NoCs have become a widespread paradigm in the system-on-chip design world, not only for multi-purpose SoCs, but also for application-specific ICs. The common approach in the NoC design world is to separate the design of the interconnection from the design of the processing elements: this is well suited for a large number of developments, but the need for joint application and NoC design is not uncommon, especially in the application-specific case. The correlation between processing and communication tasks can be strong, and separate or trace-based simulations fall often short of the desired precision. In this work, the OMNET++ based JANoCS simulator is presented: concurrent simulation of processing and communication allow cycle-accurate evaluation of the system. The potential of the proposed approach is illustrated through a simple application example. Furthermore, a detailed case study on LDPC and turbo codes parallel decoding is presented. Results analysis illustrates the need for joint simulations and demonstrates the effectiveness of the proposed JANoCS.