Agent reproduction with behaviors

Author: Lukas Breitwieser
In tutorial ST3-agent-reproduction-mortality we have explored how to add and remove agents from the simulation. In this tutorial we want to explore different behavior options to control if a new agent gets a behavior from the original agent, and if a behavior will be removed from the original one.

Let's start by setting up BioDynaMo notebooks.

%jsroot on
gROOT->LoadMacro("${BDMSYS}/etc/rootlogon.C");

INFO: Created simulation object 'simulation' with UniqueName='simulation'.

We define a simple behavior which prints has print behavior.

StatelessBehavior print_behavior([](Agent* agent) {
  std::cout << "  has print behavior" << std::endl;
});

We define the following experiment which we will run with different options of the print_behavior.
We create a cell, add a copy of the print_behavior, and run all behaviors. We expect that the following output is created.

mother: 
  has print behavior

Afterwards we print a separator ------- to indicate cell division, divide the mother cell and run the behaviors of daughter 1 and daughter 2. By definition the original mother cell turns into daughter 1 and the new agent becomes daughter 2.

void Experiment() {
    Simulation sim("my-simulation");
    auto* mother = new Cell();
    mother->AddBehavior(print_behavior.NewCopy());
    std::cout << "mother: " << std::endl;
    mother->RunBehaviors();
    std::cout << "---------------------" << std::endl;
    auto* daughter2 = mother->Divide();
    std::cout << "mother = daughter 1: " << std::endl;
    mother->RunBehaviors(); // mother = daughter 1
    std::cout << "daughter 2: " << std::endl;
    daughter2->RunBehaviors();
}

Let's run the experiment with default parameters and see what happens.

Experiment();

mother: 
  has print behavior
---------------------
mother = daughter 1: 
  has print behavior
daughter 2: 

The print_behavior was not copied to the daughter 2 cell and was not removed from the mother cell.

---

Let's try to copy the behavior from the mother cell to daughter 2.

print_behavior.AlwaysCopyToNew();
Experiment();

mother: 
  has print behavior
---------------------
mother = daughter 1: 
  has print behavior
daughter 2: 
  has print behavior

Now the print_behavior was copied to the daughter 2 cell and was not removed from the mother cell.

---

Let's try to remove the behavior from the mother cell.

print_behavior.AlwaysCopyToNew();
print_behavior.AlwaysRemoveFromExisting();
Experiment();

mother: 
  has print behavior
---------------------
mother = daughter 1: 
daughter 2: 
  has print behavior

Now the print_behavior was copied to the daughter 2 cell and was removed from the mother cell.

---

Let's reset the values to the default.

print_behavior.NeverCopyToNew();
print_behavior.NeverRemoveFromExisting();
Experiment();

mother: 
  has print behavior
---------------------
mother = daughter 1: 
  has print behavior
daughter 2: 

Behaviors provide also more fine-grained distinction. Some agents support multiple new agent events: neurite branching, neurite bifurcation, side neurite extension, etc. For each event we can specify if the behavior should be copied to the new, or removed from the existing agent.

print_behavior.CopyToNewIf({CellDivisionEvent::kUid});
print_behavior.RemoveFromExistingIf({CellDivisionEvent::kUid});
Experiment();

mother: 
  has print behavior
---------------------
mother = daughter 1: 
daughter 2: 
  has print behavior