CRISPR-Cas9 Gene Editing Simulator

Note: This is a refactored version of the original project by Nirajan2005. This version by 06navdeep06 includes alot of code improvements and bug fixes while maintaining the original functionality.

A comprehensive simulation tool for CRISPR-Cas9 gene editing experiments, now with a modular and maintainable codebase.

Features

• Interactive Web Interface: Built with Streamlit for an intuitive user experience
• Multiple Cas Variants: Supports SpCas9, SaCas9, Cpf1, and custom PAM sequences
• Realistic Simulation: Models NHEJ and HDR repair pathways
• Delivery Modeling: Simulates different delivery methods and their efficiencies
• Chromatin Context: Accounts for chromatin accessibility and histone modifications
• Visualization: Interactive visualization of editing results

Project Structure

CRISPRcas9_simV3/
├── app.py                  # Main application entry point
├── config.py               # Configuration and constants
├── models/                 # Data models and core logic
│   ├── __init__.py
│   ├── cas9.py            # Cas9 class and target finding
│   ├── scoring.py         # On/off-target scoring
│   └── simulation.py      # Delivery and editing simulation
├── utils/                  # Utility functions
│   ├── __init__.py
│   ├── sequence_utils.py  # Sequence manipulation
│   └── visualization.py   # Plotting and visualization
└── requirements.txt        # Dependencies

Installation

1. Clone the repository:

   git clone https://github.com/yourusername/CRISPRcas9_simV3.git
   cd CRISPRcas9_simV3

2. Create and activate a virtual environment (recommended):

   python -m venv venv
   source venv/bin/activate  # On Windows: venv\Scripts\activate

3. Install dependencies:

   pip install -r requirements.txt

Usage

1. Run the Streamlit application:

   streamlit run app.py

2. Open your web browser and navigate to the URL shown in the terminal (usually http://localhost:8501)

3. Use the sidebar to:

   • Input or upload a DNA sequence
   • Configure guide RNA and PAM settings
   • Set experimental parameters
   • Run the simulation

Dependencies

• Python 3.8+
• Streamlit
• Biopython
• dna-features-viewer
• Matplotlib
• NumPy

License

MIT License - see LICENSE for details.