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Martín

@mberacochea.bsky.social
114 followers 166 following 13 posts

I'm a software dev working with bioinformatics pipelines mostly. Python and Nextflow on a daily basis. @mgnifydb.bsky.social Production Project Leader at @ebi.embl.org & Nextflow ambassador @nextflow.io Unfrequent blogging - www.mberacochea.cc

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Reposted by Martín
Seqera @seqera.io · 10/08/2026
Welcoming the next cohort of 2026 @nextflow.io Ambassadors! 🎉145 active Ambassadors from 39 countries now support the global Nextflow community 🌎 by organizing events, creating content, speaking at conferences, and helping researchers adopt better workflows.
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ELIXIR Europe @elixir-europe.org · 05/02/2026
#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 👉 doi.org/10.5281/zenodo.17570133
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EMBL-EBI @ebi.embl.org · 18/11/2025
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... 🧬💻
ebi.ac.uk
A new gateway to global antimicrobial resistance data
New online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research.
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Nextflow @nextflow.io · 24/10/2025
🧩 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
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EMBL @embl.org · 01/08/2025
🌐 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 · 11/07/2025
📣 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 · 07/07/2025
Multi-omics time-series analysis in microbiome research: a systematic review www.biorxiv.org/content/10.1101/202…
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bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 07/07/2025
PIMENTO: A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants www.biorxiv.org/content/10.1101/202…
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EMBL-EBI @ebi.embl.org · 30/06/2025
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!
ebi.ac.uk
User survey to understand the value of open data resources
EMBL-EBI user survey opens – please complete it before 16 July
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mgnifydb.bsky.social @mgnifydb.bsky.social · 27/06/2025
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.
academic.oup.com
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
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mgnifydb.bsky.social @mgnifydb.bsky.social · 27/06/2025
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 · 27/06/2025
MGnify genome catalogues have close to 0.5 million genomes sourced from 12 biomes #WorldMicrobiomeDay
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Oana Stroe @oanastroe.bsky.social · 24/06/2025
🚨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 · 18/06/2025
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 · 18/06/2025
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
github.com
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...
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EMBL-EBI @ebi.embl.org · 16/06/2025
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 · 17/06/2025
I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Register here -> invt.io/1bxbsewpk7l
invt.io
I'm participating the ISMB/ECCB 2025 conference, join me!
Register now
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Reposted by Martín
nf-core @nf-co.re · 16/06/2025
Pipeline release! nf-core/proteinfamilies v1.2.0 - Aluminium Frog! Please see the changelog: github.com/nf-core/proteinfamilies/…
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Benjamin J. Buchfink @bbuchfink.bsky.social · 02/06/2025
DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...
github.com
GitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.
Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond
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Nextflow @nextflow.io · 15/05/2025
@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 · 13/05/2025
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...
washingtonpost.com
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.
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HMMER @hmmer.bsky.social · 07/05/2025
📣 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 · 17/04/2025
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 · 15/04/2025
🔗 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
forms.gle
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...
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Martín @mberacochea.bsky.social · 11/04/2025
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
mberacochea.cc
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...
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Martín @mberacochea.bsky.social · 09/04/2025
New post about @nextflow.io -- www.mberacochea.cc/posts/nextfl...
mberacochea.cc
"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 ...
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Florian Wünnemann @flowuenne.bsky.social · 10/03/2025
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...
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nf-core @nf-co.re · 03/02/2025
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/...
nf-co.re
Hackathon - March 2025 (Online / Distributed)
A virtual hackathon with local sites to develop nf-core together
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Tatiana Gurbich @tgurbich.bsky.social · 28/01/2025
🌟 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...
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Tatiana Gurbich @tgurbich.bsky.social · 28/01/2025
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
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nf-core @nf-co.re · 28/01/2025
It's fantastic seeing the number of local sites grow and grow for the upcoming @nf-co.re #hackathon ! 🎉 Already a new record and with better global spread than ever before 🌎🌏🌍 If you think you can host a site, tell us now! General registration opens in a few days 🎟 nf-co.re/events/2025/...
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Stephen Turner @stephenturner.us · 26/01/2025
mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies academic.oup.com/bioinformatics/adv… 🧬🖥️🧪 Nextflow github.com/EBI-Metagenomics/mettann…
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Martín @mberacochea.bsky.social · 21/01/2025
I've recently joined the Nextflow Ambassador program, we are using Nextflow in our team at @mgnifydb.bsky.social extensively. I'm excited to help grow the community around Nextflow. Being originally from 🇺🇾 (but now living in 🇬🇧), I want to help grow the LATAM Nextflow community.
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People Vs Profiteers @peoplevsprofiteers.bsky.social · 18/11/2024
📢 EXPOSED: While your water bills could rise by 84%, water companies sent £££billions to shareholders instead of cleaning our rivers 💩💩💩 Find out how much they took from YOU: www.greatwatercon.uk #greatwatercon
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mgnifydb.bsky.social @mgnifydb.bsky.social · 07/01/2025
At ELIXIR Europe's 2024 BioHackathon, we co-led work to improve how the metagenomics community can use RO-Crates to collectively describe and analyse more datasets, more efficiently. Our preprint envisions this as a federated microbiome analysis service: osf.io/preprints/bi...
osf.io
OSF
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Jason Koebler @jasonkoebler.bsky.social · 12/04/2024
OpenAI's training bot crawled a nonsensical set of sites set up by the author of The Internet for Dummies 3 million times in a day www.404media.co/openai-train...
404media.co
OpenAI Training Bot Crawls 'World's Lamest Content Farm' 3 Million Times in One Day
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Dan Killam @dantheclamman.blog · 11/04/2024
Hi, I'm endosymbiosis. You might remember me from hits like Mitochondria: Powerhouse of the Cell, or ¡Chloroplast! Well, let me introduce you to the newest organelle that's gonna fix your N2 and steal your heart. Meet the nitroplast! 🧪 www.nature.com/articles/d41...
nature.com
Scientists discover first algae that can fix nitrogen — thanks to a tiny cell structure
A newly discovered ‘organelle’ that converts nitrogen gas into a useful form could pave the way for engineered plants that require less fertilizer. A newly discovered ‘organelle’ that converts nitroge...
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AF the Virologist @afthescientist.bsky.social · 08/04/2024
Rabies causes 100% fatality in animals including humans (unless they get treated in time - no treatment for animals). The other diseases cause horrific symptoms and many result in death. Please vaccinate your pets. I can’t believe this is where we are at in 2024. 🫠
usatoday.com
Some pet owners are advocating against rabies vaccines. Here's why rabies is dangerous.
Hesitancy around vaccines has spilled over to pet owners, sparking concern about the resurgence of rabies, a virus that's nearly always fatal.
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