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or acute inflammation [ 27 ]. At the organismal level, we may use ABMs to consider
disease transmission vectors [ 28 , 29 ], and social and cultural effects and consequences
for infectious diseases [ 30 ].
In the following three sections, we show how agent-based models may be appro-
priate for any level of research. In Section 4.2 , we walk through the creation of a
simple ABM that mimics some of the neuronal connections made in our brains. This
is a model that was originally developed by an undergraduate student. We then present
in Section 4.3 a more complex model that suggests how the disease cholera might
spread through a small village. A more detailed version of this model was developed
by a team of undergraduate students, and within Section 4.3 we dive into how we
can use the Behavior Space function within NetLogo to replicate experiments. This
will allow us to separate the chance events that occur in a single simulation from
broader trends that accurately reflect the impact of modifications to the model or its
parameters. In Section 4.4 , we describe how ABMs are complex enough to support a
full-fledged research effort, and we give a quick overview of the way in which such
models should be presented.
4.2 AXON GUIDANCE
In this section we will develop a model of axon guidance. The motivation for this
comes from an undergraduate honors thesis titled: “Agent-based Modeling of Com-
missural Axon Guidance along the Midline" by Worku [ 31 ].
4.2.1 Background
Healthy brain development in the embryo is, in part, determined by correct electrical
and chemical pathways being established. These pathways are used by brain cells to
communicate effectively with all the other parts of the brain and the body. The human
central nervous system is bilateral; thus the transfer of information between the sides
of the body must be conducted across the midline of the brain. Neurons (nerve cells)
in the brain have axons that grow away from the cell body (Figure 4.4 ) and can cross
the midline. These axons facilitate communication between cells. To accomplish this,
the “head” of an axon (the growth cone) uses filopodia (spikes) that monitor the local
environment and uses this information to guide the direction and development of
the axon. To be affected by a given guidance cue a neuron must express a specific
receptor: think of this as a lock (receptor) and key (guidance cue), the key is useless
if it fits the wrong lock.
There are trillions of neurons in the brain, and the complexity of the connections
between all the cells is incredible. Therefore, undergraduate research tends to study
either a single guidance cue, or a neuron expressing receptors that are thought to
respond to a specific guidance cue. The aimhere is to investigate complexmechanisms
involved in the developing brain, where multiple cues are released and guide a neuron
expressing multiple receptors.
 
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