Web application that allows clinicians to quickly investigate mitochondrial mutations in sequenced or genotyped samples. Used worldwide for mitochondrial genetics research.

Django application that manages user authentication and presentation of bioinformatics deliverables. Streamlines report delivery for core facilities.

Integration Site Pipeline and Database - comprehensive toolset for managing viral integration site data processing, annotation, and analysis.

A JSON-based markup language and toolchain for describing real-time programs that coordinate parallel tracks of work with resource constraints, timing dependencies, and flexible execution patterns. Includes a CLI runner, web visualizer, and MCP server for AI-assisted schedule generation.

2025

R package for dichotomous identification keys. Build a key from a plain spreadsheet with photos, draw it as a box diagram, or turn it into an offline web wizard for the field; also imports FishBase keys and generates keys from photos (CLIP/BioCLIP), sequence alignments and trait matrices. Includes an illustrated key to Montana’s native broadleaf trees.

2020

A curated list of reproducible research case studies, projects, tutorials, and media. Community-driven resource with 356+ stars.

2017

Beginner’s tutorial to Snakemake workflow management system. Popular educational resource with 70+ stars.

2014

RNA-Seq Snakemake example with Jekyll homepage creation. Complete workflow demonstration with 20+ stars.

2014

A better seqLogo implementation for creating sequence logos in R. Enhanced visualization tool with 12+ stars.

2011

Public Ancestry Informative Markers (AIMs) dataset and tools for population genetics analysis.

2022

Validation of published GWAS studies using OpenSNP volunteered data. Binderized for reproducible analysis.

2016

Node.js web-service wrapper for fetching pairwise BLAST alignments against a fixed reference.

2013

Analysis tool to measure popularity and usage of biological ontologies across scientific literature.

2020