Assignment 2 (Due 3/9/06)

Provide a written summary of your in-class exercises using CompuCell3D. This report does not have to be very elaborate but you should briefly discuss your results and answer the questions included in the description of the exercises. Additionally if some of the results were surprising or anomalous, pleas describe them. They might be helpful in diagnosing problems with CompuCell3D and we really appreciate your feedback (and patience).

Assignment 3 (Due 3/21/06—One report required per project team)

Please write a brief one to two page summary of your class project.

Please include:

a)  A one to two paragraph introduction to your project and its importance.

b)  A brief summary of the project biology, including what happens in time and space at the tissue, cell and subcell levels. E.g., how do cells move, or differentiate? How do their properties vary from place to place or time to time? Include any relevant images, signaling and regulatory diagrams, time series,… from the literature.

c)  If there have been previous models of your phenomenon, describe them and their results briefly.

d)  Provide a simple descriptive model describing the cell types, behaviors and fields to be modeled (cell movement, adhesion, cell migration, signaling pathways, diffusive extracellular fields, mitosis, apoptisis…).

e)  Discuss how you could translate the descriptive model into a mathematical model. What parameters would you need? Which of these are available? Which ones will you have to guess? Provide a first stab at a mathematical or algorithmic model.

f)  If you will be using CompuCell3D for the project, define what modules you will need to use. If these modules are not present in CompuCell3D now, you will need to provide detailed description of what these modules are supposed to do. If you will not be using CompuCell, please provide a description of the modeling environment that you will use.

g)  A description of your preliminary data (if any).

h)  Literature citations.

Together with your team mate prepare a 10-15 min presentation about your project. You may split work however you like and we encourage you to use Power Point for the presentation.