We have released a number of software tools; here are some current and older tools. The ABD group primarily does software development in Rust, while the MEDFORD parser is written in Python. There are also some teaching tools here, developed for some of my courses.

Currently supported research software

clam is the Rust implementation of CLAM (Clustering, Learning, and Approximation on Manifolds) and includes the functionality of CHAODA for anomaly detection and CAKES for fast nearest-neighbor search $\rho$-nearest neighbor and $k$-nearest neighbor).

medford is a parser (with editor support, primarily for VS Code at present) for MEDFORD (MEtaData Format for Open Reef Data), a lightweight markup language for describing research artifacts.

TaqmanParser is a script for parsing TaqMan files, with SNP-calling rules specific to Plasmodium falciparum.

cluster-barcodes is a Haskell program for clustering Plasmodium falciparum barcodes based on longitudinal or time-invariant barcode similarities.

abd-distances is a Python wrapper around the distances crate which is part of CLAM. It provides drop-in, api-compatible replacements for the distance functions in scipy.spatial.distance.

Older research software

MICA is a compressively-accelerated metagenomic search tool (functionally similar to BLASTX) that speeds up BLASTX or DIAMOND search.

Teaching software

csc411-image is a very simplistic wrapper around the image crate for Rust. It is not intended for production use, but rather for use in some assignments in CSC 411 at URI.

rumdump is an objdump-like program for the "universal machine" used in CSC 411. It has some niceties like ANSI coloring of the binary representation of instruction words.