ai4protein/venusfactory2

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What is it?

VenusFactory2 puts protein language models, biological databases, and an Agent orchestrator in one place: upload a sequence/structure to predict, drive multi-step analysis in natural language, or fine-tune your own models.

Try online: venusfactory.bio

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Quick Start

Slow Hugging Face access: export HF_ENDPOINT=https://hf-mirror.com

git clone --recurse-submodules https://github.com/AI4Protein/VenusFactory2.git && cd VenusFactory2
# If you already cloned without submodules:
#   git submodule update --init --recursive
python scripts/setup_quickstart.py          # interactive one-click install
# python scripts/setup_quickstart.py -y     # CI / non-interactive

source .venv/bin/activate
python src/webui_v2.py --host 0.0.0.0 --port 7861
# → http://localhost:7861

The installer detects older setups (.venv / frontend / weights) and can reuse or wipe them. Press Enter for the recommended path.

After launch

1. Open the UI → Quick Tools work without an LLM key
2. Agent: set an API key in Settings, or cp .env.example .env (see .env.example)
3. Optional check: python scripts/check_env.py

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Documentation

Three layers — start at the top; dig only when needed:

中文：README_CN.md · docs/README.md

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Citation

@article{tan2026venusfactory2,
  title={Self-evolving AI agents for protein discovery and directed evolution},
  author={Tan, Yang and Zhang, Lingrong and Li, Mingchen and Yu, Yuanxi and Zhong, Bozitao and Zhou, Bingxin and Dong, Nanqing and Hong, Liang},
  journal={arXiv preprint arXiv:2603.27303},
  year={2026}
}

@inproceedings{tan2025venusfactory,
  title={VenusFactory: An Integrated System for Protein Engineering with Data Retrieval and Language Model Fine-Tuning},
  author={Tan, Yang and Liu, Chen and Gao, Jingyuan and Banghao, Wu and Li, Mingchen and Wang, Ruilin and Zhang, Lingrong and Yu, Huiqun and Fan, Guisheng and Hong, Liang and others},
  booktitle={Proceedings of the 63rd Annual Meeting of the Association for Computational Linguistics (Volume 3: System Demonstrations)},
  pages={230--241},
  year={2025}
}

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License & acknowledgement

Released under the VenusFactory Non-Commercial License: free for academic / non-commercial use; commercial use needs written approval → ****. See LICENSE / LICENSE_CN.md.

Maintained by Liang’s Lab, Shanghai Jiao Tong University.
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