Network-Based Biocomputation (NBC) circuits are computational devices that utilize biological agents to efficiently explore designed nanofabricated networks and thus solve combinatorial problems. The main advantages of NBCs are the potential to combine massively parallel computation, inherent energy efficiency of the biological agents and maturity of nanofabrication technology. We present an integrated computational-aided toolset for simulation and verification of these circuits that enables analysis of both circuit correctness and the effects of agent stochastic dynamics on circuit behavior. Our approach enables early identification of design flaws and can lead to significant savings in resources, thus playing an important role in advancing this emerging paradigm.