Homework

Individual Project #1

Final version (Proj #1): due Tue Mar 17

This assignment is part 2 of your first individual project for the class. Last week you selected one of three possible project topics and developed a preliminary version of your NetLogo simulation (due Mar 10).

This week you will complete your simulation study and turn in the final version of your project write-up (due Mar 17).

Provide the information on the 'Assignment' tab and email your responses along with a copy of your netlogo file, and any supporting figures or graphics to mcb419@gmail.com with 'proj1' in the Subject line.

This assignment is due by 11:59PM (midnight) on Tue, Mar 17.

Design Guidelines

Topic A: Area-restricted search: modulation of behavior

In Lecture 9, we discussed area-restricted search (ARS) behavior. In C. elegans, we saw that dopamine was involved in modulating the frequency of high-angle turns, such that the worm's search behavior changed depending on how much time had elapsed since the worm had last been in contact with food. For this project, you will develop a NetLogo simulation of ARS illustrating how a slow modulatory signal can mediate changes in search behavior, and how ARS can improve foraging efficiency under certain conditions. Specifically, you will use your model to provide support for the following two hypotheses:

1. When food is clustered, an area-restricted search strategy can improve foraging efficiency relative to a non-modulated search strategy.
2. When food is randomly distributed, an area-restricted search strategy does not provide any benefit relative to a non-modulated search strategy.

Topic B: Multisensory informational cues

In Lecture 6, we discussed Dusenbery's idea that certain stimuli are 'causal' whereas others are 'informational'. In his paper, Dusenbery gave an example of how the scent and color of a flower have importance to a bee only because they are associated with nectar, which has nutritional value for the bee. (nectar is 'causal'; scent and color are 'informational'). For this project, you will develop a NetLogo simulation in which two different 'informational' sensory cues are associated with the presence of food. You will then design a controller that makes use of these informational cues. For example, you might create a simulation in which food is found only in bright, warm regions of the environment. You will use your model to:

1. Demonstrate that under appropriate conditions, the use of 'informational' cues can significantly improve foraging efficiency relative to design that ignores these cues.
2. Use your simulation to clarify the factors that define 'appropriate conditions' in the above statement.

Topic C: Simulated evolution: genomic memory

In Lecture 6, we discussed the idea that an organism's genome provides a memory of what designs and strategies have been most successful in previous generations. For this project, you will develop a NetLogo simulation in which certain parameters of the bot's foraging stragegy are encoded into a set of NetLogo variables that are treated as a genome. When the bot reproduces, it passes along this genetic information to its offspring, with variation. Using a foraging scenario similar to hw05, in which bots eat, grow and reproduce, you will allow your bots to 'evolve' over multiple generations. Use this scenario to provide support for the following hypotheses:

1. Over the course of multiple generations, the processes of variation and natural selection will tend to 'converge' on a controller design that is well-matched to the foraging task in this environment.
2. The foraging performance of the 'final' design (after convergence) will be significantly improved relative to that of the initial 'seed' population.

Assignment

You can access a copy of the assignment file HERE, or copy and paste from the text below.

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MCB 419 Project #1 (Spring 2009)

When you've finished answering the questions, email a copy 
of this file along with your NetLogo file (proj1.nlogo)
and any additional figures or graphics files to
mcb419@gmail.com with 'proj1' in the Subject line. 

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1. Which one of the three project topics did you select?


2. OBJECTIVES: State the main questions or objectives of your 
project and the major hypotheses to be tested, if any. 


3. MODEL DESIGN: Describe the overall design of your simulation
model including the environment, the agent(s), their sensory 
capabilities, motor system and controller architecture.


4. EXPERIMENTAL DESIGN: Describe how you used the model to 
evaluate the questions and hypotheses listed in #2 above.
(Be specific. How were individual trials conducted?  What were 
the initial conditions? What was the main performance measure? 
How did you decide how many trials to run?  etc.)


5. RESULTS: Describe the outcome of your experimental study.
Be quantitative. Use statistical tests if appropriate. Feel
free to include tables, figures or other graphics (these can 
be included as separate attachments).


6. CONCLUSIONS: Based on the results reported in #5, what are 
your conclusions with respect to the questions and hypotheses
listed in #2. (Keep this short, a couple of sentences 
should suffice.)

 
7. DISCUSSION: What are the broader implications of this
study? Are the results relevant to biological systems? 
Are there caveats to your conclusions? Can you think of 
interesting ways that this project could be enhanced or
extended? Did this project spark any new ideas or insights?



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END OF THE ASSIGNMENT
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