Michael Murphy's Computer Systems Project Proposal 
Latimer, period 5.  9/16/05.

I.	Extending a Netlogo Simulation of the Propagation of AIDS in a controlled
population.  OR Extending or creating a similar population model in Netlogo, MASON, or Repast. 

II. 	The goal of this project is to create or to modify a behavioral model in
the Netlogo, Repast, or MASON modeling environment.

III.  	Purpose: The purpose of this project is to create or modify an existing
behavioral model to make it both more complex and more realistic.  This project
is both very interesting and significant - there are many obvious benefits and 
uses for a more accurate, and complex, model of population.  A model of the 
spread of a disease such as AIDS would obviously be a very useful one.    

IV. 	The only research I foresee that I'll have to do for this project is 
some research on the real life environment of whatever I will be modeling, such
as the transmission of AIDS in a real life environment.  I want to know what 
factors are worth including, i.e. infected people not reporting their infection
to partners, condom failure in protection of disease transmission, etc.  If I 
am modifying an already existing model, I think that I will be able to program 
with a rather large scope including many variables, as long as I implement and 
test one at a time.  The agent's base behavior in the AIDS model has already 
been defined and the developing environment that I may be working in (Netlogo) 
is specifically designed for this type of research and extension.  I would have
to do more research to be sure of this outcome, but I believe that the current 
model is overly optimistic and that, in reality, AIDS would spread much more 
fully.

V.Current research

Two packages/modeling environments, Repast and MASON, would both be fine for 
this type of work as well, and have some advantages over Netlogo, the environment
I had planned to work in.  Both Repast and MASON both do the same types of things
but on a higher level, and have the advantage of being written in Java, a 
language I am familiar with.  As time goes on, I will explore both of these 
environments and eventually I will probably choose one of them and decide on 
one of these environments to use.

http://cs.gmu.edu/~eclab/projects/mason/ y

  Start thinking about a bibliography: all references in this background and 
literature review section should be in your bibliography, but not everything 
that will be in your bibliography needs to be included here.

VI.   Procedure and Methodology.
  I will probably spend first quarter and part of second quarter doing documentation
and planning for my project.  I will also use  this time to solidify the exact 
model that I will attempt to create as well as to choose the platform in which I
will operate.  Second and third quarter, after having planned the project, I 
will begin writing code and doing the actual programming required to make the 
model work.  I will try to reserve fourth quarter for doing all the end of 
project documentation required for a tech lab project.  I will also use this 
time to experiment with my fully working model as well as to observe the achievements 
my peers have made over the course of the year.  I plan to make a time line 
that outlines the above sub task goals and check to see how I am doing on 
maintaining the time line over the course of the year.

                                
VII.
Adding or extending a model to any of the three modeling libraries will be of 
great use to anyone investigating these libraries in the future.  I expect to 
obtain a more or less fully functioning model that simulates population 
interaction, quite possibly modeling the dispersal of AIDS in a controlled population. 
I will present the final results on a project poster/power point and I will 
show the end state when the simulation is run with various changes to the 
starting setup.  Hopefully my model will be able to be extended by future 
researchers in this field.