At one level, biological cells can be thought of as "partially-mixed bags" of biological chemicals -- for the purposes<unk> s, these chemicals are mostly the mRNAs and proteins that arise from<unk>  expression.  These mRNA and proteins interact with each other with various degrees of specificity. Some diffuse around the cell. Others are bound to cell membranes, interacting with molecules in the environment. Still others pass through cell membranes and mediate long range signals to other cells in a multi-cellular organism.  These molecules and their interactions comprise a<unk> . A typical<unk>  looks something like this:
The nodes of this<unk>  are proteins, their corresponding mRNAs, and protein/protein complexes. Nodes that are depicted as lying along vertical lines are associated with the cell/environment interfaces, while the others are free-floating and diffusible. Implied are<unk> s, the DNA sequences which are transcribed into the mRNAs that translate into proteins. Edges between nodes represent individual molecular reactions, the protein/protein and protein/mRNA interactions through which the products of one<unk>  affect those of another. These interactions can be inductive (the arrowheads), with an increase in the concentration of one leading to an increase in the other, or inhibitory (the filled circles), with an increase in one leading to a decrease in the other. A series of edges indicates a chain of such dependences, with cycles corresponding to feedback loops. The<unk>  structure is an abstraction of the system's chemical dynamics, describing the manifold ways in which one substance affects all the others to which it is connected.  In practice, such<unk> s are inferred from the biological literature on a given system and represent a distillation of thec ollective knowledge about a set of related biochemical reactions.<unk> s can be viewed as nodes in the<unk> , with input being proteins such as transcription factors, and outputs being the level of<unk>  expression. The node itself can also be viewed as a function which can be obtained by combining basic functions upon the inputs (in the Boolean<unk>  described below these are Boolean functions or gates computed using the basic AND, OR and NOT gates in electronics). These functions have been interpreted as performing a kind of information processing within the cell, which determines cellular behaviour. The basic drivers within cells are levels of some proteins, which determine both spatial (tissue related) and temporal (developmental stage) co-ordinates of the cell, as a kind of "cellular memory". The<unk><unk> s are only beginning to be understood, and it is a next step for biology to attempt to deduce the functions for each<unk>  "node", to assist in modeling behaviour of a cell (see systems biology).
Mathematical models of<unk> s have been developed to allow predictions of the models to be tested. The most common modeling technique involves the use of coupled ordinary differential equations (ODEs).  Several other promising modeling techniques have been used, including Boolean<unk> s, Petri nets, Bayesian<unk> s, graphical Gaussian models, Stochastic, and Process 
Calculi.  Conversely, techniques have been proposed for<unk> rating models of<unk> s that best explain a set of time series observations.
Gene regulatory network
Gene expression
Phosphorylation cascade
Wnt signaling pathway
Transcriptome
DNA sequence
Unfolded protein response
Signal transduction