BioRuby -- Bioinformatics Library

BioRubyBioRuby― Bioinformatics Library― 生物情報科学用ライブラリNaohisa Goto / 後藤直久Genome Information Research Center, ResearchInstitute for Microbial Diseases, Osaka Univ.大阪大学微生物病研究所附属遺伝情報実験センターEmail: ngoto@gen-info.osaka-u.ac.jptwitter: @ngotogenome

BioRuby Who am I? / 自己紹介  Name: Naohisa Goto  名前: 後藤直久  Affiliation: Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University  所属: 大阪大学微生物病研究所附属遺伝情報実験センター  Twitter: @ngotogenome  Email: ngoto@gen-info.osaka-u.ac.jp  First Ruby experience: 1.2.6 (compiled in 22/Jun/1999)

BioRuby BioRuby  Bioinformatics software library and tools written in the Ruby Language  Rubyで書かれた生物情報科学（バイオインフォマティクス）用ライブラリとツール集  Free software (Ruby License)  http://bioruby.org/  https://github.com/bioruby/bioruby  % gem install bio

BioRuby DNA DNA is a chain made of the four molecules. DNAは4種類の分子からなる鎖  A (Adenine)  C (Cytosine)  G (Guanine)  T (Thymine) DNA can be treated as String. DNAは文字列として扱える。（ところで、Encoding どうしよう…） Human: Total 3GB (49-247MB/chromosome) ヒト: 合計3GB (染色体1本あたり49～247MB)図: WikiPedia: 染色体

BioRuby An example DNA data (with metadata / 付加情報含む) >gi|60459557|gb|AY948115.1| Homo sapiens alcohol dehydrogenase 1A (class I), alpha polypeptide (ADH1A) gene, complete cds GAGGGCGACAAAAGGGAACAGACCCAAAACCACAGGAGAGATGCTAGCATGACAGGGATGCAGAGACATA AAGCACAACAGTGAGATGGAGTTAATATACCTCCACGAGGGTGACCTTGTCCTGCATCTCAAATTTTGGG TAGGATTTGAATGGGCCAGAGGGACAGAAAAGAAGAGAAAGAGCATGATGAGCAAGGGCTTGAATGTTAA ATAGATTCCTCTTTGGGGGACCAGGGAGATACAAGCTTCTAAAGCACATACGCCCTGTATTGGAGAATGG GGAGGAGTAGATAGATGAGAAGGTTGAAGCCATATTACGAAGCCTTGAATGCTGAACATCAGATCTGGGG CTATATTCTTACCTTGATACATTTCAGAAGCAACTGAAATCGTAGGACCTTCCTTGCTTCTCTATTGGGT GAATGTTTCTCAGTCTTGGTGTGAGTCTCAGTGCCTACGTAGTTAAAGCTTACTGAAATGTTCCCTTTAC AATTCTAGAGAGATATGTCCTTTATGTTGACATGTTCATGCTGACAGACTGCATCTGATTAAACAGCTGC CTGTGCAATGCCTCCAAGTGTGGATAAAAGAAAAATTAAACTCATAATCTTGGACAGCCATGTGTAGACT AGTTACATTGATCAAAGGGCAATAGAAATGATCCAGTGAGGATTTGTCTGAATTTCCCACAATTATTTAA AATCTACCTCAAATACCTGTTCATCTATAATGCCTCCCCTGAGGCCTTCATTCTGAATAGTACCTCTGTC TCTGTCCCCAAAGCACTAACTGATCCCTGTGATAGCGCACTTCCCAGCCAGGCTGATATGTAGACTTGGC TGCCTGTGTATCTTTTCCCCATAGACTGTGAGCTTCCTTTTATGAATAATAATTGTAGCTAGCATTTAGT AGGGTGCTCCTACCTGTTAAACTCTATGATGAGTGCTTTACATAGATTATATCATTTATTCACTAAACAG TCCTTTAAAATGGTGCTATATTCACTAAACAGTCCTTTAAAATGGTGCTATATTCACTAAACAGTCATTT AAAATGGTATTATTCTTCTTCATCTTACAGGTAAACAAACTAAGGCAAAAAAAAAAGTGAAATAATAAGT GCCAGTACACAGAGCTAGTAAGGAATAGGGTCTGCCAGGTCCCAAAAAGCATGCCATCACCTTTGCCCCA TACTGCCTCTGGTACAGATAGAGGTAATGTCTTATTTATCACTGCCATCCACTGGACCCAGCTTAGTGCC TGACACACAGAGGGGCTCAGTCAATGCTGATTGGTTTGAGGTGGAGCAAAAATGCTTAGCAGGGTGAGCA CCTTTGCTGTGATTGAGTATCTGATTCTCTATGAAGAGAAGGGGAGTCCTGAGCCAAACACATTCCTCTG GCTCCTGGCTGTCATCTTTATTTGCCCGGCTTCTTTGCTCTTCCTCCTTCCTAACTGCACCGTTTGGATT (snip / 以下略) http://togows.dbcls.jp/entry/genbank/AY948115.1.fasta

BioRuby What BioRuby can do? / できること  Biological data analysis / 生物データの解析  DNA, RNA  Protein / タンパク質  Relation of genes / 遺伝子間の関係性  Phylogenetic tree / 系統樹  Bibliography / 文献情報 …  I/O with other software / 他のソフトの入出力  Utilize web services / ウェブサービス利用

BioRuby Code example DNA → Protein translation / DNA→タンパク質の翻訳 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

BioRuby Status Latest version: BioRuby 1.4.1 (22/Oct/2010)  Supported Ruby version: 1.8.x  Will soon be migrated to1.9 / 速やかに1.9に移行予定  Files  Library: 230 files / 35,000 lines (w/o comments, void lines)  Tests: 120 files / 22,000 lines  Sample codes: 70 files  Functionality  580 classes/modules  2,800 methods  Plugin system introduced (using gem)

BioRuby BioRuby developer’s community  Core developers (6 persons)  Toshiaki Katayama (leader) (Univ. of Tokyo, Japan)  Naohisa Goto (release manager) (Osaka Univ., Japan)  Mitsuteru Nakao (Japan)  Pjotr Prins (Wageningen University, Netherlands)  Raoul Bonnal (INGM, Italy)  Jan Aerts (Belgium)  Total >30 contributors in 10 years 10年間で延べ30人以上の貢献者  Active developers / users in the world 世界中にアクティブな開発者/利用者

BioRuby

BioRuby Brief history 11/2000 BioRuby project started 06/2001 The first version (BioRuby 0.1) 2005-2006 IPA Exploratory (未踏) Software Project 02/2006 BioRuby 1.0.0 released 09/2008 moved from CVS to Git 08/2010 Published BioRuby research paper / 学術論文 10/2010 BioRuby 1.4.1 released

BioRuby Preceding projects / 先行プロジェクト Demanded by genome projects in late 90’s 1990年代後半のゲノムプロジェクトに伴う BioPerl – since 1996 (Perl 1987) Biopython – since 1999 (Python 1991) BioJava – since 1999 (Java 1995) BioRuby – since 2000 (Ruby 1995) Together with Open Bioinformatics Foundation http://open-bio.org/ Google Summer of Code 2009, 2010, 2011

BioRuby BioHackathon  Open Bio* Hackathon (2002, 2003)  Phyloinformatics Hackathon (2006)  DBCLS BioHackathon (2008-2010)

BioRuby Academic Community / 学会 • Bioinformatics Open Source Conference • GIW / JSBi (日本バイオインフォマティクス学会) • MBSJ (日本分子生物学会) • Open Bio Japan (オープンバイオ研究会)

BioRuby Open Source Community • Ruby Kansai (関西Ruby勉強会) (2005-) • IPA Exploratory (未踏) Software Project (2005-2006) • RubyKaigi (2006-) • Google Summer of Code (2009-2011) (Open Bioinformatics Foundation)

BioRuby Recent topics  Release of new version (BioRuby 1.4.2)  Ruby 1.9.3 migration  Revolution of DNA sequencing technique DNA塩基配列決定技術の飛躍的向上

BioRuby Next-Generation Sequencer (NGS) Example: Illumina HiSeq 2000 >600GB DNA sequences in 10-days 10日間で600GB超のDNA塩基配列を決定する装置 Lack of Resources / 足りないもの • HDD • CPU • Memory • Software • Human • Money • ...

BioRuby Join us BioRuby Web http://bioruby.org ML bioruby@lists.open-bio.org GitHub https://github.org/bioruby/bioruby BioRubyユーザーが書いた本多田雅人著「Rubyではじめるバイオインフォマティクス」発売中!!

BioRuby -- Bioinformatics Library

by ngotogenome on Jul 23, 2011

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