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| <h1 align="center" style="font-weight: bold;">🤖 AIAgents4Pharma</h1> | ||
| [](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml) | ||
| [](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml) | ||
| [](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml) | ||
| [](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml) | ||
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| Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data. | ||
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| Our toolkit currently consists of three agents, each designed to simplify and enhance access to complex data in biology: | ||
| ## Introduction | ||
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| - [**Talk2BioModels**](talk2biomodels/models/intro.md): Engage directly with mathematical models in systems biology. | ||
| Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://github.com/VirtualPatientEngine) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data. | ||
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| - [**Talk2Cells**](talk2cells/intro.md) *(Work in progress)*: Query and analyze sequencing data with ease. | ||
| Our toolkit currently consists of the following agents: | ||
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| - [**Talk2KnowledgeGraphs**](talk2knowledgegraphs/intro.md) *(Coming soon)*: Access and explore complex biological knowledge graphs for insightful data connections. | ||
| - **Talk2BioModels** _(v1 released; v2 in progress)_: Engage directly with mathematical models in systems biology. | ||
| - **Talk2KnowledgeGraphs** _(v1 in progress)_: Access and explore complex biological knowledge graphs for insightful data connections. | ||
| - **Talk2Scholars** _(v1 in progress)_: Get recommendations for articles related to your choice. Download, query, and write/retrieve them to your reference manager (currently supporting Zotero). | ||
| - **Talk2Cells** _(v1 in progress)_: Query and analyze sequencing data with ease. | ||
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| - [**Talk2Scholars**](talk2scholars/intro.md) *(Coming soon)*: Access articles and receive recommendations for academic papers using state-of-the-art natural language processing | ||
|  | ||
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| ### Prerequisites | ||
| ## Getting Started | ||
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| - **Python 3.10+** | ||
| - **Git** | ||
| - Required libraries specified in `requirements.txt` | ||
|  | ||
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| ### Installation | ||
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| #### Option 1: PyPI | ||
| ```bash | ||
| pip install aiagents4pharma | ||
| ``` | ||
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| ```bash | ||
| pip install aiagents4pharma | ||
| ``` | ||
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| Check out the tutorials on each agent for detailed instrcutions. | ||
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| #### Option 2: Git | ||
| #### Option 2: git | ||
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| 1. **Clone the repository:** | ||
| ```bash | ||
| git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma | ||
| cd AIAgents4Pharma | ||
| ``` | ||
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| 2. **Install dependencies:** | ||
| ```bash | ||
| pip install -r requirements.txt | ||
| pip install . | ||
| ``` | ||
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| 3. **Initialize OPENAI_API_KEY** | ||
| ```bash | ||
| export OPENAI_API_KEY=.... | ||
| ``` | ||
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| 4. **[Optional] Set up login credentials** | ||
| ```bash | ||
| vi .streamlit/secrets.toml | ||
| ``` | ||
| and enter | ||
| ``` | ||
| password='XXX' | ||
| ``` | ||
| Please note that the password will be same for all. | ||
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| 5. **[Optional] Initialize LANGSMITH_API_KEY** | ||
| 4. **[Optional] Initialize LANGSMITH_API_KEY** | ||
| ```bash | ||
| export LANGCHAIN_TRACING_V2=true | ||
| export LANGCHAIN_API_KEY=<your-api-key> | ||
| ``` | ||
| Please note that this will create a new tracing project in your Langsmith | ||
| account with the name `<user_name>@<uuid>`, where `user_name` is the name | ||
| you provided in the previous step. If you skip the previous step, it will | ||
| default to `default` (a 128 bit unique ID created for the session). | ||
| _Please note that this will create a new tracing project in your Langsmith | ||
| account with the name `T2X-xxxx`, where `X` can be `B` (Biomodels), `S` (Scholars), | ||
| `KG` (KnowledgeGraphs), or `C` (Cells). If you skip the previous step, it will | ||
| default to the name `default`. `xxxx` will be the 4-digit ID created for the | ||
| session._ | ||
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| 6. **Launch the app:** | ||
| 5. **Launch the app:** | ||
| ```bash | ||
| streamlit run app/frontend/streamlit_app.py | ||
| streamlit run app/frontend/streamlit_app_<agent>.py | ||
| ``` | ||
| _Replace <agent> with the agent name you are interested to launch._ | ||
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| For detailed instructions on each agent, please refer to their respective modules. | ||
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| ### Contributing | ||
| --- | ||
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| ## Contributing | ||
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| We welcome contributions to AIAgents4Pharma! Here’s how you can help: | ||
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| 1. **Fork the repository** | ||
| 2. **Create a new branch** for your feature (`git checkout -b feat/feature-name`) | ||
| 3. **Commit your changes** (`git commit -m 'feat: Add new feature'`) | ||
| 4. **Push to the branch** (`git push origin feat/feature-name`) | ||
| 5. **Open a pull request** | ||
| 5. **Open a pull request** and reach out to any one of us below via Discussions: | ||
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| _Note: We welcome all contributions, not just programming-related ones. Feel free to open bug reports, suggest new features, or participate as a beta tester. Your support is greatly appreciated!_ | ||
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| - **Talk2Biomodels/Talk2Cells**: [@gurdeep330](https://github.com/gurdeep330) [@lilijap](https://github.com/lilijap) [@dmccloskey](https://github.com/dmccloskey) | ||
| - **Talk2KnowledgeGraphs**: [@awmulyadi](https://github.com/awmulyadi) [@dmccloskey](https://github.com/dmccloskey) | ||
| - **Talk2Scholars**: [@ansh-info](https://github.com/ansh-info) [@gurdeep330](https://github.com/gurdeep330) [@dmccloskey](https://github.com/dmccloskey) | ||
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| ### Current Needs | ||
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| - **Beta testers** for Talk2BioModels and Talk2Scholars. | ||
| - **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma. | ||
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| Feel free to reach out to us via Discussions. | ||
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| Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information. | ||
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| --- | ||
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| ## Feedback | ||
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| Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information. | ||
| Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Isssues` or `Discussions` 😀 |
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| # Talk2BioModels | ||
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| **Talk2BioModels** is an AI-agent designed to interact with mathematical models in systems biology. You can choose to either interact with a model available in the BioModels database or upload your own model. | ||
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| ### How to access Talk2BioModels? | ||
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| There are 2 ways to access Talk2BioModels: | ||
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| - **Set up the Streamlit app**: Follow the instructions on the home page to set up an launch the Streamlit app. | ||
| - **Use the PyPI package**: Follow the tutorial for step-by-step guidance on how to use the PyPI package. | ||
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