Figure 2
From: A method to identify and analyze biological programs through automated reasoning
Encoding sets of models and constraints in RE:IN. Shown here is how to encode a set of components, regulation conditions, interactions and constraints in RE:IN, using the toy example from Figure 1 as an illustration. This highlights how to set assumptions, such as a synchronous update scheme, whether to include the Threshold regulation conditions, and how to restrict the set of regulation conditions for a specific components (e.g., C can only use conditions 1, 3, or 5). Constraints are defined as individual experiments, in which component states are defined (using labelled predicates, if desired) at specified time points. We also highlight how to define such a state to be a fixed point.
