DDBJ Center News Archive

News from 2016

Release of genome sequence data of bitter gourd, Momordica charantia

2016年12月28日

DDBJ released genome sequence data of bitter gourd, Momordica charantia, which had been submitted by Shinshu University.

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BDCS01000001-BDCS01001052 (1,052 entries) BDCS.gz
DRA: DRR056762 (DRA004516), DRR057118-DRR057122 (DRA004548)
Services: ddbj Keywords: Data Release

JGA downtime 11th Jan. 2017, 10:00-12:00

December 28,2016

JGA downtime 11th Jan. 2017, 10:00-12:00 due to maintenance. The JGA submission/download tools can not be connected to the JGA server in this period. In addition, the JGA web services will not be available.

Services: jga Keywords: Maintenance

The list of JPO amino acid sequence data with possibility of nucleotide sequence

December 28,2016
[1] Overview
DDBJ detected amino acid sequence (AA) data with possibility of nucleotide sequence transferred from Japan Patent Office (JPO).
We checked the description of nucleotide sequence on patent publication to confirm their sequence type. In case of there is not description on patent publication, we confirmed their sequence similarity of nucleotide by using BLASTN and/or other methods.
We released the list of verified entries as JPO_AAwithN.

[2] List contents
DDBJ anonymous FTP:
ftp://ftp.ddbj.nig.ac.jp/ddbj_database/patent/

File name:
JPO_AAwithNA

Format:
Accession number[TAB]Patent publication number[TAB]Sequence number (PS line)[TAB]Validation result

Sequence number (PS line):
Sequence number is described with N. Please refer this number when you check the corresponding data of sequence listings and patent publication.
PS line is set on COMMENT block of JPO Flat File (FF).

[3] Update schedule for list
DDBJ started checking validation for all JPO AA data. We will reflect the check result to JPO_AAwithNA sequentially.
Services: ddbj Keywords: Announcement

(Dec. 27) Suspension of DDBJ FTP service due to NIG Supercomputer maintenance (Resumed)

December 26,2016

DDBJ FTP service will be unavailable due to NIG Supercomputer maintenance as follows.

 December 27 (Tue), 11:00 - 11:10 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. DDBJ FTP service is available. (December 27, 2016 at 11:15 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

DDBJ Rel. 107.0, DAD Rel. 77.0 Completed

December 21,2016

DDBJ Rel. 107.0

* From DDBJ Release 107.0, 'bulk sequence data', TSA and WGS, are also included in the statistics.bulk sequence data: entries with four-letter prefix accession numbers

DAD (DDBJ amino acid database) Rel. 77.0

  • Date: Dec. 21, 2016
  • 56,608,385 entries     17,718,176,559 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Release of genome sequence data of crown-of-thorns starfish, Acanthaster planci

December 19,2016

DDBJ released genome sequence data of crown-of-thorns starfish, Acanthaster planci, which had been submitted by Okinawa Institute of Science and Technology Graduate University.

Reference

The accession numbers are as follows. They are available on getentry or DRASearch.

CON: DF978489-DF980253 (1,765 entries)
WGS: BDGF01000001-BDGF01018088 (18,088 entries) BDGF.gz
DRA: DRR064078-DRR064083 (DRA004863)
CON: DF980254-DF983527 (3,274 entries)
WGS: BDGH01000001-BDGH01019917 (19,917 entries) BDGH.gz
DRA: DRR064073-DRR064077 (DRA004862)
Services: ddbj Keywords: Data Release

(Dec. 13) ARSA temporarily unavailable (Resumed)

December 12,2016

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 December 13 (Tue), 9:30- (JST)

We will announce on this page and Twitter when it resumes.
Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (December 13, 2016 at 10:36 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Suspension of the DDBJ activity during the New Year Holidays

December 07,2016

We at DDBJ will temporarily close for the New Year Holidays from December 29(Thu), 2016 to January 3(Tue), 2017.
Please note that DDBJ Nucleotide Sequence Submission System will be unavailable. Schedule is as follows.
NIG Supercomputer and DDBJ network services (except DDBJ Nucleotide Sequence Submission System) are available during the New Year Holidays.

During this period, DDBJ will continue to receive inquiries from E-mail and "Contact" web form.
But, please note that replies from DDBJ is after the reopening of the office in January, 2017.

DDBJ office closeDec. 29(Thu), 2016 - Jan. 3(Tue), 2017
DDBJ Nucleotide Sequence Submission SystemDec. 26(Mon), 2016 at 18:00
     - Jan. 4(Wed), 2017 at 10:00 (JST)
Data release suspensionDec. 28(Wed), 2016 - Jan. 4(Wed), 2017
Reply for inquiries
(submission, search/analysis, NIG SuperComputer)
Dec. 29(Thu), 2016 - Jan. 3(Tue), 2017
DRA, BioProject, BioSample, JGA Accession No. issueDec. 29(Thu), 2016 - Jan. 3(Tue), 2017

Thank you for your understanding and cooperation.

December 7, 2016

Services: ddbj Keywords: Announcement

DDBJ provides limited-time access service to archived fastq/SRA files

December 07,2016

Limited-time access to archived fastq/SRA files

DRA Handbook

To allow submitter to download and check archived fastq/SRA files, the files are copied to the following directories on the dradata.ddbj.nig.ac.jp server from 12th, Jan. 2017. To save disk space, the copied files are automatically deleted in one month.

Due to unexpected decrease of available disk space, copied fastq/SRA files may be deleted within one month or the copy service may be suspended. We will inform submitters on the website in advance as much as possible, however, this annoucement could be immediately before the deletion or service suspension.

  • (submitter's home)/report/dra/(DRA submission accession)/fastq/
  • (submitter's home)/report/dra/(DRA submission accession)/sra/

  • submitter/report/dra/DRA000001/fastq/DRR000001.fastq.bz2
  • submitter/report/dra/DRA000001/fastq/DRR000002.fastq.bz2
  • submitter/report/dra/DRA000001/fastq/DRR000002_1.fastq.bz2
  • submitter/report/dra/DRA000001/fastq/DRR000002_2.fastq.bz2
  • submitter/report/dra/DRA000001/sra/DRR000001.sra
  • submitter/report/dra/DRA000001/sra/DRR000002.sra
Services: bioproject,biosample,dra Keywords: Announcement

Scheduled maintenance (9:30-12:00, 21th, December)

December 07,2016
From 9:30 to 12:00 (planned), 21th, December, the DRA, BioProject and BioSample submission will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

DDBJ center starts to provide ArrayExpress mirror ftp site

November 28,2016
Based on the international collaboration between DDBJ center and European Bioinformatics Institute (EBI) ArrayExpress team, we have mirrored the public ArrayExpress data (array, experiment and atlas) to our ftp site (atlas/rnaseq directory which contains RNA-seq data is excluded). The data mirroring program was developed and executed by Project Associate Professor, Bono Hidemasa of Database Center for Life Science (DBCLS).ftp sites

To download more than 50 terabytes of data from EBI, we used the aspera software for faster file transfer. The mirroring program was executed on the SuperComputer Facilities of National Institute of Genetics.

By this mirroring realized by the collaboration between DDBJ center, EBI ArrayExpress and DBCLS, users in Japanese and neighbouring countries are able to download the ArrayExpress data from nearer DDBJ site.

          
Services: ddbj Keywords: Announcement

Feature Table Definition revised

November 18,2016

The DDBJ/ENA/GenBank Feature Table Definition is the common annotation manual of feature descriptions for DDBJ, ENA and GenBank.
It was revised to version 10.6.

Services: ddbj Keywords: Announcement

(Nov. 21) ARSA temporarily unavailable (Resumed)

November 17,2016

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 November 21 (Mon), 9:30 - (JST)

We will announce on this page and Twitter when it resumes.
Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (November 21, 2016 at 11:07 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Bug in keyword search of DRASearch

November 11,2016

In keyword search of DRA search system (DRASearch), the latest data is unavailable from 10th November, 2016.

The bug will be fixed on or after 14th November.

We apologize for all the trouble this bug has caused.

Services: dra Keywords:

Updated tools related to Mass Submission System (MSS)

November 09,2016

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.42 Released
  • Parser version 6.55 Released
  • transChecker version 2.20 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

New instrument model PacBio "Sequel" added

November 09,2016

New instrument model PacBio "Sequel" was added. xsd Handbook

Services: dra Keywords: Announcement

Registration of a locus tag prefix in D-way is unavailable due to system trouble

November 08,2016

In BioProject submission system, registration of a locus tag prefix is unavailable due to system trouble.

Please contact DDBJ BioProject team to register a locus tag prefix.

Please leave prefix box blank to complete BioProject submission.

Thank you for your understanding and cooperation.

Services: bioproject,biosample,dra Keywords:

Scheduled maintenance (9:30-11:00, 9th, November)

November 02,2016
From 9:30 to 11:00 (planned), 11th, November, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Report for DDBJ activities in NAR

October 25,2016

DDBJ activities are introduced in the following article appeared in Nucleic Acids Research, Database issue.

"DNA Data Bank of Japan"
Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Toshiaki Katayama, Yoshihiro Okuda, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Yasukazu Nakamura and Toshihisa Takagi
Nucl. Acids Res. 2016 doi: 10.1093/nar/gkw1001

Services: ddbj Keywords: Announcement

(Oct. 14-18) ARSA temporarily unavailable (Resumued)

October 14,2016

ARSA is unavailable due to NIG Supercomputer maintenance as follows.

 October 14(Fri) - October 18(Tue)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (October 18, 2016 at 14:58 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Urgent system maintenance (13:00-14:00, 13th, October)

October 12,2016
From 13:00 to 14:00 (planned), 13th, October, the DRA, BioProject and BioSample submission and search services will be unavailable due to urgent maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Provision of submitted PacBio HDF5 file as an Analysis

October 12,2016

Because PacBio HDF5 file contains valuable, re-usable data which are not retained in SRA/fastq files, DRA will provide submitted HDF5 file as an Analysis. This policy is applied to the DRA submission submitted after 12th October 2016. For details, please see the submission manual.

Services: dra Keywords:

System downtime at 26th (Wed.), October, 2016

October 05,2016

For the JGA system release, submission and search system will be unavailable from 14:00-15:00 26th (Wed.), October, 2016.

Services: jga Keywords: Announcement

Apology for the trouble of BLAST search results

October 05,2016

In BLAST, when showing a search results to web browser, we found a bug as follows.

 Period: From new BLAST system released on April 2013
 Extent of the impact: BLAST (*There is no problem with WABI BLAST.)
 Situation: If "PRE" included in BLAST search results, this character was replaced "DIV"

This problem has already been fixed and the service works normally.

We sincerely apologize for the inconvenience you have been caused by this trouble.

Services: ddbj Keywords: Maintenance

Award Winners of the DDBJ Data Analysis Challenge 2016

September 30,2016
September 30, 2016
DDBJ Data Analysis Challenge Committee
DNA Data Bank of Japan held the DDBJ Data Analysis Challenge from July 6 through August 31, 2016. The DDBJ Data Analysis Challenge is a machine learning competition using "'International Nucleotide Sequence Database", corresponding to life science big data provided by DDBJ, EBI, and NCBI. Participants need to submit their generated machine learning models to a collaborative website, UnivOfBigData. This time challenge task is "Predicting chromatin features from DNA sequence" . There were a total of 38 participants with cumulative total of 360 model submissions. We announce the top 3 Award Winners and the Student Prize winner who is the top of all student participants in DDBJ Data Analysis Challenge 2016.

DDBJ Data Analysis Challenge 2016 Award Winners

1st Prize of DDBJ Challenge Awards 2016Information and Mathematical Science and Bioinformatics Co., Ltd.
MOCHIZUKI Masahiro
2nd Prize of DDBJ Challenge Awards 2016RIKEN ACCC Bioinformatics Research Unit
MATSUMOTO Hirotaka(representative*), OZAKI Haruka(*)
*They participated in this Challenge as a team.
3rd Prize of DDBJ Challenge Awards 2016BITS Co., Ltd.
OKAYAMA Toshitsugu
Student Prize of DDBJ Challenge Awards 2016Master's Degree Program 1, Graduate School of Information Science and Technology, The University of Tokyo
KATO Takuya
 

Results

DDBJ Challenge AwardAUCModel Design Tool Version
1st Prize0.94564*2 Classifiers(Extremely Randomized Trees, CNN)
*Ensemble Learning(Stacking)
*External Data(Genomic Position, Gene Structure Annotation)
python=3.5
scikit-learn=0.17.1
chainer=1.10.0
2nd Prize0.89859*2 Classifiers(CNN, Product of Genomic Distance Decay Parameter and  Nearest Training Data Output)
*Ensemble Learning(Averaged)
*External Data(Genomic Position)
julia=0.4.6
python=2.7.10
skflow(tensorflow=0.8.0)
3rd Prize0.85428*7 Classifiers(Naive Bayes for Multivariate Bernoulli Models, Logistic Regression, Random Forest, Gradient Boosting, Extremely Randomized Trees, eXtreme Gradient Boosting, CNN)
*Ensemble Learning (Stacking)
python=2.7.11
numpy=1.10.4
scikit-learn=0.17
chainer=1.11.0
xgboost=0.4a30
Student Prize0.84318*3 Classifiers(LeNet like CNN, DeepBind like CNN, Variable filter DeepBind like CNN)
*Ensemble Learning(Soft Voting)
python=2.7
lasagne=0.2.dev1
  Contact: Please contact us from DDBJ Contact Web Form.
Services: ddbj Keywords: Announcement

Suspension of a part of services in submission system due to server trouble

September 23,2016

In BioProject, BioSample and DRA submission system, a part of services have been suspended since September 20th due to a server trouble.

D-way

  • Create a D-way account

Email notification services

  • Notification of release of BioProject, BioSample and DRA
  • Notification of coming of hold date of DRA data
  • DRA validation log

Please wait for a while until the restoration.

You can check the status of your submissions via D-way.

Please contact DRA team to obtain a D-way submission account.

Thank you for your understanding and cooperation.

Services: bioproject,biosample,dra Keywords:

DDBJ Rel. 106.0, DAD Rel. 76.0 Completed

September 21,2016

DDBJ Rel. 106.0

DAD (DDBJ amino acid database) Rel. 76.0
  • Date: Sep. 21, 2016
  • 53,463,317 entries     16,696,790,839 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

Release of genome sequence data of a water bear, Ramazzottius varieornatus

September 15,2016

DDBJ released genome sequence data of a water bear, Ramazzottius varieornatus, which had been submitted by National Institute of Genetics.

Reference

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BDGG01000001-BDGG01000199 (199 entries) BDGG.gz
fosimid clones: AP013349-AP013352 (4 entries)
mitochondrion: AP017609
DRA: DRR013908-DRR013910 (DRA001119)
Services: ddbj Keywords: Data Release

bam reference sequences can be specified by multi-fasta

September 14,2016

Submitters can specify reference sequences by the following two ways.

  • When accessioned reference is in the repository, specify by the INSDC/RefSeq accession.version.
  • When not in the repository, specify by uploading multi-fasta.

For the unmapped bam from PacBio and IonTorrent, neither the mapping table nor reference multi-fasta are not necessary.

For details, please see the manual.

Services: bioproject,biosample,dra Keywords: Announcement

The Report for the 29th International Collaborators Meeting

September 08,2016

International Nucleotide Sequence Database Collaboration (INSDC), consisted of DDBJ, EBI and NCBI, hold the international collaborators meeting every year.
In 2016, the meeting was held at EBI, 16-18 May, to discuss practical matters to maintain and update nucleotide sequence data archives; DDBJ, ENA, GenBank, Sequence Read Archive (SRA) and Trace Archive.
The outcomes of the meeting are summarized here.

Services: ddbj Keywords: Announcement

Scheduled maintenance (9:30-11:00, 14th, September)

September 07,2016
From 9:30 to 11:00 (planned), 14th, September, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome, GSS, RAD-Seq, RNA-Seq and EST data of Japanese morning glory (Ipomoea nil)

September 01,2016

DDBJ released genome, GSS, RAD-Seq, RNA-Seq and EST data of Japanese morning glory (Ipomoea nil) which had been submitted by National Institute for Basic Biology.

The accession numbers are as follows. They are available on getentry or DRASearch.

Genome
WGS: BDFN01000001-BDFN01003416 (3,416 entries) BDFN.gz
mitochondrion: AP017303
chloroplast: AP017304
DRA: DRR013917-DRR013926 (DRA001121), DRR024668 (DRA002710), DRR048755-DRR048757 (DRA004158)
GSS
GSS: GA933005-GA974698 (41,694 entries)
RAD-Seq
DRA: DRR026831-DRR027252 (DRA002758)
RNA-Seq
DRA: DRR024544-DRR024549 (DRA002647)
EST
EST: HY917605-HY949060 (31,456 entries)
Services: ddbj Keywords: Data Release

System maintenance (9:30-10:30, 22th, August)

August 19,2016
From 9:30 to 10:30 (planned), 22th, August, the DRA, BioProject and BioSample submission and search services will be unavailable due to unscheduled system maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome sequence data of Okinawa mozuku, Cladosiphon okamuranus

August 18,2016

DDBJ released genome sequence data of Okinawa mozuku, Cladosiphon okamuranus, which had been submitted by Okinawa Institute of Science and Technology Graduate University.

Reference

The accession numbers are as follows. They are available on getentry and DRASearch.

CON: DF977685-DF978416 (732 entries)
WGS: BDDF01000001-BDDF01004525 (4,525 entries) BDDF.gz
DRA: DRR059718-DRR059726 (DRA004654)
Services: ddbj Keywords: Data Release

Release of TSA data of a jellyfish, Turritopsis sp. SK-2016

August 17,2016

DDBJ released TSA (Transcriptome Shotgun Assembly) data of a jellyfish, Turritopsis sp. SK-2016, which had been submitted by Kazusa DNA Research Institute.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: IAAF01000001-IAAF01090327 (90,327 entries) IAAF.gz
DRA: DRR053671-DRR053676 (DRA004346)
Services: ddbj Keywords: Data Release

Release of genome sequence data of pink oyster mushroom (Pleurotus salmoneostramineus)

August 10,2016

DDBJ released genome sequence data of pink oyster mushroom (Pleurotus salmoneostramineus) which had been submitted by Kindai University.

The accession numbers are as follows. They are available on getentry.

WGS: BDGN01000001-BDGN01026934 (26,934 entries) BDGN.gz
Services: ddbj Keywords: Data Release

Release of transcriptome sequence data from Chinese lantern and cape gooseberry

August 10,2016

DDBJ released transcriptome sequence data from Chinese lantern (Physalis alkekengi var. franchetii) and cape gooseberry (Physalis peruviana), which had been submitted by RIKEN.

The accession numbers are as follows. They are available on getentry and DRASearch.

organism TSA accession numbers DRA accession numbers
Chinese lantern (Physalis alkekengi var. franchetii) IABG01000001-IABG01075221 (75,221 entries) IABG.gz DRR048294-DRR048297 (DRA004085)
cape gooseberry (Physalis peruviana) IABH01000001-IABH01054513 (54,513 entries) IABH.gz DRR048298-DRR048300 (DRA004085)
Services: ddbj Keywords: Data Release

Scheduled maintenance (9:30-14:00, 18th, August)

August 08,2016
From 9:30 to 14:00 (planned), 18th, August, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Bug in the Experiment page in the DRA submission system (fixed)

August 01,2016

2016-08-18 This bug has been fixed.

Due to a bug in the update release of the DRA XML schema at 13th July 2016, a system error can occur in the Experiment page of the DRA submission system.

In the Experiment page, when [Save] and [Next (RUN)] buttons are clicked when values are not provided for the required fields "Library Source" and "Library Strategy", system error is caused. The DRA submission with this error can not be used.

As a temporal solution to prevent this error, we will block [Save] and [Next (RUN)] buttons when the "Library Source" and "Library Strategy" are not entered. We will release the submission system to fix the bug in late August.

We apologize for all the trouble this bug has caused.

Services: bioproject,biosample,dra Keywords:

Release of genome sequence data of quinoa, Chenopodium quinoa

July 28,2016

DDBJ released genome sequence data of quinoa, Chenopodium quinoa, which had been submitted by Kazusa DNA Research Institute.

The accession numbers are as follows. They are available on getentry and DRASearch.

WGS: BDCQ01000001-BDCQ01024845 (BDCQ.gz) (24,845 entries)
DRA: DRR057247-DRR057301 (DRA004558)
Services: ddbj Keywords: Data Release

(Aug. 11 - Aug. 15) Suspension of some parts of DDBJ activities during Summer Holiday

July 28,2016

DDBJ will suspend our business on releasing data and answering inquiries from August 11 to August 15, 2016 for summer holiday.
DDBJ Nucleotide Sequence Submission System (NSSS) will be unavailable.
NIG Supercomputer and DDBJ network services (except NSSS) are available as usual.
Schedule is as follows.

 DDBJ office close:Aug. 11(Thu), 2016 - Aug. 15(Mon), 2016
 NSSS:Aug. 10(Wed), 2016, at 18:00 - Aug. 16(Tue), 2016, at 10:00 (JST)

During this period, DDBJ will continue to receive inquiries from E-mail and "Contact us" web form.
But, please note that replies from DDBJ is after the reopening of the office in August 16 (Tue), 2016.

Thank you for your understanding and cooperation.

July 28, 2016

Services: ddbj Keywords: Announcement

Release of genome sequence data of a sub clover, Trifolium subterraneum cv. Woogenellup

July 27,2016

DDBJ released genome sequence data of sub clover, Trifolium subterraneum cv. Woogenellup, which had been submitted by Kazusa DNA Research Institute.

Reference

The accession numbers are as follows. They are available on getentry and DRASearch.

WGS: BBPR01000001-BBPR01968279 (BBPR.gz) (968,279 entries)
DRA: DRR018261-DRR018262 (DRA002213)
Services: ddbj Keywords: Data Release

Release of EST and GSS data of a water bear, Ramazzottius varieornatus

July 26,2016

DDBJ released EST and GSS data of a water bear, Ramazzottius varieornatus, which had been submitted by National Institute of Genetics.

The accession numbers are as follows. They are available on

EST: HY377478-HY448296 (70,819 entries)
GSS: FT955276-FT997721 (42,446 entries)

Services: ddbj Keywords: Data Release

Release of genome sequence data of Japanese quail, Coturnix japonica

July 26,2016

DDBJ released genome sequence data of Japanese quail, Coturnix japonica, which had been submitted by the Tokyo University of Agriculture.
The accession numbers are as follows. They are available on getentry and DRASearch.
    scaffold CON: DF260915-DF266788 (5,874 entries)     WGS: BASJ01000001-BASJ01528405 (BASJ.gz) (528,405 entries)    raw data: DRR002288-DRR002301

Services: ddbj Keywords: Announcement

Release of TSA data of cherry salmon, Oncorhynchus masou masou

July 25,2016

DDBJ released TSA (Transcriptome Shotgun Assembly) data of cherry salmon, Oncorhynchus masou masou, which had been submitted by Hokkaido University.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: IABA01000001-IABA01097925 (IABA.gz) (97,925 entries)
DRA: DRR065944, DRR065945 (DRA004887)
Services: ddbj Keywords: Data Release

DDBJ cannot update of WGS data released from GenBank (Restored)

July 22,2016

At present, the following trouble has occurred for GenBank WGS data.

 Subject Data: WGS data released from GenBank after July 14 (Thu), 2016.
 Impact: Unable to download from DDBJ anonymous FTP, Unable to browse getentry

We apologize for the inconvenience.

This problem was resolved.
We apologize for any inconvenience this may have caused you. (August 17, 2016 at 15:10 JST)

Services: ddbj Keywords: Maintenance

Release of genome sequence data of sub clover, Trifolium subterraneum cv. Daliak

July 20,2016

DDBJ released genome sequence data of sub clover, Trifolium subterraneum cv. Daliak, which had been submitted by Kazusa DNA Research Institute.

Reference

The accession numbers are as follows. They are available on getentry and DRASearch.

CON: DF973112-DF976994 (3,883 entries)
WGS: BCLP01000001-BCLP01066167 (BCLP.gz) (66,167 entries)
DRA: DRR018263-DRR018264 (DRA002213), DRR032035-DRR032043 (DRA003274)
Services: ddbj Keywords: Data Release

DRA Experiment xsd 1.5e released

July 13,2016

DRA Experiment xsd was updated. For details, please see the Release note.

Services: dra Keywords: Announcement

Release of metagenome sequence data of museum specimens derived from Liagora japonica

July 11,2016

DDBJ released metagenome sequence data of museum specimens derived from a red algal species (Liagora japonica), which had been submitted by Kobe University.

The accession numbers are as follows. They are available on getentry and DRASearch.

Specimens WGS accession numbers DRA accession numbers
from Nada, Gobou, Wakayama BCQK01000001-BCQK01275014 (BCQK.gz)
275,014 entries
DRR041863 (DRA003813)
from Misaki, Miura, Kanagawa BCQL01000001-BCQL01381344 (BCQL.gz)
381,344 entries
DRR041864 (DRA003813)
Services: ddbj Keywords: Data Release

Scheduled maintenance (9:30-11:00, 13th, July)

July 06,2016
From 9:30 to 11:00 (planned), 13th, July, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome sequence data of Japanese white stork, red-crowned crane, and Okinawa rail

July 01,2016

DDBJ released genome sequence data of Japanese white stork, red-crowned crane, and Okinawa rail which had been submitted by National Institute for Environmental Studies.

The accession numbers are as follows. They are available on getentry.

organism WGS accession numbers
Japanese white stork
Ciconia boyciana
BDFF01000001-BDFF01505419 (BDFF.gz)
505,419 entries
red-crowned crane
Grus japonensis
BDFG01000001-BDFG01357545 (BDFG.gz)
357,545 entries
Okinawa rail
Gallirallus okinawae
BDFH01000001-BDFH01768680 (BDFH.gz)
768,680 entries
Services: ddbj Keywords: Data Release

(July 4) ARSA System Maintenance Information

July 01,2016

We will have ARSA system maintenance.
During the maintenance, ARSA is unavailable under the following search conditions.

 Date:July 4 (Mon) 9:30 - 10:00 (JST) (A few minutes interception during this time)
 Impact::When you enter any keywords, "Illegal query" is returned.

 Date:July 4 (Mon) (takes a day or two)
 Impact::ARSA will be unavailable when specifies the search filed "Reference PubmedID" using Advanced Search.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Maintenance

Release of genome sequence data of Japanese quail, Coturnix japonica

June 30,2016

DDBJ released genome sequence data of Japanese quail, Coturnix japonica, which had been submitted by the Tokyo University of Agriculture.

References

The accession numbers are as follows. They are available on getentry and DRASearch.

WGS: BASJ02000001-BASJ02009499 (BASJ.gz) (9,499 entries)
DRA: DRR002288-DRR002301 (DRA000595), DRR055128-DRR055129 (DRA004460)
Services: ddbj Keywords: Data Release

DDBJ Rel. 105.0, DAD Rel. 75.0 Completed

June 28,2016

DDBJ Rel. 105.0

DAD (DDBJ amino acid database) Rel. 75.0
  • Date: Jun. 28, 2016
  • 50,567,937 entries     15,768,083,034 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

DDBJ Data Analysis Challenge (Closed)

June 27,2016
DDBJ Data Analysis Challenge
"DDBJ Data Analysis Challenge 2016" was closed. Thank you very much for your participation.
"DDBJ Data Analysis Challenge" is a machine learning competition using "'International Nucleotide Sequence Database' data", which is one of the life science big data provided by DDBJ. Even college students and/or researchers outside of life science field, can get an opportunity of studying "Machine Learning and Data Mining", through this Challenge. And, to join this Challenge more easily, DDBJ provides NIG Supercomputer System as your computer resources.

Participants

Anyone can participate in this Challenge. And if you hope, you can use NIG Supercomputer System for your data analysis. (Use of NIG Supercomputer System is subject to "Criteria for issuing user login accounts". Please read this page before applying NIG Supercomputer System.)

Time Line and Due Dates

 Start Accepting Applications: June 27, 2016
NIG Supercomputer System application
NIG Supercomputer System OSS Installation request
 Start Date: July 6, 2016
 Deadline for Applications: August 21, 2016
NIG Supercomputer System application
NIG Supercomputer System OSS Installation request
 End Date: August 31, 2016
 Result: September 30, 2016

Challenge Task

DNA Data Bank of Japan (DDBJ) supports a big data resource called by DDBJ Sequence Read Archive (DDBJ SRA), which contains DNA sequences genearated from high-throughput DNA sequencers. The secondary analytical database, ChIP-Atlas database (Dr.Oki of Kyushu Univ.) provides the annotation data of chromatin feature regions on genome sequences. At this challenge task, please predict whether genomic regions corresponding to input DNA sequences includes chromatin feature regions. Chromatin feature region is related to on-off function of gene expression, and corresponds to peak regions on a genome sequence of the ChIP-Atlas database. In the ChIP-Atlas database, a combination of tissue/celltype conditions (CellType class) and functional Type (Antigen class) are curated as one experimental condition. Challenge's target species is a plant. The number of conditions for the target plant is often over 100. The number of conditions in the challenge is reduced and composed of eight conditions for saving time of try and error on data modelling.------------------------------------Input training data: 60,000 DNA sequenceInput test data: 10,000 DNA sequenceOutput training data: 8 conditions correct answer sets ------------------------------------- InputOne input sequence is composed of 200 bases, that is a ACGT sequence fragment with 200 length, where the sequence is encoded as 01 code [Example: AATGC ... = 10001000000100100100 ...] so that the length of a sequence is 800 digits.Corresponding code: A = 1000, C = 0100, G = 0010, T = 0001, Other exceptions = 0000  OutputOutput correct answer sets of 8 conditions is also encoded as 01 code. True answer is one, which means that the input DNA sequence contains chromatin feature regions.Likewise zero is false answer so that it does not include the chromatin feature region.On the submit stage, please submit the probability of true prediction with 10,000 rows (test axis) and 8 columns (condition axis) in BigData University website.
 Data
(1) set up in University of Big Data (DDBJ-challenge.mat)
(2) NIG Supercomputer Phase2 /home/challenge/data/DDBJ-challenge.mat

Submit a Challenge

To submit a challenge, please enroll in "University of Big Data". When you sign up, your Google account is required.Please submit the probability of true prediction with 10,000 rows (test axis) and 8 columns (condition axis) in University of Big Data website.When you submit a challenge, intermediate ranks and intermediate scores are displayed in University of Big Data website. Intermediate ranks are displayed by nickname.

Challenge Award

We will announce the Top 3 DDBJ Challenge winners on September 30, 2016. (If you wish to remain anonymous, we will announce a nickname.) Final ranks will be released by nickname in University of Big Data website on September 1, 2016, 0:00 (JST).To submit a paper about the reports on DDBJ Data Analysis Challenge, the award winners join as a co-author. For this reason, the top three Challenge winners will be submit the report for the data model. Also, we will release their reports by online.We publish all DDBJ Data Analysis Challenge participant's nickname in Acknowledgments of a paper. Award Winners of the DDBJ Data Analysis Challenge 2016 (September 30)

Use of NIG Supercomputer System

 NIG Supercomputer System application will be stated on June 27, 2016.
 NIG Supercomputer System application
At the application, please read "Criteria for issuing user login accounts".
We accept NIG Supercomputer System application request from June 27 to August 21, 2016 from here. Please fill in the Purpose of use, "DDBJ Challenge". (example form)
Your accout is valid until August 31, 2016(JST).
If you would like to continue to use NIG Supercomputer System for your own Life Science research, please apply to renew your account from here.
Please specify the following items, when you apply.
 Select topic: Please specify "NIG Supercomputer System".
 Subject: Application for Continuing DDBJ Challenge account
* At the end of each fiscal year, a report must be submitted on the results or progress made in using the NIG Supercomputer.
We send the password by postal mail, within two weeks after your application.
 If you already have NIG Supercomputer account: We create a group for DDBJ Data Analysis Challenge in Supercomputer account, please apply from here.
 NIG Supercomputer System OSS Installation request
We accept NIG Supercomputer System OSS Installation request from June 27 to August 21, 2016 from here.
* Please note that installation takes 7 - 10 days after sending your request, and in some cases installation is unavailable.
 Please refer the following site about basic procedures for using NIG Supercomputer System.
 Login connection, submit SGE job
 Set up your programming environment (R, MATLAB, Python)

Use of MATLAB

During the period, MathWorks Japan Inc. provides software of MATLAB for DDBJ Data Analysis Challenge.
 MATLAB is available only DDBJ Data Analysis Challenge participants.
 There are two ways to use MATLAB R2016a.
(1) Install on local PC
(2) NIG Supercomputer GPU node
 Download MATLAB on local PC, please apply from here.
(It can be applied regardless of student.)
Please specify the following items, when you apply.
 University name: Please enter your company name or school name.
 Team name: Please enter your name or a nickname.
 Team member: Please enter "1".

Contact us

 Question about DDBJ Data Analysis Challenge
 Question about NIG Supercomputer System application, OSS Installation request
Please send your question from "Contact us" web form.

Links

 Machine Learning Solution Page
 Deep Learning with MATLAB
 Training a Deep Neural Network for Digit Classification – Example Code for MATLAB
 Machine Learning Made Easy (Web Seminar)
 Machine Learning with MATLAB (Web Seminar)

Corporate Sponsor

 Mathworks Japan
During the period, MathWorks Japan Inc. provides software of MATLAB for DDBJ Data Analysis Challenge.
 About license configuration

DDBJ Challenge Committee

 DDBJ Challenge ComitteeEli Kaminuma, PhD : Center for Information Biology, National Institute of Genetics, Assistant ProfessorHisashi Kashima, PhD : Department of Intelligence Science and Technology, Kyoto University, ProfessorToshihisa Takagi, PhD : Center for Information Biology, National Institute of Genetics, ProfessorDDBJ Data Analysis Challenge has been approved ethical review by NIG Institutional Review Board (IRB).
Services: ddbj Keywords: Announcement

Suspension of some DDBJ services due to NIG supercomputer system trouble (Resumed)

June 27,2016

The following DDBJ services are unavailable due to the NIG Supercomputer system trouble.

  • DDBJ FTP (sralite file and srafull file)
  • Release of DRA submission

Please wait for a while until the restoration.

Thank you for your understanding and cooperation.

We have re-started these services. (June 27, 2016 at 9:55 JST)
We apologize for any inconvenience this may cause you.

Services: ddbj Keywords: Maintenance

Suspension of DDBJ services due to NIG Supercomputer maintenance (Resumed)

June 10,2016

The following DDBJ services will be unavailable due to NIG Supercomputer system maintenance.

ServicesSchedule (JST)
・DRA validationJune 16 (Thu) 14:00 - June 24 (Fri) 11:00 (JST)
・MiGAPJune 16 (Thu) 18:00 - June 28 (Tue) 10:00 (JST)
・D-way
・DRA Search
・BioProject Search
・BioSample Search
・JGA Submission/Download Tool
・JGA Meta Viewer
June 17 (Fri) 13:00 - June 23 (Thu) 24:00 (JST)
・DDBJ Nucleotide Sequence Submission SystemJune 17 (Fri) 17:00 - June 24 (Fri) 10:00 (JST)
・NIG Supercomputer
・DDBJ anonymous FTP
・getentry
・ARSA
・BLAST
・ClustalW
・DDBJ Read Annotation Pipeline
・DDBJ Homepage
June 20 (Mon) 9:00 - June 23 (Thu) 24:00 (JST)

Thank you for your understanding and cooperation.

We have re-started DDBJ services. (June 24, 2016 at 11:40 JST)
Thank you for your cooperation.

MiGAP is unavailable until June 28 (Tue), 10:00 (JST).

Services: ddbj Keywords: Maintenance

(June 20 – June 23) Suspension of DDBJ services due to NIG Supercomputer maintenance

June 10,2016

We will have NIG Supercomputer System maintenance as follows.
During this period, NIG Supercomputer System services will be unavailable.

June 20 (Mon) 9:00 - June 23 (Thu) 24:00 (JST)

DDBJ services will also be unavailable, please see the time table for details.

Thank you for your understanding and cooperation in this matter.

Services: bioproject,biosample,gea,dra,dta,jga Keywords: Maintenance

JGA is recommended as restricted-access database for human-derived data by Scientific Data, open letters published in Nature and Science

June 09,2016

DNA Data Bank of Japan (DDBJ) Center of National Institute of Genetics (Mishima, Japan) and National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (Tokyo, Japan) have operated the Japanese Genotype-phenotype Archive since October 2013 to serve as one of centralized repositories providing authorized access to individual-level human phenotype and genotype data.

International Nucleotide Sequence Database Collaboration (INSDC) advisors' letter was published in Nature and Science which reminds scientists to submit unrestricted-access sequence data to INSDC, and human phenotype and genotype data requiring restricted-access to other repositories that are not part of INSDC, such as NCBI's Database of Genotypes and Phenotypes (dbGaP), EMBL-EBI's European Genome-phenome Archive (EGA) or DDBJ's Japanese Genotype-phenotype Archive (JGA). JGA is also listed in the recommended data repositories of Scientific Data journal.

Information about available studies can be accessed freely on the JGA and NBDC websites. As of 8 June 2016, 28 studies are available at JGA.

DDBJ Center and NBDC continue to improve JGA as internationally-recognized repository to promote human data sharing and to accelerate biomedical research world-wide.

Background

To exploit personal genomic data while respecting the privacy and informed consents of study participants, it is essential to establish a centralized repository for data management and a policy for data usage. In the US, the National Institutes of Health (NIH) have established guidelines for sharing human subject data. Likewise, NBDC in Japan established guidelines for sharing human-derived data. Data submission to JGA and usage requests from researchers are reviewed by the Data Access Committee (DAC) at NBDC.

JGA accepts data that are de-identified by submitters. Acceptable data types include raw data from array-based and next-generation sequencing platforms, clinical images, and phenotype data associated with data samples. Processed and analyzed data such as alignments, assemblies and variations are also acceptable. Upon submission, the JGA team will archive the original data files in encrypted form in the database. Information in JGA is organized in a hierarchical JGA data model based on that of EGA. JGA assigns stable, unique identifiers prefixed by 'JGA' to studies and subsets of information from those studies. Once granted by DAC, approved datasets can be downloaded with secure downloading software.

Services: ddbj Keywords: Announcement

JGA is recommended as restricted-access database for human-derived data by Scientific Data, open letters published in Nature and Science

June 09,2016

DNA Data Bank of Japan (DDBJ) Center of National Institute of Genetics (Mishima, Japan) and National Bioscience Database Center (NBDC) of Japan Science and Technology Agency (Tokyo, Japan) have operated the Japanese Genotype-phenotype Archive since October 2013 to serve as one of centralized repositories providing authorized access to individual-level human phenotype and genotype data.

International Nucleotide Sequence Database Collaboration (INSDC) advisors' letter was published in Nature and Science which reminds scientists to submit unrestricted-access sequence data to INSDC, and human phenotype and genotype data requiring restricted-access to other repositories that are not part of INSDC, such as NCBI's Database of Genotypes and Phenotypes (dbGaP), EMBL-EBI's European Genome-phenome Archive (EGA) or DDBJ's Japanese Genotype-phenotype Archive (JGA). JGA is also listed in the recommended data repositories of Scientific Data journal.

Information about available studies can be accessed freely on the JGA and NBDC websites. As of 8 June 2016, 28 studies are available at JGA.

DDBJ Center and NBDC continue to improve JGA as internationally-recognized repository to promote human data sharing and to accelerate biomedical research world-wide.

Background

To exploit personal genomic data while respecting the privacy and informed consents of study participants, it is essential to establish a centralized repository for data management and a policy for data usage. In the US, the National Institutes of Health (NIH) have established guidelines for sharing human subject data. Likewise, NBDC in Japan established guidelines for sharing human-derived data. Data submission to JGA and usage requests from researchers are reviewed by the Data Access Committee (DAC) at NBDC.

JGA accepts data that are de-identified by submitters. Acceptable data types include raw data from array-based and next-generation sequencing platforms, clinical images, and phenotype data associated with data samples. Processed and analyzed data such as alignments, assemblies and variations are also acceptable. Upon submission, the JGA team will archive the original data files in encrypted form in the database. Information in JGA is organized in a hierarchical JGA data model based on that of EGA. JGA assigns stable, unique identifiers prefixed by 'JGA' to studies and subsets of information from those studies. Once granted by DAC, approved datasets can be downloaded with secure downloading software.

Services: jga Keywords: Announcement

(June 20 - June 23) Suspension of DDBJ services due to NIG Supercomputer maintenance

June 03,2016

We will have NIG Supercomputer System maintenance as follows.
During this period, NIG Supercomputer System services will be unavailable.

 June 20 (Mon) 9:00 - June 23 (Thu) 24:00 (JST)

DDBJ services will also be unavailable. We will announce if the schedule is fixed.

Thank you for your understanding and cooperation in this matter.
-----

 Suspension of DDBJ services due to NIG Supercomputer maintenance
For further details about suspension of DDBJ services, please follow this link. (June 10, 2016)

Services: ddbj Keywords: Maintenance

Urgent system release (11:00-12:00, 3th June)

June 02,2016
From 11:00 to 12:00 (planned), 3th June, the JGA submission and search systems will be unavailable due to the urgent system release. Sorry for any inconvenience.
Services: jga Keywords: Maintenance

Updates in the D-way submission interface

June 01,2016

To improve the D-way submission system, interface is updated.

Icons and explanation sentences are added, links to both English and Japanese manuals are provided in the popup.
Services: bioproject,biosample,dra Keywords: Announcement

Connection error of the JGA tool [fixed]

May 31,2016

We have updated the server certificate of the JGA server at 23th, May (Monday). Due to this update, a connection error is caused when using the JGA tool. We apologize any inconvenience this may cause.

2016-05-31 Please use the latest version (v3.0.1) of our tool.
Services: jga Keywords:

Scheduled maintenance (9:30-11:00, first June)

May 26,2016
From 9:30 to 11:00 (planned), first, June, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

2016-05-26 18:00-20:00 JGA web server re-start

May 24,2016
During 18:00-20:00, 26th May, 2016, the JGA web server will be re-started for maintenance. Connection to the server will be dis-connected. we apologize for any inconvenience.
Services: jga Keywords: Maintenance

Publication of an open letter from International Advisory Committee

May 12,2016

The members of International Advisory Committee wrote an open letter reminding scientists to submit sequence data to INSDC that was published in both Nature and Science.

Services: ddbj Keywords: Announcement

Release of genome sequence data of a mushroom (Hypsizygus marmoreus)

May 12,2016

DDBJ released genome sequence data of a mushroom (Hypsizygus marmoreus) which had been submitted by Kindai University.

The accession numbers are as follows. They are available on getentry.

WGS: BDDV01000001-BDDV01010694 (BDDV.gz) (10,694 entries)
Services: ddbj Keywords: Data Release

Release of TSA data of Tausch's goatgrass (Aegilops tauschii), 10 strains

May 12,2016

DDBJ released TSA (Transcriptome Shotgun Assembly) data of Tausch's goatgrass (Aegilops tauschii), 10 strains which had been submitted by Kobe University.

The accession numbers are as follows. They are available on getentry or DRASearch.

strain TSA accession numbers DRA accession numbers
AT76 IAAN01000001-IAAN01045723 (IAAN.gz) (45,723 entries) DRR058959 (DRA004604)
KU-2003 IAAO01000001-IAAO01055813 (IAAO.gz) (55,813 entries) DRR058960 (DRA004604)
KU-2025 IAAP01000001-IAAP01033680 (IAAP.gz) (33,680 entries) DRR058961 (DRA004604)
KU-2075 IAAQ01000001-IAAQ01065447 (IAAQ.gz) (65,447 entries) DRR058962 (DRA004604)
KU-2078 IAAR01000001-IAAR01060884 (IAAR.gz) (60,884 entries) DRR058963 (DRA004604)
KU-2087 IAAS01000001-IAAS01065827 (IAAS.gz) (65,827 entries) DRR058964 (DRA004604)
KU-2093 IAAT01000001-IAAT01053474 (IAAT.gz) (53,474 entries) DRR058965 (DRA004604)
KU-2124 IAAU01000001-IAAU01060479 (IAAU.gz) (60,479 entries) DRR058966 (DRA004604)
KU-2627 IAAV01000001-IAAV01060547 (IAAV.gz) (60,547 entries) DRR058967 (DRA004604)
PI499262 IAAW01000001-IAAW01055848 (IAAW.gz) (55,848 entries) DRR058968 (DRA004604)
Services: ddbj Keywords: Data Release

Release of genome sequence data of common buckwheat (Fagopyrum esculentum)

May 12,2016

DDBJ released genome sequence data of common buckwheat (Fagopyrum esculentum) which had been submitted by Kazusa DNA Research Institute.

Reference
Gluten-free noodle revolution: the quest for chewier, non-allergenic buckwheat

The accession numbers are as follows. They are available on getentry or DRASearch.

WGS: BCYN01000001-BCYN01387594 (BCYN.gz) (387,594 entries)
DRA: DRR046985-DRR046993 (DRA004060)
Services: ddbj Keywords: Data Release

Release of genome sequence data of matsutake (Tricholoma matsutake)

May 06,2016

DDBJ released genome sequence data of matsutake (Tricholoma matsutake) which had been submitted by Kindai University.

The accession numbers are as follows. They are available on getentry.

WGS: BDDP01000001-BDDP01088884 (BDDP.gz) (88,884 entries)
Services: ddbj Keywords: Data Release

Release of genome sequence data of 'ohi'a lehua (Metrosideros polymorpha var. glaberrima)

May 02,2016

DDBJ released genome sequence data of 'ohi'a lehua (Metrosideros polymorpha var. glaberrima) which had been submitted by Kyoto University .

The accession numbers are as follows. They are available on getentry.

WGS: BCNH01000001-BCNH01036376 (BCNH.gz) (36,376 entries)
Services: ddbj Keywords: Data Release

(April 27) ARSA temporarily unavailable (Resumued)

April 27,2016

ARSA will be unavailable due to NIG Supercomputer system maintenance as follows.

 April 27 (Wed), 10:00 - 12:00 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (April 27, 2016 at 11:56 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Announcement

Metadata fields for phenotype, disease and molecular data type were added

April 26,2016

Metadata fields for phenotype, disease and molecular data type were added to the JGA metadata excel.

Study

Required:
  • Molecular Data Type
  • Phenotype term(s)/Disease term(s)
Recommended:
  • Inclusion/Exclusion Criteria
  • Disease Type(s)

Sample

Recommended:
  • Tissue
  • Population
  • Histological Type
  • Is Tumor
Services: jga Keywords: Announcement

Suspension of DDBJ services due to NIG Supercomputer maintenance (2016-04-25)

April 20,2016

Due to NIG Supercomputer system maintenance, BioProject, BioSample and DRA services will be unavailable during 9:00-24:00. For details, please see DDBJ News. Thank you for your understanding and cooperation.

Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

Suspension of DDBJ services due to NIG Supercomputer maintenance (Resumed)

April 20,2016

The following DDBJ services will be unavailable due to NIG Supercomputer system maintenance.

ServicesSchedule (JST)
・MiGAPApril 21 (Thu) 18:00 - April 27 (Wed) 10:00 (JST)
・DRA validationApril 22 (Fri) 14:00 - April 26 (Tue) 13:00 (JST)
・D-way
・DRA Search
・BioProject Search
・BioSample Search
April 25 (Mon) 9:00 - April 25 (Mon) 24:00 (JST)
・DDBJ Nucleotide Sequence Submission SystemApril 25 (Mon) 9:00 - April 26 (Tue) 10:00 (JST)
・NIG Supercomputer Hompage
・DDBJ anonymous FTP
・getentry
・ARSA
・BLAST
・ClustalW
・DDBJ Read Annotation Pipeline
April 25 (Mon) 13:00 - April 25 (Mon) 24:00 (JST)

Thank you for your understanding and cooperation.

We have re-started DDBJ services. (April 26, 2016 at 10:42 JST)
Thank you for your cooperation.

MiGAP is unavailable until April 27 (Wed), 10:00 (JST).

Services: ddbj Keywords: Maintenance

Updated tools related to Mass Submission System (MSS)

April 20,2016

DDBJ updated tools related to Mass Submission System.

  • Utilities for MSS file Error check (UME) version 1.41 Released
  • Parser version 6.54 Released

See MSS Home in detail.

Services: ddbj Keywords: Announcement

Release of TSA data of a planarian, Dugesia japonica

April 20,2016

DDBJ released TSA (Transcriptome Shotgun Assembly) data of a planarian, Dugesia japonica, which had been submitted by Kyoto University.

The accession numbers are as follows. They are available on getentry or DRASearch.

TSA: IAAB01000001-IAAB01137201 (IAAB.gz) (137,201 entries)
DRA: DRR047187-DRR047210 (DRA004066)
Services: ddbj Keywords: Data Release

Suspension of some parts of DDBJ activities during Japanese national holidays

April 18,2016

We at DDBJ will temporarily close for the Japanese National Holidays from the end of April to the beginning of May, 2016.
For the detailed, please see DDBJ Calendar.

 DDBJ Calnedar

During the holidays, NIG Supercomputer and DDBJ network services are available.
Also, DDBJ will continue to receive inquiries from E-mail and "Contact us" web form.
Please note that replies from DDBJ is after the holidays.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Announcement

Public key in OpenSSH format can not be registered to D-way account

April 15,2016

To submit data to DRA, a public key needs to be registered to the D-way account (Handbook)。At present, a public key in OpenSSH format commonly used in Mac OS X and Unix, is not properly registered to the account. We apologize for the inconvenience caused.

This issue will be resolved at 25th, April.

If submitter wants to newly use OpenSSH keys, please follow the steps below.

1. Register a public key: Please generate key pairs by PuTTY Key Generator, and register the public key in PuTTY format to your account. Handbook (Windows)

Upload data files to the DRA server by 2 or 3.

2. Upload files in scp by using WinSCP in Windows machine. Handbook (Windows)

3. To upload files in Mac OS X and Unix machines, first convert the PuTTY-formatted private key into the OpenSSH format. Handbook. Move the converted OpenSSH private key to the Mac OS X or Unix machines and execute scp command.

Services: bioproject,biosample,gea,dra,dta Keywords:

Scheduled maintenance (9:30-11:00, 13 Apr.)

April 07,2016
From 9:30 to 11:00 (planned), 13th, April, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Release of genome sequence data of luminous mushroom (Mycena chlorophos)

April 06,2016

DDBJ released genome sequence data of luminous mushroom (Mycena chlorophos) which had been submitted by Keio University .

The accession numbers are as follows. They are available on getentry or DRASearch.

DRA: DRR018497-DRR018504 (DRA002230)
WGS: BAYG01000001-BAYG01025660 (BAYG.gz) (25,660 entries)
scaffold CON: DF837679-DF850034 (12,356 entries)
Services: ddbj Keywords: Data Release

Suspension of some DDBJ services due to NIG supercomputer system trouble

April 01,2016
The following DDBJ services are unavailable due to the NIG supercomputer system trouble.DDBJ FTP (some SRA metadata and fastq files)DRA SearchPlease wait for a while until the restoration.Thank you for your understanding and cooperation.
Services: dra Keywords:

Suspension of some DDBJ services due to NIG supercomputer system trouble [2016-04-04 9:22 resumed]

April 01,2016

The following DDBJ services are unavailable due to the NIG supercomputer system trouble.
[2016-04-04 9:22 resumed]

  • DDBJ FTP (some SRA metadata and fastq files)
  • DRA Search

Please wait for a while until the restoration.

Thank you for your understanding and cooperation.

Services: ddbj Keywords: Maintenance

Trouble in adding DRA submission grant to the account

March 31,2016
2016-04-13 11:00 This bug was fixed.
2016-03-31: Due to the D-way authentification system update carried out at 2016-03-30, DRA submission is not granted by registering public key and center name to the D-way account. We are fixing this trouble. If you need to add the DRA submission grant to your account, please contact us. We apologize for any inconvenience.
Services: bioproject,biosample,dra Keywords:

Suspension of "DDBJ Nucleotide Sequence Submission System" due to system trouble(resumed)

March 29,2016

DDBJ Nucleotide Sequence Submission System is suspended due to a system trouble.
Please wait for a while until resume of the service.
Thank you for your understanding and cooperation.

Theservice is available. DDBJ sincerely apologize for your inconvenience.(March 30, 2016 at 16:40 JST)

Services: ddbj Keywords: Maintenance

DDBJ Rel. 104.0, DAD Rel. 74.0 Completed

March 25,2016

DDBJ Rel. 104.0

DAD (DDBJ amino acid database) Rel. 74.0
  • Date: Mar. 25, 2016
  • 47,659,541 entries     14,850,873,151 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release

System unavailable due to the D-way authentication system updates (2016-03-30)

March 25,2016
March 30 (Wednesday), 2016, 9:30-17:00 (planned), to switch the D-way authentication system, the submission system (D-way) and data retrieval systems (DRASearch, BioProject/BioSample Search) will be unavailable. We apologize for any inconvenience this may cause you.
Services: bioproject,biosample,dra Keywords: Maintenance

(Mar. 24) ARSA temporarily unavailable (Resumed)

March 23,2016

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 March 24 (Thu), 10:00 - 12:00 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (March 24, 2016 at 11:55 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Release of TSA data of ants, 17 species

March 23,2016

DDBJ released TSA (Transcriptome Shotgun Assembly) data of ants, 17 species which had been submitted by Okinawa Institute of Science and Technology Graduate University.

The accession numbers are as follows. They are available on getentry or DRASearch.

organism TSA accession numbers DRA accession numbers
Formica aquilonia LH381539-LH513652 (132,114 entries) DRR042077-DRR042082 (DRA003820)
Formica cinerea LH513653-LH652103 (138,451 entries) DRR042083-DRR042088 (DRA003820)
Formica exsecta LH652104-LH973351 (321,248 entries) DRR042089-DRR042092 (DRA003820)
Formica fusca LI000001-LI121692 (121,692 entries) DRR042093-DRR042098 (DRA003820)
Formica pratensis LI121693-LI219804 ( 98,112 entries) DRR042099-DRR042104 (DRA003820)
Formica pressilabris LI219805-LI349988 (130,184 entries) DRR042105-DRR042110 (DRA003820)
Formica truncorum LI349989-LI476587 (126,599 entries) DRR042111-DRR042116 (DRA003820)
Lasius neglectus LI476588-LI563515 ( 86,928 entries) DRR042123-DRR042128 (DRA003820)
Lasius turcicus LI563516-LI670604 (107,089 entries) DRR042129-DRR042134 (DRA003820)
Linepithema humile LI670605-LI795928 (125,324 entries) DRR042117-DRR042122 (DRA003820)
Monomorium chinense LI795929-LI926639 (130,711 entries) DRR042135-DRR042140 (DRA003820)
Monomorium pharaonis LJ000001-LJ120855 (120,855 entries) DRR042141-DRR042146 (DRA003820)
Myrmica rubra LJ120856-LJ206166 ( 85,311 entries) DRR042147-DRR042152 (DRA003820)
Myrmica ruginodis LJ206167-LJ284088 ( 77,922 entries) DRR042153-DRR042158 (DRA003820)
Myrmica sulcinodis LJ284089-LJ356044 ( 71,956 entries) DRR042159-DRR042164 (DRA003820)
Solenopsis invicta LJ356045-LJ530869 (174,825 entries) DRR042165-DRR042170 (DRA003820)
Solenopsis invicta LJ530870-LJ707314 (176,445 entries) DRR042171-DRR042176 (DRA003820)
Services: ddbj Keywords: Data Release

Release of genome sequence data of a bacterium that degrades and assimilates PET, Ideonella sakaiensis

March 22,2016

DDBJ released genome sequence data of a bacterium that degrades and assimilates polyethylene terephthalate (PET), Ideonella sakaiensis, which had been submitted by Kyoto University.

Reference
Yoshida S et al. (2016). Science 351, 1196-1199. DOI: 10.1126/science.aad6359

The accession numbers are as follows. They are available on getentry

WGS: BBYR01000001-BBYR01000227 (BBYR.gz) (227 entries)

Services: ddbj Keywords: Data Release

Release of genome sequence data of zoysiagrasses, 3 species

March 22,2016

DDBJ released genome sequence data of zoysiagrasses, 3 species which had been submitted by Kazusa DNA Research Institute.

The accession numbers are as follows. They are available on getentry or DRASearch.

organism WGS accession numbers DRA accession numbers
Zoysia japonica cv. Nagirizaki BCLF01000001-BCLF01011786 (BCLF.gz) (11,786 entries) DRR047281, DRR047282, DRR047283, DRR047291 (DRA004073)
Zoysia matrella cv. Wakaba BCLG01000001-BCLG01013609 (BCLG.gz) (13,609 entries) DRR047287, DRR047289 (DRA004073)
Zoysia pacifica cv. Zanpa BCLH01000001-BCLH01011428 (BCLH.gz) (11,428 entries) DRR047288, DRR047290 (DRA004073)
Services: ddbj Keywords: Data Release

DDBJ service is unavailable due to the electric power outage (Resumed)

March 17,2016

DDBJ service is unavailable due to the electric power outage of the NIG(National Institute of Genetics) caused by failure in power transmission at electric power company which occurred on March 16.

Please wait for a while until the restoration.

Thank you for your understanding and cooperation.

DDBJ service is available. (March 18, 2016 at 12:20 JST)
We sincerely apologize for the inconvenience.

Services: ddbj Keywords: Maintenance

Scheduled maintenance (9:30-11:00, 9 Mar.)

March 03,2016
From 9:30 to 11:00 (planned), 9th, March, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra,dta Keywords: Maintenance

Order of submitted BioSamples and update of sample name

February 05,2016

After submitting BioSamples from D-way, BioSamples are sorted in alphabetical (ASCII code) order of sample_name values and NOT in order of appearance (top to bottom in tab-delimited text file). BioSample accession numbers are issued to the alphabetically-sorted BioSamples. (news). From 9th, February, 2016, BioSample accessions are issued to the BioSamples in order of appearance (top to bottom in tab-delimited text file).

Sample name had been un-editable after submission. From 9th, February, 2016, sample name can be updated after submission upon request. Order update at this site.

Services: bioproject,biosample,dra Keywords: Announcement

Scheduled maintenance (9:30-11:30, 9 Feb.)

February 04,2016
From 9:30 to 11:30 (planned), 9th, February, the DRA, BioProject and BioSample submission and search services will be unavailable due to scheduled maintenance.
Services: bioproject,biosample,dra Keywords: Maintenance

Suspension of all DRA/BioProject/BioSample services due to hardware trouble [second time]

February 02,2016

The hardware trouble occurred at 29th, January was fixed by vendor at 1st, February.
However, a similar trouble occurred again at 2nd, February.
DDBJ will stop all DRA/BioProject/BioSample services due to the repeated hardware trouble.
Our system will be re-started after 3rd, February (Wednesday).
We will announce the re-starting time if determined.

We sincerely apologize for any inconvenience this repeated suspension may cause you.

We have re-started all DRA/BioProject/BioSample services (February 4th, 2016 at 16:00 JST).
We apologize for any inconvenience this may cause you.

Services: ddbj Keywords: Announcement

Suspension of all DRA/BioProject/BioSample services due to hardware trouble [second time]

February 02,2016
The hardware trouble occurred at 29th, January was fixed by vendor at 1st, February. However, a similar trouble occurred again at 2nd, February. DDBJ will stop all DRA/BioProject/BioSample services due to the repeated hardware trouble. Our system will be re-started after 3rd, February (Wednesday). We will announce the re-starting time if determined. We sincerely apologize for any inconvenience this repeated suspension may cause you.
We have re-started all DRA/BioProject/BioSample services (February 4th, 2016 at 16:00 JST).
We apologize for any inconvenience this may cause you.
Services: bioproject,biosample,dra,dta Keywords:

Suspension of all DRA/BioProject/BioSample services due to hardware trouble

January 29,2016

DDBJ will stop all DRA/BioProject/BioSample services due to the hardware trouble. Our system will be re-started after 1st, February (Monday). We will announce the re-starting time if determined. We apologize for any inconvenience this may cause you.
[2/1 16:40 All system is available.]

Services: ddbj Keywords: Announcement

Suspension of all DRA/BioProject/BioSample services due to hardware trouble

January 29,2016
DDBJ will stop all DRA/BioProject/BioSample services due to the hardware trouble. Our system will be re-started after 1st, February (Monday). We will announce the re-starting time if determined. We apologize for any inconvenience this may cause you.
Services: bioproject,biosample,gea,dra,dta Keywords: Maintenance

(Jan. 28) ARSA temporarily unavailable (Resumed)

January 27,2016

ARSA will be unavailable due to NIG Supercomputer maintenance as follows.

 January 28 (Thu), 10:00 - 12:00 (JST)

Thank you for your understanding and cooperation.

NIG Supercomputer maintenance finished. ARSA is available. (January 28, 2016 at 11:00 JST)
Thank you for your cooperation.

Services: ddbj Keywords: Maintenance

Release of genome sequence data of Taiwan habu (Protobothrops mucrosquamatu)

January 19,2016

DDBJ released genome sequence data of Taiwan habu (Protobothrops mucrosquamatu) which had been submitted by Okinawa Institute of Science and Technology Graduate University.

Reference
previously released data

The accession numbers are as follows. They are available on getentry or DRASearch.

DRA: DRR049668, DRR049669 (DRA004189)
WGS: BCNE02000001-BCNE02167851 (BCNE.gz) (167,851 entries)
scaffold CON: LD636650-LD688929 (52,280 entries)
Services: ddbj Keywords: Data Release

Release of genome sequence data of Acropora digitifera

January 18,2016

DDBJ released genome sequence data of Acropora digitifera which had been submitted by Okinawa Institute of Science and Technology Graduate University.

Reference
previously released data

The accession numbers are as follows. They are available on getentry or DRASearch.

DRA: DRR001380-DRR001433 (DRA000447)
WGS: BACK02000001-BACK02054400 (BACK.gz) (54,400 entries)
scaffold CON: DF970692-DF973111 (2,420 entries)
Services: ddbj Keywords: Data Release

Scheduled system maintenance (9:30-11:30, 20 Jan.)

January 14,2016
From 9:30 to 11:30 (planned), 20th (Wednesday), January, the DRA, BioProject and BioSample submission services will be unavailable due to scheduled maintenance of D-way.
Services: bioproject,biosample,dra Keywords: Maintenance

DDBJ Rel. 103.0, DAD Rel. 73.0 Completed

January 07,2016

DDBJ Rel. 103.0

DAD (DDBJ amino acid database) Rel. 73.0
  • Date: Jan. 7, 2016
  • 45,660,142 entries     14,219,638,761 aa (total number of residues)
  • DAD Release Note
Services: ddbj Keywords: Data Release
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