Modeling network dynamics using Boolean formalism: An introduction
A notion of a "network" is central in modern cell biology. One of the reasons is that there are many experimental methods that can discover gene and regulatory networks in cells and the hope is that the same networks have the same function in different organisms. If so, then networks would provide a very useful abstraction: the individual chemical species do not matter, only the structure of their interactions. The conjecture that networks exhibit stereotypical behavior is false, as dynamics of complex systems will depend on the choice of the model, its parameters, and its initial conditions. Boolean formalism attempts to extract information about dynamic behavior of the networks where each node is either On or Off, and the updates of the states are based on Boolean functions. I will provide basic introduction to discrete Boolean models, review some results and shortcomings and end up with description of switching networks which embed Boolean update functions in a ODE model.