PyGen

PyGen is a dynamic cellular simulation tool designed for modelling cellular interactions within diverse three-dimensional tissue architectures. This tool leverages various mechanical, geometric, and life-event forces to mirror the adaptability of cellular spatial configurations across varied tissue landscapes.

Requirements

Ensure you have the following packages installed on a python virtual environment:

• numpy
• scipy
• h5py
• vispy
• torch
• numba

You can typically install these using pip, for instance:

pip install numpy scipy h5py vispy etc

Codebase

The project comprises two main files:

1. pygen.py: The primary script for executing simulations.
2. visuals.py: Designed for executing visualisations either in real time or offline.

Usage

To use PyGen, follow these steps:

1. Clone or download this repository to your local computer.
2. Navigate to the project directory.
3. Run the simulation using the following command:

python pygen.py

By default, the code runs a simulation with predefined parameters, for example n_steps=5000 and geometry='Drosophila' as shown in the if __name__ == "__main__": block.

Parameters:

main(
    N_cells=200,      # Change the initial number of cells
    n_steps=10000,    # Change the number of simulation steps
    dt=1e-3,          # Adjust the time step
    geometry='sphere',# Choose a different background geometry
    division=100,     # Set how many cell division events to occur
    death=50          # Set how many cell death events to occur
)

• geometric_background: Specifies the target geometry of the tissue architecture. Options include:
  • sphere
  • torus
  • wfoil
  • wknot
  • cylinder
  • beltrami

Alternatively, you can import or generate your own point clouds utilising the notebook generate_points.ipynb within tools.

Example

To run the simulation with a new configuration, simply edit the main() call as described above and execute:

python pygen.py

For example, changing N_cells=500, division=100, and death=50 would simulate a scenario where 500 cells evolve over time, with 100 division events and 50 death events.

Maintenance

For any further queries or issues, feel free to open an issue on this repository or contact the maintainer.

jesus [dot] fuentes [at] uni [dot] lu