clone-competition-simulation 0.4.0

Python simulations of clone competition during ongoing mutagenesis.

clone-competition-simulation

Python3 simulations of clone competition during ongoing mutagenesis.

Installation

First install GNU Scientific Library (homebrew) and FFMPEG (homebrew).

Then install from PyPi, e.g.

pip install clone-competition-simulation

---

Alternatively, install using the code from GitHub.

Install UV.

Clone the git repository
git clone https://github.com/michaelhall28/clone-competition-simulation.git

and install the code in this repository
uv pip install -e .

Running simulations

First, the parameters for the simulation are defined. The Parameters class checks that the parameters are appropriate for the chosen algorithm. e.g.

from clone_competition_simulation.parameters import Parameters, TimeParameters, PopulationParameters, FitnessParameters
from clone_competition_simulation.fitness import Gene, UniformDist, FitnessCalculator, multiply_fitness

# Define the effect of mutations that appear during the simulation
fitness_calculator = FitnessCalculator(genes=[Gene(name='example_gene', 
                                                   mutation_distribution=UniformDist(1, 2), synonymous_proportion=0.5)],
                                       combine_mutations=multiply_fitness)

p = Parameters(
        algorithm="WF2D",
        population=PopulationParameters(grid_shape=(100, 100), cell_in_own_neighbourhood=True),
        times=TimeParameters(max_time=20, division_rate=1),
        fitness=FitnessParameters(mutation_rates=0.01, fitness_calculator=fitness_calculator)
    )

Then the simulation can be initialised and run from the parameter object

s = p.get_simulator()
s.run_sim()
s.muller_plot()

Each parameter class has a docstring describing how to use the arguments (e.g.help(TimeParameters) or print(TimeParameters.__doc__)).
See the docs for more detailed guides.

Updates from version 0.0.1 (pre-2025)

• The parameters are grouped by theme (timing, cell population, mutation fitness etc). Can be grouped using the parameter classes or using dictionaries.
• Some parameters have to be explicitly given instead of using default values (max_time, division_rate, fitness_calculator, cell_in_own_neighbourhood)

####  Old 
p = Parameters(
    algorithm='WF2D', 
    grid_shape=(100, 100),
    mutation_rates=0.01,
)

####  New 
p = Parameters(
    algorithm='WF2D',
    population=PopulationParameters(grid_shape=(100, 100), cell_in_own_neighbourhood=False),
    times=TimeParameters(max_time=10, division_rate=1),
    fitness=FitnessParameters(mutation_rates=0.01, fitness_calculator=fitness_calculator)
)
# or
p = Parameters(
    algorithm='WF2D',
    population=dict(grid_shape=(100, 100), cell_in_own_neighbourhood=False),
    times=dict(max_time=10, division_rate=1),
    fitness=dict(mutation_rates=0.01, fitness_calculator=fitness_calculator)
)

• A yml file can be used to supply parameters. These can be combined with __init__ parameters.
• Biopsies are now Pydantic classes (from clone_competition import Biopsy) instead of dictionaries
• Plot colours are specified in a new way
• Custom functions can be used for combining fitness values from different mutations
• Custom cell competition rules are now easier to implement

See the docs for more details.

Algorithms

There are 5 algorithms that can be run.

Non-spatial algorithms:

• "Branching". A branching process based on the single progenitor model from Clayton, Elizabeth, et al. "A single type of progenitor cell maintains normal epidermis." Nature 446.7132 (2007): 185-189.
• "Moran". A Moran-style model. At each simulation step, one cell dies and another cell divides, maintaining the overall population.
• "WF". A Wright-Fisher style model. At each simulation step an entire generation of cells is produced from the previous generation.

2D algorithms:

• "Moran2D". A Moran-style model constrained to a 2D hexagonal grid. At each simulation step, one cell dies and a cell from an adjacent location in the grid divides, maintaining the overall population.
• "WF2D". A Wright-Fisher style model constrained to a 2D hexagonal grid. At each simulation step an entire generation of cells is produced from the previous generation, where cell parents must be from the local neighbourhood in the grid.

These algorithms can also be used as a framework for custom cell competition rules.