#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

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... 🧬💻

A new gateway to global antimicrobial resistance data

New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.

ebi.ac.uk

🧩 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

🌐 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

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

ebi.ac.uk

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

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

@mgnifydb.bsky.social · last yr.

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...

🚨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

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

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 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

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

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

@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. 🌍🧬

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.

washingtonpost.com

📣 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

🔗 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

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...

Nextflow@nextflow.io · last yr.

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

Calling all bioinformatics enthusiasts! Join a global network of @nextflow.io ninjas for the @nf-co.re hackathon from March 24-26, 2025 🎉 Collaborate remotely or at one of the 36+ local sites worldwide (🇦🇷🇦🇺🇧🇪🇧🇷🇨🇦🇨🇴🇨🇿🇩🇰🇪🇹🇫🇷🇩🇪🇬🇭🇬🇷🇮🇳🇮🇹🇳🇱🇳🇿🇵🇰🇵🇱🇿🇦🇪🇸🇸🇪🇨🇭🇹🇷🇬🇧🇺🇸). Registration is now open! 🎟 nf-co.re/events/2025/...

Hackathon - March 2025 (Online / Distributed)

A virtual hackathon with local sites to develop nf-core together

nf-co.re

🌟 Features include annotations by UniFIRE (UniProt's automated function prediction system), AMR, biosynthetic gene clusters 🦠 Can be used on novel & known species 💻 Try it out: github.com/EBI-Metageno...

Our paper describing mettannotator, a new prokaryotic annotation pipeline, is out: academic.oup.com/bioinformati... 📝 Mettannotator generates comprehensive structural & functional annotations ⚙️ Built with #Nextflow — scalable, no installation needed