Last updated:2014.9.8.

News for the NIG super computer system replacement in Mar., 2012

GTOP and PMD are available since April 2, 2012.

We are sorry for your inconvenience.
Please use it.

Reference : News for computer system replace in Mar., 2012 (title list)
National Institute of Genetics new supercomputer system are updated in March, we start the operation this system from March 21, 2012.

The new supercomputer system have more than 350 high‐throughput cluster machines with the latest CPU , a server with 10TB memory, large capacity storage total of 5PB. Their connected with high-speed transfer network.

For using, you need to apply for a supercomputer account from "Apply the use of super computer system (in Japanese)".
For more information, please refer to the "New supercomputer introduction (in Japanese)" and "How to use the super computer system (in Japanese)".
The computer system in the National Institute of Genetics will be replaced with an upgraded one by March, 2012. Consequently, DDBJ fulfills the provision of high-speed search and/or analysis systems, data submission systems corresponding for the explosive data increase, and other new services.

According to this replacement, currently, some DDBJ services are being suspended as of February 15, 2012.
Under suspention (resume will be notified at DDBJ HP)
 Data retrieval and analyses
BLAST & ClustalW
Resume is scheduled for the middle of March, after running the new supercomputer system. Before the services are resumed, as alternative way, please visit NCBI BLAST, EBI-ClustalWGenomenet-ClustalW(Kyoto Univ.)
DDBJ Read Annotation Pipeline
Web API
GIB · GIB-V
GTOP
PMD
 Data submission
Mass submission via massFTP
 
Continuously provided services
 DDBJ HP
DDBJ HP view by WWW
DDBJ HP update (news, notices, etc)
 Data submission, update, and release
SAKURA data submission
Mass data submission (other than massFTP)
Issue of Accession Nos.
Data update,and data release
 DRA/DTA/Bioproject data submission, update,release and data retrieval
 CIBEX data submission, update,release and data retrieval
 Data retrieval and analyses
GTPS
 Data download by anonymousFTP
 
Currently provided as new services (from Feb.15)
 
Termination of services (as of Feb. 24, 2012)
 NIG supercomputer system (supernig)
Public use of new supercomputer system will be started from early April. Call for entries will be notified at the DDBJ HP in the middle of March.
 
 
DDBJ sincerely apologizes for your inconvenience. Thank you very much for your understanding and cooperation.

Integrated entry retrieval system

DDBJ has provided the following 2 indepedent entry search/retrieval systems through WWW so far.
1. entry retrieval by database specific IDs : getentry
2. keyword search : ARSA
With the computer system replacement in NIG scheduled in March 2012, these 2 functions are unified to "ARSA".

Current individual functions of getentry and ARSA are provided as webAPI as well as web application . Although DDBJ users can select preferable one (web application or WebAPI), WebAPI is convenient method.
 
 

New getentry and New ARSA

Details will be notified on this web site soon.
 
 

Change of creating links to DDBJ entries

DDBJ has provided the method to create links from your web contents to the DDBJ flat files, using getentry. Because of the transition of getentry to the new system, this method is also changed from February 15, 2012.

If you currently set the links to the DDBJ entries, please change the settings according to the following description.
(1) GET method
http://getentry.ddbj.nig.ac.jp/getentry?database=database name&accession_number=accession number&additional parameters (optional)
(2) smart URL
http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number
http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number/?additional parameters (optional)

  Note: This new method is effective as of February 15, 2012.
 
DDBJ has provided the method to create links from your web contents to the DDBJ flat files, using getentry. Because of the transition of getentry to the new system, this method is also changed from February 15, 2012.

If you currently set the links to the DDBJ entries, please change the settings according to the following description.
(1) GET method
http://getentry.ddbj.nig.ac.jp/getentry?database=database name&accession_number=accession number&additional parameters (optional)

(2) smart URL
http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number
http://getentry.ddbj.nig.ac.jp/getentry/database name/accession number/?additional parameters (optional)

  Note: This new method is effective as of February 15, 2012.
 
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