Quickstart example for cancer simulation

Import modules

### Uncomment and execute if the next cell fails with "module not found".` Then reload the kernel.
# %cd ../../../..
# %pip install -e .
# %cd -

/opt/data/repos/cancer_software
Obtaining file:///opt/data/repos/cancer_software
Installing collected packages: CaSim
  Found existing installation: CaSim 1.0.0
    Uninstalling CaSim-1.0.0:
      Successfully uninstalled CaSim-1.0.0
  Running setup.py develop for CaSim
Successfully installed CaSim
Note: you may need to restart the kernel to use updated packages.
/opt/data/repos/cancer_software/docs/source/include/notebooks

# The cancer simulation module.
from casim import casim

#  3rd party modules.
import os, shutil
from wand.image import Image as WImage

Setup parameters

parameters=casim.CancerSimulatorParameters(
                                matrix_size=20,
                                number_of_generations=10,
                                division_probability=0.5,
                                advantageous_division_probability=0.8,
                                death_probability=0.1,
                                advantageous_death_probability=0.4,
                                mutation_probability=0.2,
                                advantageous_mutation_probability=0.8,
                                mutations_per_division=10,
                                time_of_advantageous_mutation=30000,
                                number_of_clonal=2,
                                plot_tumour_growth=True,
                                export_tumour=True
                               )

Setup the simulation engine.

if os.path.isdir('out'):
    shutil.rmtree('out')

cancer_sim = casim.CancerSimulator(parameters, seed=1, outdir='out/')

Run the simulation

cancer_sim.run()

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<Figure size 432x288 with 0 Axes>

Display the growth curve.

image_path=os.path.join(cancer_sim.outdir,'cancer_1', 'simOutput', 'growthCurve.pdf')

img = WImage(filename=image_path)

display(img)