There are various models, but their robustness varies, so which is better for model ecological interactions ?
If you are interested in marine ecosystems, look at the suite of ECOPATH models (with ECOSIM) which are available for free download (new version currently under development). Villy Christensen at UBC Vancouver is one of the key driving forces behind this effort. There is a large community of people applying the principles to ecosystems around the globe and continuing to develop the methodology. www.ecopath.org
Mathieu Colléter at the Sea Around Us Project, UBC Vancouver, is working on EcoBase; he is developing a repository for Ecopath with Ecosim (EwE) models as a way to facilitate meta-analyses as a road to further understanding marine ecosystem.
How about terrestrial ecosystems, is there something that's similar to ECOPATH....
In principle, ECOPATH should be useable also for terrestrial systems, because it's about mass balance between interacting ecological groups that make up a system. Put simply: At the origin one of the key points was to make sure specialists of particular groups would not come up with unrealistic biomass estimates because they were unaware of biomass, production and natural or other mortality of groups up and down the foodweb considering transfer rates between trophic levels. To make up a fictious case, you can hardly have 10,000 units of marine mammals if your primary production is 100,000 units - perhaps it might be mathematically ok in a model, but not in nature when you know the food composition of these marine mammals and know they don't feed directly on phytoplankton.
It's just that I have not seen such applications because my own focus is on marine, but for sure coastal models have incorporated groups in the intertidal area, seabirds, you name it, whatever ecological group is a non-negligible part of the system under study.
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