cellsystem package

Subpackages

• cellsystem.logging package
  • Subpackages
    • cellsystem.logging.core package
      • Submodules
      • cellsystem.logging.core.log module
      • cellsystem.logging.core.multi module
      • cellsystem.logging.core.weak module
      • Module contents
        • Core logging classes
  • Submodules
  • cellsystem.logging.full module
  • cellsystem.logging.geometric module
    • Geometric Logging
  • cellsystem.logging.simple module
  • cellsystem.logging.treelogs module
  • Module contents
• cellsystem.simulation package
  • Submodules
  • cellsystem.simulation.cells module
  • cellsystem.simulation.logging module
  • cellsystem.simulation.system module
  • cellsystem.simulation.world module
  • Module contents
• cellsystem.utils package
  • Submodules
  • cellsystem.utils.tree module
  • Module contents

Submodules

cellsystem.cellsystem module

The cell simulation with logging.

class cellsystem.cellsystem.CellSystem(*args, grid_shape=(100, 100), init_genome=None, **kwargs)

Bases: cellsystem.simulation.system.System

A system simulating cell growth.

A cell system is a system subclass, with the automatic initialization of three main entities:

1. Cells represented by a cell line.
2. A ‘world’ representing the space that the cells inhabit, and;
3. A ‘log’ that follows and makes a record of the cells’ actions.

Each part can be accessed by system['cells'], system['world'] and system['log'] respectively.

seed()

Place a single cell in the middle of the world.

class cellsystem.cellsystem.SimpleCells(*args, genome_alphabet=None, **kwargs)

Bases: cellsystem.simulation.cells.CellLine

A cell line representing simple cells with default behaviors.

A cell from this line performs:

• Cell division,
• Cell death,
• Cell migration,
• Cell genome mutation.

add_cell_to(site)

Add a new, initialized cell to the given site.

Return the added cell to the caller.

static death(cell)

Cellular death.

static death_probability(cell)

Cellular death probability.

static division(cell, preserve_father=False)

Cell division.

Get a new daughter of this cell and place it in a nearby neighboring site.

static division_probability(cell)

Probability that this cell will divide if selected for division.

static migration(cell)

Migrate to a neighboring cell.

static migration_probability(cell)

Migration probability for this cell.

static mutation(cell)

Do a single site mutation.

static mutation_probability(cell)

Probability to mutate if selected for it.

Module contents

class cellsystem.CellSystem(*args, grid_shape=(100, 100), init_genome=None, **kwargs)

Bases: cellsystem.simulation.system.System

A system simulating cell growth.

A cell system is a system subclass, with the automatic initialization of three main entities:

1. Cells represented by a cell line.
2. A ‘world’ representing the space that the cells inhabit, and;
3. A ‘log’ that follows and makes a record of the cells’ actions.

Each part can be accessed by system['cells'], system['world'] and system['log'] respectively.

seed()

Place a single cell in the middle of the world.