Martín @mberacochea.bsky.social · 09/09/2026Great deck, thanks for sharing. Did you happen to record the presentation? 101
Reposted by Martín Seqera @seqera.io · 10/08/2026Welcoming 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. 066
Reposted by Martín 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 0106
Reposted by Martín EMBL-EBI @ebi.embl.org · 18/11/2025Antimicrobial 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.ukA new gateway to global antimicrobial resistance dataNew online portal connects bacterial genomes with experimental resistance data to support antimicrobial resistance research. 13618
Reposted by Martín 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 111
Reposted by Martín 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... 02611
Reposted by Martín 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 082
Reposted by Martín bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 07/07/2025Multi-omics time-series analysis in microbiome research: a systematic review www.biorxiv.org/content/10.1101/202… 034
Reposted by Martín bioRxiv Bioinfo @biorxiv-bioinfo.bsky.social · 07/07/2025PIMENTO: A PrIMEr infereNce TOolkit to facilitate large-scale calling of amplicon sequence variants www.biorxiv.org/content/10.1101/202… 032
Reposted by Martín EMBL-EBI @ebi.embl.org · 30/06/2025Do 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.ukUser survey to understand the value of open data resourcesEMBL-EBI user survey opens – please complete it before 16 July 01211
Reposted by Martín mgnifydb.bsky.social @mgnifydb.bsky.social · 27/06/2025Mettannotator 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.commettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assembliesAbstractSummary. In recent years, there has been a surge in prokaryotic genome assemblies, coming from both isolated organisms and environmental samples. T 031
Reposted by Martín mgnifydb.bsky.social @mgnifydb.bsky.social · 27/06/2025It’s #WorldMicrobiomeDay! This year’s theme is Microbiome 101: What You Need to Know — here we present MGnify’s guide to microbiome data! 🔬 144
Reposted by Martín Tatiana Gurbich @tgurbich.bsky.social · 27/06/2025MGnify genome catalogues have close to 0.5 million genomes sourced from 12 biomes #WorldMicrobiomeDay 021
Reposted by Martín 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? 132
Reposted by Martín Nextflow @nextflow.io · 18/06/2025Nextflow 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 186
Martín @mberacochea.bsky.social · 18/06/2025We 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.socialgithub.comRelease v3.0.0 · EBI-Metagenomics/miassemblerMassive 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... 041
Reposted by Martín EMBL-EBI @ebi.embl.org · 16/06/2025If 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... 03131
Martín @mberacochea.bsky.social · 17/06/2025I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Register here -> invt.io/1bxbsewpk7linvt.ioI'm participating the ISMB/ECCB 2025 conference, join me!Register now 020
Reposted by Martín nf-core @nf-co.re · 16/06/2025Pipeline release! nf-core/proteinfamilies v1.2.0 - Aluminium Frog! Please see the changelog: github.com/nf-core/proteinfamilies/… 032
Reposted by Martín Benjamin J. Buchfink @bbuchfink.bsky.social · 02/06/2025DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...github.comGitHub - bbuchfink/diamond: Accelerated BLAST compatible local sequence aligner.Accelerated BLAST compatible local sequence aligner. - bbuchfink/diamond 001
Martín @mberacochea.bsky.social · 18/05/2025Interesting. I work on that space, in metagenomics to be more specific. I'll tinker with it and then will share some thoughts. 000
Martín @mberacochea.bsky.social · 18/05/2025I'm not there, but have you considered datasette for bioinformatics? A big chunk of bioinfo is wrangling csv/tsv files. 120
Reposted by Martín 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. 🌍🧬 133
Reposted by Martín Matthew Hay Brown @matthewhaybrown.bsky.social · 13/05/2025FAREWELL 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.comJosé Mujica, Marxist rebel in Uruguay who became president, dies at 89He oversaw an economic boom, a reduction in poverty and the legalization of abortion, same-sex marriage and marijuana. 417443
Reposted by Martín 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. 142
Reposted by Martín Nextflow @nextflow.io · 17/04/2025Big 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 1125
Reposted by Martín 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 supportforms.gleFAIRyMAGs Hackathon: Optimising Metagenomics Assembled Genomes buildingMetagenomics 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... 023
Martín @mberacochea.bsky.social · 11/04/2025Blog 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.socialmberacochea.ccIntroduction to Nextflow workshop in UruguayThe 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... 010
Martín @mberacochea.bsky.social · 09/04/2025New post about @nextflow.io -- www.mberacochea.cc/posts/nextfl...mberacochea.cc"Sync" Channels in NextflowNextflow 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 ... 010
Reposted by Martín Florian Wünnemann @flowuenne.bsky.social · 10/03/2025If 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... 073
Martín @mberacochea.bsky.social · 04/02/2025Look the ecosystem is collapsing, let's create an app to solve it. 010
Reposted by Martín nf-core @nf-co.re · 03/02/2025Calling 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.reHackathon - March 2025 (Online / Distributed)A virtual hackathon with local sites to develop nf-core together 2139
Reposted by Martín 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... 001
Reposted by Martín Tatiana Gurbich @tgurbich.bsky.social · 28/01/2025Our 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 1126
Reposted by Martín nf-core @nf-co.re · 28/01/2025It'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/... 085
Reposted by Martín Stephen Turner @stephenturner.us · 26/01/2025mettannotator: a comprehensive and scalable Nextflow annotation pipeline for prokaryotic assemblies academic.oup.com/bioinformatics/adv… 🧬🖥️🧪 Nextflow github.com/EBI-Metagenomics/mettann… 082
Martín @mberacochea.bsky.social · 21/01/2025I'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. 062
Reposted by Martín 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 417170
Reposted by Martín mgnifydb.bsky.social @mgnifydb.bsky.social · 07/01/2025At 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.ioOSF 001
Martín @mberacochea.bsky.social · 03/01/2025I share this crusade, same result among friends and family. Keep up the good fight ✊ 010
Reposted by Martín Jason Koebler @jasonkoebler.bsky.social · 12/04/2024OpenAI'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.coOpenAI Training Bot Crawls 'World's Lamest Content Farm' 3 Million Times in One Day 213140
Reposted by Martín Dan Killam @dantheclamman.blog · 11/04/2024Hi, 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.comScientists discover first algae that can fix nitrogen — thanks to a tiny cell structureA 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... 38132
Reposted by Martín AF the Virologist @afthescientist.bsky.social · 08/04/2024Rabies 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.comSome 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. 26472180