クリスマス明けてDFAST_QC論文アクセプトの知らせ。今年の査読あり国際誌論文は、植物2、DDBJ/INSDC2、ネコ1、イヌ1、微生物1の合計7報で、プレプリント公開&投稿中がネコ1 、植物1となりました
よいおとしを。甘いなコレ
よいおとしを。甘いなコレ
December 28, 2024 at 6:35 AM
クリスマス明けてDFAST_QC論文アクセプトの知らせ。今年の査読あり国際誌論文は、植物2、DDBJ/INSDC2、ネコ1、イヌ1、微生物1の合計7報で、プレプリント公開&投稿中がネコ1 、植物1となりました
よいおとしを。甘いなコレ
よいおとしを。甘いなコレ
Yep. ENA and DDBJ.
February 3, 2025 at 11:31 PM
Yep. ENA and DDBJ.
My introduction: Yaz Nakamura is a professor at the NIG in Japan. His expertise is genome analysis and DB construction. He also works for DDBJ, an INSDC partner. He loves cats so much that he has started cat genome research.
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
January 8, 2025 at 3:47 AM
My introduction: Yaz Nakamura is a professor at the NIG in Japan. His expertise is genome analysis and DB construction. He also works for DDBJ, an INSDC partner. He loves cats so much that he has started cat genome research.
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
The genomic information for our strains, which belong to the ‘Hodarchaeales', has been released. Due to a large-scale server replacement at DDBJ (DNA Database of Japan), the release has been delayed.
April 14, 2025 at 1:10 AM
The genomic information for our strains, which belong to the ‘Hodarchaeales', has been released. Due to a large-scale server replacement at DDBJ (DNA Database of Japan), the release has been delayed.
だいたいやね。イヌゲノムネコゲノムとINSDCとDDBJとむりくり四題噺にするところに無理があるんよね
... いやでもそりゃあもう全部乗っけで行きたいところで...
... いやでもそりゃあもう全部乗っけで行きたいところで...
February 10, 2025 at 10:18 AM
だいたいやね。イヌゲノムネコゲノムとINSDCとDDBJとむりくり四題噺にするところに無理があるんよね
... いやでもそりゃあもう全部乗っけで行きたいところで...
... いやでもそりゃあもう全部乗っけで行きたいところで...
I’ve been praying that the sharing of gene and other sequences between Genbank, EMBL and DDBJ continues.
March 21, 2025 at 6:36 AM
I’ve been praying that the sharing of gene and other sequences between Genbank, EMBL and DDBJ continues.
伴侶動物ゲノム医療情報基盤としてのイエネコ・イヌゲノム解読の戦略、また、そのような塩基配列データを格納し共有するINSDCとその日本ノードのDDBJの活動についても紹介し、NGSデータを格納し最も巨大なアーカイブとなったSRAの現状とINSDCの可能な将来像を併せて考察する
...ごちゃごちゃしてんな
...ごちゃごちゃしてんな
February 10, 2025 at 10:18 AM
伴侶動物ゲノム医療情報基盤としてのイエネコ・イヌゲノム解読の戦略、また、そのような塩基配列データを格納し共有するINSDCとその日本ノードのDDBJの活動についても紹介し、NGSデータを格納し最も巨大なアーカイブとなったSRAの現状とINSDCの可能な将来像を併せて考察する
...ごちゃごちゃしてんな
...ごちゃごちゃしてんな
will this work? www.uniprot.org/blast/
or
EMBL-EBI BLAST (European version) ➡ www.ebi.ac.uk/Tools/sss/nc...
DDBJ (Japan) BLAST ➡ blast.ddbj.nig.ac.jp/blastn
or
EMBL-EBI BLAST (European version) ➡ www.ebi.ac.uk/Tools/sss/nc...
DDBJ (Japan) BLAST ➡ blast.ddbj.nig.ac.jp/blastn
UniProt
www.uniprot.org
March 1, 2025 at 11:49 PM
will this work? www.uniprot.org/blast/
or
EMBL-EBI BLAST (European version) ➡ www.ebi.ac.uk/Tools/sss/nc...
DDBJ (Japan) BLAST ➡ blast.ddbj.nig.ac.jp/blastn
or
EMBL-EBI BLAST (European version) ➡ www.ebi.ac.uk/Tools/sss/nc...
DDBJ (Japan) BLAST ➡ blast.ddbj.nig.ac.jp/blastn
#DavidsMonthOfMusic
#MusicChallenge
Day6 : a song that begins with a G
Green and blue
m.youtube.com/watch?v=ddBj...
#MusicChallenge
Day6 : a song that begins with a G
Green and blue
m.youtube.com/watch?v=ddBj...
The Murder Capital - Green & Blue (Official Video)
YouTube video by The Murder Capital
m.youtube.com
January 7, 2026 at 5:34 AM
#DavidsMonthOfMusic
#MusicChallenge
Day6 : a song that begins with a G
Green and blue
m.youtube.com/watch?v=ddBj...
#MusicChallenge
Day6 : a song that begins with a G
Green and blue
m.youtube.com/watch?v=ddBj...
m.youtube.com/watch?v=dDbJ...
노력 없이 좋은 추억 만들고 싶어요
노력 없이 좋은 추억 만들고 싶어요
정우 - JUVENILE / 가사
YouTube video by Todaytrack
m.youtube.com
May 22, 2026 at 6:18 AM
m.youtube.com/watch?v=dDbJ...
노력 없이 좋은 추억 만들고 싶어요
노력 없이 좋은 추억 만들고 싶어요
If it is sequencing data, and as long as you submitted a sequence file (FASTQ/BAM etc), this brokered automatically GEO->GenBank->(INSDC)->ENA (and DDBJ) at source. Arrays... not the same but not so critical these days.
January 23, 2025 at 10:41 PM
If it is sequencing data, and as long as you submitted a sequence file (FASTQ/BAM etc), this brokered automatically GEO->GenBank->(INSDC)->ENA (and DDBJ) at source. Arrays... not the same but not so critical these days.
GISAID ruining science. This is a great shame.
covSPECTRUM, an invaluable tool, will continue to work with open data from the INSDC system (ENA, NCBI, DDBJ).
But historical data and data from many countries only feeding into GISAID will be unavailable.
covSPECTRUM, an invaluable tool, will continue to work with open data from the INSDC system (ENA, NCBI, DDBJ).
But historical data and data from many countries only feeding into GISAID will be unavailable.
December 19, 2025 at 7:37 AM
GISAID ruining science. This is a great shame.
covSPECTRUM, an invaluable tool, will continue to work with open data from the INSDC system (ENA, NCBI, DDBJ).
But historical data and data from many countries only feeding into GISAID will be unavailable.
covSPECTRUM, an invaluable tool, will continue to work with open data from the INSDC system (ENA, NCBI, DDBJ).
But historical data and data from many countries only feeding into GISAID will be unavailable.
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
October 4, 2025 at 6:31 PM
DFAST (sorta PGAP fromthe DDBJ)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
Not overly complicated to add custom annotation sources (blastn, blastp, rps-blast, hmm-based...)
In case GISAID does not get its act together, covSPECTRUM also runs on open data containing a lower number of sequences with more restricted geographic coverage.
Open data through the INSDC system (www.insdc.org; ENA, NCBI, DDBJ)
Here is a comparison for XFG*
Open data through the INSDC system (www.insdc.org; ENA, NCBI, DDBJ)
Here is a comparison for XFG*
October 31, 2025 at 7:08 AM
In case GISAID does not get its act together, covSPECTRUM also runs on open data containing a lower number of sequences with more restricted geographic coverage.
Open data through the INSDC system (www.insdc.org; ENA, NCBI, DDBJ)
Here is a comparison for XFG*
Open data through the INSDC system (www.insdc.org; ENA, NCBI, DDBJ)
Here is a comparison for XFG*
EBI has (basically) indepenent submission, display and transfer schemes, though EBI and NCBI (and DDBJ for ENA) are (rightfully) appropriately entangled to maintain common accession/identifier spaces (INSDC Accession numbers; MANE IDs, Project IDs, PMIDs etc etc);
February 7, 2025 at 12:41 PM
EBI has (basically) indepenent submission, display and transfer schemes, though EBI and NCBI (and DDBJ for ENA) are (rightfully) appropriately entangled to maintain common accession/identifier spaces (INSDC Accession numbers; MANE IDs, Project IDs, PMIDs etc etc);
From the @narjournal.bsky.social #NARDatabaseIssue | #DDBJ update in 2025: system integration for global data-sharing including #pathogen surveillance | #Bioinformatics #Database #Genomics #OpenScience #OpenData 🧬 🖥️🧪🔓 🇯🇵
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
DDBJ update in 2025: system integration for global data-sharing including pathogen surveillance
Abstract. The Bioinformation and DNA Data Bank of Japan Center (https://www.ddbj.nig.ac.jp/) continues to serve as a global core infrastructure for biologi
academic.oup.com
November 25, 2025 at 5:05 PM
From the @narjournal.bsky.social #NARDatabaseIssue | #DDBJ update in 2025: system integration for global data-sharing including #pathogen surveillance | #Bioinformatics #Database #Genomics #OpenScience #OpenData 🧬 🖥️🧪🔓 🇯🇵
⬇️
academic.oup.com/nar/advance-...
⬇️
academic.oup.com/nar/advance-...
My wonderful colleague at NIG running the Japanese part (DDBJ) of INSDC which includes ENA and GenBank - ie, the world's open access research DNA database, running since the 1980s, coordinated globally and underpinning so many discoveries
He is also a great researcher, around Cat genetics/genomics
He is also a great researcher, around Cat genetics/genomics
My introduction: Yaz Nakamura is a professor at the NIG in Japan. His expertise is genome analysis and DB construction. He also works for DDBJ, an INSDC partner. He loves cats so much that he has started cat genome research.
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
He lives with 4 cats, the favorite is Mr. Moushtache.
で、チェアに紹介文を送っときました。
January 8, 2025 at 8:48 AM
My wonderful colleague at NIG running the Japanese part (DDBJ) of INSDC which includes ENA and GenBank - ie, the world's open access research DNA database, running since the 1980s, coordinated globally and underpinning so many discoveries
He is also a great researcher, around Cat genetics/genomics
He is also a great researcher, around Cat genetics/genomics
GEO sequencing data brokers into Genbank / SRA and then is shared automatically across INSDC - to ENA at EBI and DDBJ at NIG. INSDC has been running since the 1980s …. Array data though was not pooled though array data is no longer as used / submitted / reprocessed
February 9, 2025 at 8:50 AM
GEO sequencing data brokers into Genbank / SRA and then is shared automatically across INSDC - to ENA at EBI and DDBJ at NIG. INSDC has been running since the 1980s …. Array data though was not pooled though array data is no longer as used / submitted / reprocessed
40 years after Unknown Pleasures, the Joy Division sound still works.
www.youtube.com/watch?v=ddBj...
www.youtube.com/watch?v=ddBj...
The Murder Capital - Green & Blue (Official Video)
YouTube video by The Murder Capital
www.youtube.com
December 7, 2024 at 9:59 PM
40 years after Unknown Pleasures, the Joy Division sound still works.
www.youtube.com/watch?v=ddBj...
www.youtube.com/watch?v=ddBj...
GEO sequence data is mirrored in INSDC (ENA/Genbank/DDBJ). Microarrays and derived files are not
January 29, 2025 at 8:10 AM
GEO sequence data is mirrored in INSDC (ENA/Genbank/DDBJ). Microarrays and derived files are not
The feature is only available on open.cov-spectrum.org which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.
If you have any questions or suggestions, please let us know! 3/4
If you have any questions or suggestions, please let us know! 3/4
August 28, 2025 at 7:41 AM
The feature is only available on open.cov-spectrum.org which uses data from INSDC (GenBank/ENA/DDBJ), we unfortunately cannot provide it for data from GISAID.
If you have any questions or suggestions, please let us know! 3/4
If you have any questions or suggestions, please let us know! 3/4
ddbjに塩基配列を登録する作業、なんとか無事にアップロードとメタデータの提出まで完了
April 29, 2025 at 12:09 AM
ddbjに塩基配列を登録する作業、なんとか無事にアップロードとメタデータの提出まで完了
Sequencing databases are run as an international collaboration though, between NCBI, EMBL-EBI and DDBJ. www.insdc.org/about-insdc/
International Nucleotide Sequence Database CollaborationAbout INSDC – International Nucleotide Sequence Database Collaboration
www.insdc.org
February 1, 2025 at 12:51 PM
Sequencing databases are run as an international collaboration though, between NCBI, EMBL-EBI and DDBJ. www.insdc.org/about-insdc/
Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important
February 22, 2025 at 9:00 PM
先進ゲノム支援とDDBJが共同でやってる情報解析講習会の録画と配布資料がちょっと前に公開されてました。
www.genome-sci.jp/lecture202511
www.genome-sci.jp/lecture202511
情報解析講習会ビデオ＜2025年度 PAGS・DDBJ合同 初級者情報解析講習会＞ ｜ 先進ゲノム支援（先進ゲノム解析研究推進プラットフォーム）
www.genome-sci.jp
December 24, 2025 at 8:42 AM
先進ゲノム支援とDDBJが共同でやってる情報解析講習会の録画と配布資料がちょっと前に公開されてました。
www.genome-sci.jp/lecture202511
www.genome-sci.jp/lecture202511