From ktym at hgc.jp Fri Mar 4 09:10:20 2005 From: ktym at hgc.jp (Toshiaki Katayama) Date: Fri Mar 4 09:05:46 2005 Subject: [BioRuby] bioruby book chapter In-Reply-To: References: Message-ID: <4219ad762a6d1857875a6b79fa60a10b@hgc.jp> I heard that this is a Dave Thomas book. Does anyone interested in writing? 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/~k/ GenomeNet/KEGG http://www.genome.jp/ Human Genome Center http://www.hgc.jp/ On 2005/03/01, at 11:12, Ara.T.Howard wrote: > > hi out there- > > i'm putting togther a book on scientific programming with ruby. i'm > looking > for bioruby users that might be interested in contributing ideas, > example > code, project descriptions, etc. > > i know nothing about bioruby and just want to test the waters: what > are people > doing with it? is it mature enough for average users? i don't even > know > where to start so suggestions are welcome! > > kind regards. > > -a > -- > ======================================================================= > ======== > | EMAIL :: Ara [dot] T [dot] Howard [at] noaa [dot] gov > | PHONE :: 303.497.6469 > | When you do something, you should burn yourself completely, like a > good > | bonfire, leaving no trace of yourself. --Shunryu Suzuki > ======================================================================= > ======== > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby From mmhohman at northwestern.edu Fri Mar 4 16:55:44 2005 From: mmhohman at northwestern.edu (Moses Hohman) Date: Fri Mar 4 16:50:46 2005 Subject: [BioRuby] bioruby book chapter In-Reply-To: <4219ad762a6d1857875a6b79fa60a10b@hgc.jp> References: <4219ad762a6d1857875a6b79fa60a10b@hgc.jp> Message-ID: I'd be interested in helping out; I was waiting for the most established BioRuby people to answer first in case they wanted to. In any case, I'm hoping you are also interested, Toshiaki, because your perspective would be invaluable. I am not a good example case of BioRuby in use because I have only been involved as a hobby, though I am a bioinformatics/bio-IT person. Moses Moses M. Hohman, Ph.D. Assoc. Director of Bioinformatics, Center for Functional Genomics Assoc. Director, Bioinformatics Core, Robert H. Lurie Comprehensive Cancer Center Northwestern University www.neuromice.org (847) 491 4108 (office) mmhohman@northwestern.edu On Mar 4, 2005, at 8:10 AM, Toshiaki Katayama wrote: > > I heard that this is a Dave Thomas book. > Does anyone interested in writing? > > 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/~k/ > GenomeNet/KEGG http://www.genome.jp/ > Human Genome Center http://www.hgc.jp/ > > > On 2005/03/01, at 11:12, Ara.T.Howard wrote: > >> >> hi out there- >> >> i'm putting togther a book on scientific programming with ruby. i'm >> looking >> for bioruby users that might be interested in contributing ideas, >> example >> code, project descriptions, etc. >> >> i know nothing about bioruby and just want to test the waters: what >> are people >> doing with it? is it mature enough for average users? i don't even >> know >> where to start so suggestions are welcome! >> >> kind regards. >> >> -a >> -- >> ====================================================================== >> ========= >> | EMAIL :: Ara [dot] T [dot] Howard [at] noaa [dot] gov >> | PHONE :: 303.497.6469 >> | When you do something, you should burn yourself completely, like a >> good >> | bonfire, leaving no trace of yourself. --Shunryu Suzuki >> ====================================================================== >> ========= >> _______________________________________________ >> BioRuby mailing list >> BioRuby@open-bio.org >> http://portal.open-bio.org/mailman/listinfo/bioruby > > _______________________________________________ > BioRuby mailing list > BioRuby@open-bio.org > http://portal.open-bio.org/mailman/listinfo/bioruby > From pjotr at pckassa.com Sat Mar 5 02:29:10 2005 From: pjotr at pckassa.com (Pjotr Prins) Date: Sat Mar 5 02:24:22 2005 Subject: [BioRuby] bioruby book chapter In-Reply-To: References: <4219ad762a6d1857875a6b79fa60a10b@hgc.jp> Message-ID: <20050305072910.GA26228@nmi-tm2.xs4all.nl> I have had some discussion with Ara - and am happy to take a lead in a team effort - if no one else does. There are three real advantages: 1. It is an opportunity to document BioRuby (rdoc and Wiki) - I know I should have done it ages ago 2. It will attract more scientists (especially if we accentuate against BioPerl) 3. It puts Ruby and BioRuby in the lime light So it is killing more birds with one stone. Ara will credit the authors of each chapter by name and organisation - important for scientists who need that as a publication in their job (I do if I book time against it). It should be more than BioRuby though - it is also about using Ruby as a programming language in the life sciences. We may want to ask Ara if we can use a modified version of the chapter in BioRuby documentation. That may help advertise the book. If the book never gets published we should be allowed to take it public too. Inside the chapter the authors of BioRuby should be credited too. I am quite happy to do it on my own, but if you think you can do a similar sized chunk of the work - and produce real text - I'd think it be really cool to have you as co-author(s). Mind, it is a big exercise. Documentation always is. Reserve a few full-time weeks for it. So let's go for it! Pj. On Fri, Mar 04, 2005 at 03:55:44PM -0600, Moses Hohman wrote: > I'd be interested in helping out; I was waiting for the most > established BioRuby people to answer first in case they wanted to. In > any case, I'm hoping you are also interested, Toshiaki, because your > perspective would be invaluable. I am not a good example case of > BioRuby in use because I have only been involved as a hobby, though I > am a bioinformatics/bio-IT person.