I need to use an agent based model package (MESA) to simulate the bone formation phase of the bone remodeling process. The agents that I am using are Osteoblasts, Osteocytes and Bone Lining Cells.
Osteoblast Functions and behavior: The function of the Osteoblasts are basically, once they sense the stress signal sent by osteocytes, they will move to the damaged bone site (empty grid cells in the surface of the MultiGrid, simulating the broken down bone). Once in the damaged bone site, they will allocate themselves in on cell and they will secrete osteoid (new bone layer) per turn it will secrete 1 unit of osteoid inside the cell. Once the grid cell gets 50% (5 units of osteoid, maximum units of osteoid per cell = 10) full, then the Osteoblast stops secreting osteoid and under goes either differentiation or apoptosis. Osteoblasts can differentiate into Osteocytes or Bone Lining Cells. 20% of the total osteoblasts will differentiate into osteocytes, 60% will undergo apoptosis and the reaming 20% will become Bone Lining cells.
Osteocyte Functions and behavior: The function of the osteocytes are basically being randomly distributed in the middle-bottom part of the grid and sending stress signal to Osteoblasts to activate them and call them to move to the damaged bone site.
Bone Lining Cell Functions and behavior: These cells will be allocated at the top surface of the grid. These cells will randomly become active an transform into osteoblasts and help during the osteoid secretion process.
The Model: The Model basically has to help visualise a grid of 10x10 where the top 2 or 3 rows are bone lining cells, and there is a "hole" in the bone surface that simulates the broken down bone and its represented by empty grid cells. The osteocytes will be randomly dispersed in the middle-bottom part of the grid.
I am a beginner in python and MESA commands, but I started this internship and I am supposed to use this package to help a research. I would really much appreciate any kind of help or guidance.
This is a "scaffold" or "Script type" that I have to follow.
import mesa
from mesa.time import RandomActivation
from mesa.space import MultiGrid
from mesa.datacollection import DataCollector
import random
# Define your custom agent classes
class Osteoblast(mesa.Agent):
def __init__(self, unique_id, model):
super().__init__(unique_id, model)
self.state = "active"
# Add more attributes and methods for osteoblasts
def step(self):
# Define agent behavior for each step
pass
class Osteocyte(mesa.Agent):
def __init__(self, unique_id, model):
super().__init__(unique_id, model)
# Add attributes and methods for osteocytes
def step(self):
# Define agent behavior for each step
pass
class BoneLiningCell(mesa.Agent):
def __init__(self, unique_id, model):
super().__init__(unique_id, model)
# Add attributes and methods for bone lining cells
def step(self):
# Define agent behavior for each step
pass
class BoneRemodelingModel(mesa.Model):
def __init__(self, width, height, num_osteoblasts, num_osteocytes, num_bone_lining_cells):
self.num_agents = num_osteoblasts + num_osteocytes + num_bone_lining_cells
self.grid = MultiGrid(width, height, True)
self.schedule = RandomActivation(self)
# Create osteoblasts
for i in range(num_osteoblasts):
osteoblast = Osteoblast(i, self)
# Add osteoblasts to the grid and schedule
x = random.randrange(self.grid.width)
y = random.randrange(self.grid.height)
self.grid.place_agent(osteoblast, (x, y))
self.schedule.add(osteoblast)
# Create osteocytes
for i in range(num_osteocytes):
osteocyte = Osteocyte(i + num_osteoblasts, self)
# Add osteocytes to the grid and schedule
x = random.randrange(self.grid.width)
y = random.randrange(self.grid.height)
self.grid.place_agent(osteocyte, (x, y))
self.schedule.add(osteocyte)
# Create bone lining cells
for i in range(num_bone_lining_cells):
bone_lining_cell = BoneLiningCell(i + num_osteoblasts + num_osteocytes, self)
# Add bone lining cells to the grid and schedule
x = random.randrange(self.grid.width)
y = random.randrange(self.grid.height)
self.grid.place_agent(bone_lining_cell, (x, y))
self.schedule.add(bone_lining_cell)
def step(self):
self.schedule.step()
# Create and run the model
model = BoneRemodelingModel(width=50, height=50, num_osteoblasts=50, num_osteocytes=100, num_bone_lining_cells=30)
for i in range(100): # Run the model for 100 steps (you can adjust this)
model.step()
