Lukas Forer
@lukfor.bsky.social
Assistant Professor of Genome Informatics. MedUni Innsbruck. Cloud Computing, Machine Learning, AI, Genotype Imputation. Open Source and Open Science. Co-Creator of Michigan Imputation Server and www.askimed.com. Creator of www.nf-test.com.
Do you remember this Prince of Persia version? 🎮 Prince of Persia 🕹 NES (PAL) 📅 1992 💡 A simplified but very playable console adaptation 👑 Prince of Persia cartridges every Saturday #PoPSaturday
Over the years, my Game Boy cartridge collection quietly grew to around 100 pieces. Last week, I decided to turn it into a small nostalgia project. One cartridge per day.
Retro Game Cartridges@retro-cartridges.bsky.social · 7mo ago🎮 Do you remember this Game Boy game? 🕹 Tetris 📅 1989 💡 For many, inseparable from the Game Boy 🧩 Easy to learn, impossible to forget When was the last time you played a round? #gameboy #retrogaming #nostalgia
After a long journey, our nf-test paper is officially out! 🚀 doi.org/10.1093/giga...
Improving the Reliability, Quality and Maintainability of Bioinformatics Pipelines with nf-test
Abstract. The workflow management system Nextflow, together with the nf-core community, has established an essential ecosystem in bioinformatics. However,
doi.org
This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...
Cameron Patrick - Some Quarto PDF formatting tips, with particular reference to thesis writing
I’ve just spent most of a day faffing around trying to get Quarto to produce a nice PDF file that I like the look of and which meets my university’s formatting requirements for a PhD thesis. Maybe my ...
cameronpatrick.com
Another Bactopia update! I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
As a post-GWAS analysis, ever thought about automatic haplotype testing @ each locus + test vs any number of traits? 👏 Amazing @dariushghasemi.bsky.social just released #Haplomics, a #Snakemake pipeline walking u all the way down to summary stats+clustering www.medrxiv.org/content/10.1... #statgen
Haplomics: A Snakemake pipeline for haplotype-based association analysis in multi-omics studies
Summary Genome-wide association studies (GWAS) generated thousands of loci associated with complex traits and diseases. However, to characterize of the pleiotropic, molecular and population genetic bo...
medrxiv.org
Really cool that the latest VSCode extension for Nextflow shows nf-test test coverage! 🚀
Nextflow@nextflow.io · last yr.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
𝐇𝐮𝐦𝐚𝐧𝐠𝐞𝐧𝐨𝐦 𝐀𝐮𝐬𝐭𝐫𝐢𝐚 ist jetzt auf Bluesky! Das österreichische Humangenomprojekt ist eine Initiative für 𝐝𝐢𝐞 𝐈𝐧𝐭𝐞𝐠𝐫𝐚𝐭𝐢𝐨𝐧 𝐠𝐞𝐧𝐞𝐭𝐢𝐬𝐜𝐡𝐞𝐫 𝐮𝐧𝐝 𝐠𝐞𝐧𝐨𝐦𝐢𝐬𝐜𝐡𝐞𝐫 𝐃𝐚𝐭𝐞𝐧 𝐢𝐧 𝐌𝐞𝐝𝐢𝐳𝐢𝐧 𝐮𝐧𝐝 𝐖𝐢𝐬𝐬𝐞𝐧𝐬𝐜𝐡𝐚𝐟𝐭 in ganz Österreich. Infos ➡️ www.humangenom.at #Genetik #Genetics #Health #Genomics #GenomeOfEurope
What a fantastic talk given by Prof. Michael Moor. Thanks to the Faculty of AI and Scientific Computing in Medicine for organizing such an important event. @i-med.ac.at @sebschoenherr.bsky.social @lukfor.bsky.social #MedSky
🎙️ #Atherotalk Episode 7 is live, don’t miss it! I had the chance to interview my mentor, Prof. Kronenberg. @i-med.ac.at @aspcardio.bsky.social @katioorni.bsky.social #MedSky #CardioSky #Lpa #FH #Podcast 🎧Spotify: open.spotify.com/episode/26Me...
Just found my first real game on some old floppy discs from around 1999: a Mastermind clone written in QBasic. I remember being super happy and proud because it was the first project I actually finished instead of stopping halfway to start another idea. 👨🏻💻
I'd like to share DSO, a command line helper to build reproducible data science projects with ease. It is an opinionated way to organize data science projects, built around data version control (DVC). github.com/Boehringer-I...
GitHub - Boehringer-Ingelheim/dso: Data Science Operations (dso) command line tool
Data Science Operations (dso) command line tool. Contribute to Boehringer-Ingelheim/dso development by creating an account on GitHub.
github.com
Our Nextflow in Genomics workshop kicks off tomorrow! Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social #nf-genomics #freeimputation
Looking forward to great discussions, learning, and sharing insights. Busy but productive days ahead!
Sebastian Schönherr@sebschoenherr.bsky.social · 2y ago🚀 Ready to kick off our Nextflow in Genomics workshop tomorrow at @i-med.ac.at! 🎉 Together with @lukfor.bsky.social & @silvidm.bsky.social we'll work on improving imputation server workflows. Big thanks to @nextflow.io, @evanfloden.bsky.social, and @ewels.bsky.social for the support.
I learned the hard way today: SimpleDateFormat in Java is NOT thread-safe! #java
Yes, but can it run Doom? `nextflow run doom` ✅ @nextflow.io (by @jordeu.bsky.social 🌟) github.com/nextflow-io/...
Für die #Geoguessr Spieler unter uns: eine Map mit ca. 9.900 locations aus #Südtirol. Viel Spaß! 📍 www.geoguessr.com/maps/678e0b0...
GeoGuessr - Südtirol
Explore this map by lukfor on GeoGuessr
geoguessr.com
Looking forward to spending two days working on the imputation server with fantastic people! Thanks to @seqera.io, @ewels.bsky.social and @chrishakk.bsky.social for sending us stickers 🙏
Sebastian Schönherr@sebschoenherr.bsky.social · 2y agoAre you working with one of the genotype imputation servers? Then this is your chance to see new features pretty soon on the server: @lukfor.bsky.social ky.social, @silvidm.bsky.social, and I are hosting our 2nd Nextflow in Genomics Hackathon to boost imputation servers here @i-med.ac.at 1/2
For anyone who hasn’t already read the article, this is a pretty great video from Prime on it. curiouscoding.nl/posts/static...
Static search trees: 40x faster than binary search
Table of Contents 1 Introduction 1.1 Problem statement 1.2 Motivation 1.3 Recommended reading 1.4 Binary search and Eytzinger layout 1.5 Hugepages 1.6 A note on benchmarking 1.7 Cache lines 1.8 S-tree...
curiouscoding.nl
Seth Stadick@ducktapeprogrammer.bsky.social · 2y ago@curiouscoding.nl You’re (more?) famous!! youtu.be/hAO7YiwOcCg?...
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Med Uni Innsbruck@i-med.ac.at · 2y agoZeit, neue Wege zu gehen: Wir haben unsere Aktivitäten auf X beendet. Bleiben Sie mit uns im Dialog – hier bei Bluesky und auf unseren anderen Kanälen. Mehr Info: https://www.i-med.ac.at/mypoint/thema/788987.html #eXit #WissXit #ByeByeX #QuitX Credit: HHU/Paul Schwaderer
2024 is ending soon and it has been an exciting year for nf-test 🎉 A lot of new features and the amazing @nextflow.io community made nf-test even better 🚀 Thank you! 🙏 💡 What was your favorite nf-test update this year? #Nextflow #Bioinformatics #recap Here's a quick look back at 2024 🧵👇
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Sebastian Schönherr@sebschoenherr.bsky.social · 2y agoThis summer, @lukfor.bsky.social and I migrated the Michigan Imputation Server to Nextflow. 2M genomes later, we can say it was a big success. As a Christmas gift, we’re excited to show you how to set up your own local server in under 10 minutes. ##freeimputation genepi.github.io/michigan-imp...
If you're looking to connect with other researchers and physicians in the cardiovascular field, join this Starter Pack. #CardioSky #MedSky #GeneSky #ImmunoSky go.bsky.app/VEqq8ML
Don't forget to open the door number 5 of the Nextflow Advent Calendar! 😍
Florian Wünnemann@flowuenne.bsky.social · 2y agoChristmas 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...
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...