Lightnews — Scholar-powered news

Reposted by Martín

EMBL @embl.org · Aug 1

🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.

💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.

www.embl.org/news/connect...

Caption+Credit: EMBL’s AI Strategy aims to transform life sciences by integrating AI across research areas like genomics, drug discovery, and imaging. Creative team/ EMBL

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HMMER @hmmer.bsky.social · Jul 11

📣 We’re pleased to announce the release of jackhmmer.
It’s now available for use, and we’d greatly value any feedback as we continue to improve the tool.

www.ebi.ac.uk/Tools/hmmer/...
Give it a try and share your thoughts!

#bioinformatics #hmmer

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 7

Multi-omics time-series analysis in microbiome research: a systematic review https://www.biorxiv.org/content/10.1101/2025.07.03.659054v1

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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · Jul 7

PIMENTO: A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants https://www.biorxiv.org/content/10.1101/2025.07.04.663168v1

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EMBL-EBI @ebi.embl.org · Jun 30

Do you use EMBL-EBI data resources? We would really appreciate your feedback!

Our Interim Director Jo McEntyre explains how you can help us demonstrate the value of our data resources: www.ebi.ac.uk/about/news/a...

Survey closes on 16 July: www.surveymonkey.com/r/QGFMBH8?ch...

Thank you!

User survey to understand the value of open data resources

EMBL-EBI user survey opens – please complete it before 16 July

www.ebi.ac.uk

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

Mettannotator academic.oup.com/bioinformati... provides a rich set of annotations for prokaryotic genomes, within a comprehensive NextFlow pipeline leveraging tools, databases and customised scripts to tap into gene functions for novel species.

mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies

AbstractSummary. In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. T

academic.oup.com

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mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

It’s #WorldMicrobiomeDay! This year’s theme is Microbiome 101: What You Need to Know — here we present MGnify’s guide to microbiome data! 🔬

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Tatiana Gurbich @tgurbich.bsky.social · Jun 27

MGnify genome catalogues have close to 0.5 million genomes sourced from 12 biomes #WorldMicrobiomeDay

mgnifydb.bsky.social @mgnifydb.bsky.social · Jun 27

Microbes can be difficult to culture in the laboratory. To tackle this we assemble their genomes directly from metagenomic data. These are called MAGs: metagenome-assembled genomes. Explore the novelty of uncultivated microbes in our biome-specific genome catalogues. www.ebi.ac.uk/metagenomics...

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Oana Stroe @oanastroe.bsky.social · Jun 24

🚨Awesome comms jobs alert!

The @ebi.embl.org Comms team is looking for two new colleagues:

🟢 Deputy Head of EMBL-EBI Communications
🟢 Communications Officer

Applications close on 20 July.

One of them is my role which I'm finishing in a few months after 9 incredible years.

Why apply?

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Nextflow @nextflow.io · Jun 18

Nextflow Training Week is Back on June 23-27, 2025! 🎉

This free, self-paced training is perfect for newcomers looking to get started with Nextflow

Sign up now: hubs.la/Q03sDmpr0

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Martín @mberacochea.bsky.social · Jun 18

We have just released a new version of the Microbiome Informatics metagenomes assembler pipeline - github.com/EBI-Metageno.... Jenny Mattock benchmarked a new contigs cleaning process that Sonya Ochkalova implemented. Great team effort with > 100 comments in the PR. #nextflow @mgnifydb.bsky.social

Release v3.0.0 · EBI-Metagenomics/miassembler

Massive work from @ochkalova and @jmattock5 What's Changed Add --iontorrent by @KateSakharova in #40 Increase memory for CANU LR by @KateSakharova in #41 Add more time to CANU LR by @KateSakharova...

github.com

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EMBL-EBI @ebi.embl.org · Jun 16

If EMBL-EBI managed data resources have ever saved you time & effort, this is your chance to give back!

Fill in a 15-minute survey to help us:
🌍Demonstrate the real-world impact of our resources
🤓Understand your needs
🌟Secure continued funding

Closes 16 July
www.surveymonkey.com/r/QGFMBH8?ch...

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Martín @mberacochea.bsky.social · Jun 17

I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Register here -> invt.io/1bxbsewpk7l

I'm participating the ISMB/ECCB 2025 conference, join me!

Register now

invt.io

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nf-core @nf-co.re · Jun 16

Pipeline release! nf-core/proteinfamilies v1.2.0 - Aluminium Frog!

Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/1.2.0

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Benjamin Buchfink @bbuchfink.bsky.social · Jun 2

DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...

GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.

Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond

github.com

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Martín @mberacochea.bsky.social · May 18

Interesting. I work on that space, in metagenomics to be more specific. I'll tinker with it and then will share some thoughts.

Martín @mberacochea.bsky.social · May 17

I'm not there, but have you considered datasette for bioinformatics? A big chunk of bioinfo is wrangling csv/tsv files.

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Nextflow @nextflow.io · May 15

@olgabot.bsky.social, CEO & Founder at @seanome.bsky.social, just gave an insightful talk on her vision to create the best protein annotator for any organism using @nf-co.re, supporting efforts to better understand global biodiversity through large-scale sequencing. 🌍🧬

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Matthew Hay Brown @matthewhaybrown.bsky.social · May 13

FAREWELL AND GODSPEED, PEPE

As a Marxist guerrilla, José Mujica was nearly killed in a shootout and tortured during 14 years in prison

As president, he oversaw an economic boom, a reduction in poverty and the legalization of same-sex marriage and marijuana.

www.washingtonpost.com/obituaries/2...

José Mujica, Marxist rebel in Uruguay who became president, dies at 89

He oversaw an economic boom, a reduction in poverty and the legalization of abortion, same-sex marriage and marijuana.

www.washingtonpost.com

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HMMER @hmmer.bsky.social · May 7

📣 We will be transitioning to a new website architecture on May 20, 2025.
We will not be running a parallel system, so you may have to make a few changes, especially if you are using the API.

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Nextflow @nextflow.io · Apr 17

Big updates for the Nextflow @vscode.dev extension! 🚀

🔍 Workflow view – Visualize logical structure of pipelines
⚙️ Process view – See all processes in one place
🌐 Seqera view – Manage connected CEs directly in the IDE
📚 Resources view – Quickly access Copilot, AI tools & training

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Bérénice Batut @bebatut.bsky.social · Apr 15

🔗 Registration: Registration is free but limited to 15 attendees onsite. Secure your spot soon!
forms.gle/KQK7arqNjqth...

Don't miss this opportunity to be part of something big!

Thanks @elixir-europe.org, @denbi.bsky.social, @ifb-elixir-fr.bsky.social for the support

FAIRyMAGs Hackathon: Optimising Metagenomics Assembled Genomes building

Metagenomics Assembled Genomes building workflows are both technically and scientifically challenging, yet they are essential tools for reducing microbial dark matter, as most microbes cannot be culti...

forms.gle

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Martín @mberacochea.bsky.social · Apr 11

Blog post about the "Introduction to Nextflow" workshop in Montevideo last week. This workshop was organized by the lovely people of the ISCB Regional Student Group Uruguay rsg-uruguay.iscbsc.org. www.mberacochea.cc/posts/worksh... @nextflow.io @iscb.bsky.social

Introduction to Nextflow workshop in Uruguay

The Regional Student Group Uruguay (RSG-Uruguay) is a non-profit academic group intended to gather young Uruguayan researchers among the bioinformatics and computational biology fields. They have been...

www.mberacochea.cc

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Martín @mberacochea.bsky.social · Apr 9

New post about @nextflow.io -- www.mberacochea.cc/posts/nextfl...

"Sync" Channels in Nextflow

Nextflow is based on the Dataflow paradigm. The operations on the data are defined in a directed acyclic graph (DAG). The nodes of the DAG are the operations that need to happen and the edges are the ...

www.mberacochea.cc

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Florian Wünnemann @flowuenne.bsky.social · Mar 10

If you want to start learning #Nextflow or brush up on your basics of #Nextflow, now is the perfect time 🕑!

New training materials and support from ambassadors and experienced community members during training week help guide you through it, at your own pace!
community.seqera.io/t/nextflow-t...

Nextflow @nextflow.io · Mar 10

The #Nextflow #Training week has begun! 🎉

New to Nextflow or need a guided intro? Watch the brand new on-demand walkthrough videos for the "Hello Nextflow" course, and learn at your own pace!

hubs.la/Q03b2-Rk0

Hello Nextflow: Intro and setup

Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

hubs.la

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