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Florian Wünnemann

@flowuenne.bsky.social
1.6K followers 132 following 88 posts

Bioinformatics engineer at Seqera (seqera.io) Genomics 🧬 | Spatial omics🔬 | technology 💻 | soccer ⚽ Working towards scalable and reproducible science with #Nextflow Living in Montreal 🇨🇦

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Florian Wünnemann @flowuenne.bsky.social · 07/10/2025
Join me today at the @nf-co.re help desk to discuss your questions about @nextflow.io and nf-core at 2pm Eastern Time! 🍏💻🧬!
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Florian Wünnemann @flowuenne.bsky.social · 19/09/2025
Join us for two days of fun in Barcelona, hacking away at nf-core projects!
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Nextflow @nextflow.io · 09/05/2025
Check out the blog post by Nextflow Ambassador Zohaib Anwar on VIRUS-MVP: a flexible and scalable workflow for genomic surveillance of priority viruses including SARS-CoV-2, Mpox, RSV, and influenza! 🦠 👉 Read now: hubs.la/Q03lM5KG0 #NextflowAmbassador @nf-co.re
hubs.la
VIRUS-MVP: A scalable and flexible pathogen surveillance workflow powered by Nextflow and nf-core | Seqera
VIRUS-MVP leverages Nextflow and nf-core to provide a modular, automated, and scalable framework for genomic surveillance of priority viruses. Designed initially for SARS-CoV-2, the workflow was later...
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Florian Wünnemann @flowuenne.bsky.social · 16/04/2025
Check out this fantastic work on neighbourhood preference in spatial omics data from the Schapiro lab 🚀! Congratulations @chiaraschiller.bsky.social and team on a wonderful project! 👏🤩
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Florian Wünnemann @flowuenne.bsky.social · 04/04/2025
You should definitely check out this amazing Nextflow podcast episode with my friend and collaborator @kbestak.bsky.social discussing microscopy and spatial omics workflows in nf-core and Nextflow! 🤩🔬🧪
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Jacques Dainat @jacquesdainat.bsky.social · 15/03/2025
My latest #Nextflow pipeline has just been published in JOSS 🎉
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Florian Wünnemann @flowuenne.bsky.social · 11/03/2025
Running Nextflow pipelines on AWS ☁️? Check out the blogpost I wrote about using resource Labels with Nextflow and Seqera to get detailed pipeline run costs 💵.
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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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Florian Wünnemann @flowuenne.bsky.social · 05/03/2025
Come and talk about your amazing projects at the #Nextflow summit in Boston 🎤! I am very sad to miss this summit this year, but it will be a fantastic event, so make sure you to submit your abstract before the deadline 🤩!
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Florian Wünnemann @flowuenne.bsky.social · 26/02/2025
Great opportunity to get together with your colleagues and friends and watch the training videos to learn Nextflow together 👥. 💬 Discussing things not clear to you and sending questions to the community forum are all great ways to accelerate your learning experience and increase the fun 🚀 🤩!
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Christina Agapakis @agapakis.com · 24/02/2025
Interesting to see doom and gloom as separate ends of a governance axis!
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Stephen Turner @stephenturner.us · 10/02/2025
New blog post: Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper doi.org/10.59350/wzt... #Rstats
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Jasmine Plummer @jasmineplummer.bsky.social · 03/02/2025
Introducing @gestaltsp.bsky.social We’re growing with already >1000 members. Come be part of spatial omics revolution!!! @ioavlachos.bsky.social @lgmartelotto.bsky.social @naturegenet.bsky.social rdcu.be/d8qHT #spatial #omics #technology #computation #tissue #singlecell
rdcu.be
Introducing the Global Alliance for Spatial Technologies (GESTALT)
Nature Genetics - This Comment outlines the creation of the Global Alliance for Spatial Technologies (GESTALT), a collaborative initiative aimed at fostering the growth and standardization of...
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Florian Wünnemann @flowuenne.bsky.social · 27/01/2025
Don't miss this chance to listen to my amazing colleagues Esha and Rob talk about how you can utilize Seqera Platform to help streamline your scientific data analysis! 🤩
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Satoshi Yoshiji, MD, PhD @satoshiyoshiji.bsky.social · 26/01/2025
📣 We are hiring! Join Yoshiji Lab at McGill University Dept of Human Genetics in Montreal, Canada! yoshiji-lab.org/joinus ✅Fully Funded Positions • 2 MSc Students • 1 PhD Student • 1 Postdoc ✅Goal: Using human genetics and multi-omics for drug target discovery and precision medicine
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Florian Wünnemann @flowuenne.bsky.social · 23/01/2025
You can now use Seqera AI with MultiQC! 🤖 Get insights from your reports and chat about potential QC issues with Seqera AI, directly from inside your MultiQC reports! Fantastic new update by everyone involved at @seqera.io !
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Diego del Alamo @delalamo.xyz · 19/01/2025
Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...
Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.
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Nextflow @nextflow.io · 14/01/2025
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities
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Piet @drpiet.bsky.social · 14/01/2025
Extra! Extra! If you're into cardiovascular development and regeneration, and you want to hobnob with all them awesome scientists, then follow @weinsteinconf.bsky.social and submit an abstract for the 2025 Weinstein Conference in Milwaukee!! #favorite #conference #ever
media.tenor.com
a close up of a chocolate chip cookie on a white surface
ALT: a close up of a chocolate chip cookie on a white surface
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Stephen Turner @stephenturner.us · 13/01/2025
Interesting concept. jetty::run() executes R code in a Docker container and passes the results back into the local environment cran.r-project.org/web/packages/jet… (source: github.com/dmolitor/jetty)
cran.r-project.org
jetty: Execute R in a 'Docker' Context
The goal of 'jetty' is to execute R functions and code snippets in an isolated R subprocess within a 'Docker' container and return the evaluated results to the local R session. 'jetty' can install…
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Florian Wünnemann @flowuenne.bsky.social · 08/01/2025
I am organizing a local site in Montreal for this @nf-co.re hackathon 🇨🇦. Anyone in the area who is interested to help organize or join this hackathon and a potential #Nextflow training before, please DM me 😊!
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Florian Wünnemann @flowuenne.bsky.social · 08/01/2025
Do you want some AI guided help to write #Nextflow pipelines or convert your old legacy pipelines to #Nextflow? Go to seqera.io and try out Seqera AI now 🤩!
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BioMassSpec @realbiomassspec.bsky.social · 05/01/2025
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing #JASMS pubs.acs.org/doi/10.1021/...
pubs.acs.org
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing
Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed N...
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Florian Wünnemann @flowuenne.bsky.social · 02/01/2025
For anyone that loves poker and card games, Balatro is such a great game! Just started playing it again on my tablet via Apple Arcade and having a blast 🎮🃏! apps.apple.com/ca/app/balat...
apps.apple.com
‎Balatro+
‎Welcome to the official Balatro+ game! Hypnotic and endlessly satisfying, Balatro is a magical mix of card games like Solitaire and Poker, that lets you twist the rules in ways never seen before! Yo...
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Florian Wünnemann @flowuenne.bsky.social · 30/12/2024
Now that advent time and Christmas is over, I wanted to share the hidden easter eggs 🥚 in my #Nextflow advent calendar, for everyone that missed them. Head to flowuenne.github.io/nextflow_adv... to discover them yourself or find all cheat codes in this 🧵...
flowuenne.github.io
Advent Calendar
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Florian Wünnemann @flowuenne.bsky.social · 24/12/2024
Today is the last day of my #Nextflow advent calender. It was fun doing this during December and I hope people discovered things they didn't know yet about the NF ecosystem ☺️! flowuenne.github.io/nextflow_adv... Merry Christmas and a Happy New Year to everyone 🎄❄️☃️🎁🎆
flowuenne.github.io
Advent Calendar
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Florian Wünnemann @flowuenne.bsky.social · 19/12/2024
I hope we get many people together across Quebec (Canada) for a local site for this hackathon. If you are interested to join our local site in person, please contact me so we can plan ahead ☺️! Excited to hack some Nextflow with many of you 👍💻
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Mike Lee @astrobiomike.org · 18/12/2024
An opportunity to work at an amazing place with amazing people! 🦠 “GeneLab is seeking a #Bioinformatics #ProgramDeveloper to drive research with #omics data from space biology experiments. Develop workflows and analyze data critical to human space exploration. 🔗 Apply now: tinyurl.com/8psb8uwn “
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Nextflow @nextflow.io · 18/12/2024
Are you looking for job opportunities where your Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities
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Florian Wünnemann @flowuenne.bsky.social · 18/12/2024
This map of Github is really cool: anvaka.github.io/map-of-githu... I feel right at home in Genomic Haven next to RWorld. Hope to visit some of these lands next year. Vuetopia and Vuestian look like cool places 😎.
anvaka.github.io
Map of GitHub
This website shows a map of GitHub. Each dot is a project. Two dots within the same cluster are usually close to each other if multiple users frequently gave stars to both projects
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Florian Wünnemann @flowuenne.bsky.social · 15/12/2024
Today is a special Nextflow advent calender entry, as you will need to have discovered the first hidden secret to solve this one. 🎅Santa needs help with his gift delivery Nextflow pipeline? Can you help him ☺️🦌🎁?! Open door 15 on: flowuenne.github.io/nextflow_adv...
flowuenne.github.io
Advent Calendar
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Florian Wünnemann @flowuenne.bsky.social · 14/12/2024
Today's content in my Nextflow advent calender door 14 is for anyone interested in bacterial genomes 🧬 👀 @rpetit3.bsky.social flowuenne.github.io/nextflow_adv...
flowuenne.github.io
Advent Calendar
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Albert Vilella, PhD. @albertvilella.bsky.social · 13/12/2024
Protenix, another third wave AF3-like model goes Apache license github.com/bytedance/Pr...
github.com
GitHub - bytedance/Protenix: A trainable PyTorch reproduction of AlphaFold 3.
A trainable PyTorch reproduction of AlphaFold 3. Contribute to bytedance/Protenix development by creating an account on GitHub.
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Florian Wünnemann @flowuenne.bsky.social · 14/12/2024
It's exciting to see so much activity and enthusiasm in the protein folding and design space. So many new tools available (Chai-1, Boltz-1, Protenix), can't wait to see many of them used in Nextflow pipelines like nf-core/proteinfold soon (github.com/nf-core/prot...) 🤩!
github.com
GitHub - nf-core/proteinfold: Protein 3D structure prediction pipeline
Protein 3D structure prediction pipeline. Contribute to nf-core/proteinfold development by creating an account on GitHub.
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Miguel Ibarra @miguelib.bsky.social · 12/12/2024
Mind blowing science with 10x @10xgenomics.bsky.social #ESSB2024
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Piet @drpiet.bsky.social · 09/12/2024
The Gregor Andelfinger and Alexandre Dubrac labs in Montreal are looking for a research assistant to investigate Multisystemic smooth muscle dysfunction syndrome. (1/3)
linkedin.com
CHU Sainte-Justine hiring Assistant (e) de recherche Niveau 2 (Dr. Andelfinger et Dr. Dubrac) in Montreal, Quebec, Canada | LinkedIn
Posted 1:45:25 AM. Le Centre de recherche Azrieli du CHU Sainte-Justine est à un stade de maturité, qui lui a permis…See this and similar jobs on LinkedIn.
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Florian Wünnemann @flowuenne.bsky.social · 09/12/2024
Over the weekend some busy elves have hidden a secret in my personal #Nextflow Advent calender 📆. Would love to hear from people whether they can find it (but don't spoil the discovery for everyone else 😉). flowuenne.github.io/nextflow_adv... Tip: Best to discover and enjoy on 💻 versus 📱
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Florian Wünnemann @flowuenne.bsky.social · 07/12/2024
Today's advent calender door has something for all of you that love open source software, that was recently announced at Nextflow Summit Barcelona 👀 Open the door here 🚪: flowuenne.github.io/nextflow_adv...
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Schapiro Lab @schapirolab.bsky.social · 04/12/2024
We are looking for a Postdoc with a strong computational background to join our team. Want to work on the development and application of computational methods in the field of translational spatial biology? Apply now! karriere.klinikum.uni-heidelberg.de/index.php?ac...
karriere.klinikum.uni-heidelberg.de
Postdoc – Computational Tissue Analysis (m/f/d)
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Luciano Martelotto @lgmartelotto.bsky.social · 05/12/2024
meetings.cshl.edu/courses.aspx...
meetings.cshl.edu
Single Cell & Spatial Transcriptomics Analysis
Cold Spring Harbor Laboratory Meetings & Courses -- a private, non-profit institution with research programs in cancer, neuroscience, plant biology, genomics, bioinformatics.
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Florian Wünnemann @flowuenne.bsky.social · 04/12/2024
Anyone that tried to open door 4 of the Nextflow advent calender today but found it closed, just pushed a fix to reset cache so it should not happen again 😅☺️ flowuenne.github.io/nextflow_adv... Today's door has something for you, if you want to learn #Nextflow!
flowuenne.github.io
Advent Calendar
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Florian Wünnemann @flowuenne.bsky.social · 04/12/2024
If you are interested in spatial omics, bioinformatics, want to live in a beautiful city in Germany and work with an awesome team, you should absolutely apply for this opportunity! ☺️🚀🤩
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Florian Wünnemann @flowuenne.bsky.social · 03/12/2024
Just added some cozy christmas background music made by suno.com to the page to round up the AI development cycle 😄.
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Florian Wünnemann @flowuenne.bsky.social · 03/12/2024
Christmas time is upon us 🎄🎅! What better way to count down the days till Christmas eve than with an Advent calender? I am one day late, but here is little Nextflow advent calender I made for everyone. Check back every day at midnight EST to open a new door: flowuenne.github.io/nextflow_adv...
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Michael Paulauski♨️ @mike10010100.com · 01/12/2024
AlphaFold is gonna revolutionize biotech. blog.google/technology/a...
blog.google
AlphaFold 3 predicts the structure and interactions of all of life’s molecules
Our new AI model AlphaFold 3 can predict the structure and interactions of all life’s molecules with unprecedented accuracy.
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Florian Wünnemann @flowuenne.bsky.social · 01/12/2024
Naive question from someone outside the protein design field: Many protein folding methods such as #alphafold use multiple sequence alignments (MSA) to model co-evolution of amino acids. But isn't using MSAs to known sequences biasing us to folding structures that we have observed before?
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Nextflow @nextflow.io · 28/11/2024
Watch the podcast on YouTube or Spotify now, or check out the webpage for links, details, a written summary and the full transcript! hubs.la/Q02ZN8l20
hubs.la
Nextflow Summit Barcelona 2024 Highlights | The Nextflow Podcast by Seqera
Seqera | The Home for Open Science | From the creators of Nextflow, Wave, and MultiQC
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Florian Wünnemann @flowuenne.bsky.social · 30/11/2024
One of the really cool things about Nextflow is that it can run your pipelines everywhere with only changing the configuration🔧. Build it on your laptop, run it on slurm, aws, gcp, or any other infrastructure 🤩! As a recent SLURM to cloud convert, I really appreciate this flexibility 👍!
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Florian Wünnemann @flowuenne.bsky.social · 29/11/2024
I was an anti Apple products person for a long time (also mostly owed to being a student without much money for most of my adult life). But damn is it smooth when you copy something on your Mac and paste it on your phone (or vice versa)... ⚡️
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