AI drug-discovery workbench — molecular design, docking, MD, and validation in one screen.
🇰🇷 한국어 README
bioflow integrates 39 external tools (AutoDock Vina, Boltz-2, Chai-1, AiZynthFinder, REINVENT 4, GROMACS, OpenMM, …), a 6-agent Co-Scientist loop, multi-modal validation, a knowledge graph, and MLflow tracking into a single Python monolith — a unified drug-discovery toolkit.
Starting with v0.10.0, a PySide6 native desktop shell ships, installable as a one-click desktop app.
| OS | Download | Install guide |
|---|---|---|
| Windows 11 | bioflow-Setup.exe |
docs/guides/INSTALL.md |
| macOS arm64 | bioflow-0.10.1.dmg |
docs/guides/INSTALL.md |
| Linux x64 | bioflow-0.10.1.AppImage |
docs/guides/INSTALL.md |
After install, double-click the desktop icon to open the 3-panel workbench.
git clone https://github.com/malamute0882-create/bioflow.git
cd bioflow
python3 -m venv .venv && source .venv/bin/activate
pip install -e ".[native,webapp,prod,llm,dev]"
# Native desktop shell
bioflow app native
# Or browser entry (legacy)
bioflow webapp --port 8000Detailed install steps: docs/guides/INSTALL.md (English) / docs/guides/INSTALL_KO.md (Korean).
| Command | Description | Since |
|---|---|---|
bioflow app native |
PySide6 native desktop shell (3-panel + chat + campaign tree) | v0.10.0 ← new default |
bioflow webapp |
Browser entry (http://localhost:8000) |
v0.7+ |
bioflow app launch |
System-tray launcher → auto-opens browser | v0.8+ |
All three call the same FastAPI backend (95 endpoints).
- REINVENT 4 de novo molecular generation (
screen/denovomodes) - AiZynthFinder retrosynthesis + synthesis-score gate
- RDKit descriptor / ADMET / fingerprint / scaffold analysis
- PoseBusters docking-pose plausibility validation
- Boltz-2 fold + binding affinity prediction
- Chai-1 MSA-free protein folding
- AlphaFold DB + AlphaMissense integration
- AutoDock Vina / DiffDock / GNINA docking
- fpocket pocket detection
- GROMACS / OpenMM MD simulation
- CHARMM-GUI workflows (GPCR-membrane / soluble kinase)
- MDAnalysis trajectory analysis
- Co-Scientist 6-agent loop (Generation / Reflection / Tournament / Proximity / Ranking / Meta-review)
- Phase A: AgentSignal confidence/uncertainty contract + Reflexion retry
- Phase B: ReasoningMemoryBank long-term memory + Self-RAG + LiteratureAgent
- Phase C: A-HMAD multi-agent debate + CheMatAgent two-tier validation
- Local LLM: Ollama Qwen3 8B (offline-friendly)
- Cloud: Anthropic Claude / OpenAI GPT (configurable)
- Knowledge Graph (PrimeKG schema)
- MLflow experiment tracking
- MOSAIC safety gate (dual-use chemistry/biology refusal)
- HPC Slurm integration
| Document | Content |
|---|---|
| docs/guides/INSTALL.md | English install guide (Windows/Mac/Linux) |
| docs/guides/INSTALL_KO.md | Korean install guide |
| docs/guides/WORKBENCH_TOUR.md | Workbench operator tour |
| docs/architecture/ARCHITECTURE.md | System architecture |
| docs/adr/ | Architecture Decision Records (32 entries) |
| docs/release-notes/v0.10.0.md | v0.10.0 release notes |
| docs/api/openapi-v0.10.1.json | OpenAPI spec (111 endpoints) |
| docs/industry/INDUSTRY_ALIGNMENT.md | Industry tool mapping |
# Tests
make test # Non-integration suite (1295 cases)
pytest tests -m integration # Integration tests (DB required)
pytest tests -m e2e # E2E (Qt + browser)
# Quality gates
make lint # ruff
make audit # pip-audit + bandit
make docs # mkdocs build
# Native build (per OS)
pyinstaller deploy/native/pyinstaller/bioflow-native.specGitHub Actions for the release workflow has been disabled to manage CI cost. Manual builds are documented in docs/guides/INSTALL.md § Developer install.
Bioflow is released under the Apache License 2.0.
Copyright 2026 Jun-Hyuck Lee
Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at
http://www.apache.org/licenses/LICENSE-2.0
Third-party dependencies are listed with their respective licenses in
NOTICE. Key components:
- PySide6 (Qt 6): LGPL-3.0 (link-only)
- PyInstaller: GPL-2.0 + bundle exception (commercial bundles permitted)
- External tools (AutoDock Vina, Boltz-2, AiZynthFinder, REINVENT 4, etc.):
invoked as subprocesses; each tool's own license applies when installed.
See
docs/industry/INDUSTRY_TOOLS.md. - Model weights (Boltz-2, Chai-1, REINVENT 4, ESM, AlphaFold, etc.): not bundled — fetched at runtime under each project's terms.
| Version | Released | Highlights |
|---|---|---|
| v0.10.1 | 2026-05-10 | Korean README + install guide + CI fix patches |
| v0.10.0 | 2026-05-10 | PySide6 native shell + Phase C debate + workbench M9-M15 + 8 lifecycle endpoints |
| v0.9.0 | 2026-05-10 | Conversational Workbench + Phase A/B agent intelligence + Codex Phase 1 (M1-M8) |
| v0.8.0 | 2026-05-09 | Windows desktop package (PyApp + Inno Setup) + local LLM (Ollama Qwen3) |
| v0.7.0 | 2026-05-07 | Open Coscientist composition + BioMCP/AlphaFold evidence + domain profiles |
| v0.6.0 | 2026-05-07 | Co-Scientist campaign state + LangGraph integration + MLflow tracking |
| v0.5.0 | 2026-05-06 | Async jobs + run DB + API key auth + distroless runtime |
Full CHANGELOG.md.