iiinova — where your digital self keeps evolving

Armin Töpfer @armintoepfer.com · 01/11/2025

What's going on in #bioinformatics? Any new cool alignment or mapping algos? Any advances in kmer hashing?

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Armin Töpfer @armintoepfer.com · 19/10/2025

When a candidate's CV matches the job description too well

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Armin Töpfer @armintoepfer.com · 18/10/2025

No updates from my side today

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Armin Töpfer @armintoepfer.com · 22/07/2025

No updates from my side today.

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Armin Töpfer @armintoepfer.com · 16/02/2025

I've been unhappy with my Sonos equipment. Last night, I've decided to take things into my own hands and created a local sonos controller in the browser with LLM help. Once I grok the full API, final frontier will be an Android app. Everything is 100% open source github.com/armintoepfer...

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Armin Töpfer @armintoepfer.com · 16/01/2025

Back in town, this time staying a few nights in SF. Good to be back and looking forward to meeting y'all @pacbio.bsky.social

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Armin Töpfer @armintoepfer.com · 16/12/2024

Testing out #cursor AI, anyone got great tips and tricks?

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Armin Töpfer @armintoepfer.com · 05/12/2024

Anyone got experience with code review bots? Are they any good? #AI

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Armin Töpfer @armintoepfer.com · 04/12/2024

I wonder if someone will sit down and write a better map-and-align tool than minimap2. If yes, will it (I) still support crappy 90% accuracy long reads or not and (II) offer interoperability being written in C or C++?

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Armin Töpfer @armintoepfer.com · 03/12/2024

Advent of code, hardcore edition Day A: Write fizz buzz in Haskell. You need to create a new DSL. You can only use letters of {A,C,G,T}. The code must be stored in DNA. You need to sequence and assemble it. Maximum coverage of 3-fold. Implicit error correction is allowed. Hint: Use HiFi.

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Armin Töpfer @armintoepfer.com · 02/12/2024

There's no traffic jam on the extra mile

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Armin Töpfer @armintoepfer.com · 30/11/2024

Things that happen if you spawn uint -1 threads on MacOS. The system instantly freezes and reboots after like 10 seconds.

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Armin Töpfer @armintoepfer.com · 29/11/2024

Performance review time of the year

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Armin Töpfer @armintoepfer.com · 29/11/2024

Trying out the new QwQ to rewrite gepard: Step 12: Think about parallelization for speed. - Given the large size of the sequence, parallel processing will be essential. - C++ allows for multi-threading, but for更大规模的并行，可以考虑使用GPGPU CUDA。 - 如果能够将计算分解为可以在GPU上并行执行的小任务，那么CUDA将是一个很好的选择。 ...yeah

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Armin Töpfer @armintoepfer.com · 28/11/2024

Just changed my handle to @armintoepfer.com pretty sweet feature

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Armin Töpfer @armintoepfer.com · 28/11/2024

I'm not used to having a normal work day from 8-4. Thanksgiving break shows me the real European work life balance that I get once per year. Usually I have 3-5 meetings between 5-9pm, 10 ppl pinging me on slack, verification churn, and chain of command asking me for updates.

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Armin Töpfer @armintoepfer.com · 24/11/2024

AI will help the ambitious to become more productive and successful. But you need to have a solid background to innovate, hands-on experience to make things really fast, must have suffered to grow, and be able to articulate and explain a hard problem. I need you to build the nexgen #PacBio. Apply

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Armin Töpfer @armintoepfer.com · 24/11/2024

Tis the season, baking with the kids

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Armin Töpfer @armintoepfer.com · 23/11/2024

Tired of chasing streaming providers, I just got this gem, forever.

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Armin Töpfer @armintoepfer.com · 22/11/2024

I made fried rice. Uncle Roger would approve.

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Armin Töpfer @armintoepfer.com · 20/11/2024

True leadership recognizes the unseen effort that prevents chaos — humility begins with appreciating the fires that never had to be fought.

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Armin Töpfer @armintoepfer.com · 20/11/2024

So, #PacBio made the jump. Where are the UK folks? Where are our friends that can only read stories?

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Armin Töpfer @armintoepfer.com · 20/11/2024

The upcoming SPRQ chemistry for #PacBio #Revio will be accompanied with a software update to improve the on-instrument 5mC methylation performance and introduce 6mA calling 🎉. Every HiFi read comes with both signals – for free. This will also enable Fiber-seq. Talk to your @pacbio.bsky.social rep!

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Armin Töpfer @armintoepfer.com · 20/11/2024

I've recently created a background for a Christmas card using #midjourney. Feel free to use ;)

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Armin Töpfer @armintoepfer.com · 20/11/2024

It's that time of the year again. The first snow is falling and self evaluation for the yearly performance review is due.

media.tenor.com

fry from futurama blowing a party horn

ALT: fry from futurama blowing a party horn

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Armin Töpfer @armintoepfer.com · 18/11/2024

I just found my next Christmas work sweater

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Armin Töpfer @armintoepfer.com · 17/11/2024

Sounds like I need to implement it on my own.

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Armin Töpfer @armintoepfer.com · 17/11/2024

What an amazing night. After 20 years last #qlimax ever. 9 hours of dancing, now back at home...time to sleep at 9:30am. I wore my swag from 2006, my first visit

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Armin Töpfer @armintoepfer.com · 16/11/2024

Three pivotal moments in long-read #PacBio DNA sequencing - HiFi for everyone - HiFi on your bench - What I'm cooking right now #bioinformatics at scale to enable science

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Armin Töpfer @armintoepfer.com · 16/11/2024

Three pivotal moments in long-read #PacBio DNA sequencing - HiFi for everyone - HiFi on your bench - What I'm cooking right now #bioinformatics at scale to enable science

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Armin Töpfer @armintoepfer.com · 16/11/2024

This is it. Me and the boys are going to the last #qlimax. Just found my swag from 2006...will wear it with pride. Back in the days, #hardstyle wasn't that commercial yet. Let's hope for some great old-school sets and DJs.

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Armin Töpfer @armintoepfer.com · 15/11/2024

Attention to detail and minimalism is a virtue that I fully support. I'm afraid to start writing in this beautiful notebook by ia.net/notebook. I would, but I didn't know what. Maybe "Scaling Genomics: My Last Decade from Fridges to Benchtops and Beyond" @pacbio.bsky.social

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Armin Töpfer @armintoepfer.com · 15/11/2024

Getting ready for the next deep learning #ML project, beefed up my current 2x64c Genoa server with 1.5 TB RAM and 9 GPUs. One PCIe slot is broken...

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Armin Töpfer @armintoepfer.com · 15/11/2024

Tomorrow, I'll visit #qlimax for the last time. Went there 2006 for the first time...time flies

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Armin Töpfer @armintoepfer.com · 15/11/2024

If you are a #C++ developer, either have a #bioinformatics or #CUDA background, and take pride in your engineering and/or algorithmic skills, I'm looking for a Senior Staff Engineer at @pacbio.bsky.social. You can work remotely. Feel free to ping me or go to pacb.com/careers Please spread the word

pacb.com

Careers - PacBio

PacBio is always looking to add the best and brightest minds to our world-class company. Our highly interdisciplinary team is best suited for individuals who are creative, forward thinking, and who ap...

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Armin Töpfer @armintoepfer.com · 15/11/2024

Does anyone have a C or C++ implementation to compute a dot plot like gepard does? The sparse matrix is sufficient. Better to ask before NIH it myself. #bioinformatics #algorithms

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Armin Töpfer @armintoepfer.com · 15/11/2024

Winter time means comfy clothes and fresh OJ

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Armin Töpfer @armintoepfer.com · 15/11/2024

New T-shirts arrived for me and my Swiss buddy

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Armin Töpfer @armintoepfer.com · 14/11/2024

Remember when @pacbio.bsky.social introduced Kinnex and customers suddenly got >40M HiFi transcripts per run? I was tasked to solve scaling up Iso-Seq reference-free clustering and had less than a month. There were a lot of #bioinformatics challenges to be solved More info on isoseq.how or read on🧵

isoseq.how

Iso-Seq Home

Scalable De Novo Isoform Discovery from PacBio HiFi Reads.

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Armin Töpfer @armintoepfer.com · 13/11/2024

Let's see how good qwen2.5-coder 32B really is.

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Armin Töpfer @armintoepfer.com · 13/11/2024

I've designed a new shirt that just shipped. Can't wait to wear this at work

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Armin Töpfer @armintoepfer.com · 13/11/2024

If you work on real-time applications with a maximum time to results for a set of data points and you are running on a NUMA system with multiple sockets, there are a few rules to ensure system stability and achieve lowest turnaround time 🧵 1/5 #HPC #Linux #BareMetal

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Armin Töpfer @armintoepfer.com · 12/11/2024

> Teams > Slack > Mails > Meetings > Recordings > 1:1s > SWAT teams > Tiger teams > Q4 OKRs > '25 planning Tired.

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Armin Töpfer @armintoepfer.com · 12/11/2024

> Teams > Slack > Mails > Meetings > Recordings > 1:1s > SWAT teams > Tiger teams > Q4 OKRs > '25 planning Tired.

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Armin Töpfer @armintoepfer.com · 12/11/2024

Incentives for a bioinformatician working on tools to process or generate HiFi data are different. Both advance science, but the latter won't go to conferences, have their names on posters or papers, and will operate mostly in the shadows. But you know that without your work, there wouldn't be HiFi.

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Armin Töpfer @armintoepfer.com · 12/11/2024

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Armin Töpfer @armintoepfer.com · 12/11/2024

Yesterday I was looking at how fast I can compact an array of 8bit ints using a mask of the same size. Single core, 1.5ms for 10M entries, using AVX512. This instruction set is great. That's only 35GB/s, so definitely not DDR5 limited. I have to check if I can compact the mask and ensure aligned mem

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