Write a draft of your final paper without the results.You should include an abstract, an introduction, a methods section.
Model and Methods section(s): You can either have one section describing both the model and the methods or make this two separate sections. The Models section explicitly defines the model you are extending an your own model, offering any necessary justifications. The Methods section describes how you will use the model to answer the questions described in the introduction. For instance, will there be a parameter sweep, will you solve for fixed points and test their stability, and how? How will results be measured, compared, etc. Be sure that these sections are concrete and specific, leaving no ambiguity about what you intend to do to produce the results section. Somebody outside of your group should be able to read the methods section and produce all of the results without having to ask you questions.
Please avoid referencing code syntax or the GUI of whatever software you use. If you are doing a NetLogo simulation it might be useful to show a screenshot of the simulation in action, and describe it in the text. But please avoid showing picture of or discussing things like sliders and buttons.
Introduction: Keep in mind that you need to answer two questions: What is the scientific question that you are addressing, and what are you doing that is new and novel to extend previous research? This means that you should not include background research which is not relevant to these questions. Save that for a thesis or a review article. You should only include the details of previous research that help the reader understand what you are doing which is novel.
Citation Style: Please use APA or Chicago citation style.
Length: Your goal should be to be as concise as possible but still answering the questions that the Intro needs to ask, and explaining the models and the methods in full detail. I'm guessing 4-6 pages, but use more or less as needed.