月に２回のINSDCエグゼクティブの日でした。10時過ぎに会議終了。やれねむい。部屋に帰ります
February 19, 2026 at 1:21 PM
月に２回のINSDCエグゼクティブの日でした。10時過ぎに会議終了。やれねむい。部屋に帰ります
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
1/ 🧬 A big #Pathoplexus milestone: you can now optionally include raw sequencing reads alongside your consensus sequences!
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
Hosting raw reads alongside consensus data helps improve reproducibility & allow in-depth analyses.
📰 Read more: pathoplexus.org/news/2026-09...
September 23, 2026 at 1:06 PM
This is a big deal for virus data sharing. Submitters can now upload raw reads, immediately share them with collaborators, and let Pathoplexus take care of the INSDC submission process on their behalf…
I finished the bi-weekly INSDC EC meeting—good night from Fukuoka.
The bath is so small, I have to sit with my knees up.
The bath is so small, I have to sit with my knees up.
September 18, 2025 at 12:43 PM
I finished the bi-weekly INSDC EC meeting—good night from Fukuoka.
The bath is so small, I have to sit with my knees up.
The bath is so small, I have to sit with my knees up.
今日は1時間遅れのINSDC国際会議終了。欧州のエグゼクティブの一人が今月いっぱいで交代となる。一抹の寂しさ
February 6, 2025 at 2:08 PM
今日は1時間遅れのINSDC国際会議終了。欧州のエグゼクティブの一人が今月いっぱいで交代となる。一抹の寂しさ
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
Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
November 25, 2024 at 12:55 PM
Our new GenSpectrum.org dashboard has finally launched! Using Influenza H5N1, RSV and SARS-CoV-2 data from INSDC and West Nile virus data from @pathoplexus.org, it enables fast and interactive analyses of genome sequencing data similar to CoV-Spectrum. 1/5
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
GlobDB: a comprehensive species-dereplicated microbial genome resource
AbstractMotivation. Over the past years, substantial numbers of microbial species’ genomes have been deposited outside of conventional INSDC databases.Resu
doi.org
November 21, 2025 at 4:21 PM
Our paper describing the GlobDB is now published in @bioinfoadv.bsky.social
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
doi.org/10.1093/bioa...
The GlobDB is the largest species dereplicated genome database currently available, containing 306,260 species representatives.
More information on globdb.org 1/5
🖥️🧬🦠
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。
To do all this, we needed to reprocess all the public SARS-CoV-2 genome data in INSDC, and it became very apparent how dominated this data was by US/UK. The second half of this project became about working with teams across the world to help them get their data into INSDC.
February 9, 2026 at 3:21 PM
To do all this, we needed to reprocess all the public SARS-CoV-2 genome data in INSDC, and it became very apparent how dominated this data was by US/UK. The second half of this project became about working with teams across the world to help them get their data into INSDC.
Notice for users submitting MAGs to INSDC
Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...
What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...
What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
Genome
Download a genome data package including genome, transcript and protein sequence, annotation and a data report
www.ncbi.nlm.nih.gov
April 10, 2026 at 2:15 PM
Notice for users submitting MAGs to INSDC
Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...
What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
Issue: MAGs submitted to INSDC without taxonomic annotations, typically listed as ‘metagenome’, are not included in GTDB. Examples: www.ncbi.nlm.nih.gov/datasets/gen...
What to do: Provide at least a domain-level taxonomic affiliation in the Taxon field.
Data is exchanged daily.
Here’s a recent (January) NAR article about the collaboration.
doi.org/10.1093/nar/...
Here’s a recent (January) NAR article about the collaboration.
doi.org/10.1093/nar/...
The international nucleotide sequence database collaboration (INSDC): enhancing global participation
Abstract. The members of the International Nucleotide Sequence Database Collaboration (INSDC; https://insdc.org) have built systems to collect, archive and
doi.org
March 2, 2025 at 5:46 PM
Data is exchanged daily.
Here’s a recent (January) NAR article about the collaboration.
doi.org/10.1093/nar/...
Here’s a recent (January) NAR article about the collaboration.
doi.org/10.1093/nar/...
One interesting thing we did is look at rate of submission bacterial sequence data to INSDC. Logistic fit is surprisingly good - inflexion during the pandemic. So, the data no longer looks like exponential growth. Projected to 2035 just for the hell of it, let's see.
February 27, 2026 at 9:02 AM
One interesting thing we did is look at rate of submission bacterial sequence data to INSDC. Logistic fit is surprisingly good - inflexion during the pandemic. So, the data no longer looks like exponential growth. Projected to 2035 just for the hell of it, let's see.
From @colmanoc.bsky.social and colleagues in #OUP 's #DATABASE journal | The INSDC specifications--foundations for a #FAIR and global INSDC | #Bioinformatics #OpenScience #OpenData #INSDC #GenBank @enasequence.bsky.social #DDBJ #NCBI CC/ @ebi.embl.org | 🧬🖥️🧪🔓
⬇️
academic.oup.com/database/art...
⬇️
academic.oup.com/database/art...
The INSDC specifications—foundations for a FAIR and global INSDC
Abstract. Members of the International Nucleotide Sequence Database Collaboration (INSDC; https://www.insdc.org/) collect, exchange, and preserve comprehen
academic.oup.com
September 8, 2026 at 12:40 PM
From @colmanoc.bsky.social and colleagues in #OUP 's #DATABASE journal | The INSDC specifications--foundations for a #FAIR and global INSDC | #Bioinformatics #OpenScience #OpenData #INSDC #GenBank @enasequence.bsky.social #DDBJ #NCBI CC/ @ebi.embl.org | 🧬🖥️🧪🔓
⬇️
academic.oup.com/database/art...
⬇️
academic.oup.com/database/art...
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
Life science research depends on global access to sequencing data but this only works when everyone speaks the same technical language.
Find out how the INSDC has updated its specifications to simplify data submission for better synchronisation across its partners.
www.ebi.ac.uk/about/news/a...
Find out how the INSDC has updated its specifications to simplify data submission for better synchronisation across its partners.
www.ebi.ac.uk/about/news/a...
New specifications for submitting nucleotide sequence data
New INSDC standards support simpler submissions and improve synchronisation of global genome sequence data.
www.ebi.ac.uk
March 18, 2026 at 3:03 PM
Life science research depends on global access to sequencing data but this only works when everyone speaks the same technical language.
Find out how the INSDC has updated its specifications to simplify data submission for better synchronisation across its partners.
www.ebi.ac.uk/about/news/a...
Find out how the INSDC has updated its specifications to simplify data submission for better synchronisation across its partners.
www.ebi.ac.uk/about/news/a...
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...
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
Pathoplexus | Pathoplexus July Update
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
July 15, 2025 at 2:05 PM
Some great new features and updates from the awesome Pathoplexus project. This is a new open pathogen genome database that can provide access to your sequences under a use-restricted license but also feed directly in to INSDC (EBI, Genbank etc) when you are ready. pathoplexus.org/news/2025-07...
Pathoplexus now has an Mpox virus instance: pathoplexus.org/mpox/
An easy upload portal with direct submission to INSDC (e.g. Genbank) after an optional embargo period.
Public access with a restricted use license if required.
Easy, reponsive, UI.
An easy upload portal with direct submission to INSDC (e.g. Genbank) after an optional embargo period.
Public access with a restricted use license if required.
Easy, reponsive, UI.
Pathoplexus | Mpox Virus - Browse
Pathoplexus is a new, open-source database dedicated to the efficient sharing of human viral pathogen genomic data, fostering global collaboration and public health response.
pathoplexus.org
December 9, 2024 at 11:43 PM
Pathoplexus now has an Mpox virus instance: pathoplexus.org/mpox/
An easy upload portal with direct submission to INSDC (e.g. Genbank) after an optional embargo period.
Public access with a restricted use license if required.
Easy, reponsive, UI.
An easy upload portal with direct submission to INSDC (e.g. Genbank) after an optional embargo period.
Public access with a restricted use license if required.
Easy, reponsive, UI.
講習会初日終了。一旦仕事を終えて10時からのINSDCエグゼクティブに備えます（なんか今日は欧州のパートナーの都合で一時間後ろになってしまった。更に眠いぞ
February 6, 2025 at 8:17 AM
講習会初日終了。一旦仕事を終えて10時からのINSDCエグゼクティブに備えます（なんか今日は欧州のパートナーの都合で一時間後ろになってしまった。更に眠いぞ
As a reminder - when data is submitted openly, or when Restricted-Use data becomes open, Pathoplexus takes care of sending it automatically to INSDC-member databases, ensuring it is available on NCBI/Genbank, ENA, and DNA Data Bank of Japan.
4/7
4/7
December 9, 2024 at 7:15 PM
As a reminder - when data is submitted openly, or when Restricted-Use data becomes open, Pathoplexus takes care of sending it automatically to INSDC-member databases, ensuring it is available on NCBI/Genbank, ENA, and DNA Data Bank of Japan.
4/7
4/7
We're pulling together the genomes for GlobDB release 232, which will be based on the upcoming GTDB release. We will also add new sources of genomes not in INSDC. Here's an overview of the data that will be included in the next GlobDB: globdb.org/news
Please contact me if we've missed something!🦠🖥️🧬
Please contact me if we've missed something!🦠🖥️🧬
News | GlobDB
globdb.org
March 7, 2026 at 7:37 PM
We're pulling together the genomes for GlobDB release 232, which will be based on the upcoming GTDB release. We will also add new sources of genomes not in INSDC. Here's an overview of the data that will be included in the next GlobDB: globdb.org/news
Please contact me if we've missed something!🦠🖥️🧬
Please contact me if we've missed something!🦠🖥️🧬
本日夜９時からのINSDC Tech Summitが延期になったのでもやし買って帰って食って寝る。今日は楽しく延期日はつらい
October 30, 2024 at 9:59 AM
本日夜９時からのINSDC Tech Summitが延期になったのでもやし買って帰って食って寝る。今日は楽しく延期日はつらい
We're on it though. Turns out uploading a lot of MAGs to INSDC databases isn't as easy as you'd think...
October 23, 2025 at 9:07 AM
We're on it though. Turns out uploading a lot of MAGs to INSDC databases isn't as easy as you'd think...
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
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/