One question that I get quite frequently concerns how I/we construct our food web models. Well, one node/taxon/species at a time. This is just a little animation of the process, in this case for one of the Caribbean coral reefs (click on the figure if your browser does not animate it automatically). More detailed discussions may be found in these publications:
Roopnarine, P. D. 2009. Ecological modeling of paleocommunity food webs. in G. Dietl and K. Flessa, eds., Conservation Paleobiology, The Paleontological Society Papers, 15: 195-220.
Roopnarine, P. D., K. D. Angielczyk, S. C. Wang, and R. Hertog. 2007. Trophic network models explain instability of Early Triassic terrestrial communities. Proceedings of the Royal Society B, 274: 2077-2086.