Python toolbox for plant tissue simulation prototypes
# PyPTS: A Python Plant Tissue Simulation tools
PyPTS is a Python package for creating cell-based simulations of plant tissue. It provides the basic building blocks for prototyping and running small to medium scale simulations of two dimensional plant tissues.
- Author: Przemyslaw Klosiewicz (firstname.lastname@example.org)
- License: BSD 3-Clause, cfr. LICENSE.txt
The standard way of installing PyPTS is either through pip:
pip install PyPTS
or downloading the sources / cloning the repository and running:
python ./setup.py install [–user]
inside the PyPTS source tree.
Currently used versions are indicated. Code possibly works with slightly older versions as well.
- Python 2.7
- NumPy (Used all throughout the code)
- SciPy (Maily for the solvers)
- h5py (I/O for tissue files)
- Matplotlib (Plotting tissue structures)
- PySide (optional; for tissue_plot.py visualization)
- MPI4Py (optional; for running bulk sweep jobs, cfr: mpi_*.py)
See pypts/examples for some example scripts