Ecological Dynamics (Spring, 2026)

BIO/ESS 156, QSB/ES 256

Info

• Class time/location: TR 12:00-1:15 in COB2 140
• Office hours: T 10-11 AM (SE1 288); F 10-11 AM (ZOOM)
• To contact me, use the INBOX feature in Canvas. Letters sent to my email address will typically be lost.
• Course Syllabus
• Course Schedule
• AI Use Policy

Welcome!

Welcome to the course website for Ecological Dynamics! The links above should connect you to all the general course information/content that you need. See the course syllabus for the required materials, grading policy, AI policy, and rules of the road. See the course schedule for the topics we are covering, required readings, etc. Check that page often, as it is subject to change at any time. Any major announcements will be listed on this main page.

This course requires the use of a textbook (Otto and Day, A Biologist’s Guide to Mathematical Modeling), and assessments will be comprised of both in-class pencil-and-paper work, as well as take-home assignments. AI-use will be integrated into some parts of class assignments, and will be prohibited in others. Quizzes and exams will be taken in class using scantron. You will be required to have a pack of scantron forms with you at every class session. You will be required to have a physical paper notebook (not an ipad or computer) for taking notes. Use of electronics (iphones, ipads, computers) is prohibited except when otherwise stated. The full list of what you need in the course can be found here.

For some assignments, AI will be allowed and encouraged in certain capacities. See the AI Use Policy for details. But in the allowed use-cases, what AI should you use? Every student has access (through their MS account) to Microsoft Copilot, which currently uses the ChatGPT 4o engine. There are also free tiers of Anthropic’s Claude, Google’s Gemini, and OpenAI’s GPT 5 models, among others. Note that AI can frequently deliver convincing answers/code that is incorrect. Be careful! You will be held responsible for the accuracy of your work whether AI is used or not!

Annoucements!

• The first day of class is Tuesday, January 20th in COB2 140!

Errata

This is the first time that I am teaching this course as a conjoined undergraduate/graduate offering. While I am excited to offer this material in a way that is accessible and useful for both undergraduate and graduate students, there will be times where I may have to make some alterations as we go along to ensure a smooth delivery.

---

Coding Resources

R

• R without RStudio - a staple language for biologists
• RStudio (should self-install R)
• RStudio webinars and tutorials
• Learn R through Swirl (requires R)
• Greg Gilbert’s transitioning to R course materials
• Try R Code School

Julia

• Julia - new language but incredibly fast
• Learning Julia
• Jupyter notebook environment
• Julia Coursera

Other

• Wolfram Alpha: Easy plotting and analysis of functions using natural language
• Mathematica, Matlab, and proprietary software supplied by UCMerced
• Python - perhaps the most widely used language across sciences
• Visual Studio text editor