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Printable syllabus

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Basic Info:

Professor

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Jonathan Gilligan
Office: SC 5735 and on Zoom (details on Brightspace)
Email: [email protected]
Office Hours: Tues. 4:00–5:00 pm, Wed. 7:00–8:00 pm (on Zoom, contact details on Brightspace), or by appointment

Graduate Teaching Assistant

Katherine “Kat” Turk
Office: SC 5743
Email: [email protected]
Office Hours: Tues. 10:00–11:00 am, Wed. 11:00 am–12:00 pm, or by appointment.

Schedule

Class meetings: TR 11:10–12:25, SC 2200

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Catalog Description

EES 4760/5760 Agent- and Individual-Based Computational ModelingApplications in natural, social, and behavioral sciences and engineering.Designing, programming, and documenting models. Using models for experiments.Examples from environmental science, ecology, economics, urban planning, andmedicine. Familiarity with basic statistics and proficiency in algebra areexpected. [3] (MNS)

Prerequisites

You should be generally numerically literate and I will assume that you arefamiliar and comfortable with basic algebra and statistics.Prior programming experience is not required.Students with significant experience in programming and statistical analysisshould find themselves well prepared but should find plenty still to learnthroughout the semester.

Narrative Description

Agent-based and individual-based modeling has become a powerful tool forresearch in many fields, including anthropology, civil engineering, computerscience, ecology, economics, epidemiology, marketing, medicine, politicalscience, public policy, robotics, sociology, transportation, and urban planning.

Agent-based modeling is used to study how individual agents (which can representpeople, animals, plants, cars, robots, or packets of information in acommunications network) making simple decisions can produce complex andunexpected collective behavior through their interactions. Agent-based modelshave been used to investigate racial segregation in American cities,traffic jams, adaptation to global warming, disease outbreaks, inflammatoryresponse to wound infections, ecosystem dynamics, impacts of changing land-useon tropical rain forests, political instability, and market penetration of homesolar-energy systems.

6.2.0

This course will provide an introduction to agent and individual-based modeling.You will learn how to design, program, and document agent-based computationalmodels using the free open-source NetLogo environment. You will usethese models scientifically to perform computational experiments and interpretthe results.

You do not need to have any prior knowledge of computer programming, but I doexpect that you are familiar with basic statistics and algebra.We will use the NetLogo environment for writing and running agent-basedmodels.NetLogo is a widely used system that is both powerful and easy to learn,so you can quickly start to program your own models.

I divide the semester into three parts:

  • Introduction to Agent-Based Models and NetLogo:The first part of the course introduces the basic concepts of computermodeling, what agent-based models are, and how to use the NetLogo environmentto write and run simple agent based models.I do not assume any prior experience with programming or computer modeling,so this part of the course will give you everything you need to get started.

  • Designing Agent-Based Models:Next, we study the essential components of agent-based models and develop asystematic approach to designing and implementing agent-based models that willbe suitable for doing real science. This section will use examples of realagent-based models that have been used for published research.

  • Using Models for Serious Research:After mastering the components that good models should have, we step back fromthe details and work at a more strategic level to consider how we can designand use models to answer research questions in social and natural sciences.

Reading Material

There is one required textbook.Supplementary reading on the Internet or in handouts will also be assignedduring the term.

Textbook

  • Steven F. Railsback and Volker Grimm, Agent-Based and Individual-Based Modeling: A Practical Introduction (Princeton University Press, 2012). ISBN: 978-0-691-13674-5

    There is a companion web site to the book,http://railsback-grimm-abm-book.com/where you can find errata in the textbook and download supporting data filesand NetLogo models for some of the exercises.

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Additional Resources

This course only scratches the surface of what is possible with agent-basedmodels, and what researchers are doing with them.I have prepared a separate handout on additional reading and computationalresources for doing research with agent-based models.This handout lists a number of helpful books, journals, web sites, and softwaretools that you may find useful or interesting if your want to learn more.

Class Web Site

In addition to the Blackboard web site, I have set up a server athttps://ees4760.jgilligan.org,where I post the web versions of class slides and interactive web-basedapplications to that can be useful for working with data output from agent-basedmodeling experiments.

Computer Software

For this class, we will write and execute agent-based models using the NetLogomodeling system. NetLogo is free software developed at Northwestern University.You can download it from .NetLogo is available for Windows, Mac OS X, and Linux.I have chosen it for this course because it is free, it runs on all the majoroperating systems, its programming language is very easy to learn; and itallows you to easily create a visual representation of your model.

Netlogo Software

You should download NetLogo version 6.2.0 fromand install it on your computer.

NetLogo has been used widely both for education and also forresearch-grade modeling. However, no computer software is perfect and for somelarge or complicated models, NetLogo may be inadequate. There are anumber of open-source agent-based modeling systems that are more powerful thanNetLogo and are better suited for large and complex models. However,these systems are much harder to learn and much harder for even experts to writemodels in. My experience is that for most modeling projects, you can get moredone in a week with NetLogo than in a month or more with the othersystems I know of.

Overview of reading assignments

I will give out detailed reading that give specific pages to read for each classand notes on important things you should understand.I expect you to complete the reading before you come to class on the dayfor which the reading is assigned,so you can participate in discussions of theassigned material and ask questions if there are things you don’t understand.

Graded Work

Mac

Homework

6.2.0

Homework must be turned in electronically to Brightspace by 11:59 pm on theday it is due.

Projects

You will do one assigned team project and one research project.On the team project you will work with a partner to program and work with amodel from the textbook,run experiments with the model, write up the results,and make a short presentation to the class.

For your research project, you will study an existing model, adapt it toinvestigate a new research question, run and analyze experiments using themodel, write up the results, and make a presentation to the class.

Note:Graduate student research projects will involve additional requirements and alonger final report than undergraduate projects, and graduate students will beassigned more homework exercises.

Tests and Examinations

There will not be any tests or examinations in this course. Your grade will bebased on class participation, homework, modeling projects, and in-classpresentations.

Basis for Grading

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Class participation5%
Homework30%
Team Project25%
Research Project40%

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I have made every effort to plan a busy, exciting, and instructive semester.I may find during the term that I need to revise the syllabus to give more timeto some subjects or to pass more quickly over others rather than covering themin depth.Thus, while I will attempt to follow this syllabus as closely as I can,you should realize that it is subject to change during the semester.