AutoBiology CLI

AutoBiology turns biological SOP text into structured automation requirements. The CLI parses procedure text, builds operation hypergraphs, generates deterministic R1-R10 requirements, optionally adds LLM-assisted candidates, and writes coverage reports with Mermaid diagrams.

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Install

npm install -g autobiology-cli
autob --help
autob update --check

The installed command is autob. The npm package contains the CLI runtime, bundled data/ knowledge base, and user documentation.

Documentation

Getting Started Install the CLI, initialize config, and run your first SOP. Configuration Set global and project JSON config without committing secrets. Blender Simulation Use the standalone Blender component to render requirement-driven MP4 simulations. Pipeline Guide Understand each stage and the files written to the output directory. LLM And Artifacts Check whether LLM inference is enabled and use the research artifacts. CLI Reference Look up commands, arguments, options, and expected behavior.

Quick Run

autob init
autob run your-sop.txt -o out

Open out/report.md first, then inspect the JSON files for structured data.

To check whether a run used the optional LLM layer:

autob config show
node -e "const fs=require('fs'); const m=JSON.parse(fs.readFileSync('out/run-meta.json','utf8')); console.log(m.config.llmModel)"
rg -n '"LLM-Candidate"' out/04-requirements.json

Knowledge Base And Artifacts

The CLI includes the curated data/ knowledge base used by the deterministic stages: synonyms, domain action patterns, parameter constraints, and the standard risk catalog. autob run loads it once and passes it through atomize, hypergraph, and requirements generation.

The GitHub repository also includes publication/ for paper-oriented methods, reproducibility notes, figures, and sample outputs, plus graphify-out/ for the generated code knowledge graph and architecture report.

See LLM And Artifacts for the LLM enablement check, deterministic and LLM responsibility boundary, and artifact usage notes.