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Key features of dynamic systems
As a large numbers of different formalisms have been used to model GRNs, it is useful to have an underlying conceptual framework that can be used to categorize and compare particular models. A common view of a regulatory network is as a dynamic system, consisting of a set of components (genes, gene products) whose properties change in response to internal interactions and external signals. The two fundamental concepts in a dynamic systems description are state and transition.
A state of a system is a description of the properties of each component at a given point in time. In a GRN model, this may include levels of gene activation, concentration of chemical species or even the number and location of individual molecules, depending on the level of resolution of the model. A related concept is a state space, the total set of possible states a system can be in. The state space of a system will have a dimensionality equal to the number of components in the system (see Figure 5).
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States in a state space are linked together by transitions, which describe how the state of a system is updated. The set of transitions that can be applied to any given state will determine the possible state or states into which a system can move. The path of a system through state space over time is often referred to as its trajectory.
Next: Logical, continuous and stochastic Up: A diversity of models Previous: Complex systems and systems Nic Geard 2004-05-06