David O'Connor
@david--oconnor.bsky.social
Embedded engineering, computational chemistry, molecular biology. Etc.
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
- Molchanica
- MolMechanica
- MolMotus
- ChemForma
December 18, 2025 at 5:31 PM
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
- Molchanica
- MolMechanica
- MolMotus
- ChemForma
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/la...
#RustLang #chemsky #ORCA 🧬🖥️
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...
docs.rs
November 25, 2025 at 2:51 PM
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/la...
#RustLang #chemsky #ORCA 🧬🖥️
Reposted by David O'Connor
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.
This was NOT AI as how the public sees "AI", and this is disingenuous.
November 23, 2025 at 9:21 AM
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.
This was NOT AI as how the public sees "AI", and this is disingenuous.
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
🧬🧪🖥️
www.athanorlab.com
Athanor — Structural Biology Software
Powerful interactive tools for exploring biological systems.
www.athanorlab.com
November 11, 2025 at 1:20 AM
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
🧬🧪🖥️
www.athanorlab.com
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
www.quantamagazine.org
Science and Math News | Quanta Magazine
Illuminating mathematics, physics, biology and computer science research through public service journalism.
www.quantamagazine.org
November 4, 2025 at 6:00 PM
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
www.quantamagazine.org
Reposted by David O'Connor
I have been charged in a federal indictment sought by the Department of Justice.
This political prosecution is an attack on all of our First Amendment rights. I’m not backing down, and we’re going to win.
This political prosecution is an attack on all of our First Amendment rights. I’m not backing down, and we’re going to win.
October 29, 2025 at 4:55 PM
I have been charged in a federal indictment sought by the Department of Justice.
This political prosecution is an attack on all of our First Amendment rights. I’m not backing down, and we’re going to win.
This political prosecution is an attack on all of our First Amendment rights. I’m not backing down, and we’re going to win.
I'm adding an organic molecule editor to Daedalus. The party trick: Fully integrated and interactive "real-time" dynamics.
October 13, 2025 at 2:33 PM
I'm adding an organic molecule editor to Daedalus. The party trick: Fully integrated and interactive "real-time" dynamics.
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
Thx to the compiler team for including this in std on v1.89
#RustLang
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.
github.com
August 7, 2025 at 8:19 PM
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
Thx to the compiler team for including this in std on v1.89
#RustLang
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/David-OConno...
#RustLang
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
github.com
July 10, 2025 at 6:29 PM
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/David-OConno...
#RustLang
Ready to share my Bio Files rust lib. Parses molecule formats, electron density, and now Amber force field parameters.
github.com/David-OConno...
#RustLang 🧬💻
github.com/David-OConno...
#RustLang 🧬💻
GitHub - David-OConnor/bio_files: Read and write common biology file formats
Read and write common biology file formats. Contribute to David-OConnor/bio_files development by creating an account on GitHub.
github.com
July 1, 2025 at 7:12 PM
Ready to share my Bio Files rust lib. Parses molecule formats, electron density, and now Amber force field parameters.
github.com/David-OConno...
#RustLang 🧬💻
github.com/David-OConno...
#RustLang 🧬💻
I'm integrating molecular dynamics into Daedalus's docking logic. Improving the bio-files lib to load Amber force fields.
June 30, 2025 at 11:24 PM
I'm integrating molecular dynamics into Daedalus's docking logic. Improving the bio-files lib to load Amber force fields.
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...
Any feedback/desired features appreciated! #RustLang 🧪🧬🖥️
github.com/David-OConno...
GitHub - David-OConnor/daedalus: Protein and molecule viewer
Protein and molecule viewer. Contribute to David-OConnor/daedalus development by creating an account on GitHub.
github.com
May 22, 2025 at 12:34 PM
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...
Any feedback/desired features appreciated! #RustLang 🧪🧬🖥️
github.com/David-OConno...
Reposted by David O'Connor
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 🧪
#scicomm #nsf 🧪
May 2, 2025 at 4:45 PM
Reposted by David O'Connor
Right Now, most of the American can relate to this message from the 90's.
April 19, 2025 at 3:28 PM
Right Now, most of the American can relate to this message from the 90's.
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/David-OConno...
#rustlang
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.
github.com
March 22, 2025 at 11:17 PM
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/David-OConno...
#rustlang
Reposted by David O'Connor
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/shorts/sLLh4...
Gotta save science!
YouTube video by Science IRL
youtube.com
January 24, 2025 at 12:01 PM
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/shorts/sLLh4...
I published a Barnes Hut algorithm library in Rust, for fast N-Body simulations: crates.io/crates/barne...
#RustLang
#Cosmology
#RustLang
#Cosmology
crates.io: Rust Package Registry
crates.io
January 18, 2025 at 6:06 PM
I published a Barnes Hut algorithm library in Rust, for fast N-Body simulations: crates.io/crates/barne...
#RustLang
#Cosmology
#RustLang
#Cosmology
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/David-OConno...
#RustLang
GitHub - David-OConnor/graphics
Contribute to David-OConnor/graphics development by creating an account on GitHub.
github.com
January 2, 2025 at 5:46 PM
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/David-OConno...
#RustLang
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
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 - David-OConnor/corvus
Contribute to David-OConnor/corvus development by creating an account on GitHub.
github.com
December 24, 2024 at 3:24 PM
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
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
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
#RustLang
na_seq - Rust
API documentation for the Rust `na_seq` crate.
docs.rs
December 20, 2024 at 2:29 PM
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
#RustLang
Reposted by David O'Connor
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 😷
Wild animal populations, on land and at sea, are collapsing. Species which existed on this Earth for millions of years are no more. It is a moral abomination for one species to seal the fate of millions of others. We need to fix it. My latest: www.donotpanic.news/p/who-will-s...
Who Will Speak For The Animals?
Wild animal populations are in free-fall, the average population size now nearly 75% smaller than just fifty years ago.
www.donotpanic.news
December 11, 2024 at 9:59 PM
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 😷
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.
December 1, 2024 at 6:55 PM
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.
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
Let me know what you think! I plan to keep adding features.
#Genomics #Bioinformatics #MolecularBiology
GitHub - David-OConnor/plascad
Contribute to David-OConnor/plascad development by creating an account on GitHub.
github.com
December 1, 2024 at 3:08 PM
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
Let me know what you think! I plan to keep adding features.
#Genomics #Bioinformatics #MolecularBiology