Bigdata meetup in Tokyo at 8 Dec. 2011 by Tazro Inutano Ohta

1. G E S C AL E
LAR
D A TA IN
E SC IE N CE

10. Update( new_suffix )
{
current_suffix = active_point
test_char = last_char in new_suffix
done = false;
while ( !done ) {
if current_suffix ends at an explicit node {
if the node has no descendant edge starting with test_char
create new leaf edge starting at the explicit node
else
done = true;
} else {
if the implicit node's next char isn't test_char {
split the edge at the implicit node
create new leaf edge starting at the split in the edge
} else
done = true;
}
if current_suffix is the empty string
done = true;
else
current_suffix = next_smaller_suffix( current_suffix )
}
active_point = current_suffix
}

12. photo by http://www.photoxpress.com/stock-photos/1814937

13. photo by @meguu

15. Large-scale data in Life Science
Contents
fontin sans fonts by Jos Buivenga (exljbris). Thank You! -> www.exljbris.com

16. NOW IS THE TION
T-G ENERA
NEX
ED ATA
CAL NCE
L ES
ARG FE SCIE
LI

17. NOW IS THE TION
T-G ENERA
NEX
ED ATA
CAL NCE
L ES
ARG FE SCIE
LI

18. DBCLS:
DATABASE CENTER
FOR LIFE SCIENCE

20. Tazro Inutano Ohta @iNut
/ Technical Specialist

24. Large-scale data in Life Science

30. or or ?
ATGCATGCATGCATGCATGCATGC
ATGCATGCATGCATGCATGCATGC
ATGCATGCATGCATGCATGCATGC
ATGCATGATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCAGCATGCAT
GCATGCATGCATGCATGCATGCAT
or or ?
GCATGCATGCATGCATGCATGCAT
GCATGCATGCATGCATGCATGCAT
photo by Togopic, Licensed under CreativeCommons 2.1 JP Attribution

31. ATGCATGCATGCATGCATGCATGC
ATGCATGCATGCATGCATGCATGC Data ID : 000001
ATGCATGCATGCATGCATGCATGC
ATGCATGATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA organism : mouse
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA cell : nervous cell
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA
TGCATGCATGCATGCATGCATGCA sequencer : 454
TGCATGCATGCATGCAGCATGCAT
GCATGCATGCATGCATGCATGCAT
date : 2011 12 08
GCATGCATGCATGCATGCATGCAT
GCATGCATGCATGCATGCATGCAT
photo by Togopic, Licensed under CreativeCommons 2.1 JP Attribution

35. Next-generation sequencing data

38. grazie per le informazioni @ma_ko * DNA exon

40. *illumina HiSeq 2000

43. https://twitter.com/#!/dritoshi/status/121817788200390656

45. short read from NGS
de novo assemble
reference
genome
reference alignment

46. short read from NGS
de novo
de novo assemble
reference
genome
reference alignment

48. Velvet
http://www.ebi.ac.uk/~zerbino/velvet/
SOAPdenovo
http://soap.genomics.org.cn/soapdenovo.html
sequence assembly in wikipedia
http://en.wikipedia.org/wiki/Sequence_assembly

49. short read from NGS
de novo assemble
reference
genome
reference alignment

50. Chr1 Chr2 Chr3
CPU1 CPU2 CPU3

52. Troubles not yet shooted

56. https://twitter.com/#!/dritoshi/status/110559890413600768

57. https://twitter.com/#!/dritoshi/status/113546074760822784

58. https://twitter.com/#!/dritoshi/status/114675417998311425

62. http://bcbio.wordpress.com/tag/galaxy/

65. ITPro http://itpro.nikkeibp.co.jp/article/NEWS/20110927/369510/

66. grazie per le informazioni @yag_ays! asahi.com http://www.asahi.com/digital/bcnnews/BCN201111240007.html