Booleanization of regulatory graphs

GINsim enables the definition of multi-valued models where some components can have several increasing activity levels. However, some other analysis tools only consider Boolean (on/off) models. Model booleanization allows to convert multi-valued models into Boolean models by mapping each multivalued component on a group of Boolean variables. The resulting Boolean model generates the same dynamical behaviour as the original multivalued model.

bioLQM uses the mapping originaly proposed by van Ham, in which a component associated with the maximal value m will be mapped on m Boolean components. For example, a component taking the values 0, 1, 2, and 3 will be encoded as 000, 100, 110, and 111.

The booleanization introduces many non-admissible states, which may require special care depending on the analysis applied on the booleanized model. This modifier makes sure that a simulation which start with an admissible state will not explore non-admissible states. It also prevents the introduction of non-admissible attractors by making sure that at least one admissible state is reachable from any non-admissible.

Exporting a multivalued model to a format limited to Boolean components triggers an implicit Booleanization step. This booleanization step can also be performed explicitely using the booleanization tool in the Actions menu.

This method was implemented in GINsim 3.0. The backend is implemented in BioLQM, enabling its programmatic use.