This is a summer course primarily for college professors and instructors who want to add individual-based modeling to their teaching and research skills.
Individual-based (or "agent-based") models (IBMs, ABMs) are a popular new technique for understanding how the dynamics of a complex system emerge from the characteristics and behaviors of its individual components and their environment, but they also have important advantages for real-world management problems.
Currently, it is not easy for most professors to teach students how to use IBMs. This technique requires skills that few of us have training in, and until now, there have been no textbooks. This course will introduce Agent-based and Individual-based Modeling: A Practical Introduction (2012; Princeton University Press), a textbook designed for classes in which even the instructors are new to IBMs/ABMs.
Topics to be covered include:
- when and why to use IBMs, for both theoretical and applied science;
- strategies for designing models that are "as simple as possible, but not simpler";
- software techniques: programming IBMs, testing software, and running simulation experiments;
- model analysis and publication: how to produce science once a model is built; and
- linking your empirical research to individual-based science.
The course will use NetLogo, a software platform that greatly reduces the effort and expertise to program and use IBMs. NetLogo is free, extremely well designed and documented, widely used in science, and great fun. At the end of the course, participants should know NetLogo well enough to build basic models, teach themselves to become expert, and use the textbook to lead a class effectively.
The primary audience of this course is university professors and instructors who are considering teaching a class in individual-based modeling. Others (e.g., graduate students, scientists wanting to use IBMs in research) will be considered as space allows.
The course instructors are ecologists, and many of the examples used in the class will be ecological, but the textbook is interdisciplinary and participants from other fields are welcome.
2018 Course Schedule
Location: Room 204b, Forestry Building
|Time||Sunday, July 29||Monday, July 30||Tuesday, July 31||Wednesday, Aug. 1||Thursday, Aug. 2||Friday, Aug. 3|
|8:30 a.m.||Welcome, introductions, and motivational examples (VG; SR)||Lecture: Design concepts (Ch. 7; VG)||Work on Project 1||Pattern-oriented modeling example: The Jamaica coffee farm model (SR)||Work on Project 2|
|9:30 a.m.||Lecture: What are models, IBMs, ABMs; and why do we use them? (Ch. 1; VG)||Group exercise: Emergence, simulation experiments, and BehaviorSpace (Ch. 8; VG)||Lecture: Independent testing of submodels (Sect. 12.3; SR)||Work on Project 2||(continued)|
|10:30 a.m.||Group exercise- Introduction to NetLogo (Ch. 2; VG)||Lecture and group exercise: Sensing; NetLogo variables (Ch 10, Sect. 10.2, Ex. 10-1; SL)||Work on Project 1||(continued)||(continued)|
|12 p.m.||Lunch (catered; discussion opportunity)||Lunch and discussion||Lunch and discussion||Lunch and discussion||Lunch and discussion|
|1 p.m.||Group exercise- Programming a first NetLogo model (Ch. 4; SR)||Lecture- Software testing (Ch. 9; SR)||Presentations of Project 1||Lecture: Analyzing and doing science with IBMs -- how to get that Nobel Prize (VG)||Project presentations and feedback|
|2 p.m.||(continued)||Software testing exercise||Guest lecture and discussion: Empirical science and individual-based modeling: how do they affect each other? (B. C. Harvey, Redwood Sciences Lab, US Forest Service)||Work on Project 2||(continued)|
|3 p.m.||Group exercise: From animations to science (Ch. 5; SR)||(continued)||Lectures: Stochasticity and random number generation (Ch. 15; SR)
Collectives and NetLogo Breeds (Ch. 16; SL)
|4 p.m.||(continued)||Lecture: Adaptive behavior and objectives (Ch. 11; SR)
Exercise: AgentSets and subsetting (Sect. 11.2.1; Ex. 11-1: SL)
|Lecture: Pattern-Oriented Modeling--The Way to do agent-based science (VG)||Grand finale- NetLogo gadgets; how to keep your momentum up; course feedback|
|4:30 p.m.||The ODD Protocol- Why and how (Ch. 3; VG)||Introduction to Project 1: Business Investor & Telemarketer models (Ex. 10-3 & 13-1, 2; SR)||Introduction to Project 2: Wild Dog & Woodhoopoe models (Ex.13-3, 4 & 19-2; SR)||Discussion- Effective learning of software development (SL)|
6-9 p.m. 231 13th St.
Download MAP (PDF: Requires Reader)
|Redwood forest stroll (~1 mile walk through the redwood forest adjacent to campus), immediately after class||Project work (independent)||Baseball at the Arcata Ballpark: Humboldt Crabs vs. S.F. Seals (7 p.m.)||Class repast: 6:30 p.m. Plaza View Room, Jacoby Storehouse, on the plaza in downtown Arcata|
- The textbook: Agent-based and Individual-based Modeling: A Practical Introduction
- The QUBES website for instructors using the textbook
- Grimm and Railsback 2005: Individual-based Modeling and Ecology
- Volker Grimm
- Individual-based modeling at Humboldt State
- A related short course for graduate students