Computer Systems Project Proposal
Annie Martin
Period 3

I.     A Model of Relationships Among the Species in an Ecosystem and the Adaptation
and Evolution they Cause.

II.    This project aims to study a ecosystem with a variety of species and a 
variety of complex relationships, including predator-prey relations, parasitic 
relations, symbiotic partnerships, competition among members of the same species
and members of different species, and studies the adaptations they make by tracking
a simplified genome that causes variation among the members of the species.  
This is a very large scoped project, and the main goals would be to  model the 
competition and to study the adaptations of three or four species, including 
producers.  More species and complex relationships would be added during the 
course of the year, though it is hypothisized that a simplistic evolutionary 
model will not be radically different from a more complex one.  Additionally, 
human interference with the environment could be added, to study the effects of
development on the survival of the species.

III.   The goal of this project is to model an existing ecosystem, preferably one
with population data available in order to improve the relevance of the project
and to measure the accuracy of the program.  Ecologies of different systems are
often not understood because of the complexities that they involve.  The study 
of the population dynamics of such a system could add some insight.


IV.    This project aims to study an ecosystem with a variety of species and a 
variety of complex relationships, including predator-prey relations, parasitic 
relations, symbiotic partnerships, competition among members of the same species
and members of different species. The project studies the adaptations they make by tracking a simplified genome that causes variation among the members of the species.  
This is a very large scoped project, and the main goals would be to model the 
competition and to study the adaptations of three or four species, including 
foliage.  More species and complex relationships would be added during the 
course of the year, though it is hypothisized that a simplistic evolutionary 
model will not be radically different from a more complex one.  Additionally, 
human interference with the environment could be added, to study the effects of
development on the survival of the species.  This project allows for many options
should time allow, but these features are not intrinsic to the experiment.

V.     The key pieces of research needed to prepare for the project are on the 
animals themselves.  How do animals recognize other of their own species or other
species?  They use different senses, depending on the animal, but always involving
the look, sound, and smell of the animal.  What differneces are found in animals
of different species as opposed to the differences found among animals of the 
same species?  How does an animal react to an animal of its own or another species
(attack, attempt to mate, run, hide, etc.).  What results should be expected 
from a ecological model? The research would all center around what the important
characteristics of animals in general are.  Also, the use of a MAML (Multiple Agent Modeling Language)
that will effectively be able to run this model will need to be studied.  What is 
the difference between different modeling languages?
    
VI.    The language used will take care of the graphics.  At this point, it will
probably be REPAST, but, if difficulties with this occur, NetLogo, MASON, or a 
similar language could also be used. All of these languages have model programs
based on predator prey relationships that can be built on.  My project will add
different relationships among the animals, natural variation, and different 
animal behaviors based on their abilities, in a way that should allow the animals
to adapt and, theoretically, evolve.  The data to compare the model to determine
if it is a realistic model is availible many places, for example at the Centre 
for Population Biology (http://cpbnts1.bio.ic.ac.uk).  The accuracy will be 
difficult to measure because of the number of factors not taken into account by
the simplified program, namely human interference.  However, the model is that 
of a sample population, and should be relevant to the general case, so a match 
to specific data will not be an intrinsic part of the project. A better 
comparison could be drawn by comparing the model to text book cases of population
genetics.