Thomas Sandmann
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thomas-sandmann.genomic.social.ap.brid.gy
Thomas Sandmann
@thomas-sandmann.genomic.social.ap.brid.gy
41 followers 4 following 23 posts
Computational biologist, biotech, neurodegeneration, genomics, learning, R, python

[bridged from https://genomic.social/@thomas_sandmann on the fediverse by https://fed.brid.gy/ ]
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Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
w00t! - jarl can now run a linter to see if you've accidentally left a browser() in your #rstats code

https://jarl.etiennebacher.com/rules/browser

(my small contribution)

I'm super excited about (crazy fast) Rust tooling making development smoother across other languages.
browser – jarl
jarl.etiennebacher.com
November 23, 2025 at 12:41 PM
Reposted by Thomas Sandmann
stephenturner.us
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)

Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/

#Rstats
November 21, 2025 at 5:39 PM
Reposted by Thomas Sandmann
preya.mastodon.social.ap.brid.gy
Im Sommer habe ich hier einen Toot gesehen, wo jemand nach einer Platform sucht, auf der "überholtes" Schulwissen gelistet wird. Also man gibt sein Abschlussjahr ein, und sieht dann welche Dinge aus dem #lehrplan inzwischen nicht mehr stimmen.
Leider gab es sowas anscheinend nicht. Also habe ich […]
Original post on mastodon.social
mastodon.social
November 20, 2025 at 9:56 AM
Reposted by Thomas Sandmann
ai6yr.m.ai6yr.org.ap.brid.gy
I hate the shopping season, but I posted this list of "Disaster Preparedness Stocking Stuffers" it seems like a century ago on Tw*tter, so reposting the list again here:

Disaster Preparedness Stocking Stuffers

It's that time of the year again, where people are thinking about holiday gifts […]
Original post on ai6yr.org
m.ai6yr.org
November 22, 2025 at 2:54 AM
Reposted by Thomas Sandmann
cutterkom.mastodon.social.ap.brid.gy
We can now encrypt @duckdb databases:

"When using DuckDB with encrypted storage, we can also simplify threat modeling when – for example – using DuckDB on cloud providers."

Detailed post on implementation and usage

https://duckdb.org/2025/11/19/encryption-in-duckdb
DuckDB中的静态数据加密
Data-at-Rest Encryption in DuckDB (duckdb.org) 03:26  ↑ 100 HN Points
duckdb.org
November 21, 2025 at 6:50 AM
thomas-sandmann.genomic.social.ap.brid.gy
Just finished "Automatic Noodle" by @annaleen - so much fun. I loved the description of San Francisco in the not-so-distant future, and the lovable and diverse characters. Highly recommended! https://us.macmillan.com/books/9781250357465/automaticnoodle/ #books #scifi #noodles #robots #california
November 20, 2025 at 5:26 AM
Reposted by Thomas Sandmann
hrbrmstr.mastodon.social.ap.brid.gy
Jarl (with a Zed Extension!) by @etiennebacher is DOPE!

https://github.com/etiennebacher/jarl

So. FAST!

Need to figure out a good way to perma-eradicate the bane that is {lintr}.
GitHub - etiennebacher/jarl: Just Another R Linter
Just Another R Linter. Contribute to etiennebacher/jarl development by creating an account on GitHub.
github.com
November 19, 2025 at 10:34 PM
Reposted by Thomas Sandmann
michcampbell.fediscience.org.ap.brid.gy
Yesterday I told my boss that I'm not going to be applying for any funding to stay in Europe (for multiple reasons. Postdocing has to end eventually, and living on the other side of the planet from my friends, family, and the Australian bush isn't working for me). He said, 'Makes sense you want […]
Original post on fediscience.org
fediscience.org
November 19, 2025 at 8:38 AM
Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
The latest issue of @rweekly is now live!

https://rweekly.org/2025-W47.html

This week's highlights:
🤖 When plotting, LLMs see what they expect to see by @simonpcouch and @sara-altman.bsky.social
🏓 Winners of the 2025 Table Contest by Rich Iannone and @Posit
🪠 How much do you know about pipes? […]
Original post on fosstodon.org
fosstodon.org
November 17, 2025 at 10:52 AM
Reposted by Thomas Sandmann
leafyericscott.hachyderm.io.ap.brid.gy
My lightning talk on {geotargets} from posit::conf(2025) is up on YouTube!

https://youtu.be/RmTtugX1CoE?si=3rER0gwnDueIsL4f

#positconf2025 #rstats #rspatial
November 16, 2025 at 7:40 PM
Reposted by Thomas Sandmann
adapalmer.wandering.shop.ap.brid.gy
Doctors in China have used lab-grown insulin-producing cells to treat a woman with type 1 diabetes. The cells were made from her own tissue, reprogrammed into stem cells, and then grown into tiny clusters that release insulin. A year after the transplant, her blood sugar remains normal without […]
Original post on wandering.shop
wandering.shop
November 15, 2025 at 6:03 PM
Reposted by Thomas Sandmann
hrbrmstr.mastodon.social.ap.brid.gy
re: "Google Docs Tracking Links" (https://mastodon.social/@hrbrmstr/115514845732795707) thing from yesterday…

https://rud.is/defang-google-docs is a single HTML file with in-browser local-only processing that sanitizes those links from epub and html docs […]

[Original post on mastodon.social]
Screenshot of a web tool called “Google Docs Link Defanger,” which strips tracking URLs from exported Google Docs EPUB or HTML files. The interface includes a drag-and-drop upload area, a description of how it removes Google’s tracking wrappers from links, and a note that all processing happens locally in the browser. light mode Screenshot of a web tool called “Google Docs Link Defanger,” which strips tracking URLs from exported Google Docs EPUB or HTML files. The interface includes a drag-and-drop upload area, a description of how it removes Google’s tracking wrappers from links, and a note that all processing happens locally in the browser. dark mode
November 9, 2025 at 11:31 AM
Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
I'll be talking about some Neo4j knowledge graph projects in Melbourne next week https://www.meetup.com/melbourne-data-engineering-meetup/events/311353364/
Melbourne Data Eng meetup, Graph Edition, Tue, Nov 11, 2025, 5:00 PM | Meetup
Hey all, please join us for our November Edition of the Melbourne Data Eng meetup which will dive deep on all things Knowledge Graphs and GraphRAG. Join us for an engaging
www.meetup.com
November 5, 2025 at 3:32 AM
Reposted by Thomas Sandmann
mariavonbolla.mastodon.social.ap.brid.gy
Ich helfe gerade zwei obdachlosen Menschen recht intensiv, die ich hier in Berlin kennengelernt habe. Sie könnten jetzt ein Smartphone oder Tablet gebrauchen. Hätte da noch wer was rumliegen in der Stadt? Oder gibt es Orte, wo sie das unkompliziert bekommen könnten? Kann 7 Jahre alt sein, egal […]
Original post on mastodon.social
mastodon.social
November 4, 2025 at 11:29 AM
Reposted by Thomas Sandmann
davidho.mastodon.world.ap.brid.gy
Forrest Smith, the only National Park Service engineer cleaning up abandoned oil and gas wells, lost his contract, leaving 93 orphaned wells on park lands unmanaged. These leaking wells release methane and toxins, threatening health and the environment, with no replacements yet hired […]
Original post on mastodon.world
mastodon.world
November 3, 2025 at 5:57 AM
Reposted by Thomas Sandmann
Since I've retired, I'll be blogging more about #bioinformatics and most likely #rstats - and to start it all off - here is the first blog post on the #quarto based blog (converted from Wordpress).
https://brianrepko.github.io/blog/posts/2025-10-31-blogging-for-real/
Blogging again…for real – Learning, Thinking, and Coding
and lots more time to do it
brianrepko.github.io
October 31, 2025 at 9:36 PM
Reposted by Thomas Sandmann
stephenturner.us
I'm doing a workshop on R package development with Positron on Jan 15 2026. Register for the virtual workshop here: sites.google.com/view/dariia-... I'll cover devtools, usethis, testthat, covr, and a few AI tools along the way to help. #Rstats
October 31, 2025 at 9:56 AM
Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
About half way through @daroczig's #user talk recording on {logger}

https://www.youtube.com/watch?v=8R8ulz4MVm0

I was admiring how extensible it was and it struck me that it was a good fit for sending logged errors via {ntfy} - I got a working proof of […]

[Original post on fosstodon.org]
logger message sent via ntfy
October 31, 2025 at 4:14 AM
Reposted by Thomas Sandmann
stephenturner.us
Come work with me! We're hiring a new *Director of Innovation* at the UVA School of Data Science jobs.virginia.edu/us/en/job/R0... 🧬🖥️🧪
October 30, 2025 at 9:07 AM
Reposted by Thomas Sandmann
simon.fedi.simonwillison.net.ap.brid.gy
This was a tough but necessary decision - I posted my own notes on this here, from the perspective of a current PSF board member https://simonwillison.net/2025/Oct/27/psf-withdrawn-proposal/
https://fosstodon.org/@ThePSF/115446659188615376
The PSF has withdrawn a $1.5 million proposal to US government grant program
The Python Software Foundation was recently "recommended for funding" (NSF terminology) for a $1.5m grant from the US government National Science Foundation to help improve the security of the Python …
simonwillison.net
October 27, 2025 at 8:36 PM
Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
The {ntfy} #rstats package has been updated on CRAN with internal improvements and tests thanks to @hadleywickham https://cran.r-project.org/package=ntfy

Send a message to your devices on-demand or when some code completes, including emoji and plot outputs. No […]

[Original post on fosstodon.org]
ggplot sent as a notification via the ntfy package
October 26, 2025 at 9:30 PM
Reposted by Thomas Sandmann
nowosad.fosstodon.org.ap.brid.gy
Want to transform the geometry of spatial data in Python? ✨🌍🐍

Chapter 4 of geocompy covers:

- Vector: simplify, buffer, centroid, clip, unions, affine transforms
- Raster: crop, resample, aggregate, align datasets

👉 https://py.geocompx.org/04-geometry-operations

#geopython #python #gischat […]
Original post on fosstodon.org
fosstodon.org
October 26, 2025 at 2:02 PM
Reposted by Thomas Sandmann
bagder.mastodon.social.ap.brid.gy
Just noticed this site exists:

https://justuse.org/curl/
Just Use Curl
Comments
justuse.org
October 21, 2025 at 1:46 PM
Reposted by Thomas Sandmann
b0rk.social.jvns.ca.ap.brid.gy
just added the MEGA TERMINAL CHEAT SHEET from "The Secret Rules of the Terminal" to our list of posters at https://wizardzines.com/#posters
October 20, 2025 at 3:22 PM
Reposted by Thomas Sandmann
jonocarroll.fosstodon.org.ap.brid.gy
If you're learning python (as I slowly am) then I recommend Rodrigo's mathspp blog and the daily python drops emails

https://drops.mathspp.com/subscribe?ref=dy06MhyDko

as well as the (free) uv cheatsheet https://mathspp.com/blog/uv-cheatsheet

Lots of helpful hints and tips.
Python drops 🐍💧
Python drops: tips & tricks that trickle into your inbox daily
drops.mathspp.com
October 19, 2025 at 12:04 AM