# virtual_lab

**Repository Path**: wzl19371/virtual_lab

## Basic Information

- **Project Name**: virtual_lab
- **Description**: testtesttest
- **Primary Language**: Unknown
- **License**: MIT
- **Default Branch**: main
- **Homepage**: None
- **GVP Project**: No

## Statistics

- **Stars**: 0
- **Forks**: 0
- **Created**: 2025-10-24
- **Last Updated**: 2025-10-24

## Categories & Tags

**Categories**: Uncategorized

**Tags**: None

## README

# Virtual Lab

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![Virtual Lab](images/virtual_lab_architecture.png)

The **Virtual Lab** is an AI-human collaboration for science research. In the Virtual Lab, a human researcher works with a team of large language model (LLM) **agents** to perform scientific research. Interaction between the human researcher and the LLM agents occurs via a series of **team meetings**, where all the LLM agents discuss a scientific agenda posed by the human researcher, and **individual meetings**, where the human researcher interacts with a single LLM agent to solve a particular scientific task.

Please see our paper [The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies](https://www.nature.com/articles/s41586-025-09442-9) for more details on the Virtual Lab and an application to nanobody design for SARS-CoV-2.

If you use the Virtual Lab, please cite our work as follows:

Swanson, K., Wu, W., Bulaong, N.L. et al. The Virtual Lab of AI agents designs new SARS-CoV-2 nanobodies. *Nature* (2025). https://doi.org/10.1038/s41586-025-09442-9


## Virtual Lab for nanobody design

As a real-world demonstration, we applied the Virtual Lab to design nanobodies for one of the latest variants of SARS-CoV-2 (see [nanobody_design](https://github.com/zou-group/virtual-lab/tree/main/nanobody_design)). The Virtual Lab built a computational pipeline consisting of [ESM](https://www.science.org/doi/10.1126/science.ade2574), [AlphaFold-Multimer](https://www.biorxiv.org/content/10.1101/2021.10.04.463034v2), and [Rosetta](https://rosettacommons.org/software/) and used it to design 92 nanobodies that were experimentally validated.

Please see the notebook [nanobody_design/run_nanobody_design.ipynb](https://github.com/zou-group/virtual-lab/blob/main/nanobody_design/run_nanobody_design.ipynb) for an example of how to use the Virtual Lab to create agents and run team and individual meetings.


## Installation

The Virtual Lab can be installed using pip or by cloning the repo and installing the required packages. Installation should only take a couple of minutes.

Optionally, first create a conda environment.

```bash
conda create -y -n virtual_lab python=3.12
conda activate virtual_lab
```

The Virtual Lab can be installed via pip.

```bash
pip install virtual-lab
```

To install a local version of the Virtual Lab, clone the repo and then install the package.

```bash
git clone https://github.com/zou-group/virtual_lab.git
cd virtual_lab
pip install -e .
```


## OpenAI API Key

The Virtual Lab currently uses GPT-4o from OpenAI. Save your OpenAI API key as the environment variable `OPENAI_API_KEY`. For example, add `export OPENAI_API_KEY=<your_key>` to your `.bashrc` or `.bash_profile`.