osn-scott.bsky.social

This tool is great. I’d love it even more if I can compare the long read assembly that I have with an NCBI reference genome! Seems to only take NCBI genomes for comparisons.

Very sad news. I was building HMMER profiles to mine the nascent Celera mouse and human genomes. Such a powerful tool.

BEFORE THE BATHROOM SCALE WAS INVENTED, THE ONLY WAY TO WEIGH PEOPLE WAS MASS SPECTROMETRY.

Love today’s #xkcd comic on
#MassSpec
🤣

We’ve uncovered Asgard chromatin structures formed by a Hodarchaeal histone : closed hypernucleosome conserved in archaea and an open form resembling the H3-H4 eukaryotic octasome. Fantastic work by @harshranawat.bsky.social!
www.biorxiv.org/content/10.1...
#Chromatin #Asgard #Archaea #cryoEM

🚨 Teaching bioinformatics? Or learning it solo?
Check out my free & open Fundamentals of Bioinformatics course materials: lectures, slides, and exercises — no coding background required.
🔬🧬👩‍💻

📚 github.com/lskatz/funda...
⭐️ Star it, share it, and level up!

#bioinformatics #opensource #STEMeducation

"As with software, open DNA & strains promotes innovation around the world. I wish to extend Open Yeast & Yeast Protein Expression Toolkits, now in 50 countries, to permit engineering of Yarrowia lipolytica & creating truly open chassis to support boots on the ground innovators."

Here's another #MegabaseSpark submission, from
@osn-scott.bsky.social: "The Open Yarrowia Collection" (detail in reply) Like and repost if you like this idea! #SynBio #RootPath

AlphaFold is amazing but gives you static structures 🧊

In a fantastic teamwork, @mcagiada.bsky.social and @emilthomasen.bsky.social developed AF2χ to generate conformational ensembles representing side-chain dynamics using AF2 💃

Code: github.com/KULL-Centre/...
Colab: github.com/matteo-cagia...

chinnadevarapu.bsky.social has updated his tiny, low cost Pocket Spectrometer design that uses an M5StickC microcontroller and AS7341 spectral sensor - simplified hardware connections and software improvements. Nice job! Details at: github.com/scientistnob...

🚀 First Bluesky Post! 🎉 VMD 2.0 Alpha is here! Released today at BPS 2025, this is the biggest update in 30 years—new UI, real-time ray tracing, fast surfaces, UHD & touchscreen support. Monthly updates coming in 2025! Try it now! #VMD #BPS2025 #MolecularVisualization
www.ks.uiuc.edu/Research/vmd...

Re DNA sequence DBs: While sequence is shared across #INSDC databases #ENA #Genbank #DDBJ, the presentation and granularity of annotations/metadata can differ notably, with diff. benefits, impacting searches and downstream analyses. All INSDC databases must be maintained - annotations are important

Quantifying metabolites using structure-switching aptamers coupled to DNA sequencing Nature Biotechnology - Metabolites can be quantified using a combination of aptamers and DNA barcodes.

Delighted to share our latest paper describing a method to read the levels of hundreds of metabolites or drugs in parallel using DNA sequencing. This method, which we call ‘smol-seq’ (Small MOLecule sequencing), harnesses the power of DNA sequencing for metabolite detection:
rdcu.be/d8xLv (1/6)

What limits rubisco function? Is it the chemical mechanism? Evolution? In this paper, @prywes.bsky.social et. al explore this question by assaying >99% of single amino acid mutants in Form II rubisco (1/7) doi.org/10.1038/s415...

New Journal Article: “Trust in #Scientists and Their Role in Society Across 68 Countries” www.infodocket.com/2025/01/20/j... #science #trustinscience

Two new studies provide some insights on red meat intake, with respect to both potential risks and how they can be mitigated.
erictopol.substack.com/p/the-update...

This paper has been a long time coming: We looked at the genomes of historical bacterial samples over a century to look for trends of antibiotic resistance genes, finding multiple instances of them in infections before the age of antibiotics, but an increase in both frequency and mobility after

FIB-SEM dataset visualized with Microscopy Nodes, data from Mocaer et al 2023

Microscopy Nodes is now up on bioRxiv! 🚀

This is a Blender extension that seamlessly integrates and visualizes 3D microscopy data (TIF & @zarr.dev).

High-quality volume rendering for anyone, in both EM and fluorescence, regardless of computational expertise! 🔬

www.biorxiv.org/content/10.1...

Open Source Alternatives To Proprietary Software The world's largest directory for open source software. Discover 500+ popular open source alternatives to proprietary software products. 100% free.

For y’all’s consideration:

Use this site to find open source alternatives to whatever app you want to ditch.

www.opensourcealternative.to?searchTerm=I...

Here it is... it is exclusive, it is arbitrary, and membership will be determined solely by me. You should be upset if you are included, and also upset if you are not included

go.bsky.app/JZc9HXe

PDB101: Molecule of the Month: Assembly Line Polyketide Synthases Large multienzyme complexes that synthesize diverse small molecules in a stepwise manner.

I'm happy and humbled to take on a new role with @rcsbpdb.bsky.social. I'll be continuing David Goodsell's work on the Molecule of the Month, starting with my first article on Assembly Line Polyketide Synthases! Check it out (animation included!)
pdb101.rcsb.org/motm/301

Build instructions for DIYNAFLUOR, a $40 fluorimeter for DNA quantification - uses 3D printed filter cube, LED source, TSL2591 sensor, cheap 10mm square bandpass filters - with full protocols for SYBR Safe dye measurements
github.com/traulab/DIYN... and www.biorxiv.org/content/10.1...

Here's an archived free copy of CL Strong's 1960 book with collected Amateur Scientist columns from Scientific American. Inspiration for citizen science. Forward by Vannevar Bush...
archive.org/details/Proj...

👆 @atinygreencell.bsky.social

Meet Agara Bio, an undergraduate-led community lab 🧪

Agara Bio is an open bio-lab run by undergraduate students at @jhu.edu.

MIT researchers introduce Boltz-1, a fully open-source model for predicting biomolecular structures Researchers in the MIT Jameel Clinic for Machine Learning in Health developed a fully open-source biomolecular structure prediction model that achieves state-of-the-art performance, at the level of Al...

After AlphaFold3 was released with a limited license, a global race began to build the first fully open source replica of the biomolecular prediction model that could be available for commercial use.

Read more in MIT News: news.mit.edu/2024/researc...

This is our latest preprint about the biogenesis of the translation proteins in a minimal translation system (PURE). www.biorxiv.org/content/10.1...

Donate to Signal Private Messenger Your donation helps pay for the development, servers, and bandwidth of an app used by millions around the world for private and instantaneous communication. Please make a donation today.

It costs around $50 million every year to ensure Signal is robust and available all over the world for anyone whenever they need it.

And as a nonprofit, that money comes from all of you; the people who believe that we all deserve a place to speak freely.

signal.org/donate/

Latin American journals are open-access pioneers. Now, they need an audience SciElo, other platforms work to help journals reach readers around the world

“There is a lot of pressure to publish in mainstream journals even if we must pay for it,” [Ana María Cetto] says. “Ultimately, our resources go to rich countries so our researchers can have prestige in the community.”

Nice piece on open access in Latin America.

www.science.org/content/arti...

Super excited to preprint our work on developing a Biomolecular Emulator (BioEmu): Scalable emulation of protein equilibrium ensembles with generative deep learning from @msftresearch.bsky.social ch AI for Science.

www.biorxiv.org/content/10.1...

Covalent Fragments Acting as Tyrosine Mimics for Mutant p53-Y220C Rescue by Nucleophilic Aromatic Substitution The tumor suppressor p53 is frequently mutated in human cancers. The Y220C mutant is the ninth most common p53 cancer mutant and is classified as a structural mutant, as it leads to strong thermal des...

Does someone have a good post scheduler for bluesky? Usually using @fedica.com, but if I post a link to a paper there, it does not generate a preview, whereas if I directly post the same link, it does. E.g. the preview below did not work with fedica. pubs.acs.org/doi/10.1021/...