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--- a/README.md +++ b/README.md @@ -1,268 +1,268 @@ -[](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) -[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml) - - - - -## Introduction - -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. - -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) - - - -## Getting Started - - - -### Installation - -_Please use version 1.26.2 or later for better support with NVIDIA NIM models._ - -#### Option 1: PyPI - - - -```bash -pip install aiagents4pharma -``` - -Check out the tutorials on each agent for detailed instructions. - -#### Option 2: Docker Hub - -_We now have `Talk2AIAgents4Pharma`, `Talk2Biomodels`, and `Talk2Scholars` available on Docker Hub._ - -##### **Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs** - -Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network. - -###### **Setup Environment Variables** - -1. Choose the app you want to use: - -```sh -# Navigate to the correct directory before setting up environment variables. -# Use one of the following commands based on the agent you want to use: -cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma -cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs -``` - -2. Copy the `.env.example` file and rename it to `.env`: - ```sh - cp .env.example .env - ``` -3. Open the `.env` file and add your API keys: - - ```plaintext - OPENAI_API_KEY=your_openai_api_key - NVIDIA_API_KEY=your_nvidia_api_key - OLLAMA_HOST=http://ollama:11434 - LANGCHAIN_TRACING_V2=true - LANGCHAIN_API_KEY=your_langchain_api_key_here - # Notes: - # The API endpoint for Ollama is already set in env.example. - # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma. - # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed. - # Langsmith API for tracing is optional for both, set it in env.example if required. - ``` - -4. Save the file. - -To start the containers, run the following command: - -```sh -docker compose --profile cpu up # for CPU mode -docker compose --profile nvidia up # for GPU mode -docker compose --profile amd up # for AMD mode -``` - -This will: - -- Pull the latest images if they are not already available. -- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network. -- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs. - -To Access the web app, open your browser and go to: - -``` -http://localhost:8501 -``` - -To stop the containers, run: - -```sh -docker compose down -``` - -##### **Run Talk2Biomodels and Talk2Scholars** - -1. **Run the containers** - - ```bash - 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 - ``` - - ```bash - 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> \ - -p 8501:8501 \ - virtualpatientengine/talk2scholars - ``` - -2. **Access the Web App** - Open your browser and go to: - - ``` - http://localhost:8501 - ``` - - _You can create a free account at NVIDIA and apply for their - free credits [here](https://build.nvidia.com/explore/discover)._ - -#### **Notes** - -- Ensure you **replace `<your_openai_api_key>`, `<your_nvidia_api_key>`, `<your_zotero_api_key>`, and `<your_zotero_user_id>`** with your actual credentials. -- Both applications use **port `8501`**, so run them on different ports if needed: - ```bash - docker run -d -e OPENAI_API_KEY=<your_openai_api_key> -p 8501:8501 virtualpatientengine/talk2scholars - ``` - Then, access it via `http://localhost:8501`. - -#### Option 3: git - - - -1. **Clone the repository:** - ```bash - git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma - cd AIAgents4Pharma - ``` -2. **Install dependencies:** - - ```bash - pip install -r requirements.txt - ``` - - ⚠️ The current version of T2KG requires additional Ollama library to be installed. - - Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download) - - As an alternative, use the following commands to install the library using terminal and to pull necessary model: - - - Ubuntu: - ``` - curl -fsSL https://ollama.com/install.sh | sh - ollama pull nomic-embed-text - ``` - - Windows: - ``` - curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip - tar -xzf .\ollama-windows-amd64.zip - start ollama serve - ollama pull nomic-embed-text - ``` - - macOS: - ``` - brew install ollama - ollama pull nomic-embed-text - ``` - A list of pulled Ollama models can be checked using the following command: - - ``` - ollama list - ``` - - ⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed. - You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/). - -3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY** - - ```bash - export OPENAI_API_KEY=.... - export NVIDIA_API_KEY=.... - ``` - - _You can create a free account at NVIDIA and apply for their - free credits [here](https://build.nvidia.com/explore/discover)._ - -4. **Initialize ZOTERO_API_KEY and ZOTERO_USER_ID** - - ```bash - export ZOTERO_API_KEY=.... - export ZOTERO_USER_ID=.... - ``` - - _Please note that ZOTERO keys are requried only if you want to launch Talk2Scholars. For all the other agents, please ignore this step._ - -5. **[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 `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._ - -6. **Launch the app:** - ```bash - streamlit run app/frontend/streamlit_app_<agent>.py - ``` - _Replace <agent> with the agent name you are interested to launch._ - -For detailed instructions on each agent, please refer to their respective modules. - ---- - -## Contributing - -We welcome contributions to AIAgents4Pharma! Here’s how you can help: - -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** and reach out to any one of us below via Discussions: - - _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!_ - -- **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) - -### Current Needs - -- **Beta testers** for Talk2BioModels and Talk2Scholars. -- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma. - -Feel free to reach out to us via Discussions. - -Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information. - ---- - -## Feedback - -Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀 +[](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) +[](https://github.com/VirtualPatientEngine/AIAgents4Pharma/actions/workflows/tests_talk2aiagents4pharma.yml) + + + + +## Introduction + +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. + +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) + + + +## Getting Started + + + +### Installation + +_Please use version 1.26.2 or later for better support with NVIDIA NIM models._ + +#### Option 1: PyPI + + + +```bash +pip install aiagents4pharma +``` + +Check out the tutorials on each agent for detailed instructions. + +#### Option 2: Docker Hub + +_We now have `Talk2AIAgents4Pharma`, `Talk2Biomodels`, and `Talk2Scholars` available on Docker Hub._ + +##### **Run Talk2AIAgents4Pharma and Talk2KnowledgeGraphs** + +Talk2AIAgents4Pharma and Talk2KnowledgeGraphs require Ollama for embedding models, so Docker Compose is used to run both containers in the same network. + +###### **Setup Environment Variables** + +1. Choose the app you want to use: + +```sh +# Navigate to the correct directory before setting up environment variables. +# Use one of the following commands based on the agent you want to use: +cd AIAgents4Pharma/aiagents4pharma/talk2aiagents4pharma +cd AIAgents4Pharma/aiagents4pharma/talk2knowledgegraphs +``` + +2. Copy the `.env.example` file and rename it to `.env`: + ```sh + cp .env.example .env + ``` +3. Open the `.env` file and add your API keys: + + ```plaintext + OPENAI_API_KEY=your_openai_api_key + NVIDIA_API_KEY=your_nvidia_api_key + OLLAMA_HOST=http://ollama:11434 + LANGCHAIN_TRACING_V2=true + LANGCHAIN_API_KEY=your_langchain_api_key_here + # Notes: + # The API endpoint for Ollama is already set in env.example. + # Both API keys (OPENAI_API_KEY and NVIDIA_API_KEY) are required for Talk2AIAgents4Pharma. + # If using Talk2KnowledgeGraphs separately, only the OPENAI_API_KEY is needed. + # Langsmith API for tracing is optional for both, set it in env.example if required. + ``` + +4. Save the file. + +To start the containers, run the following command: + +```sh +docker compose --profile cpu up # for CPU mode +docker compose --profile nvidia up # for GPU mode +docker compose --profile amd up # for AMD mode +``` + +This will: + +- Pull the latest images if they are not already available. +- Start both Talk2AIAgents4Pharma or Talk2KnowledgeGraphs and Ollama containers in the same network. +- Ensure Ollama is running first before launching Talk2AIAgents4Pharma or Talk2KnowledgeGraphs. + +To Access the web app, open your browser and go to: + +``` +http://localhost:8501 +``` + +To stop the containers, run: + +```sh +docker compose down +``` + +##### **Run Talk2Biomodels and Talk2Scholars** + +1. **Run the containers** + + ```bash + 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 + ``` + + ```bash + 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> \ + -p 8501:8501 \ + virtualpatientengine/talk2scholars + ``` + +2. **Access the Web App** + Open your browser and go to: + + ``` + http://localhost:8501 + ``` + + _You can create a free account at NVIDIA and apply for their + free credits [here](https://build.nvidia.com/explore/discover)._ + +#### **Notes** + +- Ensure you **replace `<your_openai_api_key>`, `<your_nvidia_api_key>`, `<your_zotero_api_key>`, and `<your_zotero_user_id>`** with your actual credentials. +- Both applications use **port `8501`**, so run them on different ports if needed: + ```bash + docker run -d -e OPENAI_API_KEY=<your_openai_api_key> -p 8501:8501 virtualpatientengine/talk2scholars + ``` + Then, access it via `http://localhost:8501`. + +#### Option 3: git + + + +1. **Clone the repository:** + ```bash + git clone https://github.com/VirtualPatientEngine/AIAgents4Pharma + cd AIAgents4Pharma + ``` +2. **Install dependencies:** + + ```bash + pip install -r requirements.txt + ``` + + ⚠️ The current version of T2KG requires additional Ollama library to be installed. + + Ollama can be easily downloaded and installed from the following link: [https://ollama.com/download](https://ollama.com/download) + + As an alternative, use the following commands to install the library using terminal and to pull necessary model: + + - Ubuntu: + ``` + curl -fsSL https://ollama.com/install.sh | sh + ollama pull nomic-embed-text + ``` + - Windows: + ``` + curl -L https://ollama.com/download/ollama-windows-amd64.zip -o ollama-windows-amd64.zip + tar -xzf .\ollama-windows-amd64.zip + start ollama serve + ollama pull nomic-embed-text + ``` + - macOS: + ``` + brew install ollama + ollama pull nomic-embed-text + ``` + A list of pulled Ollama models can be checked using the following command: + + ``` + ollama list + ``` + + ⚠️ `pcst_fast 1.0.10` library requires `Microsoft Visual C++ 14.0` or greater to be installed. + You can download `Microsoft C++ Build Tools` from [here](https://visualstudio.microsoft.com/visual-cpp-build-tools/). + +3. **Initialize OPENAI_API_KEY and NVIDIA_API_KEY** + + ```bash + export OPENAI_API_KEY=.... + export NVIDIA_API_KEY=.... + ``` + + _You can create a free account at NVIDIA and apply for their + free credits [here](https://build.nvidia.com/explore/discover)._ + +4. **Initialize ZOTERO_API_KEY and ZOTERO_USER_ID** + + ```bash + export ZOTERO_API_KEY=.... + export ZOTERO_USER_ID=.... + ``` + + _Please note that ZOTERO keys are requried only if you want to launch Talk2Scholars. For all the other agents, please ignore this step._ + +5. **[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 `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._ + +6. **Launch the app:** + ```bash + streamlit run app/frontend/streamlit_app_<agent>.py + ``` + _Replace <agent> with the agent name you are interested to launch._ + +For detailed instructions on each agent, please refer to their respective modules. + +--- + +## Contributing + +We welcome contributions to AIAgents4Pharma! Here’s how you can help: + +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** and reach out to any one of us below via Discussions: + + _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!_ + +- **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) + +### Current Needs + +- **Beta testers** for Talk2BioModels and Talk2Scholars. +- **Developers** with experience in Python and Bioinformatics and/or knowledge graphs for contributions to AIAgents4Pharma. + +Feel free to reach out to us via Discussions. + +Check out our [CONTRIBUTING.md](CONTRIBUTING.md) for more information. + +--- + +## Feedback + +Questions/Bug reports/Feature requests/Comments/Suggestions? We welcome all. Please use `Issues` or `Discussions` 😀