| Name | virtual-lab JSON |
| Version |
1.0.0
JSON |
| download |
| home_page | None |
| Summary | A virtual lab of large language model agents for scientific research. |
| upload_time | 2024-11-26 21:31:23 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.10 |
| license | MIT License Copyright (c) 2024 Kyle Swanson Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
llm
automated science
large language model
scientific research
virtual lab
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# Virtual Lab
[](https://badge.fury.io/py/virtual-lab)
[](https://badge.fury.io/py/virtual-lab)
[](https://pepy.tech/project/virtual-lab)
[](https://github.com/zou-group/virtual-lab/blob/main/LICENSE.txt)
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.
## 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`.
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"description": "# Virtual Lab\n\n[](https://badge.fury.io/py/virtual-lab)\n[](https://badge.fury.io/py/virtual-lab)\n[](https://pepy.tech/project/virtual-lab)\n[](https://github.com/zou-group/virtual-lab/blob/main/LICENSE.txt)\n\nThe **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.\n\n\n## Virtual Lab for nanobody design\n\nAs 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.\n\nPlease 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.\n\n\n## Installation\n\nThe 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.\n\nOptionally, first create a conda environment.\n\n```bash\nconda create -y -n virtual_lab python=3.12\nconda activate virtual_lab\n```\n\nThe Virtual Lab can be installed via pip.\n\n```bash\npip install virtual-lab\n```\n\nTo install a local version of the Virtual Lab, clone the repo and then install the package.\n\n```bash\ngit clone https://github.com/zou-group/virtual_lab.git\ncd virtual_lab\npip install -e .\n```\n\n\n## OpenAI API Key\n\nThe 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`.\n",
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