Tutorial: running a simulation through the command line interface

This tutorial will simulate a similar scenario as the interactive mode tutorial, but using the command line interface instead.

Installation

If you haven’t installed MetaSpread yet, use the following command:

pip install metaspread

or:

python -m pip install metaspread

Running metaspread

Once installed, create a folder for this tutorial project. For example, this command will create a folder called “tutorial-interactive”: .. code-block:: console

mkdir tutorial-cli

Then, navigate to this folder: .. code-block:: console

cd tutorial-cli

Running a Simulation

1. Editing the parameters: if you followed the interactive mode tutorial, you should already have changed grids_number, extravasation_probs and secondary_sites_vessels. So there is no need to change the parameters again. If you haven’t done so, follow the instructions at tutorial-interactive.

2. Start a simulation: run the following command in the terminal:

   python -m metaspread run 300 30
   

   Wait for the simulation to finish.

3. Postprocessing the simulation: once the simulation is finished, you can apply all the postprocessing tools by using the following command:

   python -m metaspread postprocess all Sim-max_steps-300-collection_period-30-cells-388-grids_number-2 10 1
   

4. Visualize the results: Enter the Videos directory inside the Sim-max_steps-300-collection_period-30-cells-388-grids_number-2 directory and check the results. You should get something like the following: