Quick Start Guide

VERA modeling

To construct VERA models, you will need to be familiar with a few special terms:

Component Types

  • Biotic Population: A group of organisms to be modeled as a population with common behaviors (e.g. phytoplankton, pika, chicken etc.)
  • Abiotic substance: Some non-biotic substance that is introduced into the ecosystem being modeled that has an effect on the Biotic Population (e.g. light, phosphorous, nitrogen etc.)
  • Habitat: A physical region in which the Biotic/Abiotic Components interact (e.g. land, shallow water, deep water etc.)
  • Relationship: A way in which the above Components can interact in a directed manner (e.g. “component X relates to component Y”) The Relationship types implemented in VERA are: “includes,” “destroys,” “consumes,” “produces,” “occupies,” and “becomes on death.”

The VERA modeling tool provides typical graphical editing support including the following:


  • Create/Save model: To create a model, go to “projects” tab in the main page, and select or add a project. Then “add a model” in the project. To save a model, go to “file” in the menu bar and select “save.”
  • Edit modeling properties: Select any component or relationship, then its modeling properties will be shown on the left in the “modeling” tab. For Biotic/Abiotic/Habitat Components, you can change the color of the Component, which will later represent the Component in the simulation. For a Relationship component, you can change the Relationship types in the drop down menu.
  • Edit simulation properties: Select any Component or Relationship, then the simulation properties will be shown on the left in the “simulation” tab. For a Biotic Population, you can change biotic properties that can affect its simulation behavior including lifespan and reproductive interval. For Abiotic substance, you can change its amount and growth-rate.
  • Run simulation: On the top right corner, click on “simulation.” An agent-based simulation will be generated based on the model and properties you have input.

VERA Simulation

A VERA model can be simulated with the NetLogo engine. simulation is automatically generated from the conceptual model. You can use the simulation to help validate (or invalidate) the hypothesis expressed in your model.

Editing simulation properties

The simulation properties on each Component and Relationship are what drive the simulation itself. These properties differ depending on the type of Component or Relationship and can be edited by clicking on the Component or Relationship you want.

On the left side of screen, you will see several properties along with their units of measure in the simulation tab. These properties control how the populations behave.

Some Relationships will also have simulation properties that can be modified. For example, “consumes” relationships in our model should show “consumption rate” and “interaction probability.” The relationship type and simulation properties affect the emergent behaviors of agents in the simulation.

Running simulation

Running a simulation generated from your model is very simple. Just click the “simulation” tab on the top right corner. This will compile your model into a simulation program and execute it. Currently all simulations are compiled into NetLogo and executed using the NetLogo engine.

  • Start: starts and resumes the simulation.
  • Stop: stops and pauses the simulation.
  • Reset: initializes your simulation or resets it if you have already run a simulation.
  • The usual workflow is to click “Start” to start a new simulation run, and click “Stop” to pause the simulation so that you can record observations, refine the properties in the “model editor” tab and start over in the “simulation” tab.


As the simulation runs, a graph showing population changes is updated. On the right side of the graph, you will see each Component represented in the colors used in the “model editor.” To exit the simulation mode, just click the “model editor” tab.

More about simulation parameters

With the exception of “reproductive maturity” the rest are related to the flow of carbon through the ecological system.

Carbon biomass

This is the amount of carbon in a typical adult organism from a biotic population. It is the analogue for energy flow in the ecosystem since research typically doesn’t measure energy (e.g. joules, watts, etc) but does and can measure the change in carbon mass of organisms.

Assimilation efficiency

When one thing consumes another, not all the carbon is assimilated by the consumer – some is burned off, some is passed as waste. This parameter is the percentage of carbon biomass retained by the consumer. Say the rate is 0.90, if they consume something that has 1kg of carbon biomass, 0.9kg is added to the consumer and 0.1kg is “lost” to the environment.

Respiratory rate

Essentially resting metabolic rate measured in loss of carbon biomass so we can model starvation/dissipation.

Photosynthesis rate

This is the rate at which photosynthetic organisms can add carbon biomass to themselves; essentially the inverse of respiratory rate.

Reproductive maturity

The age at which a biotic organism is able to begin reproducing; related to “reproductive interval” which controls how often the population’s organisms can reproduce after they reach the age of reproductive maturity.