Purpose

The fish model allows users to see the effects of different concentrations of estrogen on a freshwater ecosystem containing algae, fish, and birds. The model attempts to capture the long-term effects of estrogen on male fish, and demonstrates how sensitive a freshwater ecosystem can be to various concentrations of estrogen. The model is stochastic and it was written in NetLogo, an agent-based modeling language which allows users to view and analyze complex interactions between agents and their environment. A stochastic model employs probability to determine the behavior of its components, thus it is the best type of model to capture the randomness of an ecosystem. The model was also demonstrated to local public school teachers so that they could help their students visualize interactions between different organisms and organisms and their environment. The current lake we are simulating is fictional, however, the code has been developed in such a way that one could substitute the parameters in our model with parameters they have received from a particular lake they wish to test.

Parameter	Value (if applicable)	Reasoning (if applicable)
water-color	blue	Aesthetic purposes. Static value.
male-fish-color	cyan	Aesthetic purposes. Static value.
female-fish-color	pink	Aesthetic purposes. Static value.
feminized-fish-color	yellow	Aesthetic purposes. Static value.
bird-color	orange	Aesthetic purposes. Static value.
algae-color	green-scale	Aesthetic purposes. Static value. Darker green squares correspond to more algae.
fish-stride	0.8	The distance traveled each tick. Static value.
bird-stride	0.5	The distance traveled each tick. Static value. Birds should be a little slower than the fish so that the fish are not decimated.
fish-size	0.8	Relative size of the fish. Static value.
bird-size	1.2	Relative size of the birds. Static value. Birds should be bigger than their prey.
fish-reproduction-age	20	The age at which a fish is mature enough to reproduce. Static value.
bird-reproduction-age	20	The age at which a bird is mature enough to reproduce. Static value.
fish-max-age	100	The age at which a fish will die of old age. Static value.
bird-max-age	100	The age at which a bird will die of old age. Static value.
max-fish-offspring	2	Maximum number of offspring a female fish can produce each time she successfully reproduces. Static value. DO NOT CHANGE as the value must always be greater than the max number of offspring a bird can produce but almost all computers cannot handle a value of > 2.
max-bird-offspring	1	Maximum number of offspring a female bird can produce each time she successfully reproduces. Static value. DO NOT CHANGE as the value must always be less than the max number of offspring a fish can produce but almost all computers cannot handle a value of > 1.
male?	true/false	Assigned when an agent is born. Static at birth. 50% chance of being true.
energy	≤ 100	Initialized to 100 when an agent is born. If it is less than or equal to 0, then the agent dies. Increases as the agent consumes food, up to a max value of 100. Decreases by a fixed amount each tick.
current-age	0-100	The age of an agent. Initialized to 0 when an agent is born. Incremented by one each tick.
estrogen-concentration	≥ 0	Initialized to 0. Represents the current concentration of estrogen (ppt) in the water. Decreases over time and as fish are feminized. Can be increased by the user.
estrogen-resistance	200	The ability of a male fish to resist feminization. Static value. Higher number corresponds to higher base resistance (different types of fish resist estrogen to various extents so the model can be used to simulate different freshwater sources).
estrogen-accumulated-max	0.1	Essentially captures how much estrogen can be accumulated in the fat tissue of a male fish over time. Static value.
estrogen accumulated	≤ estrogen-stored-max	The current amount of estrogen accumulated in a male fish due to exposure to estrogen from environment. As this number increases the chance a male fish is feminized also increases.
algae-energy	0-100	The amount of algae present in a square. If it equals 0, then there is no algae present in the square and the square is blue.
algae-growth-rate	10	The amount of energy an algae tile gains each time it reproduces. Static value.
algae-growth-delay	15	The amount of time the algae needs to wait before it can reproduce. Static value.
algae-max-energy	100	The maximum amount of algae that can be located in a tile. Static value.
fish-survival	0.30	Probability that a fish makes it out of infancy. Static value.
bird-survival	0.15	Probability that a bird makes it out of infancy. Static value.
fish-find-egg	10	The more male fish there are the greater the chance is that an egg is fertilized. Increasing this number increases the number of male fish needed to fertilize eggs (a large body of water will have a greater value for this parameter).
bird-egg	1	The more male birds there are the greater the chance is that an egg is fertilized. Increasing this number increases the number of male birds needed to fertilize eggs (a large body ecosystem will have a greater value for this parameter).

Team:Carnegie Mellon/Fish

From 2014.igem.org

Purpose

Outline

The Parameters

Insight

Results

Code

References