In general, the simulation scripts for any particular figure involves the following:

1. a main tcl file which simulates the topologies and flows (ns input script)
2. a tcl file that runs the main tcl file over and over again to generate many outputs
3. an averaging or percent computation script that post-processes the data produced from simulations.
4. a plot file that generates a postscript graph.

the (2) (tcl file for running simulations over and over) also runs the post processing and plot file in most cases.

The simulation scripts assume the location of ns to be ~/ns-allinone-2.1b7a/ns-2.1b7a/ns. You may need to either put ns in that location or replace that with your location of ns in the simulation scripts. Rest all the simulation scripts will run themselves generating relevant postscript files (whose name are there in plot files). Exception are simulation scripts for figures 4 and 5.

For figures 4 and 5, you need to manually split the output file generated (avg-result-RED) into 5 files (for each of the SlowCC algorithm). You need to name these files, avg-result-RED-1 through avg-result-RED-6. Replace the second column (which corresponds to b parameter in the files for TCP, TCP(1/8) and SQRT) with a value 1-1/x if x is the value of the second colum entry (eg. replace 0.5 by 2, 0.875 by 8 and 0.995 by 256). Then, plot the output.