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.

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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

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Running the GUI

Run the following command to start the GUI:

bash gui.sh

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