by David M Diez, Christopher D Barr, and Mine Çetinkaya-Rundel

Chapters Used:

• Chapter 1: Introduction to Data
• Chapter 4: Foundations of Inference
• Chapter 7: Introduction to Linear Regression
• Chapter 8: Multiple and Logistic Regression

by David R. Anderson

Chapters Used:

• Chapter 1:  Introduction: Science Hypotheses and Science Philosophy
• Chapter 2:  Data and Models
• Chapter 3:  Information Theory and Entropy
• Chapter 4:  Quantifying the Evidence About Science Hypotheses

by Steven F. Railsback and Volker Grimm

Chapters Used:

• Chapter 1: Models, Agent-Based Models, and the Modeling Cycle
• Chapter 2: Getting Started with NetLogo
• Chapter 3: Describing and Formulating ABMs:  The ODD Protocol
• Chapter 4: Implementing a First Agent-Based Model
• Chapter 5: From Animations to Science
• Chapter 6: Testing Your Program
• Chapter 7: Introduction to Part II
• Chapter 8: Emergence

by Dan Graur and Wen-Hsiung Li

Chapters Used:

• Chapter 2: Dynamics of Genes in Populations

by Brian P. Ingalls

Chapters Used:

• Chapter 1: Introduction
• Chapter 2: Modeling of Chemical Reaction Networks
• Chapter 3: Biochemical Kinetics
• Chapter 4: Analysis of Dynamic Mathematical Models
• Chapter 5: Metabolic Networks
• Chapter 6: Signal Transduction Pathways
• Chapter 7: Gene Regulatory Networks