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Onedcellsim

Onedcellsim is a project designed to simulate one-dimensional cell migration using Julia, based on a biomechanical model as developed by Amiri et al. (2023). Additionally, it uses simulation-based inference in Python via SBI to infer biomechanical cell parameters from observed data.

Installation

Prerequisites

  • Python 3
  • Linux or Mac OS

Steps

  1. Clone the repository: 
    git clone https://github.com/miguelatienza/onedcellsim.git
  2. Navigate to the project directory: 
    cd onedcellsim
  3. Set up a virtual environment: 
    python -m venv venv
source venv/bin/activate
  4. Install onedcellsim: 
    pip install git+https://github.com/miguelatienza/onedcellsim@main
  5. Install additional dependencies: 
    pip install -r requirements.txt
  6. Install Julia: 
    python install_julia.py

Running the GUI

Run the following command to start the GUI:

bash gui.sh

Feel free to contribute or report issues on the GitHub repository.