iiinova — where your digital self keeps evolving

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 · 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 · 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 · 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 · 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 · 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 · 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 · 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 · 16/02/2026

The Expedition 33 soundtrack may be my favorite album. The Une Vie trilogy, in particular, are masterpieces.

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David O'Connor @david--oconnor.bsky.social · 30/01/2026

Go home clippy, you're drunk! > warning: the loop variable `i` is used to index `lines` - for i in first_atom_line..last_atom_line { + for (i, <item>) in lines.iter().enumerate().take(last_atom_line).skip(first_atom_line) { #RustLang

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David O'Connor @david--oconnor.bsky.social · 24/01/2026

We hold ourselves in the US to a higher standard. The world now and through history has had more brutal leaders, more government-led violence. Authoritarians are common. That is no excuse for tolerating that behavior here; it's what sets us apart, and what has made me proud to be a US citizen.

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Radley Balko @radleybalko.bsky.social · 19/01/2026

At about the 35-second mark the officer says "IF YOU FUCKING MOVE I'LL FUCKING TASE YOU," followed immediately by "GET OUT OF THE FUCKING CAR RIGHT NOW." Which contradictory order are you supposed to follow, knowing that either could get you tased? Or worse? bsky.app/profile/petr...

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David O'Connor @david--oconnor.bsky.social · 16/01/2026

Nothing the Trump admin and his private army are doing is novel or unusual; they're just below the standard we have held ourselves to in the US.

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Radley Balko @radleybalko.bsky.social · 15/01/2026

This is what they’ve wanted all along. This is the goal.

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David Burbach 🇺🇸 @dburbach.bsky.social · 15/01/2026

Non-protesting dad just trying to hustle his kids, as young as 6mo, out of the neighborhood. ICE threw a flash-bang INTO HIS car, all 6 kids in the hospital now. If anyone wondered how things turn against occupying armies there's a case study playing out in front of you.

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Status Coup News @statuscoupnews.bsky.social · 15/01/2026

🚨"This is nuts! What the f*ck is going on, this is insane! ICE is just trying to scare people; they tell you it's only immigrants—it's f*cking anybody!" -furious Minneapolis resident tells our @zdroberts.bsky.social after ICE shot a man in the leg tonight. LIVE NOW ⬇️

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Don Moynihan @donmoyn.bsky.social · 10/01/2026

This is the second time in three months a DHS agent called a US citizen a "bitch" as he shot her. donmoynihan.substack.com/p/whos-threa...

The video also allegedly shows the CBP agent saying “Do something, bitch” before shots were fired. In private Signal chats, the CBP agent boasted to other officers: “I fired 5 rounds and she had 7 holes. Put that in your book boys.” If he felt comfortable enough communicating that to fellow employees, it speaks to an irredeemable organizational culture.

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Radley Balko @radleybalko.bsky.social · 08/01/2026

Yes, JD. Let’s ask them if they think a stay at home mom, avowed Christian, and widow of a veteran deserved to be shot in the face and left to bleed out in her own car after dropping her 6-year-old off at school, for the crime of looking out for her neighbors. Let’s ask everyone running for office.

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Radley Balko @radleybalko.bsky.social · 08/01/2026

A 6-year-old just lost his mother. A woman was shot in the face in front of her wife. The swift, lockstep attempt to dehumanize and villainize Renee Nicole Good might be the most depraved thing we've seen yet from these ghouls and their supporters. These people are utterly fucking dead inside.

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David O'Connor @david--oconnor.bsky.social · 18/12/2025

Looking for help choosing a more unique name for my molecule viewer/editor/dynamics program. Thoughts on these? (Latin names age well, right?) - Molchanica - MolMechanica - MolMotus - ChemForma

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David O'Connor @david--oconnor.bsky.social · 25/11/2025

I added initial ORCA integration in bio_files. This makes it easy to integrate quantum chem workflows into applications written in Rust. I'm using it to integrate ORCA's geom opt and MD into software I'm writing. docs.rs/bio_files/la... #RustLang #chemsky #ORCA 🧬🖥️

docs.rs

bio_files::orca - Rust

For interop with the ORCA quantum chemistry software package. For example, This module constructs inputs for ORCA, and can either save them to disk, or run them directly if ORCA is available in the sy...

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Emily Hunt @emily.space · 23/11/2025

My family are useful canaries of what news the public actually sees from astro, and only yesterday did my mum ask me about a study (one article of many linked below) who said they "trained an AI" to simulate the Milky Way. This was NOT AI as how the public sees "AI", and this is disingenuous.

space.com

AI helps build the most detailed Milky Way simulation ever, mapping 100 billion stars

Simulating a billion years using previous best-resolution simulations would take almost 36 years of real computing time.

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David O'Connor @david--oconnor.bsky.social · 11/11/2025

Launched a new site for my structural biology tools. And made a new Daedalus release; can infer MD force fields for arbitrary molecules, and better solvent initialization. Fixes for viewing electron density too. 🧬🧪🖥️ www.athanorlab.com

athanorlab.com

Athanor — Structural Biology Software

Powerful interactive tools for exploring biological systems.

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David O'Connor @david--oconnor.bsky.social · 04/11/2025

Quanta Magazine is a treasure. It's one of the highest-quality existent journalism sources. Isn't trying to pump metrics, sell products, or trigger emotions. Respects the reader's intelligence. Exemplary of what news should be. www.quantamagazine.org

quantamagazine.org

Science and Math News | Quanta Magazine

Illuminating mathematics, physics, biology and computer science research through public service journalism.

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David O'Connor @david--oconnor.bsky.social · 13/10/2025

I'm adding an organic molecule editor to Daedalus. The party trick: Fully integrated and interactive "real-time" dynamics.

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David O'Connor @david--oconnor.bsky.social · 07/08/2025

Updated [lin-alg](github.com/David-OConno...) with 512-bit SIMD support (f64x8, f32x16). Std-compatible floats, Vec3, Vec4, and Quaternion types. Thx to the compiler team for including this in std on v1.89 #RustLang

github.com

GitHub - David-OConnor/lin-alg: Operations on matrices, vectors, and quaternions

Operations on matrices, vectors, and quaternions. Contribute to David-OConnor/lin-alg development by creating an account on GitHub.

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David O'Connor @david--oconnor.bsky.social · 10/07/2025

Released v2.0 of Stm32-HAL. This applies the latest PAC (Thanks stm32-rs team!), which allows better peripheral support, esp for L5, C0, G0, and H5. github.com/David-OConno... #RustLang

github.com

GitHub - David-OConnor/stm32-hal: This library provides access to STM32 peripherals in Rust.

This library provides access to STM32 peripherals in Rust. - David-OConnor/stm32-hal

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David O'Connor @david--oconnor.bsky.social · 01/07/2025

I'm integrating molecular dynamics into Daedalus's docking logic. Improving the bio-files lib to load Amber force fields.

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David O'Connor @david--oconnor.bsky.social · 22/05/2025

I published an open-source protein and ligand viewer. Goal: fast and easy-to-use. Long-term: a platform for docking and molecular dynamics. I'm gradually splitting it into standalone libs. Any feedback/desired features appreciated! #RustLang 🧪🧬🖥️ github.com/David-OConno...

github.com

GitHub - David-OConnor/daedalus: Protein and molecule viewer

Protein and molecule viewer. Contribute to David-OConnor/daedalus development by creating an account on GitHub.

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Reposted by David O'Connor

Molly Edwards, PhD @science-irl.bsky.social · 02/05/2025

Yesterday Tr*mp froze all NSF funds, today he announced a 56% budget cut. This is going to devastate science in the US. I've spent the morning calling my reps to raise hell and applying for jobs as it's clear I can't sustain my freelance scicomm business on NSF funding anymore (1/n) #scicomm #nsf 🧪

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Saganism @sagan.bsky.social · 19/04/2025

Right Now, most of the American can relate to this message from the 90's.

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David O'Connor @david--oconnor.bsky.social · 22/03/2025

I updated my vector and quaternion lib with SIMD support. e.g. `Vec3x8`, `Quaternionx8` etc types. Works on stable rust. Uses `f64x4` etc types and syntax similar to `core::simd`, but on stable rust. github.com/David-OConno... #rustlang

github.com

GitHub - David-OConnor/lin-alg: Operations on matrices, vectors, and quaternions

Operations on matrices, vectors, and quaternions. Contribute to David-OConnor/lin-alg development by creating an account on GitHub.

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Molly Edwards, PhD @science-irl.bsky.social · 24/01/2025

I made this video about action steps you can take to speak up for the NIH 🧪 The comments are nottttt passing the vibe check rn but at least the trolls are driving views: youtube.com/shorts/sLLh4...

youtube.com

Gotta save science!

YouTube video by Science IRL

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David O'Connor @david--oconnor.bsky.social · 18/01/2025

I published a Barnes Hut algorithm library in Rust, for fast N-Body simulations: crates.io/crates/barne... #RustLang #Cosmology

crates.io

crates.io: Rust Package Registry

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David O'Connor @david--oconnor.bsky.social · 02/01/2025

I open-sourced my 3D visualization framework. It's an integration of GUI, and WGPU with a simple engine. I use it to make applications that include both a GUI, and 3D graphics, generally for scientific visualizations. github.com/David-OConno... #RustLang

github.com

GitHub - David-OConnor/graphics

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

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David O'Connor @david--oconnor.bsky.social · 24/12/2024

I open-sourced my quadcopter flight-controller firmware: github.com/David-OConno... It supports control radios, OSD, GPS, acro and attitude flight modes. Uses STM32 flight controllers. I released the code as a demo of how to do this in rust. #RustLang

github.com

GitHub - David-OConnor/corvus

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

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David O'Connor @david--oconnor.bsky.social · 20/12/2024

I'd like to share a bio primitives lib I've been working on and using: docs.rs/na_seq/lates.... It has data structures and utilities for nucleotides, amino acids, and related. Open to any and all critique and suggestions! Currently using it in my plasmid editor. #RustLang

docs.rs

na_seq - Rust

API documentation for the Rust `na_seq` crate.

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luckortraining @luckortraining.bsky.social · 11/12/2024

Per @natebear1.bsky.social the most profoundly ethical question human society can ask itself is how billions of living beings who have no agency to physically alter their world CAN LIVE SAFELY alongside the one species that does #science🔬💉 #EvoSky 🌎 #EcoSky #Conservation 🛟 #socialjustice 😷

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David O'Connor @david--oconnor.bsky.social · 01/12/2024

My favorite quality of #rustlang: Mutability semantics. It may be the only language that allows mutation to happen only explicitly, *and* with simple syntax. Including `&mut` in a fn signature seems obvious in hindsight, and I miss it elsewhere.

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David O'Connor @david--oconnor.bsky.social · 01/12/2024

I'm building an OSS plasmid editor - PlasCAD: github.com/David-OConno.... Small standalone application; emphasis on performance, ease, and practical workflows. It sets up and QCs primers too. Let me know what you think! I plan to keep adding features. #Genomics #Bioinformatics #MolecularBiology

github.com

GitHub - David-OConnor/plascad

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

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