For example, Bayesian approaches have been used to model biological pathways and the effects of gene deletion [8].
To model biological pathways from selected genes located within the redefined Aec2 genetic region, Pathway Studio version 5.0 software (Ariadne Genomics, Rockville, MD, USA) and the ResNet mammalian database were used.
To gain insight into the interaction and regulation of biological systems, mathematical frameworks such as ordinary differential equations have been widely applied to model biological pathways and interpret the temporal data.
ODEs are a common method of modeling biological pathways and have been used to model a range of signal transduction processes [29], [33] [41].
Different kinds of Petri nets have been developed and applied for modelling biological pathways including metabolic pathways, gene regulatory networks, signal transduction pathways and integrated signalling-regulatory systems.
Since the exact parameter settings in modeling biological pathways are generally difficult because of the limited amount of available experimental data [ 54], we took a simple approach in constructing the OT model.
However, when modeling biological pathways, it has been noticed that several useful extensions should be applied for modeling and simulating more complicated biopathway processes (e.g., activities of enzymes for a multi-modification protein) and other biological processes that are not normally treated in biological pathways (e.g., alternative splicing and frameshifting) [ 18].
A number of different computational techniques have been proposed and investigated for modeling biological pathways, including Stochastic Petri Nets (e.g., [ 26]), P Systems (e.g., [ 27]), Brane Calculus (e.g. [ 28]), Rule-Based Modeling (e.g., [ 29]), combination approaches (e.g., [ 30]), etc.
The effectiveness of our method suggests that the information-flow based model with dissipation, saturation and direction may provide an excellent framework to model the biological pathways.
This model takes into account explicitly the common features of the information transmission and provides a general framework to model the biological pathways.
As previously said, we don't want to insert our model at the level of the languages used for simulation and modeling of biological pathways.
