Large-scale data in life science

G E S C AL ELAR D A TA IN E SC IE N CE

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 nodes next char isnt 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}

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photo by @meguu

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

NOW IS THE TION T-G ENERANEX ED ATA CAL NCE L ES ARG FE SCIE LI

DBCLS:DATABASE CENTER FOR LIFE SCIENCE

Tazro Inutano Ohta @iNut/ Technical Specialist

Large-scale data in Life Science

or or ?ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAGCATGCATGCATGCATGCATGCATGCATGCAT or or ?GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT photo by Togopic, Licensed under CreativeCommons 2.1 JP Attribution

ATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGC Data ID : 000001ATGCATGCATGCATGCATGCATGCATGCATGATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA organism : mouseTGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA cell : nervous cellTGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCA sequencer : 454TGCATGCATGCATGCAGCATGCATGCATGCATGCATGCATGCATGCAT date : 2011 12 08GCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCATGCAT photo by Togopic, Licensed under CreativeCommons 2.1 JP Attribution

Next-generation sequencing data

grazie per le informazioni @ma_ko * DNA exon

*illumina HiSeq 2000

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

short read from NGSde novo assemble reference genome reference alignment

short read from NGS de novode novo assemble reference genome reference alignment

Velvethttp://www.ebi.ac.uk/~zerbino/velvet/SOAPdenovohttp://soap.genomics.org.cn/soapdenovo.htmlsequence assembly in wikipediahttp://en.wikipedia.org/wiki/Sequence_assembly

short read from NGSde novo assemble reference genome reference alignment

Chr1 Chr2 Chr3CPU1 CPU2 CPU3

Troubles not yet shooted

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

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

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

http://blog.livedoor.jp	70
http://paper.li	6
http://a0.twimg.com	5

Large-scale data in life science

by Tazro Ohta on Dec 08, 2011

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Large-scale data in life science — Presentation Transcript