The Bonham lab is committed to open, reproducible science, and to the Julia scientific computing ecosystem as a home for high-performance, expressive bioinformatics tooling. We develop and maintain Julia packages that fill gaps in the microbiome and spatial omics analysis landscape, and contribute to the broader Julia community.
We "eat our own dogfood", building the tools that we use or want to use in our own lab. Microbiome.jl and BiobakeryUtils.jl — provide data structures for working with microbial community profiles and utilities for parsing the output of the bioBakery suite of metagenomic analysis tools, including MetaPhlAn, HUMAnN, and Kneaddata. Both are registered Julia packages maintained under the EcoJulia organization. A more recent effort, SpatialOmics.jl, provides analogous infrastructure for spatial transcriptomics data.
Beyond analysis packages, the lab also maintains ObsidianXranklin.jl, the tool that powers this wiki by syncing notes from an Obsidian vault to a Franklin.jl-based static site. Research software should be written to be shared — with good documentation, open licenses, and attention to the needs of users outside the lab.