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Peptaloid Database - User Manual

Introduction

The Peptaloid Database is designed to manage and analyze peptaloid-related data. It provides a user-friendly interface for adding, searching, and analyzing data associated with peptaloids.

Installation

Requirements:

  • Python 3.x
  • FastAPI
  • PostgreSQL
  • React (for frontend)
  • Node.js (for frontend dependencies)

Installation Steps:

  1. Clone the Repository:

     git clone https://github.com/your-repository/peptaloid-database.git

  2. Backend Installation (FastAPI):

    • Navigate to the backend folder.

        cd backend

    • Install dependencies via pip:

        pip install -r requirements.txt

    • Create the database and apply migrations:

        alembic upgrade head

  3. Frontend Installation (React):

    • Navigate to the frontend folder.

        cd frontend

    • Install dependencies via npm:

        npm install

  4. Run the Application:

    • Start the backend server:

        uvicorn main:app --reload

    • Start the frontend development server:

        npm start

Usage

  1. Access the Web Interface

    Once both the frontend and backend servers are running, access the application by visiting:

    http://localhost:3000

  2. User Authentication

    • Create a new account or log in if you already have one.
    • Upon logging in, you'll be redirected to the dashboard, where you can manage data.

  3. Managing Data

    • Adding New Data

      • Navigate to the "Add Data" section.
      • Fill in the necessary fields, including SMILES string, properties, and relevant annotations.
      • Submit the form to add the data.

    • Searching the Database

      • Use the search bar in the dashboard to query data using SMILES strings, molecule properties, or other parameters.
      • Results will be displayed in a table format with options to view or edit entries.

    • Data Analysis

      • Access the analysis tools to visualize data trends, compare molecules, or export results for further research.

Error Handling

In case of issues, the application will display error messages, particularly when:

  • Invalid SMILES strings are submitted.
  • The database connection fails.

Maintenance

Database Backups

Perform regular backups of the PostgreSQL database using pg_dump:

pg_dump peptaloid_db > backup.sql

Updating the Application

Pull the latest changes from the repository:

git pull origin main

Re-run the installation and migration steps if there are updates to the database schema.