The 3rd Open Science Award

The 3rd Open Science Award

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Tazro Inutano Ohta

March 17, 2016
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  1. None
  2. Award! What/Why

  3. Nominate,! Vote,! Honor! by the community

  4. Award! to encourage the open science! in Japanese Biomedical research

  5. Award! to honor to people contributing to! the activity which

    may not be published
  6. The! 3rd! Award

  7. Nominated Products

  8. Best Database ChIP-Atlas! AOE (All Of gene Expression)! RDF Portal

    for NBDC! RefEx! DNApod! BRCϚ΢εϦιʔεදݱܕϝλσʔλ! BRCࡉ๔Ϧιʔεදݱܕϝλσʔλ! JCMඍੜ෺Ϧιʔεϝλσʔλ! NBRPϝμΧදݱܕϝλσʔλ! Integrative Japanese Genome Variation Database! ཧݚϝλσʔλϕʔε
  9. Best Software meshr! mudi - mutation discovery! ΫϦοΫͪΌΜ! CRISPRdirect! smbt!

    Centroidfold! FuncTree! Gendoo! UMATracker! Cnocglas MolBrowser! Bayes Linux! GhostX! MEGADOCK
  10. Best Website/Article RͰԘج഑ྻղੳ/RͰϚΠΫϩΞϨΠσʔλղੳ! ύοΫϚϯͷ௅ઓ! ฏ੒27೥౓NGSϋϯζΦϯߨशձ - ChIP-Seqղੳجૅ! ʮ΍ʔ͍͓લͷ෕ͪΌΜόΠΦΠϯϑΥʔʂʯ! ੜ໋ՊֶݚڀΛߟ͑ΔΨνٞ࿦ˏୈ36ճ೔ຊ෼ࢠੜ෺ֶձ! ͳͥόΠΦΠϯϑΥϚςΟΫεͷղੳ͸λμͰ͸ͳ͍ͷ͔!

    NGSσʔλղੳසग़୯ޠू! NGS͸೉͍͠ (Ծ)! όΠΦΠϯϑΥͰ࣮ݧϊʔτΛऔΖ͏! biopapyrus! CloudBioLinuxΛ༻͍ͯϩʔΧϧαʔόʹNGSղੳ؀ڥΛߏங͢Δ! bio෼໺޲͚ͷDockerίϯςφΛͭ͘Δ on MacOSX
  11. Winners

  12. Best Database

  13. Best Database 1st! ChIP-Atlas, RDF Portal for NBDC! ! 3rd!

    RefEx
  14. ChIP-Atlas

  15. ChIP-Atlas SRAͷChIP-SeqσʔλΛશ෦࠶ղੳͯ͠ՄࢹԽͱൺֱ͕Մೳʹɻਓྗ ΞϊςʔγϣϯʹΑΔσʔλͷ੔ཧͱෳ਺ͷσʔλղੳΛαϙʔτɻ! ! ։ൃऀ (۝भେֶ ԭਅ໻͞Μ) ͔Βͷίϝϯτ:! ʮΊͪΌͪ͘Ό͏Ε͍͠Ͱ͢ʂड৆ࣜ͸ NY

    ʹ͍·͢ͷͰࢀՃͰ͖ͳ ͍ͷ͕࢒೦Ͱ͢ʯ
  16. RDF Portal for NBDC

  17. RDF Portal for NBDC ड৆ऀߨԋ! DBCLS ઒ౡ लҰ͞Μ

  18. RefEx

  19. RefEx ड৆ऀߨԋ! DBCLS খ໺ ߒխ͞Μ

  20. http://refex.dbcls.jp/ -JDFOTFEVOEFSB$$#:˜খ໺ߒխ %#$-4 Ҩ఻ࢠൃݱϦϑΝϨϯεσʔληοτ ʰRefExʱ ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ খ໺ ߒխ

  21. -JDFOTFEVOEFSB$$#:˜খ໺ߒխ %#$-4 3FG&Yͷಛ௕ ๏ਖ਼ৗ૊৫ɾଁثͷҨ఻ࢠൃݱঢ়گΛͻͱ໨Ͱ ๏ ͭͷҟͳΔ࣮ݧख๏ʹΑͬͯಘΒΕͨछྨͷਖ਼ৗ૊৫ɾଁث
 ʹ͓͚ΔҨ఻ࢠൃݱσʔλΛฒྻʹදݱ ๏ ࿦จͰݟ͔͚ͨೃછΈͷͳ͍Ҩ఻ࢠ͕ͲͷଁثͰൃݱ͍ͯ͠Δͷ͔
 ࣮ࡍͷଌఆσʔλ͔Βݚڀऀࣗ਎ͷ໨Ͱ؆୯ʹ֬ೝ


    ๏ௐ΂͍ͨҨ఻ࢠΛΑΓ୳͠΍͘͢ΑΓ෼͔Γ΍͘͢ ๏ ň૊৫ಛҟతҨ఻ࢠʼnΛଌఆσʔλ͔Βಠࣗʹࢉग़͠ɺ૊৫͝ͱʹ
 ҰཡՄೳ ๏ "EWBODFETFBSDI΍ߜΓࠐΈݕࡧΛ࢖ͬͯෳࡶͳݕࡧ৚݅΋
 ࢦఆՄೳͰɺ໨తͱ͢ΔσʔλΛ؆୯ʹݕࡧ ๏௚ײతͳՄࢹԽͰ৽ͨͳ஌ࣝൃݟɾԾઆߏஙΛ ๏ ૊৫ؒͷൺֱͱଌఆख๏ؒͷൺֱΛཱ྆ͤͨ͞૬ରൃݱྔͷ
 όʔνϟʔτ΍ਓମ%ϞσϧʹൃݱྔΛ൓өͤͨ͞ώʔτϚοϓ ๏ ೚ҙͰબΜͩ࠷େͭͷҨ఻ࢠͷൃݱσʔλΛฒྻʹൺֱͰ͖Δ
 Ϧετػೳ
 ๏࠶ར༻ՄೳͰ༗༻ͳύϒϦοΫσʔλͷ׆༻ྫ ๏ ੜ໋Պֶσʔλͷڞ༗͓Αͼ࠶ར༻ͷ׆༻ྫͷͻͱͭͰ͋Γɺ
 σʔλۦಈܕݚڀͷͨΊͷπʔϧͱͯͩ͠ΕͰ΋ࣗ༝ʹར༻Մೳ
  22. -JDFOTFEVOEFSB$$#:˜খ໺ߒխ %#$-4 '"/50.$"(&σʔλ ๏ ώτछ ๏ Ϛ΢εछ w ࡉ๔ג w

    ॳ୅ഓཆࡉ๔ w ੒ମ૊৫ w ଻ࣇ૊৫ ๏ ଞͷσʔλʹઌۦ͚ͯ
 3%'Խ w ϏϡʔΞ࡞੒த w ελϯβԽ΁
  23. -JDFOTFEVOEFSB$$#:˜খ໺ߒխ %#$-4 5IF3FG&YBOBMZTJT ๏ ࣮ݧͰݟग़ͨ͠ඪతɾ ީิҨ఻ࢠͷൃݱྔ͕ ਖ਼ৗ૊৫ͰۃΊͯ
 ௿͍͜ͱΛ֬ೝ ๏ ͜ΕΒͷҨ఻ࢠΛ


    ࣏ྍඪతͱͨ͠৔߹ʹ ਖ਼ৗ૊৫΁ͷӨڹ͕
 খ͍͞Ŋͱ༧ଌͰ͖ͨ
 ๏ 3FG&YσʔλΛࣗ෼Ͱ
 Ճ޻ͯ͠ŊਤΛ࡞੒
  24. Best Software

  25. Best Software 1st! CRISPRdirect! ! 2nd! ΫϦοΫͪΌΜ! 3rd! Bayes Linux

  26. CRISPRdirect

  27. CRISPRdirect ड৆ऀߨԋ! DBCLS ಺౻ ༤थ͞Μ

  28. ϥΠϑαΠΤϯε౷߹σʔλϕʔεηϯλʔ %#$-4  ɹ ɹ ɹ ɹ ɹ ɹ 

    ಺ ౻ ༤ थ 
 ɹ ɹ ɹ ɹ ɹ   !NFTP@DBDBTF ɹήϊϜฤूͷͨΊͷ
 ΨΠυ3/"ઃܭπʔϧ 5XFFU0, CRISPRdirect
  29. $3*413ͷΨΠυ3/"഑ྻઃܭ ˙/((ʹྡ઀͢ΔԘجΛબ୒ ˙Φϑλʔήοτͷগͳ͍഑ྻΛબ୒ ˠ$3*413EJSFDUΛެ։ Naito, Hino, Bono, Ui-Tei
 CRISPRdirect: software

    for designing CRISPR/ Cas guide RNA with reduced off-target sites.
 Bioinformatics (2015) CRISPRdirect
  30. $3*413EJSFDU

  31. $3*413EJSFDU ɹʴछ ʢ২෺͸छʣ

  32. $3*413EJSFDU ɹʴछ ʢ২෺͸छʣ

  33. $3*413EJSFDU

  34. $3*413EJSFDU chr1:562688-562700 chr1:793957-793969 chr1:957810-957824 chr1:1085660-1085674 chr1:1373831-1373844 chr1:1482921-1482934 chr1:1526112-1526124 562688 793957

    957810 1085660 1373831 1482921 1526112 Mismatches G G C A C G Matches are highlighted with blue background. and indels are marked in red. GAAGAAAGGGGAGTGGGCACGAAATACTAC AACGAAGTCCCTCTGTCTGTGTGTGCCTAT AGGCTGCTGGCCTGGAAGGTAGTCACGTGG ATGAGATTGGAAAGTAGTAATAAGCCATGT TCAACTCCAGCCTCATGCGGATCACCCTGC TGGAGTTCTGTGTGGAAGGTGCGTGGTGGG CAGACACACAGGCCCACCCAGGTGGGTCCC GCCTTGCCTGCCCTGTGTTCCTTCCTGGAG GGGGATGGGAAGAAAGTGGCCCAGGCACCC AAGATCCTGATAGCTTTAACCCAGCGCAGA CTAGACCTGCAAGCCCCACCAGAGGCTGTG ACCAAAGGGACCACAGACCAAGCCATGAGC TACTTGGGAGGTCGAGGCAGGAGAATGGCG CGGAGCTTGCAGTGAGCAGAGATCGCACCA AGAACCTGCA- -G- -GG AGAACC- -GCAGGA- -G GAACCTG AGGAGG AG ACCTGCAGGA G AG A- -CTGCAGGAGG AG ACCTG- -AGGAGG AGAACCTGC- -- -GAGG
  35. ˙/((ʹྡ઀͢ΔԘجΛબ୒ ˙ήϊϜͷ΄͔ͷྖҬͱ͸Ԙج഑ྻ͕
 ɹҰகͤͣɺඪతͱ͢Δ෦Ґͱ͚ͩ
 ɹ׬શҰக͢Δ഑ྻΛબ୒ ˙ͱ͘ʹ1".ۙ๣ͷNFS·ͨ͸
 ɹNFSͷಛҟੑΛॏࢹ $3*413EJSFDU Naito, Hino, Bono,

    Ui-Tei
 CRISPRdirect: software for designing CRISPR/ Cas guide RNA with reduced off-target sites.
 Bioinformatics (2015) CRISPRdirect
  36. ΫϦοΫͪΌΜ

  37. ΫϦοΫͪΌΜ ड৆ऀߨԋ! ܚጯٛक़େֶ ߥ઒ ࿨੖͞Μ

  38. None
  39. 2011 2012 2013 2014 2015 2016 2010 2017 *#.8BUTPO͕+FPQBSEZͰ༏উ ୈճΦʔϓϯόΠΦݚڀձ

    ʮ8BUTPOΫΠζ൪૊΁ͷ௅ઓɺΛ௒͑Ζʂͦͷ໊͸$SJDLʯࠤ౻ݡೋ ୈճΦʔϓϯόΠΦݚڀձ4*(.#* ςʔϚɿόΠΦ൛4JSJʢԾশɿΫϦοΫͪΌΜʣ։ൃʹ͍ͭͯٞ࿦ ʮʬΫϦοΫͪΌΜʭΛ૑ΔͨΊʹ͸Կ͕ඞཁ͔(MBOHVBHF1SPKFDUͷΞϓϩʔνʯߥ઒࿨੖ #JP)BDLBUIPO ʮ(&/*&ʯ(MBOHVBHF1SPKFDU “Finally, the project that generated the most “buzz” among the participants in BioHackathon 2012 was Genie - a “Siri for Biologists”. “ J. Biomed. Semantics. (2014) /#%$%#$-4ڞಉݚڀܭը ʮNCBD/DBCLS ࣭ٙԠ౴γεςϜʯยࢁढ़໌ ࣗવݴޠͰɺ୯ޠͰ͸ͳ͘ɺจΛݕࡧ͢ΔγεςϜ
  40. ࣭໰ ߏจղੳ ࣭໰Ͱ͸ͳ͘ձ࿩ʁ ΫΤϦ֦ு ఆܕ࣭໰ɿήϊϜղੳ༻ ԣஅݕࡧɿϖʔδ ׬શจநग़ Heuristic Scoring Filtering

    τοϓ̑ީิ ׬શจͰ۩ମతͳ࣭໰͕ඞཁ Problem: ࣗવʹձ࿩ɾର࿩Λͨ͘͠ͳΔ ϢʔβΠϯλϑΣΠε Goal: Ϧιʔε͕ͳ͍͔Β͕͔͔࣌ؒΔ Problem: ଴ͭࣄ͕ۤʹͳΒͳ͍ ϢʔβΠϯλϑΣΠε Goal: ਫ਼౓͸ͦ͜·ͰݟࠐΊͳ͍ Problem: ؒҧͬͯ΋ڐͪ͠Ό͏ ϢʔβΠϯλϑΣΠε Goal:
  41. Bayes Linux

  42. Bayes Linux ʮ࠶ݱੑͷ͋ΔόΠΦΠϯϑΥ؀ڥͷߏஙʯΛίϯηϓτʹΦʔϓϯ ιʔεͰ։ൃɾ഑෍͞Ε͍ͯΔVMɻ৴པੑͷߴ͍඼࣭؅ཧɺݱ৔Ͱ ࣮ӡ༻͞Ε͍ͯΔ࣮੷ͰධՁ͕ߴ͍ɻ! ! ։ൃऀ (ཧݚACCC BiT ೋ֊ಊѪ͞Μ)

    ͔Βͷίϝϯτ:! ʮͪΐ͏Ͳ৽͍͠όʔδϣϯΛϦϦʔε༧ఆͰͨ͠ (஫: 3/11ʹϦϦʔ ε͞Ε·ͨ͠) ɻBH, Open-bioࢀՃͰ͖ͳ͍ͷ͕࢒೦Ͱ͢ʯ
  43. Best Website

  44. Best Website 1st! biopapyrus! RͰԘج഑ྻղੳ/RͰϚΠΫϩΞϨΠσʔλղੳ! ͳͥόΠΦΠϯϑΥϚςΟΫεͷղੳ͸λμͰ͸ͳ͍ͷ͔

  45. biopapyrus

  46. biopapyrus ੜ෺౷ܭ/ੜ෺৘ใͷجૅ஌͕ࣝ෯޿͘঺հ͞Ε͍ͯΔ΢ΣϒαΠ τɻ೔ຊશࠃͷֶੜͷఆظࢼݧΛॿ͚͍ͯΔʢ͸ͣʣɻ! ! ։ൃऀ (౦ژେֶ ଙݐڧ͞Μ) ͔Βͷίϝϯτ:! ʮॳΊ͸γέϓϦతʹ࡞͍ͬͯ·͕ͨ͠ɺͦͷ͏ͪࣗ෼༻ͷϝϞாత ͳײ͡ʹͳΓɺ࠷͸ଞͷϢʔβʔ͕ݟ͍ͯΔͱ͍͏͜Λҙࣝͯ͠࡞੒

    ͍ͯ͠·͢ɻ·ͩ·ֶͩੜͰ͢ͷͰɺ΢Σϒϖʔδʹॻ͍ͯ͋Δ͜ͱ ΛӏವΈʹ͠ͳ͍Ͱ͍ͩ͘͞ʯ
  47. RͰԘج഑ྻղੳ/! RͰϚΠΫϩΞϨΠσʔλղੳ

  48. RͰԘج഑ྻղੳ/! RͰϚΠΫϩΞϨΠσʔλղੳ ݴΘͣͱ஌Ε໊ͨ෺ςΩετɻ͜ΕΛݩʹߨशձ͕։࠵͞ΕͨΓɺຊ ͕ग़൛͞ΕͨΓ͍ͯ͠·͢ɻܧଓͯ͠Ξοϓσʔτɺख๏ͷൺֱ΍ච ऀͷίϝϯτͳͲඇৗʹ༗༻Ͱ͢ɻ! ! ։ൃऀ (౦ژେֶ ໳ా޾ೋ͞Μ) ͔Βͷίϝϯτ:!

    ʮࣗ෼Ͱࣗ෼͚ͩʹ౤ථ͍ͯ͠Ε͹୯ಠҰҐͩͬͨͷͰ͢Ͷw ݴ͍ͨ ͍์୊΍Γ͍ͨ์୊ͷ໳ాʹ΋౤ථͯͩ͘͠͞Δํ͕Ұఆͷׂ߹Ͱ͍ Βͬ͠ΌΔͷ͸͋Γ͕͍ͨ͜ͱͰ͢ɻ͜Ε͔Β΋ϙδγϣϯ͕ଓ͔͘ ͗ΓɺͰ͖Δ͚ͩΞοϓσʔτΛ͢ΔॴଘͰ͢ʯ
  49. ͳͥόΠΦΠϯϑΥϚςΟΫε ͷղੳ͸λμͰ͸ͳ͍ͷ͔

  50. ͳͥόΠΦΠϯϑΥϚςΟΫε ͷղੳ͸λμͰ͸ͳ͍ͷ͔ γʔέϯεʹ͸༧ࢉܭ্͢Δ͚ΕͲ΋σʔλॲཧ͸λμͰͰ͖Δͱࢥͬ ͍ͯΔਓ΁ૹΔఏݴɻࢧ࣋ͷ޿͞͸ະͩຒ·Β͵΢Σοτ/υϥΠͷ ߔͷਂ͞ނͰ͠ΐ͏͔ɻ! ! ։ൃऀ (DBCLS େాୡ࿠͞Μ) ͔Βͷίϝϯτ:!

    ʮ”ରՁΛ͖ͪΜͱ෷͏͜ͱ͕ͦ͜ϓϩδΣΫτΛ੒ޭͤ͞Δൿ݃Ͱ ͋Δ"ͱ͍͏ϑϨʔζʹάοͱ͖ͨͷͰҰؾʹ༁͠·ͨ͠ɻϓϦϯτΞ ΢τͯ͠഑Γา͍͍ͯͩ͘͞ʯ
  51. Messages! from! Community

  52. •ྑ͍اըͰ͢! •ΫϦοΫͪΌΜ ͔ΘE! •͍ͭ΋͋Γ͕ͱ͏͍͟͝·͢ (^^)! •೰·͍͠ɻɻͱͯ΋೰·͍͠ɻɻ! •஌Βͳ͍αʔϏεΛ஌Δ͜ͱ͕Ͱ͖ͯษڧʹͳΓ·͢! •ީิϦετΛݟΔ͜ͱͰຖ೥ษڧ͍͖͍ͤͯͨͩͯ͞·͢! •ຖ౓ɺ͓͔ͭΕ͞·Ͱ͢! •ࠓ೥͸Φʔϓϯιʔεʹߩݙ͢Δ೥ʹ͍ͨ͠ͱߟ͍͑ͯ·͢!

    •օ༷ͷ͓͔͛Ͱ೔ʑͷղੳ͕ਐΊΒΕ·͢ɻ͋Γ͕ͱ͏͍͟͝·͢ɻ! •͍ͭ΋͓ੈ࿩ʹͳ͍ͬͯΔ΋ͷͩͬͨΓɺॳΊ·ͯ͠ͷ΋ͷͩͬͨΓɺࠓճ΋ 1ͭ1͕ͭษڧʹͳΓ·ͨ͠ɻ! •͜ͷاը͸ࠓޙ΋ͥͻܧଓͯ͠Լ͍͞ɻڱٛͷόΠΦΠϯϑΥϚςΟΫεͰ͸ ͳ͘ɺԠ༻όΠΦΠϯϑΥϚςΟΫεʹؔ͢Δ೔ຊͷίϛϡχςΟʔͷ౒ྗͷ ྺ࢙͕ࠁ·Ε͍ͯΔͱࢥ͍·͢ɻ
  53. Thank you!