Welcome to the Isom Lab on GitHub
We study how cells sense and respond to their environment, with a focus on acidity, dark proteins, and intercellular cooperativity and communication.
Software
New to the lab’s tools? Two short guides cover everything the tools below have in common: Setting up your computer, the one-time, no-typing setup (Mac or Windows), then Getting started with a lab tool — downloading, launching, updating and troubleshooting any of them.
Our tools are being packaged as installable Python projects. Released tools live in their own repositories under the isomlab organization; the remaining projects are documented here while they are migrated.
Released
- pHinder — ionizable-residue network and surface analysis for protein structures · project page
- pam_scanning — CRISPR/Cas9 guide RNA and chimera-insertion primer design across an ORF, with synonymous PAM silencing and BLAST+ off-target screening · v1.0.1 · Bioconda recipe under review
- bioleads — mine biomedical literature for enriched terms, co-occurrence networks, and Swanson-style hypothesis leads · v0.1.0
- litlog — local-first tracker for the papers you read and how they interconnect, written as LLM-trainable tagged text · v0.1.1
- vesicle_colocalization_quantifier — interactive two-channel vesicle co-localization for microscopy images · v1.0.0 · project page
- bpp_identifier — quantify bridges, projections and protrusions at cell–cell boundaries · v1.0.0 · project page
- vesicle_triangulator — reconstruct the topology of vesicle-transfer events by Delaunay triangulation · v1.0.0 · project page
Shared code
- isomlab — the three modules used by more than one tool: computational geometry and PDB/mmCIF parsing. Each released tool ships its own copy, so you do not need this to install or run them; it is the upstream source of truth where fixes are made.