Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression
This might relate to issue #15 , specifically, we're going to have to write a new parser for the free_fix file for issue #15 , that is an obvious place to fix the pis.
Pi parameter is not getting used in the code, it needs to be fixed inside the code as a temporary solution. In long term, we would like to remove pi.