Paper Info
Title
DDBJ new system and service refactoring.
Abstract
The DNA data bank of Japan (DDBJ, http://www.ddbj.nig.ac.jp) maintains a primary nucleotide sequence database and provides analytical resources for biological information to researchers. This database content is exchanged with the US National Center for Biotechnology Information (NCBI) and the European Bioinformatics Institute (EBI) within the framework of the International Nucleotide Sequence Database Collaboration (INSDC). Resources provided by the DDBJ include traditional nucleotide sequence data released in the form of 27 316 452 entries or 16 876 791 557 base pairs (as of June 2012), and raw reads of new generation sequencers in the sequence read archive (SRA). A Japanese researcher published his own genome sequence via DDBJ-SRA on 31 July 2012. To cope with the ongoing genomic data deluge, in March 2012, our computer previous system was totally replaced by a commodity cluster-based system that boasts 122.5 TFlops of CPU capacity and 5 PB of storage space. During this upgrade, it was considered crucial to replace and refactor substantial portions of the DDBJ software systems as well. As a result of the replacement process, which took more than 2 years to perform, we have achieved significant improvements in system performance.
Year
DOI
Venue
2013
10.1093/nar/gks1152
NUCLEIC ACIDS RESEARCH
Keywords
Field
DocType
internet,genomics
European Nucleotide Archive,Data bank,Biology,Software system,Genomics,Software,Genetics,Code refactoring,Sequence Read Archive,The Internet
Journal
Volume
Issue
ISSN
41
D1
0305-1048
Citations 
PageRank 
References 
10
0.81
10
Authors
7
Name
Order
Citations
PageRank
Osamu Ogasawara112423.46
Jun Mashima28916.21
Yuichi Kodama318522.55
Eli Kaminuma49918.33
Yasukazu Nakamura533857.89
Kousaku Okubo618252.06
Toshihisa Takagi7858102.84