If you want an integrated IDE, you can use omnet++, there is an academic version that is free and they offer the source code of the models and the simulator. it offers and GUI with the animation of the simulation.
I would recommend Contiki/Cooja simulator (http://www.contiki-os.org/) which is the most sought after open source simulator for IOT and it even supports WSN simulations. Also coding with Cooja is simpler as it uses embedded 'C' and provides good GUI support. The code can be easily ported from simulation to real-time deployment as well.
I would definitely recommend NetSim. The source codes are well documented and simple to modify. NetSim UI is easy to use. The complete list of technologies supported is available at https://tetcos.com/technology-libraries.html
Thanks all for your suggestions and time. Currently I am working on SciLab script for PHY task. Once I move to next task of MAC, will explore the options you shared, and share feedback too.
in addition to all the benefits mentioned, NetSim provides c++ source code for its protocol implementation so researchers can tweak to their research interest
NetSim is our preferred tool because it speeds up protocol R & D. We can quickly learn the GUI for both scenario creation and results analysis. The C code that is reliable and well documented for Researchers to understand to develop their own algorithms.
I recommend you the Cooja Simulator from Contiki-NG, it allows the emulation of common sensor network platforms like TelosB, Zolertia, etc. More over, Contiki implements 6LoWPAN which brings the abitlity to build sensor networks based on IP addressing, you can access to MAC protocol implementations because is open source and that brings the oportunity of disccus your results compared with standard or other related works imprlemented using Contiki and Cooja simulator. The emulation feature brings several adventajes for debuging, testing communication and other things.
Though not free, Netsim Simulator offers a very user friendly GUI. It has emulators and different modules for IoT applications. We were able to publish papers on IoT security using it. I would strongly recommend it for your research interests.