This page lists various pieces of software I have developed. Although usability may vary widely, everything is still maintained and should be functional.
Genetics
Moonshine.jl
Ancestral recombination graph inference in Julia. This package's primary objective is to provide user-friendly facilities for fast model-based ARG inference. As shown in the quickstart guide, even a first-time Julia user can infer ancestries from a sample in a few lines of code. Conveniently, samples can be generated directly from msprime without ever leaving Julia's REPL. Genealogies sampled by our package are tightly integrated with Julia's graph ecosystem making their treatment as graph-theoretical objects easy and natural. At the moment, Moonshine is not quite ready for prime time. However, we aim for integration with OpenMendel in the near future in order to streamline data acquisition and analysis.
Hooch.jl
Phenotype modeling via algebraic treatment of the ancestral recombination graph. Not public yet!
Lineage
A small Asymptote library to simplify drawing ancestral recombination graphs. Still a work in progress, but very usable.
Containers
container-waypipe
Base image to serve graphical applications via Waypipe and/or X11 forwarding. Built on top of Alpine Linux, it runs an SSH server that is conveniently configured to accept the user’s certificate authority. The readme contains somewhat general user-friendly instructions on how to set up CA authentication for ssh on a small network; worth a read if you are interested in those kinds of things.
Julia
JCheck.jl
Property-based testing in Julia. Below is the talk in which I presented it at JuliaCon 2022.
The package is currently usable and available in Julia’s general registry. Its development is on hold however because of lack of time on my part. I intend to pick up where I left in the near future.