Example Projects
Applied software systems for conservation planning, biodiversity informatics, and ecological research.
Amplicon Sequence Variant Registry
A web platform for managing and exploring eDNA data across ocean monitoring projects. Developed for the Smithsonian Institution and Jonah Ventures, it integrates taxonomic assignment, spatial analysis, and standardized biodiversity export workflows.
optimTFE
An open-source R package for multi-species spatial conservation prioritization, implementing a stochastic greedy algorithm to optimize recovery areas. Applied to threatened species planning in Hawaiʻi and originally published in Conservation Biology.
Laboratory Information Management System
A cloud-native laboratory information management system (LIMS) for tracking environmental DNA samples from client intake through DNA extraction, assay processing, and reporting. Built as a modular R Shiny application backed by a custom API deployed to AWS Lambda with DynamoDB.
MitoPilot
A reproducible mitogenome assembly and annotation system integrating Nextflow orchestration, containerized bioinformatics tools, and a database-backed Shiny interface. Designed for scalable genome skimming workflows across HPC and cloud environments.
Conservation Expert Feedback Platform
An interactive web application that captures structured feedback from conservation experts, improving species distribution models and planning data for landscape-scale optimization.
Conservation Footprint Manager
A collaborative Shiny application for fine-tuning and managing species conservation footprints across multiple taxonomic groups in Hawaiʻi.
Termion
A Rust-based terminal interface for real-time monitoring and control of Oxford Nanopore sequencing runs. Streams live telemetry via gRPC and enables SSH-based oversight of sequencing operations in production environments.
gghoneycomb
An open-source R package extending ggplot2 to create honeycomb-style hexagonal waffle charts for proportional data visualization. Originally developed to visualize plant species abundance in honey using eDNA, the package combines domain-driven design with graph-based layout algorithms.
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