Omnet Inet and Wireshark are tools I used in our most recent lab. They enabled me to see how a network works at a very fine level of detail. The level of detail even went down to interactions between various OSI layers on a host, and the length of delay on a wire. I found it fascinating. It helped me to better understand how things fit together.
Wireshark is very easy to use. I had a much harder time making sense of the other two tools.
I think it would be interesting to get a hold of some real network traces and analyze them. Real data, rather than simulated, probably has a lot more to say. I would be interested to see what research has been done in the area of inferring characteristics of network traffic from data. Doing so would involve ways to analyze very large amounts of data.
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