Primitive Cells Colony Simulation - very simple simulator of cells colony growth on square nutrient medium.

• Nutrient matrix with constant shape
  • Color
    • black - resource = 1
    • grey - resource = (0, 1)
    • white - resource = 0
  • Matrix is being resupplied with constant rate
• Every cell colony started from 1 cell.
  • number of colonies is specified (No more than 6 colonies are currently available)
  • cells consume resources nearby (within a 3 x 3 submatrix) from the maximum resource level box with a certain frequency specific to each cell colony
  • cells divides when reach "division resource level"
  • they divide in the direction of maximum resource level nearby (3 x 3 submatrix)
  • if there are not enough resources nearby, the cell dies.
• Animation are saved as .gif file
  • Number of rounds (frames) is specified

NB! Tool is not parallelized! All calculations are performed sequentially. Thus, the larger the number of colonies and the size of the matrix, the longer it takes to complete the animation.

Install

git clone https://github.com/vladissta/PCeCoS
cd PCeCoS

Virtual environment setting

python -m venv venv
source ./venv/bin/activate
pip install -r requirements.txt

Usage

usage: process.py [-h] [-c [COLONY_NUMBER]] [-m MATRIX_SHAPE MATRIX_SHAPE] [-f [FRAMES]] [-r [RESUPPLY_RATE]] [-d [DIVISION_LEVEL]] [--output [OUTPUT]]

Primitive Cell Colony Simulator

options:
  -h, --help            show this help message and exit
  -c [COLONY_NUMBER], --colony-number [COLONY_NUMBER]
                        Number of colonies (default: 2)
  -m MATRIX_SHAPE MATRIX_SHAPE, --matrix-shape MATRIX_SHAPE MATRIX_SHAPE
                        Matrix shape (default: 30 30)
  -f [FRAMES], --frames [FRAMES]
                        Number of rounds (frames) (default: 30)
  -r [RESUPPLY_RATE], --resupply-rate [RESUPPLY_RATE]
                        Resupply rate of resource (default: 0.05)
  -d [DIVISION_LEVEL], --division-level [DIVISION_LEVEL]
                        Division resource level (default: 1)
  --output [OUTPUT]     Output filename (default: animation.gif)

Example of result visualization

Parameters

COLONIES_NUMBER = 5
MATRIX_SHAPE = 100, 100
DIVISION_RESOURCE_LEVEL = 1
ROUNDS_NUMBER = 60
RESUPPLY_RATE = 0.05