By specifying a threshold per gene for "presence" or "absence". As the stae of a knot may be influenced by several activators and inhinitors, you will need to define some appropriate integration functions for the incoming links to the knots.

You may check these papers:

A Tutorial on Analysis and Simulation of Boolean Gene Regulatory Network Models

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2808677/

Boolean Modeling of Genetic Regulatory Networks

http://users.phys.psu.edu/~ralbert/pdf/springer_final.pdf

Boolean Network Model Predicts Knockout Mutant Phenotypes of Fission Yeast

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0071786

Modeling mechanistic biological networks: An advanced Boolean approach

http://bioinformatics.oxfordjournals.org/content/28/4/557.long