Martín

#Opensource software and workflows are doing a lot of heavy lifting 🏋️ in the life sciences! Let's revisit ✨ ELIXIR's report on "Open source software and workflows: a driving force for innovation in life sciences" to find out the importance of #OSSWs 👉 https://doi.org/10.5281/zenodo.17570133

Great news! We will be there :)

A new gateway to global antimicrobial resistance data New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.

Antimicrobial resistance (AMR) is a growing health threat, making infections harder to treat and complicating routine medical care.

EMBL-EBI’s new AMR portal brings together laboratory resistance data and bacterial genomes in one open platform.

#WAAW2025 #ActOnAMR

www.ebi.ac.uk/about/news/t...
🧬💻

🧩 Evangelos Karatzas from @ebi.embl.org presented @nf-co.re/proteinfamilies - a scalable @nextflow.io pipeline that groups uncharacterized metagenomic proteins into families, enabling functional annotation transfer

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

🌐 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...

📣 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

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

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

User survey to understand the value of open data resources EMBL-EBI user survey opens – please complete it before 16 July

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!

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

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.

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

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

🚨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?

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

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...

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

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...

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

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

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

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

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

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

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

@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. 🌍🧬

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.

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...

📣 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.

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

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...

🔗 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

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

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

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...