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DDBJ Mail Magazine
No.36    Mar. 4, 2008
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mt.fuji
On the our HP top of page, we have a new photo of Mt Fuji, has sunrise colour. (Currently, he is more covered with white snow than before.) We can always see him from DDBJ building. This magnificent view welcome to any visiters for DDBJ and they always appreciate him. However, we are used to seeing him and tend to forget how lucky we are. It is ashame, isn't it?
If you have any questions and suggestions about DDBJmag, please do not hesitate to write ddbjmag@ddbj.nig.ac.jp . We would like to hear from you!!
 How to release millions of entries from DDBJ: What has the new computer system in a year brought with?
In February 2007, DDBJ replaced the computer system and upgraded some of the application programs. In the meantime, DDBJ has been required to process millions of entries. The question here is if the new system has been able to satisfy the emerging requirements. You might recognize that you can hold your entries in a certain period or until the relevant paper are published. DDBJ should not disclose these Hold-Until-Published entries to the public. To retain them inside DDBJ, DDBJ stores these entries in a separate server from servers for data dissemination, e.g. getentry server. In the daily data release procedure shown in the following figure, DDBJ convert entries into the flat file format from the server for in-house data management to transfer them to other servers for such services to the public as getentry, ARSA, homology search and anonymous FTP.

In January 2008, DDBJ released about 1,500,000 entries only in two days; about 1,000,000 entries in the first day, and about 500,000 entries in the second day. It is to be noted that this process was completed as smoothly as designed. With the previous system, we were able to process only 350,000 entries in a day, namely, we had to spend more than 4 days to complete 1.5M entries. Although the mission was completed this time, we learned some lessons to improve the procedure further. You may claim that "2 days" is not quick enough. The system engineers in charge started the discussion to improve the concordance of several servers to gain higher throughput than ever. We would appreciate it very much, if you remember the group of hard working system engineers especially when you see the announcement of massive data release.
  DDBJ started RSS delivery service; Watch NEW/UPDATED information by RSS
GIB (Genome Information Broker) started the delivery of update information by RSS. You will be notified whenever new genomes are added or existing genomes are updated, if you register the GIB RSS site by use of an RSS reader.

What is RSS?
RSS is a shortened name of Rich Site Summary or Really Simple Syndication, and a number of web site has used to push the information on headline, outline, update date, the link to the web site and so on to the user.

How to read RSS ?
You can subscribe to RSS of any Web site by Google, Yahoo! and other portal sites, if you are a registered user of the portal site. Please find the example of subscription in the following in the case of Goole:



Why you should use RSS? You need not visit the site every morning to find what's new. You will be notified by the site that the site is updated. In the case of GIB RSS, the list of new genomes and updated genomes is delivered to you. You click the genome of you interest in the list and you are directly guided to the web page of the genome that you choose.

How to register to the GIB RSS
You may want to install a program of RSS reader by yourself, instead of using Google, Yahoo! or other portal sites. We explain the usage of RSS program installed in Windows machine:
  1. Install a RSS reader. The following figure is RssReader (http://www.rssreader.com/).
  2. Register RSS delivery site of GIB (http://gib.genes.nig.ac.jp/rss.php) to the installed RSS reader.
  3. The line of GIB is added.
  4. Select the GIB line (the box 3 in the figure) and the list from GIB is displayed.
  5. Choose one of the genomes in the list (the box 4 in the figure) and you will know if it is updated or newly added.

Please forward your request to this type of alert system and we will expand RSS to other DDBJ services
  Release of MASS sequence data from DDBJ
Release of new Japanese macaque (Macaca fuscata) GSS 167,159 entries
DDBJ newly released Japanese macaque (Macaca fuscata) GSS 167,159 entries, which had been submitted by RIKEN Genomic Sciences Center. These entries were released as DDBJ daily updates on 12/18, and are available by anonymous FTP. Reference URL: http://hgp.gsc.riken.jp/

Release of new collared flagellate (Monosiga ovata) EST 69,143 entries and GSS 60,757 entries
DDBJ newly released collared flagellate (Monosiga ovata) EST 69,143 entries and GSS 60,757 entries, which had been submitted by RIKEN Genomic Sciences Center. These entries were released as DDBJ daily updates on 12/18, , and are available by anonymous FTP.
The accession numbers and corresponding file names are as follows. Reference URL: http://stt.gsc.riken.jp/
 DDBJ Rel. 72 Completed
The nucleotide sequence database collected and maintained by DDBJ is quarterly released online to the public. We completed DDBJ Release 72 in December 25, 2007. DDBJ Release 72 consists of 79,004,098 entries, and the number of bases reached 82,592,245,487. The periodical release and the new data are available by FTP download from the "FTP/Web API" page. As was already notified, DDBJ proceeded deletion of the both phone and fax numbers, and E-mail address from the flat files of the entries submitted to DDBJ. The retrofit of the all entries was completed by the issue of this release 72. Hereafter, database users become difficult to contact submitters based on the information described in the DDBJ flat files. When you wish to contact to the submitter(s) of an entry of your interest, please contact us using the prescribed inquiry form placed in the DDBJ HP.
 Report for DDBJ activicies in NAR
The new and significant DDBJ activities of the year 2007 were introduced in the following paper appeared in Nucleic Acids Research Vol.36 Database Issue (Jan, 2008)

"DDBJ with new system and face"
(written by H. Sugawara, O. Ogasawara, K. Okubo, T. Gojobori and Y. Tateno)
Nucleic Acids Research, 2008, Vol. 36, Database issue D22-D24
Summery: DDBJ activitiew of 2007 (Data submissions and release, New Computer System, ARSA ( New keyword search
system ) enhancement, etc.

"The H-Invitational Database ( H-InvDB ), a comprehensive annotation resource for human genes and transcripts"
Genome Information Integration Project And H-Invitational 2
( written by DDBJ member of T.Okido, J.Mashima, K-B.Lee, A.Nozaki, K.Sakai, Y.Suzuki, K.Ikeo, N.Saitou,
H.Sugawara, S.Fukuchi, Y.Tateno and T.Gojobori )
Nucleic Acids Research, 2008, Vol. 36, Database issue D793-D799
Summery: About H-Invitational Database (H-InvDB)
  

Published by:
DNA Data Bank of Japan (DDBJ)
Center for Information Biology and DNA Data Bank of Japan (CIB-DDBJ)
National Institute of Genetics (NIG)
Research Organization of Information and Systems
1111 Yata, Mishima, Shizuoka 411-8540, JAPAN