VCell BioModel Chatbot Demo

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Try It Online

You can test the live chatbot application here:

https://kacemath-vcell-demo.hf.space/

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About the Project

This demo presents a chatbot for querying and interpreting BioModels stored in the VCell BioModel Database. Developed as a demo for Google Summer of Code 2025 under the NRNB organization, the app enables users to interact with biological models using natural language, receiving structured outputs, downloadable files, and real-time visualisations.

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Overview

The chatbot can:

• Understand natural language queries
• Extract structured query parameters
• Query the VCell BioModel API
• Generate human-readable summaries using a language model
• Visualise model diagrams
• Provide download links for SBML and VCML files

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Features

• Natural Language Interface — Ask simple questions like “List all models by user ion”
• LLM-Powered Extraction — LLaMA 3 extracts query parameters from your prompt
• VCell API Integration — Dynamically fetches real model data
• Summarisation — Converts raw data into clear, helpful answers
• Visual Diagrams — Renders model reaction networks
• Download Options — Instantly download SBML and VCML formats
• Streamlit UI — Clean, responsive, deploy-ready interface

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Technologies Used

• Python 3.10+
• Streamlit
• Groq API (LLaMA 3.3 70B)
• VCell Public API
• Pydantic
• Dotenv

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Getting Started

Prerequisites

• Python 3.10 or later
• A valid Groq API key

Installation

git clone https://github.com/KacemMathlouthi/VCell-Demo.git
cd VCell-Demo
python -m venv .venv
source .venv/bin/activate
pip install -r requirements.txt

Configuration

Create a .env file at the root with your Groq API key:

LLM_API_KEY=your_groq_api_key_here

Run the App

streamlit run app.py

Visit http://localhost:8501 in your browser.

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Example Prompts

You can ask the chatbot things like:

• List all public models by user ion
• Find the model with ID 201844485
• Show VCell models related to calcium
• Get educational BioModels created after 2020

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Project Structure

VCell-Demo/
├── app.py                     # Main Streamlit app
├── requirements.txt           # Project dependencies
├── .env                       # Environment variables
├── .streamlit/config.toml     # Theme config
├── vcelldb/
│   ├── vcell_api.py           # VCell API wrapper
│   ├── diagram.py             # Diagram & file URL utils
│   └── params_model.py        # Pydantic model schema
└── utils/
    ├── llm_helper.py          # Groq API + LLM prompt handling
    └── params_extraction.py   # Prompt-to-parameter logic

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License

This project is licensed under the MIT License. You are free to use, modify, and distribute it with proper attribution.