Uses ChimeraX contact prediction to create circos-style plots for protein and DNA structures (.cif or .pdb files)

A feature-rich offline kanji/hanzi exploration tool in the terminal (or a simple window), aimed at scholars and enthusiasts

Using embeddings to find poorly conserved orthologs of synaptonemal complex proteins in Pristionchus

Amber or CHARMM relaxation of AF3 structures including protein, nucleic acid, PTMs, ligands

Collection of plotting apps for sequence, umap visualizations, etc

Attempting to create code that plots MS/MS spectra with y/b ions etc

simple content-showing app in ncurses

Plots UMAP <x,y> for DNA, shows chromosome position and selected sequence as text

utils to get minimal prefixes of string lists

Simulations of asymmetric chromosome partitioning

Config files for my GitHub profile.

Miscellaneous quantitative routines and scripts for analyzing Deltavision images

Exploring 12-mer distribution in genomes

Visualization and comparison of protein and DNA sequence embeddings

literature-scanning robot for mastodon and twitter

Convert your BibDesk library to a format that can be imported *with attachments* into Zotero (translator included)

Routines for averaging the intensity of 3D fluorescence microscopy images in concentric shells defined by DAPI staining of nuclei

Exploring questions raised by bees and zero by this paper in Science: (doi)10.1126/science.aar4975

C simulation of SYP-1 phosphorylation

For the ILAS Practical Computing for Biologists class

Use Slack to get notified of new papers added to your Zotero group library, and who added them

fvlib is a minimalistic 3D point-spring solver library for Processing and Java, built with high-performance in mind.