iiinova — where your digital self keeps evolving

David O'Connor @david--oconnor.bsky.social · 12/10/2026

> I'm begging the media to show a shred of journalistic integrity I have long lost confidence in their ability to do this broadly.

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David O'Connor @david--oconnor.bsky.social · 11/10/2026

There will be a death (Or something close to it), and rebirth. Through this, A will advance in a Kuhnian leap - habits will be broken as incentives changed, and paths ignored will be explored. Insights will flow to the sciences. I'm excited! 2/2

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David O'Connor @david--oconnor.bsky.social · 11/10/2026

The crisis in Math exposes a conflation between A: The broad concept of [abstract] Mathematics and B: The contemporary Mathematics culture and community. This crisis is directly in B only. B will adapt: In how it attributes value, status, hierarchy, and career. 1/2

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David O'Connor @david--oconnor.bsky.social · 11/10/2026

The streamlined choice this vid highlights nails it - and I like the small parking lots. Same reason - faster process; less walking through parking lots, isles etc. I wonder if the cashier forced-friendliness rubs off on customers? People seem happy to be their compared to other stores.

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David O'Connor @david--oconnor.bsky.social · 10/10/2026

Of interest, (or the opposite?) KCD2 has the most realistic (superficially?) of any game I've played.

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David O'Connor @david--oconnor.bsky.social · 08/10/2026

These embedded crates are peak software quality. Thank you for making durable software that serves as a foundation: - cortex_m - probe_rs - defmt - svd2rust - heapless #rustlang

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David O'Connor @david--oconnor.bsky.social · 08/10/2026

Nordic scooped themselves on the nRF53 - there's no reason to use one now that the 54L and H are out! It had a small window where it made sense, but I suspect most people never picked it up, and will jump 52 -> 54.

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David O'Connor @david--oconnor.bsky.social · 08/10/2026

I <3 rust, but it's not *screamingly performant*; it just starts you on level ground with C, C++ etc. Ie the language is not the limit, but that's it.

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David O'Connor @david--oconnor.bsky.social · 08/10/2026

This misses the point: Shallow mimicry isn't what makes software like Photoshop enduring. A big chunk (Not the only; marketing inertia play a role too) is being honed over years and decades to meet user's needs.

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David O'Connor @david--oconnor.bsky.social · 03/10/2026

Well said! Broadly, I especially like your point about BioArxiv's stance, as a generalization (And both are IMO a move in the right direction). Weeding out a majority of spam submissions should be straightforward through bans. Associating bans with identities has subtleties, but this doesn't disQ it

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David O'Connor @david--oconnor.bsky.social · 02/10/2026

Could you elaborate on this? Sorry; missing some context.

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David O'Connor @david--oconnor.bsky.social · 01/10/2026

I am pretty sure everyone who ignored the warnings over the years and decades and held is now doing quite well! This is a wild take given the charts.

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David O'Connor @david--oconnor.bsky.social · 19/09/2026

I set up a website to make it easy to run common structural Bio/ML tools like RFDiffusion, structure prediction, and sequence prediction tools (ESMFold, ProteinMPNN, Chai-1 etc). athanortools.com I'm using this for a specific protein design project and learning journey.

athanortools.com

Athanor Bio Tools

Athanor Bio Tools provides small web interfaces and JSON APIs for computational biology software.

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David O'Connor @david--oconnor.bsky.social · 14/09/2026

Stated another way: This is a strawman.

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David O'Connor @david--oconnor.bsky.social · 14/09/2026

Hey! The US military works with, is allied with, and coordinates with many Muslim nations and people. Prejudices (Media-stoked included) of some common people are not relevant here. The WSO in the interview is, by coincidence, a devout Christian; more so than most in the line of work. That's it.

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David O'Connor @david--oconnor.bsky.social · 12/08/2026

I've heard this argument for not having helmet laws for bicycles (In Europe primarily IIRC?) for years!

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David O'Connor @david--oconnor.bsky.social · 10/08/2026

I made a CLI program, Rust and Python lib that makes it easy to install and run bio / drug design tools. (structure pred, seq pred etc): github.com/David-OConno... `pip install bio_tools_app` `bio_tools install boltz2` `bio_tools run boltz2 --version` 🧬🖥️

github.com

GitHub - David-OConnor/bio_tools

Contribute to David-OConnor/bio_tools development by creating an account on GitHub.

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David O'Connor @david--oconnor.bsky.social · 02/08/2026

Rust is a fantastic language that earns my choice by virtue of pro/con balance. Thoughtful syntax, nice enums, great error messages, exquisite tools. I still regularly hear "If you're not using ownership abstractions, and safety-oriented design, why use it?". BC it's a nice lang! #rustlang

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David O'Connor @david--oconnor.bsky.social · 30/07/2026

The Wilson and Fagles translations are my favorites! Eye or audio. (Claire Danes and Ian McKellen narrators respectfully; both crush it). I did some back-to-back listens. The former is more plain-spoken; the latter uses more flowery ("Literary"?) language.

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David O'Connor @david--oconnor.bsky.social · 23/07/2026

New Molchanica release. Highlights: - OpenDDE GUI interface for protein structure prediction - Built-in Mol DBs (HMDB; ChEBI) - Misc UI improvements github.com/David-OConno... 🧬🖥️

github.com

GitHub - David-OConnor/molchanica: Protein and molecule viewer, editor, simulator

Protein and molecule viewer, editor, simulator. Contribute to David-OConnor/molchanica development by creating an account on GitHub.

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David O'Connor @david--oconnor.bsky.social · 07/07/2026

Typst too! Big one; best in class, and what an important class!

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David O'Connor @david--oconnor.bsky.social · 07/07/2026

Mathematica slaps and should be used more often! An incredibly powerful lang/tool honed to perfection over decades. CUDA; the subset of C++ it uses to make integrating host and device code for kernels and tiles. Excited about the tile interface! Those are the only ones which comes to mind.

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David O'Connor @david--oconnor.bsky.social · 06/07/2026

A shell/terminal application I've been working on. Makes it easy to access commonly-used and recent dirs and commands. Bookmarks, syntax highlighting, practical history and autocomplete, ssh integration. github.com/David-OConno... #rustlang

github.com

GitHub - David-OConnor/shell: A terminal/shell designed for convenience

A terminal/shell designed for convenience. Contribute to David-OConnor/shell development by creating an account on GitHub.

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David O'Connor @david--oconnor.bsky.social · 27/06/2026

Unfortunately, we need to tune mute/block/custom-feed filters to be aggressive. This will result in false positives, but the spam rate is too high. In other words: I think you have to immediately block or mute an account if your first interaction with it is something like the one you're describing.

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David O'Connor @david--oconnor.bsky.social · 15/06/2026

I wonder about, when possible, for digital displays, using a 3d model (rendering of a globe). Maybe have a few snapshots at different angles. Dodges the problem, but can't see the whole globe at once, and is dependent on the current rotatation.

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David O'Connor @david--oconnor.bsky.social · 04/06/2026

This reminds me both of people complaining about Aloy + Ciri's appearances in pre-release promo material, and Youtube's plan to add real names to comments a while back in the hope it would reduce toxicity.

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David O'Connor @david--oconnor.bsky.social · 25/05/2026

She ran against 2 other left candidates in a district she was new to.

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David O'Connor @david--oconnor.bsky.social · 11/05/2026

Following this to its logical conclusion, given that many or most software engineers have adopted LLMs into their workflows to varying degrees: Have you lost respect for all of your colleagues? It seems like this is something that will have to be reconciled.

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David O'Connor @david--oconnor.bsky.social · 11/05/2026

Uhoh... I just ordered 60mL syringes, filters, and primers for these genes: 16S, 18S, COI, ITS, 12S, MatK and rbcL... #ecology #environment

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David O'Connor @david--oconnor.bsky.social · 09/04/2026

Planes fly because their wing leading edges are packed with bumblebees. It works like the Hubble lens repair.

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David O'Connor @david--oconnor.bsky.social · 06/04/2026

Rust on some microncontrollers (ARM Cortex-M, ESP RISC-V especially) is a nice experience. Much easier build experience; i.e. you just do `cargo run` and it builds/flashes/debugs. You can use whatever IDE you want, e.g. one designed for the language instead of the hardware.

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David O'Connor @david--oconnor.bsky.social · 06/04/2026

Red Bull Wololo 2026 finals: So excited! Hera is the hero and the one to beat, but I think Liereyy can do it

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David O'Connor @david--oconnor.bsky.social · 06/04/2026

I just added GROMACS integration to my Molchanica program. It provides a GUI interface to launch GROMACS runs (Or its own MD backend) for arbitrary molecules, then immediately view results. Also works as a general playback tool now, for TRR, XTC, and DCD. 🧬 & 🖥️ www.athanorlab.com/docs

athanorlab.com

Molchanica Documentation

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David O'Connor @david--oconnor.bsky.social · 25/03/2026

I would like to reflect upon how both ORCA and GROMACS documentation are S-tier. And their logos are exceptionally tasteful

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David O'Connor @david--oconnor.bsky.social · 13/03/2026

An open-ended question which may help crystallize this: Does a table saw materially improve your life? A CNC machine? A torque wrench? A low-level programming language? PCR? A nanopore sequencer? A multichannel pipette?The answer will depend on the person, and the definition of "materially improve"

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David O'Connor @david--oconnor.bsky.social · 13/03/2026

I use LLMs to make code changes. This includes fixing errors, and integrating known algorithms. Recent example: Creating ribbon meshes for protein rendering. You might talk to software engineers - I described one of the more restrained patterns. The Overton window spread on this topic is wild!

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David O'Connor @david--oconnor.bsky.social · 08/03/2026

Default pub struct fields. I end up having to make almost all of mine pub, with the style I use. This isn't viable to do in a backwards compatible way, and it's not a limitation, but it would make an immediate readability across my code.

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