PyCafe - Solara - Agent-Based Model of Biofilm Formation

agent.py
app.py
model.py
requirements.txt
app.py
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sat Nov 23 14:54:30 2024

@author: griffinkd
"""

#Import dependencies
import mesa
from mesa.visualization import (
    Slider,
    SolaraViz,
    make_space_component,
)
from agent import Environment
from model import BiofilmFormation

def convert_to_color(concentration):
    """Convert a concentration of resource to an RGB color."""
    scaled_conc = int(255 * max((1 - concentration/100), 0))
    return '#%02x%02x%02x' % (scaled_conc, scaled_conc, 255)

def agent_portrayal(agent):
    """Agent visualization."""
    portrayal = {'size': 20}
    if isinstance(agent, Environment):
        portrayal['color'] = convert_to_color(agent.nutrient_concentration)
        portrayal['edgecolors'] = 'green' if agent.biofilm_state == 'biofilm' else 'none'
        portrayal['marker'] = 's'
        
    return portrayal

model_params = {
    "prop_biofilm": Slider("Proportion of Biofilm", 0, 0, 1, 0.1),
    "biofilm_viscosity_multiplier": Slider("Biofilm Viscosity Multiplier", 2, 1, 5, 0.5),
    "radius_nutrient": Slider("Radius of Nutrient Particles (um)", 1, 1, 10, 1),
    "temperature": Slider("Ambient Temperature (C)", 25, 10, 50, 1)
}
     
        
model = BiofilmFormation()

def post_process_space(ax):
    ax.set_aspect("equal")
    ax.set_xticks([])
    ax.set_yticks([])
    ax.get_figure().set_dpi(600)

space_component = make_space_component(
    agent_portrayal, draw_grid=False, post_process=post_process_space
)

page = SolaraViz(
    model,
    components=[space_component],
    model_params=model_params,
    name="Physics-Controlled Biofilm Formation",
    play_interval = 1,
)
page
Py.Cafe

biofilm-formation

Agent-Based Model of Biofilm Formation
