Martín
@mberacochea.bsky.social
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 - https://www.mberacochea.cc
@mgnifydb.bsky.social Production Project Leader at @ebi.embl.org & Nextflow ambassador @nextflow.io
Unfrequent blogging - https://www.mberacochea.cc
Reposted by Martín
🧩 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
October 24, 2025 at 2:57 PM
🧩 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
Reposted by Martín
🌐 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...
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
August 1, 2025 at 7:15 AM
🌐 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...
💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.
www.embl.org/news/connect...
Reposted by Martín
📣 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
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
July 11, 2025 at 7:09 AM
📣 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
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
Reposted by Martín
Multi-omics time-series analysis in microbiome research: a systematic review https://www.biorxiv.org/content/10.1101/2025.07.03.659054v1
July 7, 2025 at 3:48 AM
Multi-omics time-series analysis in microbiome research: a systematic review https://www.biorxiv.org/content/10.1101/2025.07.03.659054v1
Reposted by Martín
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
July 7, 2025 at 3:48 AM
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
Reposted by Martín
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!
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
June 30, 2025 at 10:42 AM
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!
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!
Reposted by Martín
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
June 27, 2025 at 1:46 PM
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.
Reposted by Martín
It’s #WorldMicrobiomeDay! This year’s theme is Microbiome 101: What You Need to Know — here we present MGnify’s guide to microbiome data! 🔬
June 27, 2025 at 1:46 PM
It’s #WorldMicrobiomeDay! This year’s theme is Microbiome 101: What You Need to Know — here we present MGnify’s guide to microbiome data! 🔬
Reposted by Martín
MGnify genome catalogues have close to 0.5 million genomes sourced from 12 biomes #WorldMicrobiomeDay
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...
June 27, 2025 at 1:53 PM
MGnify genome catalogues have close to 0.5 million genomes sourced from 12 biomes #WorldMicrobiomeDay
Reposted by Martín
🚨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?
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?
June 24, 2025 at 9:08 AM
🚨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?
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?
Reposted by Martín
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
This free, self-paced training is perfect for newcomers looking to get started with Nextflow
Sign up now: hubs.la/Q03sDmpr0
June 18, 2025 at 1:46 PM
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
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
June 18, 2025 at 4:14 PM
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
Reposted by Martín
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...
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...
June 16, 2025 at 10:20 AM
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...
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
June 17, 2025 at 8:36 PM
I'm attending #ISMBECCB2025 in Liverpool, United Kingdom from July 20-24. Register here -> invt.io/1bxbsewpk7l
Reposted by Martín
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
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/1.2.0
June 16, 2025 at 8:06 AM
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
Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/1.2.0
Reposted by Martín
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
June 2, 2025 at 4:23 PM
DIAMOND v2.1.12 provides support for the new NCBI taxonomic ranks and various other fixes. github.com/bbuchfink/di...
Reposted by Martín
@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. 🌍🧬
May 15, 2025 at 4:59 PM
@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. 🌍🧬
Reposted by Martín
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...
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
May 13, 2025 at 9:53 PM
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...
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...
Reposted by Martín
📣 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.
We will not be running a parallel system, so you may have to make a few changes, especially if you are using the API.
May 7, 2025 at 2:19 PM
📣 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.
We will not be running a parallel system, so you may have to make a few changes, especially if you are using the API.
Reposted by Martín
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
🔍 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
April 17, 2025 at 1:36 PM
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
🔍 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
Reposted by Martín
🔗 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/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
April 15, 2025 at 2:13 PM
🔗 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/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
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
April 11, 2025 at 3:10 AM
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...
"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
April 9, 2025 at 2:43 AM
New post about @nextflow.io -- www.mberacochea.cc/posts/nextfl...
Reposted by Martín
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...
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...
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
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
March 10, 2025 at 3:28 PM
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...
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...
Reposted by Martín
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/...
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
February 3, 2025 at 12:56 PM
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/...
Collaborate remotely or at one of the 36+ local sites worldwide (🇦🇷🇦🇺🇧🇪🇧🇷🇨🇦🇨🇴🇨🇿🇩🇰🇪🇹🇫🇷🇩🇪🇬🇭🇬🇷🇮🇳🇮🇹🇳🇱🇳🇿🇵🇰🇵🇱🇿🇦🇪🇸🇸🇪🇨🇭🇹🇷🇬🇧🇺🇸).
Registration is now open! 🎟
nf-co.re/events/2025/...