly improved. The code is developed by Pjotr Prins. KEGG PATHWAY and KEGG MODULE parsers are added: The code is developed by Kozo Nishida and Toshiaki Katayama. Bio::KEGG::GENES and Bio::KEGG::GENOME bug fixes and new methods: Some of them are due to the file format changes. Test codes are added and improved: They are developed by Kazuhiro Hayashi, Kozo Nishida, John Prince, and Naohisa Goto. Bug fixes in Bio::Tree: some methods did not work correctly. Platform-dependent bug when calling external programs: Detection of platform is improved not to call fork(2) on platforms that do not support it (e.g. JRuby). In addition, many changes have been made, including incompatible changes. For more information, see RELEASE_NOTES.rdoc and ChangeLog. The archive is available at: http://bioruby.org/archive/bioruby-1.4.1.tar.gz Gem file is also available at: http://bioruby.org/archive/gems/bio-1.4.1.gem We also put RubyGems package at RubyGems.org. You can easily install by using RubyGems. First, check the version number by using search command: % gem search ?remote bio and find ?bio (1.4.1)? in the list. Then, % sudo gem install bio Finally, we are sorry that many new features are waiting to be merged to BioRuby, including HMMER3 support. These will be included in the next major release version. Hope you enjoy. -- Naohisa Goto ng at bioruby.org / ngoto at gen-info.osaka-u.ac.jp From yannick.wurm at unil.ch Wed Oct 27 07:19:58 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Wed, 27 Oct 2010 14:19:58 +0700 Subject: [BioRuby] logo & mailing list Message-ID: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Hello, I've just moved to Jakarta (the city, not the framework!), and have been asked to give a small overview of bioinformatics & bioruby at the Jakarta.rb ruby user group meeting on Sunday. I have two questions: - is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png is very petite. - I could not find a searchable mailing list archive? Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) Thanks & all the best, Yannick -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html From tomoakin at kenroku.kanazawa-u.ac.jp Wed Oct 27 11:50:46 2010 From: tomoakin at kenroku.kanazawa-u.ac.jp (Tomoaki NISHIYAMA) Date: Wed, 27 Oct 2010 20:50:46 +0900 Subject: [BioRuby] logo & mailing list In-Reply-To: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Hi, > - I could not find a searchable mailing list archive? > Is there a reason to not mirror the mailing list on Gmane or > another service? (it can be read-only) Perhaps just short of human resource to do that. Current list archive is in fact indexed by google and perhaps other search engines. If you want to search the list, for example, "HMMER" you can ask google like: HMMER site:http://lists.open-bio.org/pipermail/bioruby So, there is little incentive to setup a dedicated search system. If you are not decided to search only that mailing list, a simpler query like: HMMER bioruby works to search a broader information and usually returns some good information if present. Best wishes, -- Tomoaki NISHIYAMA Advanced Science Research Center, Kanazawa University, 13-1 Takara-machi, Kanazawa, 920-0934, Japan From biopython at maubp.freeserve.co.uk Wed Oct 27 12:44:53 2010 From: biopython at maubp.freeserve.co.uk (Peter) Date: Wed, 27 Oct 2010 13:44:53 +0100 Subject: [BioRuby] logo & mailing list In-Reply-To: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: On Wed, Oct 27, 2010 at 8:19 AM, Yannick Wurm wrote: > > Hello, > > I've just moved to Jakarta (the city, not the framework!), and have been > asked to give a small overview of bioinformatics & bioruby at the > Jakarta.rb ruby user group meeting on Sunday. > I have two questions: > ? ? ? ?- is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png ?is very petite. This is 150 by 150 pixels, and might be more suitable: http://www.open-bio.org/w/images/5/5a/BioRuby_logo_tiny.png But I agree, a large version would be nicer. Peter From yannick.wurm at unil.ch Sat Oct 30 06:03:56 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Sat, 30 Oct 2010 13:03:56 +0700 Subject: [BioRuby] logo & mailing list In-Reply-To: <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Message-ID: Dear Tomoaki-san, thank you for your reply. I think the problem with the google search is first that novice users (biologists that have never programmed before) are unlikely to know about google's "site:" feature. Second, navigating the thread hierarchy is not as user-friendly in the pipermail archives as on a dedicated service. This is why when I need something about bioconductor, I systematically go to the gmane bioconductor mirror (http://news.gmane.org/gmane.science.biology.informatics.conductor ). Having bioruby archived on GMANE would only require filling out the following form: http://gmane.org/subscribe.php . I am happy to set it up if nobody is opposed. (FYI, all email addresses remain hidden in obfuscated images) Thanks & all the best, yannick On 27 Oct 2010, at 18:50, Tomoaki NISHIYAMA wrote: > Hi, > >> - I could not find a searchable mailing list archive? >> Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) > > > Perhaps just short of human resource to do that. > Current list archive is in fact indexed by google > and perhaps other search engines. > If you want to search the list, for example, "HMMER" > you can ask google like: > HMMER site:http://lists.open-bio.org/pipermail/bioruby > > So, there is little incentive to setup a dedicated search system. > If you are not decided to search only that mailing list, > a simpler query like: > HMMER bioruby > works to search a broader information and usually returns > some good information if present. > > Best wishes, > -- > Tomoaki NISHIYAMA > > Advanced Science Research Center, > Kanazawa University, > 13-1 Takara-machi, > Kanazawa, 920-0934, Japan > -------------------------------------------- yannick . wurm @ unil . ch Ant Genomics, Ecology & Evolution @ Lausanne http://www.unil.ch/dee/page28685_fr.html From yannick.wurm at unil.ch Sat Oct 30 06:06:00 2010 From: yannick.wurm at unil.ch (Yannick Wurm) Date: Sat, 30 Oct 2010 13:06:00 +0700 Subject: [BioRuby] logo & mailing list In-Reply-To: References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> Message-ID: <3B781E5A-0925-42D4-A631-24CE2011B3C8@unil.ch> Thanks Peter, I'm not sure all of that is the logo? I think only the guitarpick is the logo :) http://bioruby.org/images/bioruby-gem.png Best, yannick On 27 Oct 2010, at 19:44, Peter wrote: > On Wed, Oct 27, 2010 at 8:19 AM, Yannick Wurm wrote: >> >> Hello, >> >> I've just moved to Jakarta (the city, not the framework!), and have been >> asked to give a small overview of bioinformatics & bioruby at the >> Jakarta.rb ruby user group meeting on Sunday. >> I have two questions: >> - is there a higher-resolution logo? The one at http://bioruby.org/images/bioruby-gem.png is very petite. > > This is 150 by 150 pixels, and might be more suitable: > > http://www.open-bio.org/w/images/5/5a/BioRuby_logo_tiny.png > > But I agree, a large version would be nicer. > > Peter From pjotr.public14 at thebird.nl Sat Oct 30 06:48:40 2010 From: pjotr.public14 at thebird.nl (Pjotr Prins) Date: Sat, 30 Oct 2010 08:48:40 +0200 Subject: [BioRuby] logo & mailing list In-Reply-To: References: <4EF118CE-3B94-40D0-BEA3-56790DE994F9@unil.ch> <82050E00-EFB4-4171-A285-11777264EEFC@kenroku.kanazawa-u.ac.jp> Message-ID: <20101030064840.GA24484@thebird.nl> Maybe we could add a specialised google search box on the site, or somewhere, which does the site search? If it would list, or log, last searches it may even be informative for what people are looking for. Ignoring privacy concerns ;) Any Ajax gurus out there? Pj. On Sat, Oct 30, 2010 at 01:03:56PM +0700, Yannick Wurm wrote: > Dear Tomoaki-san, > > thank you for your reply. > I think the problem with the google search is first that novice users (biologists that have never programmed before) are unlikely to know about google's "site:" feature. Second, navigating the thread hierarchy is not as user-friendly in the pipermail archives as on a dedicated service. > > This is why when I need something about bioconductor, I systematically go to the gmane bioconductor mirror (http://news.gmane.org/gmane.science.biology.informatics.conductor ). > > > Having bioruby archived on GMANE would only require filling out the following form: http://gmane.org/subscribe.php . > I am happy to set it up if nobody is opposed. (FYI, all email addresses remain hidden in obfuscated images) > > Thanks & all the best, > yannick > > > > > On 27 Oct 2010, at 18:50, Tomoaki NISHIYAMA wrote: > > > Hi, > > > >> - I could not find a searchable mailing list archive? > >> Is there a reason to not mirror the mailing list on Gmane or another service? (it can be read-only) > > > > > > Perhaps just short of human resource to do that. > > Current list archive is in fact indexed by google > > and perhaps other search engines. > > If you want to search the list, for example, "HMMER" > > you can ask google like: > > HMMER site:http://lists.open-bio.org/pipermail/bioruby > > > > So, there is little incentive to setup a dedicated search system. > > If you are not decided to search only that mailing list, > > a simpler query like: > > HMMER bioruby > > works to search a broader information and usually returns > > some good information if present. > > > > Best wishes, > > -- > > Tomoaki NISHIYAMA > > > > Advanced Science Research Center, > > Kanazawa University, > > 13-1 Takara-machi, > > Kanazawa, 920-0934, Japan > > > > > > -------------------------------------------- > yannick . wurm @ unil . ch > Ant Genomics, Ecology & Evolution @ Lausanne > http://www.unil.ch/dee/page28685_fr.html > > > > _______________________________________________ > BioRuby Project - http://www.bioruby.org/ > BioRuby mailing list > BioRuby at lists.open-bio.org > http://lists.open-bio.org/mailman/listinfo/bioruby