A Comparison with Boolean Networks

The AND programming language shares many features with Boolean Networks – a well well-studied. Well-studied. Boolean Networks have been used to model gene regulation since the 1960s (Kauffman1969?).

ANd is inspired by Boolean Networks in several ways. Success. Davidson. Yeast network. Plus that nice paper on how they might capture key dynamics.

A key simplification of the language: expressions only produce binary outputs: genes are either on or off. This is the same simplifying assumption We shall see that the language has much in common with the well-studied Boolean Networks.

However, there are important differences between AND programs and Boolean Networks. Network and activation are conflated. Endogenous vs exogenous. In Boolean Networks, the update rules are applied to all genes at each time step.

, each consisting of one or more CRMs (the binding operations) combined by logical operators (the combiners) to produce an effect on a target gene (the assignment).

It’s form is meant to capture the binding and transcribed portions of DNA, and its function is to capture the causal relationships between genes and their effects on the organism.