Tools & Workflows

Software and tools I use for clinical AI development, evaluation, and biomedical research.

Agents & Clinical AI

Claude Code - Where most of my work happens. Multi-repo orchestration, custom skills, subagents for parallel search and review.

Claude Agent SDK - Building harness capabilities: orchestrator/subagent structure, tool definitions, deterministic gates.

AWS Bedrock / Azure AI Foundry - Model access across families, useful for cross-family de-confounding.

MCP servers - Custom ones where the integration matters: Zotero for the shared library, a docs server for architecture knowledge.

pytest - Regression-first. Every bug fix starts with a test that reproduces the failure through the same gate the runtime uses.

LLM-as-judge pipelines - Custom judges calibrated against clinician adjudication, with positive and negative controls.

DSPy / GEPA - Prompt optimization on held-out splits.

Docker + AWS Fargate - Containerized eval runs, sharded for parallelism, with cost circuit breakers.

Python - Primary language. Polars over pandas, plus numpy, scipy, statsmodels.

R - Secondary, for specialized packages (MatchIt for matching, SAIGE for genetic association testing).

Streamlit - Fast internal review tools for clinical adjudication workflows.

Jupyter - Exploratory analysis and reproducible reporting.

Carried over from the NIH years, still what I reach for when the question is genetic.

PLINK2 - Genetic data QC and association testing.

SAIGE - Mixed model association testing at biobank scale.

GATK - Variant calling pipelines, parallelized with GNU parallel.

bcftools/samtools - VCF manipulation and processing.

Google Cloud - dsub for batch job orchestration at scale.

BigQuery - OMOP CDM queries against All of Us.

GNU parallel - Simple but powerful parallelization.

Notion - Research notes, literature tracking, and a daily work log.

Zotero - Reference management, wired into Claude via a custom MCP server.

LaTeX - Documents where layout matters and I want the source diffable.

This page inspired by uses.tech. Last updated July 2026.