aiagents4pharma 1.30.3__tar.gz → 1.31.0__tar.gz

aiagents4pharma-1.31.0/PKG-INFO

@@ -0,0 +1,362 @@
+Metadata-Version: 2.4
+Name: aiagents4pharma
+Version: 1.31.0
+Summary: AI Agents for drug discovery, drug development, and other pharmaceutical R&D.
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.12
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: copasi_basico==0.78
+Requires-Dist: coverage==7.6.4
+Requires-Dist: einops==0.8.0
+Requires-Dist: gdown==5.2.0
+Requires-Dist: gravis==0.1.0
+Requires-Dist: huggingface_hub==0.26.5
+Requires-Dist: hydra-core==1.3.2
+Requires-Dist: joblib==1.4.2
+Requires-Dist: langchain==0.3.7
+Requires-Dist: langchain-community==0.3.5
+Requires-Dist: langchain-core==0.3.40
+Requires-Dist: langchain-experimental==0.3.3
+Requires-Dist: langchain-nvidia-ai-endpoints==0.3.9
+Requires-Dist: langchain-openai==0.2.5
+Requires-Dist: langchain_ollama==0.2.3
+Requires-Dist: langgraph_supervisor==0.0.9
+Requires-Dist: matplotlib==3.9.2
+Requires-Dist: openai==1.59.4
+Requires-Dist: ollama==0.4.7
+Requires-Dist: pandas==2.2.3
+Requires-Dist: pcst_fast==1.0.10
+Requires-Dist: plotly==5.24.1
+Requires-Dist: pubchempy==1.0.4
+Requires-Dist: pydantic==2.9.2
+Requires-Dist: pylint==3.3.1
+Requires-Dist: pypdf==5.2.0
+Requires-Dist: pytest==8.3.3
+Requires-Dist: pytest-asyncio==0.25.2
+Requires-Dist: pyzotero==1.6.9
+Requires-Dist: streamlit==1.39.0
+Requires-Dist: sentence_transformers==3.3.1
+Requires-Dist: tabulate==0.9.0
+Requires-Dist: torch==2.2.2
+Requires-Dist: torch_geometric==2.6.1
+Requires-Dist: transformers==4.48.0
+Requires-Dist: mkdocs==1.6.1
+Requires-Dist: mkdocs-jupyter==0.25.1
+Requires-Dist: mkdocs-material==9.5.47
+Requires-Dist: mkdocstrings-python==1.12.2
+Requires-Dist: mkdocs-include-markdown-plugin==7.1.2
+Requires-Dist: mkdocstrings==0.27.0
+Requires-Dist: streamlit-feedback
+Requires-Dist: anndata==0.11.3
+Requires-Dist: h5py==3.13.0
+Requires-Dist: igraph==0.11.8
+Requires-Dist: ipykernel==6.29.5
+Requires-Dist: ipython==8.32.0
+Requires-Dist: nbformat==5.10.4
+Requires-Dist: scipy==1.15.2
+Requires-Dist: tqdm==4.67.1
+Requires-Dist: umap-learn==0.5.7
+Requires-Dist: plotly-express==0.4.1
+Requires-Dist: seaborn==0.13.2
+Requires-Dist: scanpy==1.11.0
+Dynamic: license-file
+
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://bmedx.com/research-teams/artificial-intelligence/team-vpe/) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **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.
+- **Talk2AIAgents4Pharma** _(v1 in progress)_: Converse with all the agents above (currently supports T2B and T2KG)
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+### Installation
+
+#### Option 1: Docker (stable-release)
+
+_We now have all the agents available on Docker Hub._
+
+##### **To run Talk2AIAgents4Pharma / Talk2KnowledgeGraphs**
+
+Both agents require [Ollama](https://ollama.com/) to run embedding models like `nomic-embed-text`. We use a **single startup script** that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.
+
+##### **1. Clone the repository and navigate to the agent directory**
+
+```sh
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+
+cd AIAgents4Pharma/aiagents4pharma/<agent>
+```
+
+Replace `<agent>` with either:
+
+- `talk2aiagents4pharma`
+- `talk2knowledgegraphs`
+
+##### **2. Setup environment variables**
+
+Copy and configure your `.env` file:
+
+```sh
+cp .env.example .env
+```
+
+Then edit `.env` and add your API keys:
+
+```env
+OPENAI_API_KEY=...                  # Required for both agents
+NVIDIA_API_KEY=...                  # Required for both agents
+OLLAMA_HOST=http://ollama:11434     # Required for AA4P / T2KG
+LANGCHAIN_TRACING_V2=true           # Optional for both agents
+LANGCHAIN_API_KEY=...               # Optional for both agents
+```
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+###### Notes for Windows Users
+
+If you are using Windows, it is recommended to install **Git Bash** for a smoother experience when running the bash commands in this guide.
+
+- For applications that use **Docker Compose**, Git Bash is **required**.
+- For applications that use **docker run** manually, Git Bash is **optional**, but recommended for consistency.
+
+You can download Git Bash here: [Git for Windows](https://git-scm.com/downloads).
+
+When using Docker on Windows, make sure you **run Docker with administrative privileges** if you face permission issues.
+
+To resolve for permission issues, you can:
+
+- Review the official Docker documentation on [Windows permission requirements](https://docs.docker.com/desktop/setup/install/windows-permission-requirements/).
+- Alternatively, follow the community discussion and solutions on [Docker Community Forums](https://forums.docker.com/t/error-when-trying-to-run-windows-containers-docker-client-must-be-run-with-elevated-privileges/136619).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+##### **3. Start the application**
+
+Run the startup script. It will:
+
+- Detect your hardware configuration (NVIDIA GPU, AMD GPU, or CPU). Apple Metal is unavailable inside Docker, and Intel SIMD optimizations are automatically handled without special configuration.
+- Choose the correct Ollama image (`latest` or `rocm`)
+- Launch the Ollama container with appropriate runtime settings
+- Pull the required embedding model (`nomic-embed-text`)
+- Start the agent **after the model is available**
+
+```sh
+chmod +x startup.sh
+./startup.sh        # Add --cpu flag to force CPU mode if needed
+```
+
+##### **4. Access the Web UI**
+
+Once started, the agent is available at:
+
+```
+http://localhost:8501
+```
+
+##### **To Run Talk2Biomodels / Talk2Scholars**
+
+1. **Run the containers**
+
+###### Talk2Biomodels
+
+```docker
+docker run -d \
+  --name talk2biomodels \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2biomodels
+```
+
+###### Talk2Scholars
+
+```docker
+docker run -d \
+  --name talk2scholars \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e ZOTERO_API_KEY=<your_zotero_api_key> \
+  -e ZOTERO_USER_ID=<your_zotero_user_id> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2scholars
+```
+
+2. **Access the Web App**
+   Open your browser and go to:
+
+   ```
+   http://localhost:8501
+   ```
+
+To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+If you are using docker on Windows, please follow these [Windows Setup Notes](#notes-for-windows-users).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+#### Notes
+
+- Be sure to **replace the placeholder values** with your actual credentials before running any container:
+
+  - `<your_openai_api_key>`
+  - `<your_nvidia_api_key>`
+  - `<your_zotero_api_key>`
+  - `<your_zotero_user_id>`
+
+- All agents default to **port `8501`**. If you plan to run multiple agents simultaneously, make sure to assign **different ports** to avoid conflicts.
+
+  Example (Talk2Scholars on port `8502`):
+
+  ```docker
+  docker run -d \
+    --name talk2scholars \
+    -e OPENAI_API_KEY=<your_openai_api_key> \
+    -e ZOTERO_API_KEY=<your_zotero_api_key> \
+    -e ZOTERO_USER_ID=<your_zotero_user_id> \
+    -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+    -p 8502:8501 \
+    virtualpatientengine/talk2scholars
+  ```
+
+  Then access the app at: [http://localhost:8502](http://localhost:8502)
+
+#### Option 2: git (for developers and contributors)
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+1. **Clone the repository:**
+   ```sh
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+
+   ```python
+   pip install -r requirements.txt
+   ```
+
+3. **Initialize API Keys**
+
+   ```env
+   export OPENAI_API_KEY=....          # Required for all agents
+   export NVIDIA_API_KEY=....          # Required for all agents
+   export ZOTERO_API_KEY=....          # Required for T2S
+   export ZOTERO_USER_ID=....          # Required for T2S
+   export LANGCHAIN_TRACING_V2=true    # Optional for all agents
+   export LANGCHAIN_API_KEY=...        # Optional for all agents
+   ```
+
+To use **Talk2AIAgents4Pharma**, **Talk2BioModels**, **Talk2KnowledgeGraphs**, or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you must have **Ollama** installed. Follow installation instructions for your OS [here](https://ollama.com/download).
+
+After installing, pull the `nomic-embed-text` model and start the server by running:
+
+```sh
+ollama pull nomic-embed-text && ollama serve
+```
+
+More details about the model are available [here](https://ollama.com/library/nomic-embed-text).
+
+Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.  
+You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `AA4P` (Main Agent),
+`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._
+
+4. **Launch the app:**
+   ```sh
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+   _Replace `<agent>` with the agent name you are interested to launch:_
+
+- `talk2aiagents4pharma`
+- `talk2biomodels`
+- `talk2knowledgegraphs`
+- `talk2scholars`
+- `talk2cells`
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+#### Option 3: pip (beta-release)
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+```sh
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instructions.
+
+## Contributing
+
+We welcome your support to make **AIAgents4Pharma** even better.  
+All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.
+
+#### How to contribute
+
+1. Star this repository to show your support.
+2. Fork the repository.
+3. Create a new branch for your work:
+   ```sh
+   git checkout -b feat/your-feature-name
+   ```
+4. Make your changes and commit them:
+   ```sh
+   git commit -m "feat: add a brief description of your change"
+   ```
+5. Push your branch:
+   ```sh
+   git push origin feat/your-feature-name
+   ```
+6. Open a Pull Request.
+
+#### Areas where you can help
+
+- Beta testing for Talk2BioModels and Talk2Scholars.
+- Development work related to Python, bioinformatics, or knowledge graphs.
+
+#### Contacts for contributions
+
+- **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)
+
+Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
+
+## Feedback
+
+If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.  
+Please open an `issue` or start a `discussion`

aiagents4pharma-1.31.0/README.md

@@ -0,0 +1,296 @@
+[![Talk2BioModels](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2biomodels.yml)
+[![Talk2Cells](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2cells.yml)
+[![Talk2KnowledgeGraphs](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2knowledgegraphs.yml)
+[![TESTS Talk2Scholars](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2scholars.yml)
+[![TESTS Talk2AIAgents4Pharma](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml/badge.svg)](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml)
+![GitHub Release](https://img.shields.io/github/v/release/VirtualPatientEngine/AIAgents4Pharma)
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+![Talk2AIAgents4Pharma Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2aiagents4pharma?label=Talk2AIAgents4Pharma%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2Scholars Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2scholars?label=Talk2Scholars%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2BioModels Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2biomodels?label=Talk2BioModels%20Pulls&color=blue&logo=docker&style=flat-square)
+![Talk2KnowledgeGraphs Pulls](https://img.shields.io/docker/pulls/virtualpatientengine/talk2knowledgegraphs?label=Talk2KnowledgeGraphs%20Pulls&color=blue&logo=docker&style=flat-square)
+
+## Introduction
+
+Welcome to **AIAgents4Pharma** – an open-source project by [Team VPE](https://bmedx.com/research-teams/artificial-intelligence/team-vpe/) that brings together AI-driven tools to help researchers and pharma interact seamlessly with complex biological data.
+
+Our toolkit currently consists of the following agents:
+
+- **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.
+- **Talk2AIAgents4Pharma** _(v1 in progress)_: Converse with all the agents above (currently supports T2B and T2KG)
+
+![AIAgents4Pharma](docs/assets/AIAgents4Pharma.png)
+
+## Getting Started
+
+### Installation
+
+#### Option 1: Docker (stable-release)
+
+_We now have all the agents available on Docker Hub._
+
+##### **To run Talk2AIAgents4Pharma / Talk2KnowledgeGraphs**
+
+Both agents require [Ollama](https://ollama.com/) to run embedding models like `nomic-embed-text`. We use a **single startup script** that automatically detects your hardware (NVIDIA, AMD, or CPU) and handles container startup, model loading, and service orchestration.
+
+##### **1. Clone the repository and navigate to the agent directory**
+
+```sh
+git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+
+cd AIAgents4Pharma/aiagents4pharma/<agent>
+```
+
+Replace `<agent>` with either:
+
+- `talk2aiagents4pharma`
+- `talk2knowledgegraphs`
+
+##### **2. Setup environment variables**
+
+Copy and configure your `.env` file:
+
+```sh
+cp .env.example .env
+```
+
+Then edit `.env` and add your API keys:
+
+```env
+OPENAI_API_KEY=...                  # Required for both agents
+NVIDIA_API_KEY=...                  # Required for both agents
+OLLAMA_HOST=http://ollama:11434     # Required for AA4P / T2KG
+LANGCHAIN_TRACING_V2=true           # Optional for both agents
+LANGCHAIN_API_KEY=...               # Optional for both agents
+```
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+###### Notes for Windows Users
+
+If you are using Windows, it is recommended to install **Git Bash** for a smoother experience when running the bash commands in this guide.
+
+- For applications that use **Docker Compose**, Git Bash is **required**.
+- For applications that use **docker run** manually, Git Bash is **optional**, but recommended for consistency.
+
+You can download Git Bash here: [Git for Windows](https://git-scm.com/downloads).
+
+When using Docker on Windows, make sure you **run Docker with administrative privileges** if you face permission issues.
+
+To resolve for permission issues, you can:
+
+- Review the official Docker documentation on [Windows permission requirements](https://docs.docker.com/desktop/setup/install/windows-permission-requirements/).
+- Alternatively, follow the community discussion and solutions on [Docker Community Forums](https://forums.docker.com/t/error-when-trying-to-run-windows-containers-docker-client-must-be-run-with-elevated-privileges/136619).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+##### **3. Start the application**
+
+Run the startup script. It will:
+
+- Detect your hardware configuration (NVIDIA GPU, AMD GPU, or CPU). Apple Metal is unavailable inside Docker, and Intel SIMD optimizations are automatically handled without special configuration.
+- Choose the correct Ollama image (`latest` or `rocm`)
+- Launch the Ollama container with appropriate runtime settings
+- Pull the required embedding model (`nomic-embed-text`)
+- Start the agent **after the model is available**
+
+```sh
+chmod +x startup.sh
+./startup.sh        # Add --cpu flag to force CPU mode if needed
+```
+
+##### **4. Access the Web UI**
+
+Once started, the agent is available at:
+
+```
+http://localhost:8501
+```
+
+##### **To Run Talk2Biomodels / Talk2Scholars**
+
+1. **Run the containers**
+
+###### Talk2Biomodels
+
+```docker
+docker run -d \
+  --name talk2biomodels \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2biomodels
+```
+
+###### Talk2Scholars
+
+```docker
+docker run -d \
+  --name talk2scholars \
+  -e OPENAI_API_KEY=<your_openai_api_key> \
+  -e ZOTERO_API_KEY=<your_zotero_api_key> \
+  -e ZOTERO_USER_ID=<your_zotero_user_id> \
+  -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+  -p 8501:8501 \
+  virtualpatientengine/talk2scholars
+```
+
+2. **Access the Web App**
+   Open your browser and go to:
+
+   ```
+   http://localhost:8501
+   ```
+
+To use **Talk2BioModels** or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+If you are using docker on Windows, please follow these [Windows Setup Notes](#notes-for-windows-users).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+#### Notes
+
+- Be sure to **replace the placeholder values** with your actual credentials before running any container:
+
+  - `<your_openai_api_key>`
+  - `<your_nvidia_api_key>`
+  - `<your_zotero_api_key>`
+  - `<your_zotero_user_id>`
+
+- All agents default to **port `8501`**. If you plan to run multiple agents simultaneously, make sure to assign **different ports** to avoid conflicts.
+
+  Example (Talk2Scholars on port `8502`):
+
+  ```docker
+  docker run -d \
+    --name talk2scholars \
+    -e OPENAI_API_KEY=<your_openai_api_key> \
+    -e ZOTERO_API_KEY=<your_zotero_api_key> \
+    -e ZOTERO_USER_ID=<your_zotero_user_id> \
+    -e NVIDIA_API_KEY=<your_nvidia_api_key> \
+    -p 8502:8501 \
+    virtualpatientengine/talk2scholars
+  ```
+
+  Then access the app at: [http://localhost:8502](http://localhost:8502)
+
+#### Option 2: git (for developers and contributors)
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+1. **Clone the repository:**
+   ```sh
+   git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma
+   cd AIAgents4Pharma
+   ```
+2. **Install dependencies:**
+
+   ```python
+   pip install -r requirements.txt
+   ```
+
+3. **Initialize API Keys**
+
+   ```env
+   export OPENAI_API_KEY=....          # Required for all agents
+   export NVIDIA_API_KEY=....          # Required for all agents
+   export ZOTERO_API_KEY=....          # Required for T2S
+   export ZOTERO_USER_ID=....          # Required for T2S
+   export LANGCHAIN_TRACING_V2=true    # Optional for all agents
+   export LANGCHAIN_API_KEY=...        # Optional for all agents
+   ```
+
+To use **Talk2AIAgents4Pharma**, **Talk2BioModels**, **Talk2KnowledgeGraphs**, or **Talk2Scholars**, you need a free **NVIDIA API key**. Create an account and apply for free credits [here](https://build.nvidia.com/explore/discover).
+
+Only for **Talk2Scholars**, you also need a **Zotero API key**, which you can generate [here](https://www.zotero.org/user/login#applications). _(For all other agents, the Zotero key is not required.)_
+
+To use **Talk2AIAgents4Pharma** or **Talk2KnowledgeGraphs**, you must have **Ollama** installed. Follow installation instructions for your OS [here](https://ollama.com/download).
+
+After installing, pull the `nomic-embed-text` model and start the server by running:
+
+```sh
+ollama pull nomic-embed-text && ollama serve
+```
+
+More details about the model are available [here](https://ollama.com/library/nomic-embed-text).
+
+Additionally on **Windows**, the `pcst_fast 1.0.10` library requires **Microsoft Visual C++ 14.0 or greater**.  
+You can download the **Microsoft C++ Build Tools** [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/).
+
+**LangSmith** support is optional. To enable it, create an API key [here](https://docs.smith.langchain.com/administration/how_to_guides/organization_management/create_account_api_key).
+
+_Please note that this will create a new tracing project in your Langsmith
+account with the name `T2X-xxxx`, where `X` can be `AA4P` (Main Agent),
+`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._
+
+4. **Launch the app:**
+   ```sh
+   streamlit run app/frontend/streamlit_app_<agent>.py
+   ```
+   _Replace `<agent>` with the agent name you are interested to launch:_
+
+- `talk2aiagents4pharma`
+- `talk2biomodels`
+- `talk2knowledgegraphs`
+- `talk2scholars`
+- `talk2cells`
+
+For detailed instructions on each agent, please refer to their respective modules.
+
+#### Option 3: pip (beta-release)
+
+![Python Version from PEP 621 TOML](https://img.shields.io/python/required-version-toml?tomlFilePath=https%3A%2F%2Fraw.githubusercontent.com%2FVirtualPatientEngine%2FAIAgents4Pharma%2Frefs%2Fheads%2Fmain%2Fpyproject.toml)
+
+```sh
+pip install aiagents4pharma
+```
+
+Check out the tutorials on each agent for detailed instructions.
+
+## Contributing
+
+We welcome your support to make **AIAgents4Pharma** even better.  
+All types of contributions are appreciated — whether you're fixing bugs, adding features, improving documentation, or helping with testing, every contribution is valuable.
+
+#### How to contribute
+
+1. Star this repository to show your support.
+2. Fork the repository.
+3. Create a new branch for your work:
+   ```sh
+   git checkout -b feat/your-feature-name
+   ```
+4. Make your changes and commit them:
+   ```sh
+   git commit -m "feat: add a brief description of your change"
+   ```
+5. Push your branch:
+   ```sh
+   git push origin feat/your-feature-name
+   ```
+6. Open a Pull Request.
+
+#### Areas where you can help
+
+- Beta testing for Talk2BioModels and Talk2Scholars.
+- Development work related to Python, bioinformatics, or knowledge graphs.
+
+#### Contacts for contributions
+
+- **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)
+
+Please refer to our [CONTRIBUTING.md](CONTRIBUTING.md) for more detailed contribution guidelines.
+
+## Feedback
+
+If you have questions, bug reports, feature requests, comments, or suggestions, we would love to hear from you.  
+Please open an `issue` or start a `discussion`