Frequently Asked Questions

Below are some questions that we receive a lot. Please contact us if you can't find the answer of your question here.

What type of models can EcoNet run?
Any process that can be represented as a stock-flow diagram, related to Ecology or not, can be implemented in EcoNet.

Can I download EcoNet?
Currently EcoNet is accessible only through its web interface.

How can I cite EcoNet?
Please cite EcoNet as follows: Kazancı, C., 2007. EcoNet: A new software for ecological modeling, simulation and network analysis, Ecol. Model., Vol 208/1 pp 3-8.

Can EcoNet plot only certain compartments? Can I zoom into the graph?
This is possible by downloading the data and using Octave or Matlab (or your favorite graphing software) to create the plot again. This requires only a couple of lines and is easy to do. Here we describe how to do it. Note that Octave is a free software.

Can EcoNet be used for modeling biological networks?
Actually yes. The numerical engine behind EcoNet was initially developed for modeling large biochemical reaction networks. However EcoNet web interface currently does not allow for non-linear reactions, such as "A + 2 B -> C", even though the numerical engine can easily handle such reactions. This is mainly because ecological network analysis part of EcoNet is not designed for such networks. Please contact us if you are interested in such a computational tool.

How does EcoNet compute the flow rate (or amount) from one compartment to another?
EcoNet currently features donor controlled, and donor-recipient controlled flow types. We plan to update EcoNet interface to accommodate any user-defined flow-type, while keeping its simple user onterface. Please see here for more information. You can contact us with your suggestions.

My EcoNet figure does not look smooth, why?
No matter how many iterations were needed for the simulation, EcoNet uses 200 time points to create the time course plot for efficiency. If not, please opt for the Fixed time-step method rather than the Adaptive time-step algorithm.

My simulation results look unrealistic...
This is probably because the numerical solution is not accurate. If you are using the Adaptive time-step method, decrease the Sensitivity parameter. If you are using the Fixed time-step method, decrease the Step size parameter. This action will increase accuracy, but Econet will take a little longer to finish the simulation. If it takes too long; then try decreasing the Maximum time parameter.

EcoNet does not return my results, just tells me to wait...
This is probably because the simulation takes too long to run. You can either decrease the Maximum time or increase the Sensitivity (or Step size) parameter. Note that increasing Sensitivity (or Step size) will decrease the accuracy of numerical solution. Still, very high accuracy is not needed in most cases. EcoNet will not run longer than two minutes.

Why does EcoNet terminate my simulation early?
EcoNet simulations are limited to two minutes, which should be enough to run even very large models. If you are using the deafult Adaptive time-step method, increasing the Sensitivity value will most likely solve the problem. If this does not work, we suggest that you switch to Fixed time-step method, and experiment with various step-size values. EcoNet will always return accurate results in a couple of seconds for small enough Step-size and Total-time parameters, no matter how complicated the model is.