What is EcoNet?

EcoNet is a simulation and network analysis software for ecological systems that can be expressed as a set of compartments, and flows among these compartments. Flow currency can be energy, biomass, or a specific element such as C, N or P. Compartments can represent anything from accumulated organic matter to a group of species.

EcoNet is designed to simplify the model building, simulation and analysis effort. The simplicity of EcoNet interface not only encourages first time modelers to access a powerful modeling tool, but also minimizes the model building effort for experienced users, closing the gap between the thought process and the results.

Actually, any process that can be represented as a stock-flow diagram, related to Ecology or not, can be implemented in EcoNet within a few minutes. EcoNet performs deterministic or stochastic dynamical simulation from a given initial condition, and then performs ecological network analysis after the system reaches steady-state. Users can utilize EcoNet for dynamical simulation only and disregard the network analysis results. Or one can enter a model which is already at steady-state and use EcoNet only for steady-state network analysis. EcoNet is a versatile software that offers unique features on both aspects.

EcoNet requires no installation. Instead, users enter their models on a web browser, in a simple and intuitive text-based format. For user convenience, the website already contains a simple model, and default options for numerical methods and parameters are pre-selected. Anyone can try and run EcoNet immediately without needing any prior knowledge.

User simply clicks on Run Model to submit a model to EcoNet server. The server evaluates the model and unless there are errors detected in the model, a sequence of C++ codes, compiled Matlab routines and unix shell scripts work together to generate the simulation and analysis results. EcoNet server then creates a new web-page that contains these results which is then loaded into the user's browser. Typically this process takes less than four seconds.

EcoNet was first online in June 2006. We initially developed its numerical engine back in 2001 at Carnegie Mellon University to analyze statistical properties of large biochemical networks. Failing to find software able to simulate biochemical networks involving over 10,000 molecules and reactions, we developed ours from scratch in C++. This numerical engine can handle non-linear models that contain up to 105 compartments and 105 flows. Besides deterministic methods, EcoNet features fast stochastic simulation algorithms based on Langevin Equation [10] and Gillespie's Stochastic Algorithm [8].

Next: How to create an EcoNet model?

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