Blatant Why

Open-source protein design agent for Claude Code

Commercial platforms wrap open-source tools behind paywalls and call it a revolution.
BY gives you direct access through Claude Code. No platform fees. Your tools, your compute, your designs.

_{Source: trust us bro}

Quick Start (5 minutes)

You don't need to be a developer. If you can open a terminal and paste commands, you can run BY.

1. Install prerequisites

2. Create your project

mkdir my-campaign && cd my-campaign
npx blatant-why init

This scaffolds everything: 11 MCP servers, 21 agents, 19 skills, 13 slash commands, and a CLAUDE.md orchestration file. Takes about 30 seconds.

3. (Optional) Configure compute

BY defaults to local GPU if one is available. Otherwise the first-run questionnaire will help you pick between local, HPC (RunPod / Modal / SLURM), or Tamarind cloud. See Compute Options below.

cp .env.example .env
# Add keys for whichever compute provider you'll use

4. Start designing

claude

Then just tell it what you want:

> "Design VHH nanobodies against PD-L1"

Or use the guided workflow:

> /by:plan-campaign

Or if it's your first time:

> /by:welcome

That's it. Claude Code handles the rest -- research, design, screening, and ranking.

What It Does

Give it a target protein. It researches across PDB, UniProt, and SAbDab. It plans a design campaign with statistical-strategy debate when the target is novel. It runs compute jobs on your local GPU (default), on your HPC (RunPod / Modal / SLURM via the by-deploy-compute skill), or on Tamarind Bio cloud. It screens every design for structural quality, sequence liabilities, and developability. It ranks candidates by composite score. When you submit them to the lab and the results come back, it ingests the CSVs, diagnoses which in-silico features predicted reality, and feeds the calibration back into the next round.

The whole pipeline runs inside Claude Code. No platform. No dashboard. No vendor lock-in.

What's Inside

... View full README on GitHub