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David Kouřil

@dvdkouril.xyz

data visualization, postdoc @ Harvard Medical School. phd from TU Wien. davidkouril.com

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01.12.2023
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Latest posts by David Kouřil @dvdkouril.xyz

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playing around with umap-js today.

27.02.2026 17:59 👍 3 🔁 1 💬 0 📌 0
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Instead, I can have Claude figure out stuff like library API changes, or even mock responses from data servers that are no longer up. In the end, I can actually interact with the tool and see what's realistically possible.

24.02.2026 18:04 👍 2 🔁 0 💬 0 📌 0
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HiC-3DViewer: a new tool to visualize Hi-C data in 3D space - Quantitative Biology Background Although significant progress has been made to map chromatin structure at unprecedented resolution and scales, we are short of tools that enable the intuitive visualization and navigation a...

For example, this is a research software that hasn’t been touched in 7 years (according to Github). Making it run manually would probably take way too much time and effort so I’d default to making assumptions based on the paper. link.springer.com/article/10.1...

24.02.2026 18:02 👍 0 🔁 0 💬 1 📌 0
A screenshot of a paper figure with caption. Highlighted text in the caption reads "Pink arrowheads indicate the 2D to 3D mapping of the highlighted region in Hi-C heat map on the 3D model. The green arrowhead indicats the 2D to 1D mapping of the selected region in 1D yeast genome (shown in orange for the recently selected region). Each selected region will be mapped to an individual 1D genome."

A screenshot of a paper figure with caption. Highlighted text in the caption reads "Pink arrowheads indicate the 2D to 3D mapping of the highlighted region in Hi-C heat map on the 3D model. The green arrowhead indicats the 2D to 1D mapping of the selected region in 1D yeast genome (shown in orange for the recently selected region). Each selected region will be mapped to an individual 1D genome."

A nice use case for Claude Code in my work: reviving old research prototypes. When it comes to surveying interactive features of past tools, we often have to rely on static figures and descriptions in text. Sometimes there’s a video. That can be pretty limiting.

24.02.2026 18:01 👍 1 🔁 1 💬 1 📌 0
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we’ve got some selections going!

23.02.2026 15:54 👍 2 🔁 0 💬 0 📌 0
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revisiting my webgpu-based 3D scatterplot library after a year.

22.02.2026 16:33 👍 3 🔁 0 💬 0 📌 0

I closed that account on August 14, 2024. The bio on the fake profile is taken verbatim from my Github, same as the cover photo.

18.02.2026 17:54 👍 0 🔁 0 💬 0 📌 0
A screenshot of my previous twitter profile (@dvdkouril). Highlighted are two dates: one showing 'Joined January 2015' and the most recent repost of a post dated October 13, 2023.

A screenshot of my previous twitter profile (@dvdkouril). Highlighted are two dates: one showing 'Joined January 2015' and the most recent repost of a post dated October 13, 2023.

A screenshot of a fake profile using the same handle (@dvdkouril). Highlighted is: 'Joined April 2020'

A screenshot of a fake profile using the same handle (@dvdkouril). Highlighted is: 'Joined April 2020'

A screenshot of email conversation with X Support, showing that I reported Impersonation on this account. All the options are irrelevant as they are concerned with restoring my account.

A screenshot of email conversation with X Support, showing that I reported Impersonation on this account. All the options are irrelevant as they are concerned with restoring my account.

Just so you know: if you delete your twitter/x account, it will come back up at some point, and show that it’s been active from an arbitrary, impossible date. Reporting impersonation is also useless.

18.02.2026 17:51 👍 0 🔁 0 💬 1 📌 0

I also really like the part around 27min mark, where he talks about the visualizations that people make of the problems. That's what I would often default to...naturally...

08.02.2026 20:58 👍 0 🔁 0 💬 0 📌 0
Keynote: Advent of Code, Behind the Scenes - Eric Wastl
Keynote: Advent of Code, Behind the Scenes - Eric Wastl YouTube video by CppNorth

TIL that Advent of Code was invented in Salem, Massachusetts www.youtube.com/watch?v=uZ8D...

08.02.2026 20:56 👍 0 🔁 0 💬 1 📌 0
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i can’t be the only one who procrastinates on work by making tools for tracking and visualizing work

08.02.2026 15:21 👍 1 🔁 1 💬 0 📌 0
photo of an ebook, with the following text highlighted: It is well known that the majority of the cost of software is not in its initial development, but in its ongoing maintenance.

photo of an ebook, with the following text highlighted: It is well known that the majority of the cost of software is not in its initial development, but in its ongoing maintenance.

31.01.2026 13:30 👍 2 🔁 0 💬 0 📌 0
a snowed in car

a snowed in car

larger street covered in snow, a snow plowing truck approaching an intersection

larger street covered in snow, a snow plowing truck approaching an intersection

a person knee deep in snow

a person knee deep in snow

haven’t seen that much snow in a while!

26.01.2026 13:00 👍 1 🔁 0 💬 0 📌 0
a calendar view of 2025, divided by months. each day is color coded based on exercise type or gray which means no exercising that day

a calendar view of 2025, divided by months. each day is color coded based on exercise type or gray which means no exercising that day

Made a little visualization of my workouts from last year.

05.01.2026 23:04 👍 1 🔁 0 💬 0 📌 0
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hello, marimo

18.12.2025 16:38 👍 1 🔁 0 💬 0 📌 0
screenshot of very many colorful circles

screenshot of very many colorful circles

17.12.2025 17:31 👍 0 🔁 0 💬 0 📌 0
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even more colorful balls

17.12.2025 17:26 👍 0 🔁 0 💬 1 📌 0
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instead of advent of code, i’m spending my december on this #webgpu

17.12.2025 17:25 👍 0 🔁 0 💬 1 📌 0

So there won’t be any streaming for the whole conference, huh? That’s a huge bummer.

03.11.2025 14:10 👍 1 🔁 0 💬 0 📌 0
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My #IEEEVIS 2025 paper explorer is live! 🎉
👉 johnguerra.co/viz/ieeevis2... 👈

An interactive #dataviz to explore 300+ papers by similarity. Perfect for:
✨ Discovering papers related to your interests
✨ Planning which sessions to attend
✨ Creating your own paper list (new!)

Pls help me distribute it

02.11.2025 13:28 👍 30 🔁 10 💬 1 📌 0
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FOOL TIME, Part 1 of 4 | Pretty Good | Secret Base Get more from Secret Base on Patreon

after spending all year behind the paywall, part 1 of my documentary series FOOL TIME is now unlocked and free to watch for everybody: www.patreon.com/posts/fool-t...

15.10.2025 17:30 👍 710 🔁 131 💬 8 📌 34
Abdennur, Lekschas, & Manz - Bring your __repr__’s to life with anywidget | SciPy 2024
Abdennur, Lekschas, & Manz - Bring your __repr__’s to life with anywidget | SciPy 2024 YouTube video by SciPy

if interested in creating anywidgets of your own, our tutorial was finally shared to youtube:

www.youtube.com/watch?v=frEo...

07.08.2025 20:00 👍 7 🔁 3 💬 2 📌 1
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I have been playing with filtering of 3D structures (represented as Arrow tables) via duckdb-wasm… It’s been going pretty well!

25.07.2025 17:36 👍 3 🔁 0 💬 0 📌 0
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GitHub - manzt/juv: Create, manage, and run Jupyter notebooks with their dependencies Create, manage, and run Jupyter notebooks with their dependencies - manzt/juv

Maybe juv can be useful for cases like this, has been for me! github.com/manzt/juv @manzt.sh

24.07.2025 21:08 👍 3 🔁 0 💬 1 📌 0
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not completely done reading it yet, but this is definitely one of my favorite survey papers: onlinelibrary.wiley.com/doi/10.1111/...
interactive browser: uclab.fh-potsdam.de/unfoldables/
@uclab.bsky.social

13.06.2025 14:02 👍 2 🔁 0 💬 0 📌 0
screenshot of a browser window showing an online CV

screenshot of a browser window showing an online CV

totally unrelated to anything happening these days, but I now have a CV on my webpage: davidkouril.com/cv

23.05.2025 14:52 👍 4 🔁 0 💬 0 📌 0
boy do i have some bad news for you...this is gonna be a pie chart https://www.youtube.com/watch?v=lOR_45wZL2I Internals

terrible, terrible code at: observablehq.com/d/a6e42e6b6f...

18.05.2025 02:15 👍 0 🔁 0 💬 0 📌 0
GOD HATES A COWARD | PRETTY GOOD, EPISODE 18
GOD HATES A COWARD | PRETTY GOOD, EPISODE 18 YouTube video by Secret Base

inspired by: youtu.be/lOR_45wZL2I?...

18.05.2025 02:14 👍 0 🔁 0 💬 1 📌 0
a…3D pie chart

a…3D pie chart

“boy do I have some bad news for you…this is gonna be a pie chart”

reproduced this beauty from @jonbois.bsky.social

18.05.2025 02:14 👍 1 🔁 0 💬 1 📌 0
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Why users cannot create Issues directly · Issue #3558 · ghostty-org/ghostty Users are not allowed to create Issues directly in this repository - we ask that you create a Discussion first. Unlike some other projects, Ghostty does not use the issue tracker for discussion or ...

IMHO, make this the default, github: github.com/ghostty-org/...

22.04.2025 15:02 👍 190 🔁 28 💬 17 📌 2