#bioinformatics

See tagged statuses in the local BookWyrm community

50% of is just joins on poorly constructed primary keys..

select * from 'log_tpm.csv' exp join 'b_mapping.csv' bm on bm.b_number = exp.column000 join 'dh10b_2.csv' dh on dh.gene_name = bm.gene_name limit 1

Hi lazywell,

is there a standard CLI tool that can be used to extract all the descendants (rdf:subClass ? ) of a given term from a local OWL ontology file ?

I wrote a stupid java xml tool but I'd like a tool that understands the OWL spec (I don't)

📣 Calling all Bioconductor users and developers! 🧬 ✨

We’re launching a new online quarterly seminar series showcasing contributor innovations and sparking conversations about how packages work together. Expect 30 minutes of insight, 15 minutes of guided discussion, and 15 minutes of open Q&A.

📅 Date: Dec 2, 2025
🕒 Time: 9 PM CET / 3 PM EST / 12 PM PST
➡️ Register: https://dfci.zoom.us/webinar/register/WN_0nAabJt1Qeyd8QsJjvEzOQ
📑 Paper: https://pmc.ncbi.nlm.nih.gov/articles/PMC12328236/

Bioconductor Seminar Series flyer. Title: “Deep-learning-based Gene Perturbation Effect Prediction Does Not Yet Outperform Simple Linear Baselines.” Event on Dec 2, 2025 at 9 PM CET / 3 PM EST / 12 PM PST. Speakers: Constantin Ahlmann-Eltze, Wolfgang Huber, Simon Anders. Discussant: Davide Risso. Includes a “Register for Zoom Link” button, QR code, and Bioconductor logo.

Any lab out there interested in having their Natrialba species sequenced on ONT r10 up to about 3Kx read depth for free? I'll send back annotated assembly, methylation data and raw signal files. I need at least one more species for a paper from a particular phylogenetic clade within the genus.

Please feel free to DM & boost!

For people:

I want to do a short workshop / demo for , , and bioinfo undergrads. It should last maybe 10 minutes. I was thinking of some sort of gamified use of algorithms to solve problems, for example sequence alignment...

I'd love suggestions about existing options (websites, games, concepts) that you could know. Else I could print parts of sentences and have them assemble them by overlap...? I hope to find something more exciting ;)

Please re-post!

Today I gave a talk entitled "Computational reproducibility and the struggle for reliable science"

I've uploaded the slides here: https://ziemann-lab.net/2025/08/14/plenery-presentation-deakin-graduate-research-conference/

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Title slide for Mark Ziemann's plenery presentition entitled "Computational reproducibility and the struggle for reliable science" Other details include the event: LES Graduate Researcher Conference Date: 2025-08-14 Licence: CC-BY-4.0

Harvard researcher Dr. Kseniia Petrova wrote an Op-Ed in the NYT this week about her experience in ICE detention, where she has been living in 1 room with 100 other women for 3 months, and what it means for her research, and our research community more broadly: https://www.nytimes.com/2025/05/13/opinion/ice-detention-russian-scientist.html?unlocked_article_code=1.HE8.XkID.iSc5Vm8s9DXy&smid=url-share

Background on Kseniia's journey to the United States and her jailing by ICE in February: https://www.nytimes.com/2025/04/11/science/russian-scientist-ice-detained-harvard.html?unlocked_article_code=1.HE8.GpNt.Y_FhDbbuqfb0&smid=url-share

Kseniia Petrova, a Harvard scientist, in 2021. She has been in a Louisiana prison since Feb. 16.
In rat testis a complex structure of the spermatozoa tails nest in a central spiral. NoRI’s findings about the testes may one day help us treat testicular cancer.
“Any problem I have with data, she has a solution,” a colleague said. A photograph taken from her desk at Harvard showing a cheerful hand-drawn note that says "hello, Kseniia!" decorated with a heart and lots of tiny colorful flowers
A rat small intestine