We introduce monotone Boolean functions through two quite different examples from biology. The first is in metabolic networks, where they enumerate both the elementary modes and the minimal knock out strategies in a network. The second is in ancestral genome reconstruction, where they generate minimal obstacles (Conflicting Sets) to the consecutive-ones property for binary matrices.

Generating these functions is an interesting computational challenge. We use the package <cl-jointgen>, which implements an algorithm of Fredman and Khachiyan.