iiinova — where your digital self keeps evolving

Sebastian Schönherr @sebschoenherr.bsky.social · 14/03/2025

Last November, we migrated the Michigan Imputation Server (imputationserver.sph.umich.edu) to a new software stack, including Nextflow. After some turbulence, we are more and more returning to normal operations, processing around 800.000 full human genomes per month.

imputationserver.sph.umich.edu

Michigan Imputation Server 2

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Sebastian Schönherr @sebschoenherr.bsky.social · 06/03/2025

Today @michaelmoor.bsky.social took a train from Zurich to Innsbruck to kick-off our new Faculty of "AI and Scientific Computing"! 🎉 He talked about LLMs and Medical AI Agents. Exciting science and great discussions! Thanks! More info about our faculty: aiscm.i-med.ac.at #ai #scientificcomputing

aiscm.i-med.ac.at

Faculty of AI and Scientific Computing in Medicine (AISCM) Medical University of Innsbruck

Faculty of AI and Scientific Computing in Medicine

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Sebastian Schönherr @sebschoenherr.bsky.social · 29/01/2025

Silvia is excited, we are so excited. Follow Silvia for great science and great fun. www.youtube.com/watch?v=8iwB...

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Sebastian Schönherr @sebschoenherr.bsky.social · 29/01/2025

🚀 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.

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Sebastian Schönherr @sebschoenherr.bsky.social · 21/01/2025

If you didn't hear back from me today, it's because I had to solve a 4th grade math test first.

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Sebastian Schönherr @sebschoenherr.bsky.social · 16/01/2025

Almost forgot: Shout out to @nextflow.io for sending us stickers to get a bit of conference vibe here in innsbruck 🎉

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Sebastian Schönherr @sebschoenherr.bsky.social · 16/01/2025

Details about the workshop can be found here: genepi.i-med.ac.at/workshops/ne... Please feel free to reply directly to this thread for feature requests or via Github: github.com/genepi/imput... 2/2

genepi.i-med.ac.at

Nextflow In Genomics 2025 - Genepi Innsbruck

Institute of Genetic Epidemiology, Medical University of Innsbruck

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Sebastian Schönherr @sebschoenherr.bsky.social · 16/01/2025

Are 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

genepi.i-med.ac.at

Nextflow In Genomics 2025 - Genepi Innsbruck

Institute of Genetic Epidemiology, Medical University of Innsbruck

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Reposted by Sebastian Schönherr

Sebastian Schönherr @sebschoenherr.bsky.social · 28/12/2024

Publishing software is often easier than maintaining it - but we’re committed to keeping ours up to date! 🛠️ We've enhanced the documentation for our mtDNA variant calling pipeline, with detailed guides for both graphical and command-line use with Nextflow: mitoverse.readthedocs.io/mtdna-server...

mitoverse.readthedocs.io

mtDNA-Server 2 - Mitoverse

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Sebastian Schönherr @sebschoenherr.bsky.social · 28/12/2024

Btw, you can now set the mean minimum coverage when submitting a job, making it easier to work with low-coverage data. Let us know which features you’d like to see next. For graphical job execution click here: mitoverse.i-med.ac.at

mitoverse.i-med.ac.at

mitoverse

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Sebastian Schönherr @sebschoenherr.bsky.social · 28/12/2024

mitoverse.readthedocs.io

mtDNA-Server 2 - Mitoverse

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Sebastian Schönherr @sebschoenherr.bsky.social · 19/12/2024

And I almost forgot the most frightening moment in this journey: shutting down the old server after 9 years. #byebyehadoop

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Sebastian Schönherr @sebschoenherr.bsky.social · 19/12/2024

Our framework AND pipeline are now used by all the major imputation servers - Michigan, Topmed, Munich - which makes us quite proud. It’s also great to see @stephenturner.us covering us in his recent blog: tinyurl.com/5tp9tz7e. We would love to hear from more imputation servers around the world. 🌏

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Sebastian Schönherr @sebschoenherr.bsky.social · 19/12/2024

This 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...

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Sebastian Schönherr @sebschoenherr.bsky.social · 16/12/2024

Last week was fun! We had the pleasure of welcoming a MINT high school to our institute to talk about A.I 🤖. We also dived into Genetics (by @stncsn.bsky.social), Medicine, and discussed their project on AI-powered shark detection. 🧬🩺🦈 #STEM #MINT #Education #AI #Genetics @meduniibk.bsky.social

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Sebastian Schönherr @sebschoenherr.bsky.social · 13/12/2024

Today @silvidm.bsky.social delivered an impressive talk on her latest research on repetitive regions in the human genome - could they hold the key to the missing heritability? Huge thanks to the Biocenter @meduniibk.bsky.social for hosting this. #ukb #nextflow #lpa #vntrs

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Sebastian Schönherr @sebschoenherr.bsky.social · 05/12/2024

We believe this work will help others analyze VNTRs from short-read sequencing data and understand their impact on numerous human phenotypes, potentially explaining parts of the missing heritability. end.

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Sebastian Schönherr @sebschoenherr.bsky.social · 05/12/2024

For the first time, we were able to analyze the LPA VNTR in >199,000 samples from the UKB. This approach successfully revealed new, strong Lp(a)-lowering effects for KIV-2 variants, with a protective effect against coronary artery disease, and also validated previous findings. 5/n

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Sebastian Schönherr @sebschoenherr.bsky.social · 05/12/2024

And yes, we can! We developed a computational approach to resolve intra-repeat variation in the KIV-2 VNTR region using widely available short-read sequencing data, and we also applied it to 5 other medically relevant VNTRs 4/n

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Sebastian Schönherr @sebschoenherr.bsky.social · 05/12/2024

We specifically focused on the "dark" region of the cardiovascular disease gene LPA – the so-called KIV-2 VNTR. We wanted to determine if we could decipher this region using short-read sequencing data 3/n

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Sebastian Schönherr @sebschoenherr.bsky.social · 05/12/2024

A typical shot from my life as a researcher at @meduniibk.bsky.social. Standing in the HPC center with Silvia Di Maio and looking at dark genome regions What's the story behind? 1/n

(c) Medical University of Innsbruck, Cristof Simon

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Sebastian Schönherr @sebschoenherr.bsky.social · 25/11/2024

🌍 The imputation servers running on our software stack: 🛰️ Our Main Instance: imputationserver.sph.umich.edu 🛰️ TOPMed: imputation.biodatacatalyst.nhlbi.nih.gov 🛰️ MUC: imputationserver.helmholtz-munich.de 💡 Are there other imputation servers flying around?

imputationserver.sph.umich.edu

Michigan Imputation Server 2

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Sebastian Schönherr @sebschoenherr.bsky.social · 22/11/2024

Check out @lukfor.bsky.social and my latest work to run Nextflow graphically. Cloudgene3 powers major genotype imputation servers (Michigan, TOPMed, Helmholtz Munich—you name it). It’s like a referee in football—when no one is complaining, you know it’s doing an excellent job! ⚽ 🧬 shorturl.at/pdeGk

shorturl.at

Cloudgene 3: Transforming Nextflow Pipelines into Powerful Web Services

Nextflow has emerged as a flexible and scalable workflow system for building computational pipelines in life sciences. Simultaneously, Software-as-a-Service platforms enable researchers to concentrate...

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