Ecological Modeling
PBIO 5940 (3 credits)


Fall 2023 (Online)
Instructor: Brian Beckage (Brian.Beckage@uvm.edu)
Office Hours (remote by appointment)



Course Description

Pre-requisites or Co-requisites

Course Goals

Grading

Readings

Media

Schedule


----> CLICK HERE TO GET STARTED <----



Course Description

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Ecological Modeling will provide a comprehensive overview of the modeling of ecological systems to include biological and environmental systems. We will survey the methods used to model ecological systems with a focus on system dynamics and agent-based modeling. We will explore the complexity of ecological systems, including emergent properties, nonlinearities and feedbacks between system components. We will utilize the system dynamics software Stella and the agent-based programming language Netlogo.


Course Requisites or Co-requisites

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Graduate Level standing


Course Goals

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    Course objectives

  1. The student will be able to describe system feedbacks, emergence, and other properties of complex ecological systems.
  2. The student will be able to describe the fundamental properties of systems and system dynamics modeling.
  3. The student will be able to describe the structure and characteristics of agent-based models.
  4. The student will apply system dynamic and agent-based modeling approaches to model ecological systems and their relationship to the climate and human components of the Earth system.
  5. The student will apply system dynamic and agent-based modeling approaches to construct a model of an ecological system, then calibrate, validate, and analyze the model, and produce a written description of the model and its behavior.

Class Structure. Students will achieve course objectives through readings, other media, online discussions and individual and group model-building exercises.


  1. Readings. Students will complete assigned readings from course texts and other assigned sources.

  2. Media. Students will watch a variety of videos and other media that reinforce and supplement the assigned readings. These may include full length documentaries, shorter video presentations, and podcasts. The online discussions and learning assessments will integrate material from all media.

  3. Online discussions. Students will participate in online discussions that examine and analyze the concepts presented in the readings and assigned media for each course module.

  4. Exercises. Students will complete assigned exercises in building ecological models. This will involve learning basic modeling concepts and becoming proficient in using the programming platforms Stella and Netlogo.

  5. Research paper and presentation. Students will construct, parameterize, and analyze a model of an ecological system. The students will present this model in class and write a research paper using the model.

  6. Learning Assessments. Quizzes will assess student understanding of assigned readings and videos for each course module, while a cumulative final exam will assess student understanding of content across modules.


Grading

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Student grades will be based on the following components:

  1. Analysis and discussion (on Yellowdig) of assigned materials: 20% of course grade.
  2. Learning assessments on assigned materials: 20% of course grade.
  3. Completion of exercises: 20% of course grade.
  4. Research paper: 10% of course grade.
  5. Research presentation: 5% of course grade.
  6. Final exam: 25% of course grade.
  7. Grading Scale:

Percentage

Grade

  • 98-100
  • 93-97
  • 90-92
  • 88-89
  • 83-87
  • 80-82
  • 78-79
  • 73-77
  • 70-72
  • A+
  • A
  • A-
  • B+
  • B
  • B-
  • C+
  • C
  • C-

Grades less than 70 are considered failing for grad courses.


Readings

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Students will also be assigned readings from the following set of books (below). These books will be required for this class and are available as ebooks from the publisher or other online sources (e.g., Amazon, etc.) or in the university bookstore.

  1. Uri Wilensky and William Rand. 2014. An Introduction to Agent-Based Modeling: Modeling Natural, Social, and Engineered Complex Systems with NetLogo. Link to book.
  2. Bruce Hannon and Matthias Ruth. 2014. Modeling dynamic biological systems. ISBN: 9783319056159 eBook ISBN: 9783319056142 Link to book.
  3. Meadows, D.H., 2008. Thinking in systems: A primer. Chelsea Green Publishing. ISBN: 9781603580557. Link to book.


Media

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We will watch a variety of documentaries, video lectures, and podcasts. I try to find free sources of these media, but you may have to rent, purchase, or find them through a subscription service (e.g., Amazon Prime, Netflix, Apple TV, etc.).


GETTING STARTED

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  1. Watch these introductory videos:
    1. In Introductory Video 1 (7 mins), you'll learn a little about me and my approach to teaching this course, receive an orientation to the course objectives, and learn about the grading schema.
    2. In Introductory Video 2 (8 mins), you'll learn about our course readings and videos, how to get started, and an overview of the Module structure of our course.
  2. Review the course objectives and course texts above.
  3. Log onto Blackboard class page and click on the Yellowdig link on the left sidebar and make a post introducing yourself. Here is a short youtube video (3 mins) describing how to use Yellowdig and here is a video (4 mins) specific to using Yellowdig in our class.
  4. Go to the course Schedule to view the activities and assignments.


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