README.md

Agent based simulation of in-vitro intestinal crypt patterning

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Pre-requisites

• Linux OS.

• A CUDA-capable GPU.

• CUDA.

• The ya||a source code repository.

Installation

• Clone the ya||a repository.

• Clone this repository in the same folder where the ya||a repository is, e.g.

some_folder/
├── crypt_patterning_simulation
└── yalla

• Compile the code by running the following command (ou may need to replace sm_86 to a different value, depending on your specific GPU model),

nvcc -std=c++14 -arch=sm_86 crypt_patterning.cu

Running the simulation

Run the simulation with sample parameter values with the following command.

./a.out 0 1.67 10 1.56 0.098 0.09 2.55 9.24 0

Simulation output files will be saved in the output folder inside the repository folder.

To visualize the simulation output, you need a 3D visualization software that supports VTK (e.g. ParaView).