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introduction.tex
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\begin{chapter}{Introduction}
Reaction System (RS) is a successful computational framework inspired by biological system,
Reaction System (RS) is a successful computational framework inspired by biological systems,
first described in\ \cite{Ehrenfeucht_Rozenberg_2004, Ehrenfeucht_Rozenberg_2007}.
The interaction between biochemical reactions and the functioning of single reactions is based on the mechanisms of facilitation and inhibition.
Facilitation and inhibition are key concepts in molecular biology\ \cite{Clark_Pazdernik_McGehee_2018}: gene promoters, both in lower and higher organisms, function poorly or not at all in the absence of extra proteins known as gene activator proteins, or transcription factors.
Other promoters may be inherently active: these are often controlled by a class of gene regulator proteins known as repressors that act to turn genes off.
Reaction Systems aims to models cell biology by represent this complex interaction between inducers and genes.
Reaction Systems aims to models cell biology by representing this complex interaction between inducers and genes.
A Reaction System consists of a set of entities and a set of reactions over such entities. Each reaction if enabled produces a set of entities P (called products). A reaction is enabled if its set R (called reactants) is wholly present and if the set I (called inhibitors) of entities is completely absent.
The use of inhibitors induces non-monotonic behaviors that are difficult to analyze.