From hase at umbc.edu Mon Aug 1 23:28:49 2005 From: hase at umbc.edu (HASE) Date: Mon Aug 1 23:19:04 2005 Subject: [BioRuby] Bioinformatics Software Development Survey Message-ID: <2012.68.49.173.177.1122953329.squirrel@68.49.173.177> Hello, As part of our research at UMBC, we are studying the characteristics of software development in the bioinformatics domain. We believe that this study should be guided by the people who are actively involved in bioinformatics. This research is our first step towards enabling the production of high quality bioinformatics software with less time and effort. Therefore, your feedback is very important to us. We seek your input in the form of a survey questionnaire that will take around 15 minutes of your time. We solicit general demographic information, information about the products that you have developed, your work practices, and your software development process. So, if you are a bioinformatics professional doing software development or a software developer working in the bioinformatics domain, please provide us with your valuable input. We assure you that this information will be used only for academic purposes and will be completely confidential. Please follow the link below to start the survey: http://www.is.umbc.edu/bio-survey/ We appreciate your participation in advance. Regards, HASE (Human Aspects of Software Engineering) 1000 Hilltop Circle Department of Information Systems University of Maryland Baltimore County Baltimore, MD, 21250 hase@umbc.edu From pjotr at pckassa.com Mon Aug 22 13:55:42 2005 From: pjotr at pckassa.com (Pjotr Prins) Date: Mon Aug 22 13:45:14 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <20050613211634.GA28151@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> Message-ID: <20050822175542.GA25133@tm2.nmi-agro.nl> The following documents are in the ./doc directory: -rw-r--r-- 1 wrk pacs 9597 2004-08-24 01:41 BioRuby.rd.ja -rw-r--r-- 1 wrk pacs 12043 2002-07-02 03:40 Design.rd.ja -rw-r--r-- 1 wrk pacs 35298 2004-08-24 02:21 KEGG_API.rd.ja -rw-r--r-- 1 wrk pacs 3109 2004-08-24 02:18 TODO.rd.ja -rw-r--r-- 1 wrk pacs 33969 2004-08-24 02:19 Tutorial.rd.ja I notice these are all in Japanese and contain nuggets of gold ;-). Would anyone be interested in translating these into plain English? Especially the Tutorial is of interest. Don't worry about 'bad' English - I will clean it up. It would really be helpful if someone could do a quick and dirty translation - even if it were an MP3 recording. Anyone? Regards, Pj. From trevor at corevx.com Tue Aug 23 18:46:43 2005 From: trevor at corevx.com (trevor) Date: Tue Aug 23 18:36:11 2005 Subject: [BioRuby] BioRuby development In-Reply-To: <20050822175542.GA25133@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> Message-ID: <430BA753.8050007@corevx.com> I would like to start commiting updates to the BioRuby development branch. Is there a formal process for this - do I need to have an account setup or should I go through a staff member? Also, is there a developers mailing list to discuss features and improvements? This particular list seems to be relatively low-traffic. From ngoto at gen-info.osaka-u.ac.jp Wed Aug 24 00:09:49 2005 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Tue Aug 23 23:59:25 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <20050822175542.GA25133@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> Message-ID: <200508240359.j7O3xCTv032390@portal.open-bio.org> Hi, On Mon, 22 Aug 2005 19:55:42 +0200 pjotr@pckassa.com (Pjotr Prins) wrote: > The following documents are in the ./doc directory: > > -rw-r--r-- 1 wrk pacs 9597 2004-08-24 01:41 BioRuby.rd.ja > -rw-r--r-- 1 wrk pacs 12043 2002-07-02 03:40 Design.rd.ja > -rw-r--r-- 1 wrk pacs 35298 2004-08-24 02:21 KEGG_API.rd.ja > -rw-r--r-- 1 wrk pacs 3109 2004-08-24 02:18 TODO.rd.ja > -rw-r--r-- 1 wrk pacs 33969 2004-08-24 02:19 Tutorial.rd.ja There is English version of KEGG_API.rd.ja at: http://www.genome.jp/kegg/soap/doc/keggapi_manual.html (but not included in BioRuby distribution. Licence problem?) For other four documents, though the contents of them are a little bit obsolete, > I notice these are all in Japanese and contain nuggets of gold ;-). > Would anyone be interested in translating these into plain English? > Especially the Tutorial is of interest. Don't worry about 'bad' > English - I will clean it up. It would really be helpful if someone > could do a quick and dirty translation - even if it were an MP3 > recording. Yes. All BioRuby developers in Japan (including me) are now interested in writing and/or translating documents in English. -- Naohisa GOTO ngoto@gen-info.osaka-u.ac.jp Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan From pjotr at pckassa.com Wed Aug 24 10:56:06 2005 From: pjotr at pckassa.com (Pjotr Prins) Date: Wed Aug 24 10:45:54 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <200508240359.j7O3xCTv032390@portal.open-bio.org> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508240359.j7O3xCTv032390@portal.open-bio.org> Message-ID: <20050824145606.GA6031@tm2.nmi-agro.nl> On Wed, Aug 24, 2005 at 01:09:49PM +0900, GOTO Naohisa wrote: > There is English version of KEGG_API.rd.ja at: > http://www.genome.jp/kegg/soap/doc/keggapi_manual.html > (but not included in BioRuby distribution. Licence problem?) I'll read that! > All BioRuby developers in Japan (including me) are now > interested in writing and/or translating documents in English. Great. Will it be possible to translate those documents in the coming one or two weeks. Like I wrote, quick and dirty approach is fine. Probably best we use the CVS repository for that so everyone can keep track of changes. Pj. From ktym at hgc.jp Fri Aug 26 09:19:28 2005 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri Aug 26 09:10:08 2005 Subject: [BioRuby] BioRuby development In-Reply-To: <430BA753.8050007@corevx.com> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <430BA753.8050007@corevx.com> Message-ID: <27137233-CC57-40DC-ADF2-B41A9FE7423F@hgc.jp> Hello trevor, Sorry for the delay in responding and thank you for your participation to the BioRuby development. You and all other members on this list are welcome to use this list to discuss features and improvements on BioRuby. Through the discussion, committers decide whether and how your patch should be incorporated. You will also become a committer whenever staff members need your frequent developments. :) Regards, Toshiaki Katayama On 2005/08/24, at 7:46, trevor wrote: > I would like to start commiting updates to the BioRuby development branch. Is there a formal process for this - do I need to have an account setup or should I go through a staff member? Also, is there a developers mailing list to discuss features and improvements? This particular list seems to be relatively low-traffic. > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From ktym at hgc.jp Fri Aug 26 09:35:04 2005 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri Aug 26 09:24:30 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <20050824145606.GA6031@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508240359.j7O3xCTv032390@portal.open-bio.org> <20050824145606.GA6031@tm2.nmi-agro.nl> Message-ID: <546CB664-E9A4-4012-85D2-F787E464C0CE@hgc.jp> On 2005/08/24, at 23:56, Pjotr Prins wrote: > On Wed, Aug 24, 2005 at 01:09:49PM +0900, GOTO Naohisa wrote: > >> There is English version of KEGG_API.rd.ja at: >> http://www.genome.jp/kegg/soap/doc/keggapi_manual.html >> (but not included in BioRuby distribution. Licence problem?) >> > > I'll read that! The document is written by me so there is no license problem to include it in the BioRuby distribution. When I finished the 1st version of this document in Japanese, I included it just for the advertisement of the KEGG API service. Now the service has its own site (shown above) and it is a general web service (means not restricted to the BioRuby), so I don't know I should keep including the document. How do you think? >> All BioRuby developers in Japan (including me) are now >> interested in writing and/or translating documents in English. >> > > Great. Will it be possible to translate those documents in the coming > one or two weeks. Like I wrote, quick and dirty approach is fine. > Probably best we use the CVS repository for that so everyone can keep > track of changes. One or two weeks would be difficult, but we'll try to include and update the draft translation in the CVS during this September. Toshiaki Katayama From trevor at corevx.com Tue Aug 30 16:46:19 2005 From: trevor at corevx.com (Trevor Wennblom) Date: Tue Aug 30 16:35:40 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <546CB664-E9A4-4012-85D2-F787E464C0CE@hgc.jp> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508240359.j7O3xCTv032390@portal.open-bio.org> <20050824145606.GA6031@tm2.nmi-agro.nl> <546CB664-E9A4-4012-85D2-F787E464C0CE@hgc.jp> Message-ID: <4314C59B.6070306@corevx.com> I think now would be a good time to start documenting the source code with RDoc formatted comments. For ease of use, I've included generated RDoc webpages here: http://corevx.com/bioruby-doc/ http://corevx.com/bioruby-dev-doc/ The only difference between the two is that 'bioruby-dev-doc' includes private and protected objects. I plan on keeping these up-to-date every week or two. I hope this helps. Trevor From ngoto at gen-info.osaka-u.ac.jp Wed Aug 31 08:51:00 2005 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Wed Aug 31 08:52:17 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <20050822175542.GA25133@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> Message-ID: <200508311250.j7VCoPiQ016228@idns103.gen-info.osaka-u.ac.jp> Hi, I translated Tutorial.rd.ja into English. It will soon be put into the ./doc directory in CVS. I also put it into BioRuby English Wiki. http://bioruby.org/wiki/English/?Tutorial.rd.en Please mail to this mailing list when editing the Wiki page because we want to keep CVS document up-to-date. Because I have poor English skill and I've translated it very quickly and roughly, it may contain many errors. I tried to use translation software and several sentences were translated by the software, but generally it was useless. In addition, I found some eratta and wrong points in Japanese document and I'll fix them soon. Would you please clean up? On Mon, 22 Aug 2005 19:55:42 +0200 pjotr@pckassa.com (Pjotr Prins) wrote: > I notice these are all in Japanese and contain nuggets of gold ;-). > Would anyone be interested in translating these into plain English? > Especially the Tutorial is of interest. Don't worry about 'bad' > English - I will clean it up. It would really be helpful if someone > could do a quick and dirty translation - even if it were an MP3 > recording. -- Naohisa GOTO ngoto@gen-info.osaka-u.ac.jp Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan From pjotr at pckassa.com Wed Aug 31 09:11:30 2005 From: pjotr at pckassa.com (Pjotr Prins) Date: Wed Aug 31 09:32:47 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <200508311250.j7VCoPiQ016228@idns103.gen-info.osaka-u.ac.jp> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508311250.j7VCoPiQ016228@idns103.gen-info.osaka-u.ac.jp> Message-ID: <20050831131130.GA14210@tm2.nmi-agro.nl> Great! I will work on it. On Wed, Aug 31, 2005 at 09:51:00PM +0900, GOTO Naohisa wrote: > Hi, > > I translated Tutorial.rd.ja into English. > It will soon be put into the ./doc directory in CVS. From ngoto at gen-info.osaka-u.ac.jp Wed Aug 31 09:52:59 2005 From: ngoto at gen-info.osaka-u.ac.jp (GOTO Naohisa) Date: Wed Aug 31 09:42:12 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <20050831131130.GA14210@tm2.nmi-agro.nl> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508311250.j7VCoPiQ016228@idns103.gen-info.osaka-u.ac.jp> <20050831131130.GA14210@tm2.nmi-agro.nl> Message-ID: <200508311342.j7VDg8AH028193@portal.open-bio.org> Hi, > I translated Tutorial.rd.ja into English. > It will soon be put into the ./doc directory in CVS. I put ./doc/Tutorial.rd into BioRuby CVS repository. I changed name of Wiki page from Tutorial.rd.en to Tutorial.rd. http://bioruby.org/wiki/English/?Tutorial.rd In the document, I wrote many "TRANSLATOR'S NOTE". They are not only memos for readers but also reminders to change original Japanese document. On Wed, 31 Aug 2005 15:11:30 +0200 pjotr@pckassa.com (Pjotr Prins) wrote: > Great! I will work on it. Thanks!!! -- Naohisa GOTO ngoto@gen-info.osaka-u.ac.jp Department of Genome Informatics, Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Japan From pjotr at pckassa.com Wed Aug 31 13:03:37 2005 From: pjotr at pckassa.com (Pjotr Prins) Date: Wed Aug 31 12:52:49 2005 Subject: [BioRuby] BioRuby Documentation effort In-Reply-To: <200508311342.j7VDg8AH028193@portal.open-bio.org> References: <20050613211634.GA28151@tm2.nmi-agro.nl> <20050822175542.GA25133@tm2.nmi-agro.nl> <200508311250.j7VCoPiQ016228@idns103.gen-info.osaka-u.ac.jp> <20050831131130.GA14210@tm2.nmi-agro.nl> <200508311342.j7VDg8AH028193@portal.open-bio.org> Message-ID: <20050831170337.GA15193@tm2.nmi-agro.nl> Yes, also better not use the Wiki - I prefer version control. Pj. On Wed, Aug 31, 2005 at 10:52:59PM +0900, GOTO Naohisa wrote: > Hi, > > > I translated Tutorial.rd.ja into English. > > It will soon be put into the ./doc directory in CVS. > > I put ./doc/Tutorial.rd into BioRuby CVS repository. > > I changed name of Wiki page from Tutorial.rd.en to Tutorial.rd. > http://bioruby.org/wiki/English/?Tutorial.rd > > In the document, I wrote many "TRANSLATOR'S NOTE". They are > not only memos for readers but also reminders to change original > Japanese document. > > On Wed, 31 Aug 2005 15:11:30 +0200 > pjotr@pckassa.com (Pjotr Prins) wrote: > > > Great! I will work on it. > > Thanks!!! > > -- > Naohisa GOTO > ngoto@gen-info.osaka-u.ac.jp > Department of Genome Informatics, Genome Information Research Center, > Research Institute for Microbial Diseases, Osaka University, Japan > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby