Kevin Bonham, PhD
I am an assistant professor at Tufts Medical Center with nearly 11 years in computational biology and bioinformatics, much of that time spent coding in Julia. I study the relationship between the gut microbiome and human development. I am a co-maintainer of the BioJulia organization and maintain or contribute to packages in the Biology, Data, Ecology, and Statistics ecosystems, and have worked on educational material for Pumas.ai and JuliaHub.
Sessions
The BioJulia organization began as Bio.jl circa January 2014 (julia v0.2 era) and has grown into a loosely organized collection of packages for computational biology, from plotting protein structures (BioMakie.jl) to performing matrix manipulations on single-cell RNA sequencing data (SingleCellProjections.jl) to low-level biological file type I/O (Automa.jl, FASTX.jl, XAM.jl). Here, we will provide a brief history of the Org and recent efforts to provide more structure for the community, as well as growth areas and a vision for the future.
Spatial transcriptomics (sTx) is a cutting edge technology combining microscopy and high-throughput sequencing or molecular probes to measure transcription in the context of cells within their tissue context, enabling researchers to achieve single-cell resolution and identify spatial relationships between cell types. While this technology opens up many new avenues for investigation, proprietary analysis applications provided by the manufacturers of sTx machines are typically slow (often requiring cloud-based compute), feature-poor, and do not generalize across technologies. SpatialOmics.jl is a new package that combines functionality from JuliaImages, JuliaGeo, and JuliaData to offer open source and extensible end-to-end analysis tools for spatial 'omics applications.