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antomicblitz/README.md

Ahoy there

Molecular biologist and entrepreneur in Basel. I'm working on agentic lab automation and drug discovery. I make open-source instrument drivers and bioinformatics tools that I use in my work and my own lab. I also help build peptide drug discovery pipelines for myself and SP2TX. Even though I don't have formal training in software development, I enjoy tinkering and building things. I use AI, but I remain in the driver's seat as much as possible. See the AI code quality disclosure below.

Current focus

  • Building Lambda Biolab, a BSL-1 shared lab and open tooling for bioengineering, since 2022.
  • Reverse-engineering lab instruments into open Python APIs, from PCR machines to plate readers to electronic pipettes.
  • Running local LLM inference and agent tooling for wet-lab workflows.

Projects I'm working on

Affordable, low-cost, distributed computing in genomics and structural biology

  • deepvariant-linux-arm64: Google's DeepVariant, rebuilt to run on cheap Arm64 processors.
  • vastai-gpu-runner: Scalable structural biology batch GPU orchestration on Vast.ai with robust R2 storage and crash recovery.

Instrument control and lab automation

  • bentolab: reverse-engineered BLE/Wi-Fi protocol for Bento Lab PCR workstations, with async client, FastAPI wrapper, and CLI.
  • wallac-victor2-api: REST/JSON API for a PerkinElmer Victor2 multimode plate reader, driven from Linux.
  • dpette-usb-driver: open USB driver for DLAB dPette electronic pipettes.
  • i3mega-pipettebot: an Anycubic i3 Mega turned into a sub-$150 disposable-tip pipetting robot (collaboration with qte77).

Structure prediction

  • biolab-runners: modular runners for Boltz-2 structure prediction and OpenMM MD.

Code quality, and a note to haters

Just because I didn't formally study software development doesn't mean that I blindly trust all agent-generated code. I dislike low-effort vibe slop as much as the next person, but manually reviewing thousands of lines of agent-generated code doesn't scale, and pretending that line-by-line inspection alone guarantees correctness is misguided. Nonetheless, I strive to ship robust, working software that I feel confident my collaborators and I can use. Every repository has quality gates designed to catch most obvious defects, unsafe changes, and shallow implementations. For instance:

  • ruff and pyright with tests treated as first-class code
  • pytest with coverage, plus branch coverage on changed files
  • cognitive-complexity limits and mutation testing on changed code
  • bandit, secret scanning, actionlint, markdownlint
  • actions pinned to commit SHAs

How to reach me

Pinned Loading

  1. Lambda-Biolab/deepvariant-linux-arm64 Lambda-Biolab/deepvariant-linux-arm64 Public

    DeepVariant for Linux ARM64 (Graviton, Ampere, RK3588, Jetson) with hardware-accelerated inference via ONNX Runtime + ACL. Open-source variant calling on cheap ARM cloud and edge hardware.

    Python 5 1

  2. Lambda-Biolab/bentolab Lambda-Biolab/bentolab Public

    Python BLE/Wi-Fi control library for Bento Lab PCR workstations — reverse-engineered protocol, async client, FastAPI HTTP wrapper, and Typer CLI.

    Python

  3. Lambda-Biolab/biolab-runners Lambda-Biolab/biolab-runners Public

    Standalone modular runners for Boltz-2 structure prediction and OpenMM MD simulations

    Python

  4. Lambda-Biolab/dpette-usb-driver Lambda-Biolab/dpette-usb-driver Public

    Opensource USB driver for dpette and dpette+ electronic pipettes

    Python

  5. Lambda-Biolab/i3mega-pipettebot Lambda-Biolab/i3mega-pipettebot Public

    Forked from qte77/i3mega-pipettebot

    Turn an Anycubic i3 Mega into a sub-$150 disposable-tip pipetting robot driven by a DLAB dPette electronic pipette and Python.

    Python

  6. Lambda-Biolab/vastai-gpu-runner Lambda-Biolab/vastai-gpu-runner Public

    Structural Biology Cloud GPU orchestration framework for Vast.ai — batch deployment, R2 storage, worker lifecycle, crash recovery.

    Python