2008
           Biological Simulation Techniques: Term Project

Objective
The goal of the term assignment is to allow you to exercise your newly-acquired
simulation skills using a "real-world" model of significance and interest to
yourself.  The project is worth 30% of your final grade.

General Approach
From the scientific or technical literature, find a paper or article that
discusses a model of  some biological, environmental, or biomedical process.
The paper should include a quantitative expression of the model.  It will be
helpful to you if the paper includes som results of simulation based on the
model.

After finding the paper, you should implement a BASIC program of the model, and
obtain some simulation output.  Submit your program and the resulting output
together with a write-up of the problem.

Selecting the Model
The biological, biochemical and biomedical literature is filled with
quantitative models.  A suitable model should be easy to find if you have any
knowledge of the primary literature of your specific field of interest.  You can
go directly to the appropriate journals online or in the library and browse
through them for an interesting model.  If this is difficult for you, then you
might begin by consulting references contained in advanced textbooks from your
fields of interest.  The Journal of Theoretical Biology has many quantitative
models at all levels of biological organization, from molecules to mongoose
predation.

The model you choose should be about as complex as the more advanced, 4-to-10
point models in the textbook.  If you attempt a model more complex than this,
you may be overwhelmed.  This is one of the reasons for requiring a preliminary
submission of a copy of your source paper (see below). In the early stages of
your project, you may need some assistance and direction from the instructor.
  
Your paper should have a publication date of 2003 or later.

Preliminary Approval
Before you begin to work on writing a program for the selected model, you should
submit a photocopy of the paper that you have selected.  With this submission
include notes, explanations, etc., that indicate which equations will probably
be used in your simulation, and what values variables might take.  Include
sketches of graphs with labelled axes, etc. If the paper includes graphs of some
simulation output, you might indicate that you intend to try to mimic some part
of that output as part of your simulation.  You may write explanatory notes in
the margins of the photocopy you submit.  Be sure that the photocopy of the
paper you submit is complete, including references.

The paper will be returned to you as promptly as possible, indicating whether
your proposed work is approved, along with suggestions.


Written Work
You should write up your model as though you were producing an exercise for the
textbook.  Write it at a level appropriate for a moderately competent under-
graduate with programming ability typical of students nearing the end of this
course.  Follow the textbook format.

  (1) Write introductory material that explains the process and general
      concepts involved in the model.  Include simplifying assumptions.
      Diagrams may be helpful.

  (2) A clear statement of the exercise is important.  It should include
      values for constants, initial values of variables, any necessary data
      for use with curfit05 or polyft05 to estimate coefficients, etc.  The
      input data to start the simulation should be taken from the source
      literature, or be "reasonable".  As a preliminary to programming the
      model, you may want to produce a rough draft of the write-up.  This
      may help to clarify your thinking in identifying parameters, variables,
      etc.

Your write-up should be printed.  Keep a copy for yourself, because the
submitted copy will not be returned.  Be sure you include the photocopy of the
original paper with your submitted work.

Output
To your write-up of the exercise, attach the material that you would expect a
student in this class to produce in response to your exercise.  This should
include a flowchart, a listing of the BASIC program, and the graphical or
tabular output.

Questions?
This project should be a do-it-yourself exercise as far as possible.  You
certainly may question the instructor about procedures which may not be clear on
this handout.  However, after Monday, 21 April, you should not have to ask very
many questions regarding your model and simulation.  Only specific questions
about your simulation will be answered.

Questions such as "Is this OK?" or "Is this worth full credit?" are not
specific.  Neither is "Did I program this simulation correctly?".  Specific
questions will always involve a consultation of a flowchart of your program, a
printout of the program, and the output of the program.  Try to save your
questions until you are absolutely at a loss as to how to proceed.

The project will be graded on the quality of your write-up, including how well
it matches the description of the model in the literature you submit.  Also,
your program will be graded for correctness; for example, did you handle "Euler
loops" properly.  To a limited extent the complexity of your model will be
evaluated.  Avoid models that are too simple or too complex.

Deadlines

  1) Monday, 7 April 2008
     Submit to the instructor a complete copy (printout or photocopy) of the
     paper containing the model you want to use.  It will be returned with
     comments to you in class in 2-3 days.  Lateness penalty for this
     submission:  4 percentage points per day, assessed against the 30
     percentage points possible for this exercise.

  2) Friday, 25 April 2007, 5 pm
     Submit the completed write-up with attachments to the instructor.

     NOTE: a no-penalty extension of this deadline will be granted upon request.
     If you make this request, the absolute deadline will be Thursday, 1 May
     2008, 5 pm. Lateness penalty: a score of zero will be recorded because
     there will not be sufficient time to grade any projects submitted after
     this deadline.