I made a map of 3.4 million Bluesky users - see if you can find yourself!
bluesky-map.theo.io
I've seen some similar projects, but IMO this seems to better capture some of the fine-grained detail
thereโs nothing better than reaching into a bag of pistachios and pulling out one thatโs already open...
...thereโs also nothing worse than reaching into that same bag and pulling out just an empty shell.
Mars Express image of Olympus Mons volcano showing frost, 2024
In the difficult years ahead, we should remember that the snows of Olympus lie silent beneath the stars, waiting for our grandchildren.
- Arthur C. Clarke
Happy new year nerds! Episode 2 is out! Go listen to my conversation with Dr. Swetha Murthy and learn how she found her confidence through her science ๐งฌ Available now everywhere you listen to podcasts!
Austin Schubert (Saunders Lab) won "Most Innovative Approach" at the Cure SYNGAP1 conference. His poster was titled "Brainโwide discovery of when, where, and how SYNGAP1 haploinsufficiency alters neurodevelopment through single cell RNA profiling.โ
cc: @trill-nye.bsky.social @your-arpy.bsky.social
Full house for our Bi[o]hub workshop on Day 3!
Communities arenโt just built, they are co-created.
Together, weโre shaping an open, connected world of all-things-single-cell research, where sharing tools and ideas drives discovery.
Screenshot of blog post at https://dirk.eddelbuettel.com/blog/2025/10/26#duckdb-mlpack_0.0.2 announcing that mlpack is now a duckdb community extension
duckdb-mlpack 0.0.2: mlpack is now a duckdb community extension
Bringing mlpack machine learning to duckdb SQL
dirk.eddelbuettel.com/blog/2025/10...
Huge congratulations to my awesome lab mates, @your-arpy.bsky.social, and their collaborators @pasteur.fr on publishing their new paper showing how rabies hijacks brain cells and revealing a rare astrocyte subtype that boosts viral transcription ๐งช #SingleCell
www.sciencedirect.com/science/arti...
Probably just the duck from DuckDb running a quick query. It'll be gone soon.
Happy to share my first publication! AnnSQL leverages DuckDB to create a relational database based on each AnnData layer, enabling fast queries on massive, atlas-sized single-cell datasets. ๐งฌ๐ฅ๏ธ
#Bioinformatics #SingleCell #DuckDb
We're excited to offer the first #SQL based single-cell exploration and analysis tool. If you encounter anomalies or bugs, please report to the AnnSQL GitHub issue board: github.com/ArpiarSaunde...
๐ฆ๐ฝ๐ฒ๐ฒ๐ฑ: AnnSQL was built for querying large datasets.
tl;dr; If your dataset is > ~100k cells or out of memory, consider using AnnSQL. If your dataset is < ~100k cells or within memory, Scanpy or Seurat are the winners.
๐๐ป๐๐ฒ๐ฟ๐ผ๐ฝ๐ฒ๐ฟ๐ฎ๐ฏ๐ถ๐น๐ถ๐๐: AnnSQL databases (.asql) can be shared and also play nicely with a variety of languages; even R!
docs.annsql.com/interoperabi...
๐ ๐ฒ๐บ๐ผ๐ฟ๐: Using the #DuckDb in-process database engine behind the scenes, AnnSQL is memory respectful. AnnSQL also enabled a chunking parameter for all preprocessing methodsโ making it a powerful ally capable of processing massive datasets on a laptop.
๐๐ผ๐ฐ๐๐บ๐ฒ๐ป๐๐ฎ๐๐ถ๐ผ๐ป: Tutorials and API usage can be viewed at: docs.annsql.com
๐ก๐ฒ๐ ๐๐ฒ๐ฎ๐๐๐ฟ๐ฒ๐:
- Save raw layer
- Filter by cell & gene counts
- Highly variable gene selection
- PCA (experimental)
- Leiden clustering, UMAP, Diff Expression
- Various plotting utilities
๐ฃ๐ฟ๐ฒ๐ฝ๐ฟ๐ถ๐ป๐: In our updated preprint, we runtime profile filters vs queries using AnnSQL, AnnData, and Seurat.
www.biorxiv.org/content/10.1...
๐๐ป๐ป๐ฆ๐ค๐ v1 has landed! Explore atlas sized single-cell datasets, with minimal resources using SQL that's powered by the #DuckDb database engine. #SingleCell ๐งฌ ๐ฅ๏ธ ๐
github.com/ArpiarSaunde...
Happy to see lots of DuckDuckGoers. It's also worth considering Brave search. ๐ฆ
search.brave.com
Whoa, that's dedication ๐ช Hope you find what you're looking for soon!
Currently using ScEasy or SeuratDisk. Both are great tools and I've had some success using both, however, they sometimes can fail depending on the dataset and the layers present. The interoperability page you linked has some options I've yet to explore. Thank you for sharing!
I spend way too much time converting AnnData objects into Seurat objects and haven't found a tool or pipeline that just works, while retaining all data layers. What are some tools or pipelines to ease this process? ๐งฌ ๐ฅ๏ธ #SingleCell
By extension, Wikipedia says DeepSeek trained on its data and asks for $5 donation.
Learning about some of the magic behind the #DeepSeek R1 paper: "Optimisations actually began at chip level, below even CUDA, with DeepSeek engineers writing assembly language to overcome H800 bandwidth throttling. This in itself is an extraordinary technical feat"
SQL is way underappreciated in #bioinfo. Our lab just dropped a preprint for a tool (AnnSQL) that uses DuckDb for single-cell analysis.
www.biorxiv.org/content/10.1...
Usually I try to reduce it to an easily digestible analogy. Something like... Biology is like a giant puzzle and we use computers to try and put all the pieces together.
โItโs easier to fool a man than to convince him that heโs been fooled.โ - Mark Twain
Well, someone tried to tell me that Mark Twain never actually said that, but I donโt believe them
Commander Data from Star Trek The Next Generation as a change my mind meme stating "AI is just matrix multiplication. Change my mind."
The numbers speak for themselves.
#startrek #startrekmemes #data #ML #AI ๐
Named after a sci-fi series whose most notable AI component, the Replicators, sought to consume humans and all other resources in the galaxy ๐
A vending machine at OHSU Knight Cancer Research Building that is a pick up and dropoff for cancer risk screening.
Remember when vending machines were just for snacks? Happy to see OHSU researchers spearheading this screening program to help improve cancer early detection.
www.healthyoregonproject.com
๐งช #healthtech #genomics
