- LPF represents Ladybird Pattern Formation.
- LPF is a framework for exploring the biological pattern formation exemplified by ladybird beetles.
- LPF can be utilized as an educational framework for understanding biological dynamics, pattern formation, and complexity.
- Reaction-diffusion PDE models for the color pattern formation of ladybird beetles.
- Evolutionary search based on PyGMO providing the concept of island and archipelago.
- GPU optimization of the reaction-diffusion PDE solver for a batch of parameter sets based on CuPy.
- 🐍 Anaconda is recommended to use and develop LPF.
- 🐧 Linux distros are tested and recommended to use and develop LPF.
After installing anaconda, create a conda virtual environment for LPF.
In the following command, you can change the Python version
(e.g.,python=3.7 or python=3.9).
conda create -n lpf python=3.9
Now, we can activate our virtual environment for LPF as follows.
conda activate lpf
In the repository directory under the active anaconda environment, execute the following command.
python setup.py develop
After installing the package, we can update the package with git pull command.
This is why we install this package with python setup.py develop instead of python setup.py install.
git pull
💡 To optimize the solver for a batch of parameter sets based on GPU computing, install CuPy. However, if you want to use only the cpu, you can omit it.
The order of installing the following packages is important to avoid version conflicts.
Install PyTorch following the official documentation.
Install the packages in requirements.
pip install -r requirements.txt
Install PyGMO as follows.
conda install pygmo -c conda-forge
- Daewon Lee, "LPF: a framework for exploring the wing color pattern formation of ladybird beetles in Python", Bioinformatics, 39(7), btad430, July 2023.