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Biological simulation of biofilm production

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Using the Simulator

  1. Ensure java and python are installed
  2. Install the following python packages with pip install <package_name>: msgpack, numpy, imageio[ffmpeg], moderngl
  3. Navigate to the directory containing Simulator.jar in your terminal
  4. Run java -jar Simulator.jar to view the list of possible command line arguments
  5. Run java -jar Simulator.jar <your_args> to run the simulation
  6. The output video will be stored as video_gpu.mp4 upon completion of the program

How to build the project

  1. Clone the git repository
  2. Open the Simulator directory as a project in IntelliJ
  3. Build and run the project as usual

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Biological simulation of biofilm production

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