Stochastic simulation (SSA) of microtubules in neurites, implemented using jit from numba (numba.cuda.jit) for fast parallel processing on a GPU. Programmed in a generalized fashion, to be used for stochastically simulating any model with different species, with optional properties for each species member, in an arbitrary spatial domain.
The example under \scripts contains a simple simulation of MTs in the neurite running on a GPU.
Note: Execution on CPUs currently not supported. Will be added again in the future.
The package was developed and tested in Windows.
- If you don't already have Anaconda installed: Download and install Anaconda from https://www.anaconda.com/.
- If you don't already have git installed: Download and install git from https://git-scm.com/downloads
- Open an Anaconda terminal, navigate to the folder where you want to put cytotorch and clone the cytostoch repository:
- Navigate into the folder of the repository (cytostoch):
cd cytostoch
- Create environment for cytotorch with Anaconda:
conda env create -f environment.yml
- Activate environment in anaconda:
conda activate cytostoch
- Install cytostoch locally using pip:
pip install -e .
- You can now import cytotorch to build and simulate your model:
import cytostoch