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BioRuby

Naohisa Goto / Genome Information Research Center, Research Institute for Microbial Diseases, Osaka Univ.Email: ngoto@gen-info.osaka-u.ac.jptwitter: @ngotogenome

BioRubyBioRuby1Who am I? / Name: Naohisa Goto: : :

Twitter: @ngotogenomeEmail: ngoto@gen-info.osaka-u.ac.jp

BioRubyRuby 1995http://www.ruby-lang.org/(WikiPedia: Yukihiro_Matsumoto.JPG)

BioRubyBASICCC++C#COBOLDFortranHaskellJavaJavaScriptLispMLPascalPerlPHPPL/IPrologPythonRRubySmalltalkBioRubyRuby?Ruby on Rails , BioRubyTwitter, BioRubyBioRubyRuby 1.4.32012822http://bioruby.org/

BioRuby6BioRubyFormatsI/OWeb ServiceGenBankEMBLUniProtKEGGPDBMEDLINEREBASEFASTA FASTQ GFFABIFSCFGCGMSFLasergeneGONewickPhyloXMLNEXUSToolsDDBJKEGG APINCBIEBITogoWSPSORT TargetP PTS1 SOSUI TMHMM Bio::FlatFileBioFetchBioSQLFlatFile indexingDASDesign SiRNARestriction enzymeBLAST FASTA EMBOSS HMMER InterProScan GeneScan BLAT Sim4 MEMEClustal W MUSCLE MAFFT T-Coffee ProbCons PHYLIP PAML Molecular weightCodon tableConvert sequence formatColor SchemeContingency TableUtilityAnalysis (Bio::Sequence) (Bio::Features) (Bio::Locations) (Bio::Pathway) (Bio::Reference) (Bio::Tree)BioRubyCompared to other projects, BioRuby covers broad range of bioinformatics databases and tools equivalent to others.

7BioRuby2000/11BioRuby2001/06 (BioRuby 0.1)2001/10 BioRuby 0.3:2005/06-2006/03 IPA2006/02 BioRuby 1.0.0:2010/08Bioinformatics:2012/08 BioRuby 1.4.3

Goto, N., Prins, P., Nakao, M., Bonnal, R., Aerts, J. and Katayama, T. (2010) BioRuby: Bioinformatics software for the Ruby programming language.Bioinformatics, 26(20),2617-2619.BioRubyNow, bioruby is in 10th anniversary. Here, brief history of BioRuby is shown. In November 2000, bioruby project was started.In June 2001, the first version was released. In 2005, we were funded by IPA Exploratory Software Project, also called MITO project.And, in 2010, in August, the BioRuby paper was published. The latest version 1.4.1 was released in October.8BioRuby: BioRuby 1.4.3 (2012/8/22)Library: 230 filesTests: 120 filesSample codes: 70 filesLibrary: 35,000 linesTests: 22,000 lines/, 580 classes/modules2800 methods

BioRubyBioRubyToshiaki Katayama (leader) (DBCLS)Naohisa Goto (release manager) (RIMD, Osaka Univ.)Pjotr Prins (Wageningen University, Netherlands)Raoul Bonnal (INGM, Italy)Jan AertsMitsuteru NakaoFrancesco Strozzi30BioRuby: http://github.com/bioruby/biorubyBioRubyHackathonan event when programmers meet to do collaborative computer programming (from WikiPedia)formed from the intellectual slang hack and marathon2002/02 BioHackathon (Arizona and Cape town) (Katayama)2003/02 BioHackathon (Singapore) (Katayama)

2006/12 Phyloinformatics Hackathon (Durham) (Katayama, Goto)

2008/02 DBCLS BioHackathon2008 (Tokyo)2009/03 DBCLS BioHackathon2009 (Tokyo, Okinawa)2010/02 DBCLS BioHackathon2010 (Tokyo)2010/10 DBCLS BH10.10 (Shizuoka)2011/08 NBDC / DBCLS BioHackathon2011 (Kyoto)2012/09 NBDC / DBCLS BioHackathon2012 (Toyama)BioRuby

Ruby2009 3,255

2008 4,095BioRubyBioRubyRubyWindows http://rubyinstaller.org/ 2012/8Ruby 1.9.3-p194Mac OS X LeopardXcodeRubyHomebrew, MacPorts, fink BioRubyBioRubyWindows Ruby 1.9.3-p194Ruby 1.9.3-p194Start Command Prompt with Rubygem install bioEnterRubyMacTerminal.appsudo gem install bioEnterBioRubyBioRubyRubyMachttp://rubygems.org/downloads/bio-1.4.3.gem http://bioruby.org/archive/gems/bio-1.4.3.gem Terminal.appcd Desktopsudo gem install bio-1.4.3.gemBioRubyRubyWindows Ruby 1.9.3-p194Ruby 1.9.3-p194Start Command Prompt with RubyOKirbEnter

BioRubyRubyMacTerminal.appBasicirbEnter

BioRubyRubyirbRuby

1+2 * 3Enter: 7((1+2) * (3+4) + 5) * 6: 156BioRuby: 10 / 3 10.0 / 3 10 / 3.0 10.quo(3)

BioRuby

_ = a = 1 b = 2 c = a + b aaa = c * 3BioRuby

a = 1 a = 2 a = a * 3 a = xxxBioRuby" ' " ' a = "this is a string" b = 'testtest' a = a + b * 2BioRuby[..] [, ]

a = "atgccgta" a[0..2] a[2,4]

BioRubyArray

[] /[..][, ] a = [ 3, 4, 5 ] b = [ 1, 2 ] c = a + b c[2] c[2] = 9BioRubyprintputsp a = "this is test" b = 1 print a print a, b puts a puts a, b p a

BioRubyBioRubyBioruby Shell WindowsRuby 1.9.3-p194Start Command Prompt with RubybiorubyEnterMacTerminalbiorubyEnter

BioRubyBioruby ShellirbRubybiorubyBioRubyBioRuby Shell codontable

BioRubyBioRuby ShelldoublehelixDNA

BioRubyBioRuby ShellDNA music MIDI # s = Bio::Sequence::NA.new("atgccc") # DNA musicmidifile("test.mid", s)

BioRubyBioRubyBioRuby # s = Bio::Sequence::NA.new("atgccc") # puts s.length # puts s.molecular_weight # puts s.composition # puts s.complement # puts s.reverse # puts s.translateBioRubyBioRubyBioRubyWindowsC:\Ruby193\lib\ruby\gems\1.9.1\gems\bio-1.4.3 doc sample # a = Bio::Sequence::AA.new("DTPGHVDF") # puts a.molecular_weight # puts a.composition # 3 puts a.codes

BioRuby Bio::FlatFile.open("") do |ff| f.each do |e| # puts e.definition # puts e.naseq end end

BioRubyBioRubyirb / BioRuby Shell exit EnterBioRubyRubyWindowsRuby 1.9.3-p194Start Command Prompt with RubyMacTerminalcdruby .rbBioRubyRubyWindowsTeraPad, xyzzy Macmi (http://www.mimikaki.net/), CotEditor Microsoft Word BioRubyDNA

translate.rb ruby translate.rb > require "rubygems" require "bio"

f = Bio::FlatFile.open(ARGF) f.each do |entry| dna = entry.naseq aa = dna.translate seq = Bio::Sequence.new(seq) print seq.output_fasta(e.definition) end

BioRubyBioRubyRubyhttp://www.ruby-lang.org/

BioRubyBioRubydoc/ Tutorial.rd.html Tutorial.rd.ja.htmlsample/ sample/demo_*.rb test/data

http://bioruby.org/

BioRuby

Ruby2009 3,255

2008 4,095BioRuby