In silico modeling of Gene Regulatory Networks (GRN) has recently aroused a lot of interest in the biological community for modeling and understanding complex pathways. Boolean Networks (BN) are a common modeling tool for in silico dynamic analysis of such pathways. Although they are known to have effectively modeled many real and complex regulatory networks, they are deterministic in nature and have shortcomings in modeling non-determinism that is inherent in biological systems. Probabilistic Boolean Networks (PBN) have been proposed to counter these shortcomings. The capabilities of PBNs have been so far under-utilised because of the lack of an efficient PBN toolbox. This work addresses some issues associated with traditional methods of PBN representation and proposes efficient algorithms to model gene regulatory networks using PBNs.