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# 🧬 Biological Network Analyzer
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An intelligent assistant for analyzing biological networks from **text or image input**. This app can extract reaction networks from uploaded diagrams using **Gemini Vision API**, parse them into graph structures, and generate:
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- 📈 ODEs (Ordinary Differential Equations)
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- 🧮 Jacobian matrices
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- 🔄 Cyclic dependency checks
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- 📊 Graph stats (edges, variables)
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All via a **Gradio-based conversational interface**.
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---
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## 🚀 Features
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- 🔤 **Text input** (e.g. `A + B -> C, C <-> D`)
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- 🖼️ **Image input** (upload scanned or digital diagrams)
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- 🧠 Google Gemini API integration to extract text-based reactions from images
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- 🧪 ODE system generation using mass-action kinetics
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- 🧠 Jacobian matrix computation via symbolic algebra (SymPy)
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- 🔁 Cycle detection and variable/edge counting
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- 🤖 LLM-based fallback Q&A via `flan-t5-base`
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- 🎨 Customizable Gradio theme (e.g. `Soft`, `Glass`, etc.)
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---
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## 🧰 Tech Stack
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| Component | Technology |
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|---------------|-------------------------------|
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| Frontend UI | [Gradio](https://gradio.app) |
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| LLM Query | [Flan-T5](https://huggingface.co/google/flan-t5-base) |
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| Image-to-Text | [Gemini API](https://ai.google.dev/) (Vision multimodal API) |
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| Graph Parsing | [NetworkX](https://networkx.org) |
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| Symbolic Math | [SymPy](https://www.sympy.org/) |
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---
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## 🖥️ Running the App on your device
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### ✅ Prerequisites
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- Python ≥ 3.8
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- Install dependencies:
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```bash
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pip install gradio transformers networkx sympy google-generativeai python-dotenv pillow
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````
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* Set your Gemini API key in a `.env` file:
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```
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GEMINI_API=your_api_key_here
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```
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### ▶️ Run
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```bash
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python your_script.py
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```
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Or use inside a [Google Colab notebook](https://colab.research.google.com/) for instant testing.
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---
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## 📷 Example Inputs
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### Text:
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```
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A + B -> C, C <-> D, D -> E
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```
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### Image:
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* Upload PNG or JPG of a biological reaction network
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* Gemini will parse it automatically
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---
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## 📌 Future Additions
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* Export ODEs/Jacobian as LaTeX/PDF
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* Stoichiometry & reaction rate customization
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---
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## 🧑🔬 Author
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Built by \[Devansh] for a project on **LLM-based Equation Discovery from Biological Networks**.
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---
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## 📝 License
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MIT License
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---
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title: Network Analyzer
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emoji: 🦀
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---
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title: Network Analyzer
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emoji: 🦀
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