Dev
A showcase and list of the tools I've built, along with notes on my development work.
Dev environment
My environment is managed declaratively with Nix (and Home Manager), and on top of that I lean on tools like uv and pixi.
I used to be a Python person, but since I started working with AI coding agents I've stopped being precious about languages — I pick whatever fits the task, and lately I lean on Zig a lot. I mostly let the agents handle the implementation, using Codex and Claude Code together.
Rather than inventing a new algorithm from scratch, I prefer to build on and extend what already exists. I also whip up little utilities and extensions whenever an idea strikes.
GitHub activity
As of 2026/06 (built with GitHub Readme Stats)
Dev blog
No dev posts yet.
Contributions
- RosettaCommons/atomworksContributor
A generalized computational framework for biomolecular modeling.
- cbouy/mols2gridContributor
An interactive viewer for 2D molecular structures powered by RDKit.
- dbcls/togomcpContributor
MCP server for the RDF Portal.
- chemical-space-explorerAdopted into marimo's official gallery
An interactive chemical-space explorer notebook, adopted into marimo's official examples gallery.
Tools & extensions I've built
- zsasaZig
High-performance SASA calculation in Zig, with Python bindings.
Structural bioinformatics - ztrajZig
High-performance molecular dynamics trajectory analysis library.
Structural bioinformatics - zdsspZig
DSSP secondary-structure assignment, implemented in Zig.
Structural bioinformatics - mmcif-dict-cliZig
CLI tool for querying mmCIF/PDBx dictionary definitions.
Structural bioinformaticsmmCIFCLI - chimerax-rdkit-conformerPython
Generate 3D conformers from SMILES/InChI directly in ChimeraX using RDKit.
ChimeraXChemoinformatics - mmcif-rainbow-vscodeTypeScript
Rainbow syntax highlighting and dictionary hover for mmCIF files in VS Code.
Editor extensionmmCIF - mmcif-rainbow-neovimLua
Rainbow column highlighting for mmCIF files in Neovim.
Editor extensionmmCIF - pdb-mine-builderPython
Build a Mine-schema PostgreSQL database from PDB data, with RDKit chemical search.
DatabaseStructural bioinformatics - ccd2rdmolPython
Lightweight library/CLI to convert PDB CCD files into RDKit molecules.
ChemoinformaticsCLI - chemspace-marimoPython
A chemical space viewer built with marimo.
Chemoinformatics