Protein Evolution Explorer

Full-stack bioinformatics platform for protein sequence analysis.

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Architecture

The project is organized into three independent components that communicate with each other:

🐍 Protein Analyzer

Python + FastAPI

Responsible for:

• FASTA parsing
• physicochemical calculations
• sequence analysis
• generating protein analysis data

Repository:

protein-evolution-analyzer

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☕ Backend API

Spring Boot + PostgreSQL

Responsible for:

• REST API
• communication between frontend and analyzer
• data persistence
• protein analysis management

Repository:

protein-evolution-backend

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⚛️ Frontend

React + TypeScript + Tailwind

Responsible for:

• protein explorer interface
• visualization of analysis results
• interaction with backend API

Repository:

protein-evolution-frontend

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Project Structure

The main repository works as the orchestrator of the complete application.

The final structure should be:

Protein-Evolution-Explorer/
├── docker-compose.yml
├── README.md
│
├── protein-evolution-analyzer/
├── protein-evolution-backend/
└── protein-evolution-frontend/

The three component repositories must be cloned inside the main project directory.

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Running the Application

1. Clone the main repository

Clone the main repository:

git clone https://github.com/fran9300/protein-evolution-explorer

Move into the project directory:

cd Protein-Evolution-Explorer

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2. Clone the component repositories

Clone the three required components inside the main project directory:

git clone https://github.com/fran9300/protein-evolution-analyzer

git clone https://github.com/fran9300/protein-evolution-backend

git clone https://github.com/fran9300/protein-evolution-frontend

The final structure should match:

Protein-Evolution-Explorer/
├── docker-compose.yml
├── README.md
│
├── protein-evolution-analyzer/
├── protein-evolution-backend/
└── protein-evolution-frontend/

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3. Start the complete environment

From the root project directory run:

docker compose up --build

Docker Compose will automatically:

• build each service image
• create the internal network
• start PostgreSQL
• start the FastAPI analyzer service
• start the Spring Boot backend
• start the React frontend

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Services

Once running:

Service	Technology	Port
Frontend	React	80
Backend API	Spring Boot	8080
Protein Analyzer	FastAPI	8000
Database	PostgreSQL	5432

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Service Communication

The application uses Docker internal networking.

Communication flow:

Frontend
    ↓
Spring Boot Backend
    ↓
FastAPI Analyzer
    ↓
PostgreSQL Database

The services communicate using Docker service names instead of localhost.

Example:

• Backend communicates with the analyzer using the Docker service name.
• Backend connects to PostgreSQL using the database container name.

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Development Workflow

Each component can also be developed independently.

Recommended workflow:

• Use local execution for active development and debugging.
• Use Docker Compose to test the complete integrated environment.

Docker Compose is intended to provide:

• unified environment setup
• easier deployment
• consistent service communication

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Current Status

The platform is currently integrated with:

• frontend and backend communication
• backend and analyzer communication
• PostgreSQL persistence
• Docker-based environment setup

The complete system can be started using a single Docker Compose command.

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Stopping the Application

To stop all running services:

docker compose down

To remove containers and stored database data:

docker compose down -v

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Future Plans

• interactive bioinformatics visualizations
• automated testing
• production deployment
• advanced protein comparison features

Author

Francisco Kin

• Bioinformatics Student | Backend Development | Data Analysis
• GitHub: @fran9300