Tweet
Tweet

Slide 1

Slide 1 text

Ϋϥ΢υΛ׆༻ͨ͠ήϊϜ৘ใղੳͷݱঢ় 22 July 2016 | ৘ใॲཧֶձ ࿈ଓηϛφʔ 2016 ୈ2ճ Ϋϥ΢υ େా ୡ࿠! େֶڞಉར༻ػؔ๏ਓ ৘ใɾγεςϜݚڀػߏ " σʔλαΠΤϯεڞಉར༻ج൫ࢪઃ " ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ ಛ೚ݚڀһ" [email protected] Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS)

Slide 2

Slide 2 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Agenda! # 1. ࠓੜ໋Պֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔" # 2. ࠓͲͷΑ͏ͳܭࢉػ͕ٻΊΒΕ͍ͯΔͷ͔" # 3. Ϋϥ΢υΛ׆༻ͯ͠໰୊Λղܾ͢Δ

Slide 3

Slide 3 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) 1. ࠓੜ໋Պֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔

Slide 4

Slide 4 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ࠓੜ໋Պֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔ # ࣮ݧػցͷਐาʹΑͬͯσʔλͷαΠζͱྔ͕૿Ճ" # ήϊϜ෼໺Ͱ͸ʮ࣍ੈ୅DNAγʔΫΤϯαʔʯ͕ొ৔" # σʔλͷ஝ੵʹΑͬͯܭࢉػੜ෺ֶ͕੝Μʹͳ͍ͬͯΔ" # λϯύΫཱ࣭ମߏ଄σʔλɺը૾σʔλ" # σʔλॲཧɾղੳͷޮ཰Խ͸ࠓͳ͓ٸ຿" # ΞϧΰϦζϜͷਐาΛ଴͍ͬͯΔ࣌ؒ͸ͳ͍" # ϋʔυ΢ΣΞͷੑೳͰ໰୊Λղܾ͢Δ৔߹΋

Slide 5

Slide 5 text

λϯύΫཱ࣭ମߏ଄ղੳͷྫ! MEGADOCK: ౦޻େळࢁݚڀࣨ େ্ॿڭΒͷϓϩδΣΫτ http://www.nii.ac.jp/csi/openforum2016/track/pdf/20160526AM_TOUKOUDAI_akiyama2.pdf

Slide 6

Slide 6 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ήϊϜՊֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔ # ࣮ݧػցͷਐาΛཚ๫ʹྫ͑ΔͳΒ…" # ւ = ήϊϜ, ڕ = Ҩ఻ࢠ" # ʮͲΜͳڕ͕͍Δ͔ௐ΂Δ͜ͱͰւΛಛ௃͚ͮΔʯ" # ٕज़ͷਐาͰಓ۩ͷੑೳ͕޲্ͨ͠" # ௼Γ؄͕ఈҾ͖໢ʹͳͬͨ

Slide 7

Slide 7 text

ࣸਅࠨ: πϦόΧϝϥ @kazzwatabe https://tsuriba.camera/posts/XQeP3qmIp6A ࣸਅӈ: photo by atramos https://www.flickr.com/photos/atramos/5508960637 ࣮ݧػց͕ਐา͢Δͱ݁Ռͷղऍʹίετ͕͔͔Δ ͜Ε·ͰͷDNAγʔέϯαʔͷग़ྗσʔλ͸໨Ͱݟͯ֬ೝͰ͖ͨ ࠓͷDNAγʔέϯαʔͷग़ྗ͸ܭࢉػ͕ͳ͍ͱԿ΋Ͱ͖ͳ͍

Slide 8

Slide 8 text

https://flxlexblog.wordpress.com/2014/06/11/developments-in-next-generation-sequencing-june-2014-edition/ ←௼؄ ←ఈҾ͖໢ DNAγʔέϯα ػछ͝ͱͷੑೳൺֱ

Slide 9

Slide 9 text

No content

Slide 10

Slide 10 text

http://www.ncbi.nlm.nih.gov/Traces/sra/ ެڞσʔλϨϙδτϦͷσʔλαΠζͷ৳ͼ

Slide 11

Slide 11 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) DNAγʔέϯα͔ΒಘΒΕΔσʔλ # ʮήϊϜΛղಡ͢ΔʯͱҰݴͰݴ͏΋ͷͷ…" # ੜମαϯϓϧ͔ΒDNAΛநग़͢Δ" # நग़ͨ͠DNAΛ୹͍෼ࢠʹஅยԽ͢Δ" # DNAγʔέϯαͰղੳ͢Δ" # ୹͘அยԽ͞ΕͨԘج഑ྻͷϦετͰग़ྗ͞ΕΔ" # େྔͷDNAஅยͷ৘ใ͔ΒݩͷDNAΛ෮ݩ͢Δ! # de novo Assemble" # Reference Alignment" "

Slide 12

Slide 12 text

https://speakerdeck.com/michaelbarton/ranking-genome-assemblers-with-docker-containers-dockercon-eu-2014 DNAγʔέϯα͔Βग़ྗ͞ΕΔσʔλ͸அยԽ͍ͯ͠Δ

Slide 13

Slide 13 text

https://speakerdeck.com/michaelbarton/ranking-genome-assemblers-with-docker-containers-dockercon-eu-2014 DNAγʔέϯαΛγϡϨομʔʹྫ͑Δͱ…

Slide 14

Slide 14 text

https://speakerdeck.com/michaelbarton/ranking-genome-assemblers-with-docker-containers-dockercon-eu-2014 ήϊϜΞηϯϒϧ = ຊͷ෮ݩ

Slide 15

Slide 15 text

https://speakerdeck.com/michaelbarton/ranking-genome-assemblers-with-docker-containers-dockercon-eu-2014 ήϊϜΞηϯϒϧ = ຊͷ෮ݩ

Slide 16

Slide 16 text

http://www.historyofnimr.org.uk/mill-hill-essays/essays-yearly-volumes/2010-2/bringing-it-all-back-home-next-generation- sequencing-technology-and-you/ ϦϑΝϨϯεΞϥΠϯϝϯτ! = खຊ (ϦϑΝϨϯε) ʹԊͬͯฒ΂ͯ෮ݩ

Slide 17

Slide 17 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) σʔλղੳιϑτ΢ΣΞ (ղੳπʔϧ) # ଟ͘ͷղੳπʔϧ͕ΦʔϓϯιʔεͰެ։͞Ε͍ͯΔ" # ର৅σʔλͷੑ࣭ʹΑͬͯ࠷దͳπʔϧ͕ҟͳΔ" # σʔλղੳऀ (ੜ෺ֶऀ) ͕σʔλղੳΛߦ͏" # πʔϧ։ൃऀ(࣮૷ऀ)ͱར༻ऀ͸ಉҰͰ͸ͳ͍" # ར༻ऀ͕πʔϧͷڍಈΛ׬શʹ೺Ѳ͍ͯ͠Δͱ͸ݶΒͳ͍" # ղੳऀ͸ৗʹσʔλղੳΛ͍ͯ͠ΔΘ͚Ͱ͸ͳ͍" # ੜ෺࣮ݧͷยखؒʹղੳΛ͢Δݚڀऀ΋ଟ͍

Slide 18

Slide 18 text

ΦʔϓϯιʔεͰެ։͞Ε࣮ͨ૷Λ༻͍ͯղੳ https://omictools.com/de-novo-genome-sequencing-category

Slide 19

Slide 19 text

ΦʔϓϯιʔεͰެ։͞Ε࣮ͨ૷Λ༻͍ͯղੳ https://omictools.com/whole-genome-resequencing-category

Slide 20

Slide 20 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ࠓੜ໋Պֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔! # ·ͱΊ" # σʔλͷྔͱ਺͕ٸܹʹ૿͓͑ͯΓɺࠓޙ΋૿͑Δ" # ໨తʹΑͬͯҟͳΔπʔϧɾΞϧΰϦζϜ͕࢖༻͞ΕΔ" # σʔλղੳऀͱπʔϧ։ൃऀ(࣮૷ऀ)͸ҟͳΔ͜ͱ͕ଟ͍

Slide 21

Slide 21 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) 2. ࠓͲͷΑ͏ͳܭࢉػ͕ٻΊΒΕ͍ͯΔͷ͔

Slide 22

Slide 22 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ࠓͲͷΑ͏ͳܭࢉػ͕࢖ΘΕ͍ͯΔͷ͔ # PC" # PCΫϥελ" # ڌ఺εύίϯ" # ࠃཱҨ఻ֶݚڀॴ εʔύʔίϯϐϡʔλγεςϜ

Slide 23

Slide 23 text

࣍ੈ୅γʔΫΤϯαʔ%3:ղੳڭຊ ࡉ๔޻ֶผ࡭ ΑΓ ڭຊʹ͸MacΛങ͑ͱॻ͍ͯ͋Δ

Slide 24

Slide 24 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ͲͷΑ͏ͳܭࢉػ͕ٻΊΒΕΔͷ͔ # ର৅σʔλ͕େ͖͘ͳΔ/૿͑Δͱ௨ৗͷPCͰ͸ݫ͍͠" # ղੳσʔλ͕ͲΜͲΜཷ·Δ" # ಡΈॻ͖͕ߴ଎ͰڊେͳετϨʔδ! # πʔϧ͕Out of memoryͰམͪΔ" # େن໛ϝϞϦ! # όονॲཧΛେྔͷαϯϓϧʹର࣮ͯ͠ߦ͢Δ" # ෼ࢄ࣮ߦδϣϒεέδϡʔϦϯάγεςϜ! # େܕڞ༻ܭࢉػ΁ͷཁٻͷߴ·Γ" # Ҩ఻ֶݚڀॴSCͷಋೖ (2012~) => ·ͩे෼Ͱ͸ͳ͍

Slide 25

Slide 25 text

େֶڞಉར༻ػؔ๏ਓ ৘ใɾγεςϜݚڀػߏ ࠃཱҨ఻ֶݚڀॴ SuperComputer Facilities of National Institute of Genetics photo from http://sc.ddbj.nig.ac.jp/index.php/ja-gallery

Slide 26

Slide 26 text

No content

Slide 27

Slide 27 text

૿͑ଓ͚ΔϢʔβ਺ Ҩ఻ݚDDBJηϯλʔ খּݪ͞ΜͷൃදࢿྉΑΓ

Slide 28

Slide 28 text

ṧഭ͢ΔσΟεΫ https://sc.ddbj.nig.ac.jp/index.php/ja-nig-statistics

Slide 29

Slide 29 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ݱ৔Ͱ͸Կ͕ϘτϧωοΫͳͷ͔! εύίϯϢʔβձͳͲͷώΞϦϯάΑΓ # ܭࢉػʹෆ׳ΕͳϢʔβͷ೰Έ" # ܭࢉػ͝ͱʹԿ͕Ͱ͖ͯԿ͕Ͱ͖ͳ͍ͷ͔Θ͔Βͳ͍" # େن໛ͳܭࢉػΛඞཁͱ͢Δ͕CUI͕࢖͑ͳ͍" # ܭࢉػΛ࢖͍͜ͳ͢ਓͷ೰Έ" # ܭࢉػ͕ࠞΜͰ͍ͯδϣϒ͕ྲྀͤͳ͍" # σʔλͷղੳ΍อଘʹे෼ʹ༧ࢉΛ౤ೖͰ͖ͳ͍! # ؀ڥߏஙʹίετ͕͔͔Δ" # ܭࢉػͷ໘౗Λݟͨ͘ͳ͍

Slide 30

Slide 30 text

ʮੜ෺࣮ݧʹ͸͓͕͔͔ۚΔ͕ɺ
 ɹσʔλղੳʹ͸ͦΕ΄Ͳ͓͕͔͔ۚΒͳ͍ʯͱࢥΘΕ͍ͯΔ http://trattoriainutano.tumblr.com/post/132214903857/

Slide 31

Slide 31 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ͲͷΑ͏ͳܭࢉػ͕ٻΊΒΕ͍ͯΔͷ͔ # ·ͱΊ" # ର৅σʔλͱ໨తʹΑͬͯཁٻʹ͕ࠩ͋Δ" # ήϊϜ෼໺Ͱ͸ετϨʔδ΍ϝϞϦͷ೰Έ͕ਂࠁ" # ϢʔβͷܭࢉػϦςϥγʹ΋෯͕͋Δ" # ϢʔβͷϨϕϧʹΑͬͯٻΊΔϨΠϠʔ͕ҧ͏

Slide 32

Slide 32 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) 3. Ϋϥ΢υΛ׆༻ͯ͠໰୊Λղܾ͢Δ

Slide 33

Slide 33 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Ϋϥ΢υΛ׆༻ͯ͠໰୊Λղܾ͢Δ # Ϋϥ΢υͰղܾͰ͖Δ໰୊" # ಋೖίετ" # ϊʔυͷࠞࡶ" # ϝϯςφϯείετ" # Ϋϥ΢υར༻ʹ͓͚Δ՝୊" # ετϨʔδͷίετ" # ݚڀඅͰͷࢧ෷͍" # ະൃදσʔλ / ݸਓ৘ใΛؚΉσʔλͷѻ͍

Slide 34

Slide 34 text

Ϋϥ΢υ׆༻ࣄྫ (SaaS)! Google Genomics https://cloud.google.com/genomics/v1/analyze-variants

Slide 35

Slide 35 text

Ϋϥ΢υ׆༻ࣄྫ (IaaS)! 1000ਓήϊϜσʔλ on AWS https://aws.amazon.com/jp/1000genomes/

Slide 36

Slide 36 text

The NIH Commons! ถࠃͰ͸ϑΝϯσΟϯάଆ͕Ϋϥ΢υར༻Λଅਐ “The Commons is a shared virtual space where scientists can work with the digital objects of biomedical research, i.e. it is a system that will allow investigators to find, manage, share, use and reuse data, software, metadata and workflows.” - https://datascience.nih.gov/ commons

Slide 37

Slide 37 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Ϋϥ΢υ׆༻ࣄྫ (PaaS/SaaS)! ήϊϜղੳύΠϓϥΠϯ on ΞΧσϛοΫɾΠϯλʔΫϥ΢υ # JST CREST: ΠϯλʔΫϥ΢υΛ׆༻ͨ͠ΞϓϦέʔγϣϯத৺ܕΦʔόʔ ϨΠΫϥ΢υٕज़ʹؔ͢Δݚڀ (୅ද: NII߹ాઌੜ)" # ΞΧσϛοΫɾΠϯλʔΫϥ΢υͷࢼΈ" # Ҩ఻ݚεύίϯΛ৘ใݚΫϥ΢υଞࠃ಺ͷΞΧσϛοΫΫϥ΢υͱ࿈ܞ" # ղੳʹ༻͍ΒΕΔ֤πʔϧΛDockerԽ͢Δ͜ͱͰΞϓϦέʔγϣϯΛ ϙʔλϒϧʹ" # ༧ΊπʔϧΛ૊Έ߹ΘͤͨϫʔΫϑϩʔΛߏங͠GUIΛఏڙ" # ղੳσʔλ͝ͱʹ࠷దͳϦιʔεΛׂΓ౰ͯͨܭࢉػΛ্ཱͪ͛

Slide 38

Slide 38 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Ϋϥ΢υΛ׆༻ͯ͠໰୊Λղܾ͢Δ # ·ͱΊ: Ϋϥ΢υར༻ʹ͓͚Δ՝୊" # ετϨʔδͷίετ" # ܭࢉ࣌͸ߴ଎ͳI/OΛཁٻ" # อ؅࣌͸௿ίετͳετϨʔδ" # (঎༻Ϋϥ΢υͷ৔߹) ݚڀඅͰͷࢧ෷͍" # ݸਓ৘ใΛؚΉσʔλͷѻ͍" # ҆શੑͷཱ֬ - ར༻࣮੷ͷ஝ੵ" # ΨΠυϥΠϯ౳ͷࡦఆ

Slide 39

Slide 39 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) େֶ΍පӃͰ͸ήϊϜ৘ใ͕࣍ʑʹ! AMEDͳͲͷػߏʹΑͬͯήϊϜ෼໺͕ਪਐ͞Ε͍ͯΔ

Slide 40

Slide 40 text

Secure cloud computing for genomic data! Datta, Somalee, Keith Bettinger, and Michael Snyder. "Secure cloud computing for genomic data." Nature Biotechnology 34.6 (2016): 588-591.! ήϊϜσʔλղੳʹΫϥ΢υΛ༻͍Δ͋ͨΊʹඞཁͳηΩϡϦςΟ͸ ݚڀػؔͱΫϥ΢υϓϩόΠμͷ࿈ܞʹΑͬͯ੒͞ΕΔඞཁ͕͋Δ

Slide 41

Slide 41 text

Secure cloud computing for genomic data! Datta, Somalee, Keith Bettinger, and Michael Snyder. "Secure cloud computing for genomic data." Nature Biotechnology 34.6 (2016): 588-591.! # Security requirements" # The data privacy agreement / σʔλͷऔѻʹ͍ͭͯͷݚڀػؔͱͷ߹ҙ" # Physical and logical security / ෺ཧ/࿦ཧͰͷηΩϡϦςΟ" # Encryption data / σʔλͷอ؅/సૹ࣌ͷ҉߸Խ" # Authentication / Ϣʔβೝূ " # Principle of Least Privilege / ࠷খݖݶͷݪଇ" # Firewalls / ϑΝΠϠʔ΢Υʔϧ" # Logging and monitoring / ϩΪϯάͱϞχλϦϯά" # Training / ηΩϡϦςΟ΍ೝূʹ͍ͭͯͷτϨʔχϯά" # Security and privacy / ݸਓ৘ใͷอޢ

Slide 42

Slide 42 text

ݸਓ৘ใͷऔΓѻ͍ͱݚڀར༻ͷؔ܎! ೔ຊܦࡁ৽ฉʮҩֶݚڀͱݸਓ৘ใͷཱ྆Λ ʯΑΓ! http://www.nikkei.com/article/DGXKZO05121060S6A720C1EA1000/ ݸਓ৘ใΛؚΉݚڀσʔλ͸පؾͷݪҼղ໌΍࣏ྍʹඇৗʹॏཁ ηΩϡΞͳ؀ڥ͕͋Ε͹ݚڀΛਪਐ͢Δେ͖ͳ෢ثʹͳΔ

Slide 43

Slide 43 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Summary

Slide 44

Slide 44 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) Summary # ࠓੜ໋Պֶͷ෼໺ͰԿ͕ى͖͍ͯΔͷ͔" ○ େن໛ͳσʔλͷ஝ੵʹΑΓܭࢉػधཁ͕ߴ·͍ͬͯΔ" # ࠓͲͷΑ͏ͳܭࢉػ͕ٻΊΒΕ͍ͯΔͷ͔" ○ ήϊϜ෼໺Ͱ͸ετϨʔδ΍ϝϞϦ͕ॏࢹ͞ΕΔ" ○ ར༻ऀʹΑͬͯཁٻ͕ࡉ͔͘ҧ͏" # Ϋϥ΢υΛ׆༻ͯ͠໰୊Λղܾ͍͖͍ͯͨ͠" ○ Ϋϥ΢υͷརศੑΛ͞ΒʹߴΊ͍ͯ͘" ○ ར༻ࣄྫΛ૿΍͢͜ͱ͕ॏཁ

Slide 45

Slide 45 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ࢀߟࢿྉ

Slide 46

Slide 46 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔʹ͍ͭͯ # ϥΠϑαΠΤϯε෼໺ʹ͓͚Δσʔλϕʔε౷߹ʹࢿ͢Δٕज़ ։ൃΛ୲͏" # ج൫ٕज़։ൃ" # ηϚϯςΟοΫ΢Σϒٕज़΍ࣗવݴޠॲཧΛ༻͍ͨϑΣσ Ϩʔγϣϯܕσʔλ౷߹ͷͨΊͷٕज़։ൃ΍ࠃࡍඪ४ͷࡦ ఆʹऔΓ૊Ή" # DDBJ࿈ܞ" # େن໛ήϊϜσʔλΛ࢝Ίͱ͢Δσʔλͷ׆༻ͷ
 ͨΊͷٕज़։ൃΛߦ͏

Slide 47

Slide 47 text

Licensed under CC-BY 4.0 ©2016 Tazro Ohta (DBCLS) ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔʹ͍ͭͯ # JSTͷηϯλʔ NBDC ͱڞಉͰσʔλϕʔεࣄۀΛਐΊΔ" # DDBJͱ͸ಉ͡૊৫ (ROIS, NII΋ಉ͡) Ͱ࿈ܞ͍ͯ͠Δ http://dbcls.rois.ac.jp/about