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

GTOP and PMD have been resumed 2012.04.03

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)

NIG starts the application for new supercomputer system 2012.03.23

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)".

Temporary suspension of databank activities(as of Feb. 15) 2012.02.20

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.

(Important) Notice for the temporary suspension of databank activities

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-ClustalW，Genomenet-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)

getentry

ARSA

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.

DDBJ provides a new entry retrieval system from Feb.15, 2012 2012.02.14

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.

Change of creating links to DDBJ entries 2012.02.13