P is a finite set of places {p1,…, pm} ∈ P,
depicted by ellipses (Fig. 12). Each
place p possesses a color c_p ∈ C and a
bag b_p
⊆
B of tokens of color c_p.
G is a guard function. It maps each
transition t ∈ T to a guard expression g. The
output of the guard expression should
evaluate to a Boolean value (true or false). If
false, t cannot be fired.
I is an initialization function. It maps each
place p into an initialization expression i.
The initialization expression must evaluate a
multiset of tokens with a color
corresponding to the color of the place C(p).
Colored Petri nets offer an enhanced
representation that allows for a more detailed and
nuanced analysis of complex systems, particularly in
the context of molecular and biochemical signaling
pathways. Colored Petri nets take the concept of
traditional Petri Nets a step further by introducing the
notion of colors or values assigned to tokens. Unlike
traditional Petri nets, which use uniform tokens,
colored Petri nets allow for the assignment of
different colors to tokens, enabling the representation
of various types of molecules, receptors, enzymes,
chemical signals, gene expression changes, and more
(Lee D-Y. 2006).
The introduction of colors or values to tokens in
colored Petri nets enhances the ability to represent
and model the intricate behavior of molecular and
biochemical signaling pathways. By assigning
specific colors to tokens, researchers can differentiate
between different molecular species, their functional
states, concentrations, or other relevant properties.
This enables a more comprehensive and detailed
representation of the system's behavior, taking into
account and concentration of the diverse components
and their interactions within the biological system.
With the capability to differentiate tokens based on
colors, colored Petri nets provide a powerful tool for
analyzing complex biological systems. Researchers
can investigate the dynamics and behavior of
molecular and biochemical signaling pathways,
observe the effects of different inputs or
perturbations, and gain insights into the overall
functioning of the system. The use of colored Petri
nets in modeling molecular and biochemical
signaling pathways offers numerous advantages. It
allows for a more precise representation of the
system, facilitating the identification of crucial
interactions, bottlenecks, feedback loops, and other
key characteristics. Additionally, the ability to assign
colors to tokens aids in the analysis of specific
molecules, signaling cascades, and regulatory
mechanisms, contributing to a deeper understanding
of complex biological processes (Liu F. 2012).
2 AN OVERVIEW OF IMMUNE
SYSTEM
The immune system plays a crucial role in protecting
our bodies against pathogens, such as bacteria and
viruses. One of the key components of the immune
system is the T helper cell, specifically the naive T
helper cell. Naive T helper cells are a type of white
blood cell that circulates in the bloodstream,
constantly surveying for potential threats. Naive T
helper cells are "naive" because they have not
encountered any specific antigens or foreign
substances before. Their activation is a complex
process that involves interactions with antigen-
presenting cells (APCs) and the recognition of
specific antigens (Gullo F. et all 2015).
The process of naive T helper cell activation
begins when an APC, such as a dendritic cell or
macrophage, encounters a foreign antigen. The APC
internalizes the antigen and presents small fragments
of it on its surface using a protein called major
histocompatibility complex II (MHC II). This MHC
II-antigen complex serves as a signal for the naive T
helper cell to recognize the antigen. When a naive T
helper cell encounters an APC presenting an antigen
that matches its specific T cell receptor (TCR), a
series of molecular interactions occur. The TCR on
the T helper cell binds to the MHC II-antigen
complex on the APC, initiating a signaling cascade
within the T cell (Paul, W. E et all 2010).
This signaling cascade leads to the activation of
the naive T helper cell. The T helper cell undergoes
proliferation, or rapid cell division, to produce a
population of activated T helper cells specific to the
antigen. This clonal expansion ensures a robust
immune response to the pathogen. Furthermore,
during activation, the naive T helper cell receives
additional signals from the APC in the form of co-
stimulatory molecules, such as CD28, CD4 and B7.
These co-stimulatory signals are necessary for full
activation and optimal function of the T helper cell.
Once activated, T helper cells differentiate into
various subsets, such as Th1, Th2, or Th17 cells. Each
subset has specialized functions and produces
specific cytokines to regulate different aspects of the
immune response. Activated T helper cells play a
central role in orchestrating the immune response by
secreting cytokines that activate other immune cells,
such as B cells, cytotoxic T cells, and macrophages.