Projects

Each one starts with a bottleneck someone in the lab actually had. Software and models first; the research projects behind them follow.

CodeMay 2026 – Oct 2026

FDE Research

Nine agent skills behind one entry point that turn a vague enterprise AI request into a project plan you can defend: evidence first, human sign-off last.

  • 9 specialist skills behind one /fde-research entry
  • 4 deliverables: findings, proposal, technical design, delivery plan and quotation
  • Human the agent drafts and checks; a person signs off
  • Enterprise AI
  • Agent Skills
  • Claude Code
  • Python
  • Markdown

CodeMar – Aug 2026

NGS Intelligent Workflow Assistant

An AI agent that lets bench scientists run TCR and antibody sequencing pipelines on a shared HPC cluster by describing what they need in plain language.

  • < 5 min from request to submitted job, no command line
  • Audited every run reproducible and traceable by default
  • Skills new analyses plug in as skills, not rewrites
  • Harness
  • Vibe Coding
  • Claude Agent SDK
  • MCP
  • TypeScript
  • React
  • Node.js
  • SLURM
  • HPC

Research + codeSep 2025 – Mar 2026

TCR Pathology Classifier

A protein language model that ranks T-cell receptors by the disease they likely recognize, so the lab screens a short list instead of a whole repertoire.

  • 35% validated hit rate among model-prioritized clones (11 of 31)
  • ~10× smaller search space, from ~7,000 clones to 572
  • 8 wk → 10 d from raw repertoire to a testable shortlist
  • Transformer
  • NGS
  • PyTorch
  • ESM2
  • Hugging Face
  • Flask
  • pandas
  • scikit-learn

Code2026

Full-Chain Development Skills

Twenty-one open-source agent skills that walk a project from idea to release — research, PRD, spec, design, test-driven build, and retrospective — with real stop points.

  • 21 skills covering 11 stages of development
  • 11 structural checks, each with its own tests
  • MIT licensed, usable chained or one at a time
  • Vibe Coding
  • Spec-Driven Development (SDD)
  • Test-Driven Development (TDD)
  • Agent Skills
  • Claude Code
  • Python
  • MCP
  • Markdown

Research + code2022 – 2026

CAR-T vs. CAR-NKT in solid tumors

Following two cell therapies through tissues and time to learn why one of them does better in solid tumors — and which checkpoint each one needs.

  • Homing CAR-NKT cells infiltrated and localized in tumors better
  • Persistence CAR-NKT cells lasted longer in vivo
  • TIGIT vs CD96 a different checkpoint partner for each product
  • Cell Therapy Discovery
  • Stem Cell-derived CAR-T
  • NKT Cell
  • Cell Chat
  • scRNA-seq
  • scTCR-seq
  • Seurat
  • Scanpy
  • R
  • Python