Project Showcase
Explore our portfolio of bioinformatics projects, web applications, and consulting work.
Beginning Python for Bioinformatics
Educational repository with code examples from the blog series teaching Python programming for bioinformatics applications.
WormBase REST API
RESTful API to the WormBase Datomic database, providing data to the WormBase website on a per-widget basis and powering tools like BLAST.
vcfclick
Small VCF databases, one per cohort. Embedded ClickHouse engine for variants, embedded DuckDB for annotations, MCP natural-language layer, and an optional local web UI. Trio/family analysis and a GATK3-CombineVariants reimplementation. No daemon, no server.
Alliance of Genome Resources MCP Server
Model Context Protocol server enabling Claude Code to access Alliance of Genome Resources genomics tools and data.
BlueGenes
Friendly next-generation interface for genomic data discovery powered by InterMine. Modern ClojureScript/re-frame application.
abifpy
Python module for reading Applied Biosystems .ab1 trace files (Sanger sequencing chromatograms).
ISCN Authenticator
Validator for ISCN (International System for Human Cytogenomic Nomenclature) karyotype strings used in clinical genetics.
Python SQLite wxPython Example
Tutorial demonstrating how to use wxPython and SQLite to create simple database GUIs in Python.
Clinical NGS Pipelines
Production pipelines for clinical next-generation sequencing including variant calling, annotation, and reporting for diagnostic labs.
Variant Database Systems
Design and implementation of variant databases for clinical genomics labs, including integration with laboratory information systems.
InterMine Data Warehouse
Contributions to InterMine, a powerful open source data warehouse system for integrating biological data.
dbNSFP-RAG
Retrieval-augmented pipeline over the dbNSFP functional-prediction dataset for natural-language variant-annotation queries. FAISS vector store with a local Ollama model.
PopGeneS2
28-module interactive population-genetics simulation suite running entirely in the browser. A modern reimplementation of the original PopGene.S desktop package.
bioinfo_health
Mines GitHub URLs from PubMed abstracts and scores scientific-software repository health across nine dimensions, surfacing results in a web app.
code-review-7b
A fine-tuned 7B code-review LLM: tree-sitter code parsing, trained with Apple MLX, served via llama-cpp + FastAPI, with the GGUF model published to HuggingFace.
strandline
Compliance and code-acceptance platform with a hash-chained, tamper-evident audit ledger and OIDC/PKCE authentication. FastAPI + Vue 3 + Celery.
Technologies & Skills
Full stack of tools and technologies across our projects