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FAQ and Glossary

What is BioVoice?

BioVoice is a local research prototype for voice control of PyMOL and ChimeraX. It is built for structural biology workflows such as ligand-pocket walkthroughs, AlphaFold overlays, Rosetta reviews, and cryo-EM map stories.

Can I use BioVoice without an OpenAI API key?

Yes. Offline rehearsal is a first-class path. You can start the local server, inspect the UI, dry-run workflows, and run direct recipe/API routes without live voice.

Start here:

npm run agent:start -- pymol --offline --clean-target

Which voice provider does BioVoice support today?

OpenAI Realtime API only. That is the only supported and documented live voice provider in this release.

Does BioVoice support Anthropic live voice, Gemini live voice, or local speech providers?

No. Those are not implemented or supported today. BioVoice does not currently expose a provider-selection interface.

Does my PDB, CIF, or cryo-EM map leave my machine?

No. Molecular file contents stay local. During live voice sessions, microphone audio, transcripts, and structured tool-call text go to OpenAI.

Is local .env still the normal setup?

Yes. Real credentials belong in your local .env. That file stays ignored and local. The tracked .env.example file is a safe template and should remain tracked.

Which local paths stay outside the remote/public repo?

These locations are expected to stay local-only:

  • .env
  • .runtime/
  • local/
  • private/
  • tmp/
  • output/

They are kept out of git so you can use the app normally on your own machine without publishing local state.

Can I use BioVoice on Linux or Windows?

Partially. The local backend and browser UI can run, but macOS is the only platform with built-in autolaunch today. On Linux or Windows, start PyMOL or ChimeraX manually first.

Do I need both PyMOL and ChimeraX installed?

No. You can use either one. Many workflows have a recommended target, but BioVoice does not require both applications to be present.

What are the best first workflows to try?

  • Ligand pocket story for the fastest polished visual win
  • AlphaFold overlay for prediction-versus-experiment demos
  • Rosetta compare for scaffold-versus-design storytelling
  • ChimeraX map fit for a cryo-EM-oriented walkthrough

See Getting Started and the tutorial pages in docs/.

How do I test AlphaFold workflows locally?

Use the validated showcase or rehearsal commands:

npm run showcase:chimerax:overlay
npm run rehearse:workflow -- alphafold_vs_experiment_overlay --target chimerax --capture --model examples/data/local/af-p69905.pdb --experimental examples/data/local/4hhb.pdb

How do I test Rosetta workflows locally?

Use the validated showcase or rehearsal commands:

npm run showcase:pymol:rosetta
npm run rehearse:workflow -- rosetta_top_design_compare --target pymol --capture --model examples/data/local/rosetta_demo/reference_scaffold.pdb --bundle examples/data/local/rosetta_demo --scorefile examples/data/local/rosetta_demo/score.sc --top-n 2

What should I redact before filing a public issue?

Redact:

  • API keys and access tokens
  • full browser URLs
  • local filesystem paths you do not want public
  • transcript text you would not want indexed
  • screenshots that reveal sensitive structures, prompts, or machine details

See SUPPORT.md and SECURITY.md.

Glossary

PyMOL

A molecular visualization application widely used for structure inspection, presentation figures, and scripting-heavy workflows.

ChimeraX

A molecular visualization application with strong support for modern rendering, contact analysis, assemblies, maps, and structural comparison workflows.

AlphaFold

A protein-structure prediction system. In BioVoice, AlphaFold workflows usually mean confidence review, overlay, interface triage, or cryo handoff.

Rosetta

A computational modeling suite often used for design, interface optimization, and scaffold-versus-design comparison workflows.

Cryo-EM

Cryo-electron microscopy. In BioVoice, cryo-EM workflows focus on density maps, fitted atomic models, cutaways, and map-fit presentations.

OpenAI Realtime API

The live voice backend BioVoice uses today for real-time speech interaction over WebRTC.

WebRTC

The browser transport used for live audio streaming between the BioVoice UI and OpenAI Realtime.