# Model Plan

## Contents

## Introduction

An important skill in pursuing any long term goal is the ability to set up a realistic plan for the intermediate steps, and follow through on that plan.

To help you with this process, we would like you to post on the wiki your detailed plan for the reconstruction of your model during the second half of the semester. This plan is worth 1/2 points toward class participation.

In Chapter 11 of the book, which you should read by the first class after spring break, the process of developing a complex model is carefully described and illustrated.

Use this as a guide to developing your own plan for re-creating and extending your model during the second half of the semester.

## Hypothesis

The central focus of your term paper is the hypothesis. Is it vague, or is it clearly formulated and readily testable?

The "hypothesis quiz" that we administered to you before spring break, as well as the feedback we gave you on your hypothesis, should help you develop a clear hypothesis.

Your plan should state the hypothesis, and highlight it, and your plan should address how the model will test the hypothesis.

## State Variables and Parameters

As part of the plan, please provide a detailed listing (if possible, in table format) of the state variables and the parameters of the model.

Make sure to provide brief verbal descriptions of each of the state variables, and each of the parameters, and spell out any abbreviations.

This will form part of your term paper Model Description, so incorporating it into your plan will be very useful as your proceed; it will also help you to make sense of each of the equations of your model.

## Calculations

What needs to be calculated?

For example:

- Do you need to generate time plots based on simulating coupled differential equations? How will you do this?

- Do you need to compute algebraic quantities based on the outputs of differential equations? How will you do this?

- Do you need to calculate a bifurcation plot? How will you do this?

## Realistic intermediate goals

Establish realistic intermediate goals, and estimate how long it will take to achieve them.

For example, if you have a model that consists of seventeen coupled differential equations:

- Is it possible to construct sub-parts of the model, holding certain terms constant, so you can confirm that sub-components of the model are working correctly?

- Is it possible to combine several of the sub-parts together without necessarily constructing the entire model so you can confirm that these parts interact correctly?

- Is it possible to finally reconstruct the entire model?

- Is it possible to validate the model based on figures and data presented in the original paper? What specific steps will you do first, second, and so on, to be sure that your model is working correctly?

- Is it possible to extend the model? What are the specific changes in the model that you propose to make? How will you test that you have made these changes correctly?

## Timetable

Associated with each of the realistic intermediate goals should be a specific date by which you expect that goal to be completed.

You may need to update your timetable over the course of the second half of the semester, so make sure to set up your text so that it is easy to do this.