MicroRNA is a type of short non-coding RNAs, which post-transcriptionally regulate gene expressions. It has been well-documented that human microRNAs contribute in the disease development, such as cancers and obesity. While most microRNA functional studies heavily rely on the regulatory interactions between microRNAs and their target messenger RNAs, the accumulating evidence has shown that the altered availability of microRNAs, their target, and other types of endogenous RNAs competing are able to affect the microRNA-target interactions efficiently, which reflects the dynamic and conditional property of microRNA-mediated gene regulation. Here we present a new computational pipeline, miRDR-OSG, that utilizing the high-throughput computing resource provided by Open Science Grid to study the dynamic regulation of microRNAs in cancer development with the consideration of both competing and cooperative mechanisms. A large-scale genomic dataset from over four thousand patients with 9 major types of cancer was used to demonstrate the usage of miRDR-OSG. As a result, we identified 10,726 microRNA regulatory interactions that only occurred in a specific stage and/or cancer type. This observation demonstrated the dynamic and conditional microRNA regulation during cancer progression. miRDR-OSG is freely available at http://sbbi.unl.edu/miRDR.