BIO 202. Mathematics of Life: Introduction to Quantitative Biology

Schedule of Topics, Readings, and Assignments

Winter 2018 (4 credits)

Unless otherwise noted, readings and exercises are in Bodine, Lenhart, & Gross.

IMPORTANT NOTE: Each “Matlab skills” section should be replaced with the corresponding “R skills” section. The latter are found in the R supplement. The R scripts mentioned can be found here. Throughout, when the book directs you to work something out in Matlab, do it in R instead.

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Back to course syllabus

Thu 4 Jan

Topics:
- Introductions
- Orientation to the course
- The nature of biological data
- Getting started with R
- Pretest

Tue 9 Jan

Due: pretest
Reading: Chapter 1
Exercises 1 due: 1.1, 1.3, 1.5, 1.7, 1.8, 1.9, 1.10, 1.11
R tutorial §1–6
Topics:
- Data structures in R
- Data munging

Thu 11 Jan

Reading: Chapter 2
Exercises 2 due: 2.1, 2.3, 2.6, 2.9, 2.10 [Remember: do the “R skills” instead of the “Matlab skills” (§2.5).]
R tutorial §9.1–13.2
Topics:
- Data munging
- Data visualization and the grammar of graphics
Transcript of R session

Tue 16 Jan

Reading: Chapters 3–4
Exercises 3 due: 3.2, 3.3, 3.5, 3.8, 4.1, 4.2, 4.3, 4.4, 4.6, 4.7, 4.10, 4.12, 4.14
Quiz 1
Topics:

Thu 18 Jan

Reading: §§5.1–5.4
Quiz 2
Topics:
- Work on Challenge 1-1.
- Biological systems and feedback loops

Tue 23 Jan

Due: Challenge 1-1
Reading: §§5.5–5.7
Exercises 4 due: 5.1, 5.2, 5.3, 5.4, 5.5, 5.6, 5.8, 5.9, 5.11, 5.12
Topics:
- Solving first order difference equations analytically
- Biological systems and feedback loops
- Working with difference equations in R
- Challenge 1-1: peer review
Transcript of R session

Thu 25 Jan

Due: Peer review of Challenge 1-1
Reading: Chapter 6
Exercises 5 due: 6.2, 6.3, 6.5, 6.6, 6.7, 6.9
Quiz 3
Topics:
- Working with difference equations in R
- Work on Challenge 1-2
Transcript of R session

Tue 30 Jan

Reading: §§7.1–7.2
Exercises 6 due: 7.1, 7.2, 7.3, 7.4, 7.5
Due: Challenge 1-2
Quiz 4
Topics
- Pharmacokinetic modeling with difference equations
- Challenge 2: Designing a dose schedule
Transcript of R session

Thu 1 Feb

Reading: §7.3
Exercises 7 due: 7.6, 7.7, 7.8, 7.9, 7.10
Quiz 5
Topics:
- Work on Challenge 2-1.
Transcript of R session

Tue 6 Feb

Due: Challenge 2-1.
Reading: §§8.1–8.2
Exercises 8 due: 8.1, 8.2, 8.3, 8.4, 8.5
Quiz 6
Topics:
- Peer review of Challenge 2-1.
- Projection matrices and equilibria
- Eigenvalues and eigenvectors

Thu 8 Feb

Due: Peer review of Challenge 2-1.
Reading: §§8.3–8.4
Exercises 9 due: 8.6, 8.7, 8.8, 8.9
Quiz 7
Topics:
- Projection matrices and equilibria
- Leslie matrix models
- Peer review of Challenge 2-1.
- Work on Challenge 2-2.
Transcript of R session

Tue 13 Feb

Due: Challenge 1-3.
Reading: §§9.1–9.3
Exercises 10 due: 9.1, 9.2, 9.3, 9.4, 9.5, 9.6, 9.7
Quiz 8
Topics:
- Leslie matrix models
- Projection matrices and equilibria
- Work on Challenge 2-2.
- More on eigenvalues and eigenvectors
Transcript of R session

Thu 15 Feb

Due: Challenge 2-2.
Reading: §9.4
Exercises 11 due: 9.9, 9.10, 9.13, 9.14
Quiz 9
Topics:
- Challenge 3
- Modeling population growth using nonlinear difference equations
Transcript of R session

Tue 20 Feb

Due: Challenge 3-1
No class meeting
Reading: §§10.1–10.4
Exercises 12 due: 10.1, 10.2, 10.4, 10.5, 10.7, 10.8, 10.9
Peer review of Challenge 3.1

Thu 22 Feb

Due: Peer review of Challenge 3-1
No class meeting
Reading: §10.5, §§11.1–11.2
Exercises 13 due: 10.11, 10.12, 10.13, 10.15, 11.1, 11.2, 11.3

26 Feb–2 Mar

Spring Break: no class meetings

Tue 6 Mar

Reading: §§11.3–11.4
Exercises 14 due: 11.4, 11.5, 11.6, 11.7, 11.8, 11.9, 11.10, 11.11
Quiz 10
Topics:
- Introduction to probability
- Stochastic simulation
- Work on Challenges 2-3 and 3-2.
Transcript of R session

Thu 8 Mar

Due: Challenge 3-2
Reading: §§12.1–12.3
Exercises 15 due: 12.1, 12.5, 12.6, 12.9, 12.10
Quiz 11
Topics:
- Some counting problems
- Work on Challenge 2-3
- Bernoulli, binomial, and Poisson distributions

Tue 13 Mar

Due: Challenge 2-3
Reading: §§13.1–13.2
Exercises 16 due: 13.1, 13.2, 13.4, 13.5, 13.6, 13.7, 13.8, 13.14 (see errata), 13.15
Quiz 12
Topics:
- Bayes’ theorem
- Modeling population growth using nonlinear difference equations

Thu 15 Mar

Reading: none
Quiz 13
Topics:
- Dynamics of growth
- One-species population growth models.
Transcript of R session

Tue 20 Mar

Reading: none
Due: Challenge 3-3
Topics:
- Dynamics of competition
- Two-species population growth models.
- Challenge 4
Transcript of R session

Thu 22 Mar

Reading: none
Topics:
- Work on Challenge 4

Tue 27 Mar

Due: Challenge 4-1
Reading: §§14.1–14.2
Quiz 14
Exercises 17 due: 14.1, 14.2, 14.3, 14.4, 14.6, 14.7, 14.8, 14.9
Topics:
- Peer review of Challenge 4-1
- Population genetics
- Binomial distribution. Sampling.
Transcript of R session

Thu 29 Mar

Due: Peer review of Challenge 4-1
Reading: §§15.1–15.2
Quiz 15
Exercises 18 due: 15.1, 15.2, 15.3, 15.4
Topics:
- Work on Challenge 4
- Challenge 5

Tue 3 Apr

Due: Challenge 4-2
Reading: §§15.3
Quiz 16
Exercises 19 due: 15.5, 15.8, 15.10, 15.11, 15.12
Topics:
- Deterministic one-locus, two-allele model
- Poisson, binomial, and multinomial distributions
- Work on Challenge 5

Thu 5 Apr

Reading: §§16.1–16.4
Quiz 17
Exercises 20 due: 15.13, 16.1, 16.2, 16.3, 16.4, 16.6, 16.7
Topics:
- Work on Challenge 4-3
Transcript of R session

Tue 10 Apr

Due: Challenge 5-1
Reading: §§ 17.1–17.4
Quiz 18
Exercises 21 due: 17.1, 17.2, 17.3, 17.4, 17.5
Topics:
- Peer review of Challenge 5-1
- Work on Challenges

Thu 12 Apr

Due: Challenge 5-2
Reading: §§ 17.5–17.7, 18.1–18.2
Exercises 22 due: 17.7, 17.8, 17.9, 17.10, 18.1, 18.2
Quiz 19
Topics:
- Work on Challenges
Transcript of R session

Fri 13 Apr

Extra office hour: 10am–12:30pm

Mon 16 Apr

Extra office hour: 10am–12:30pm

Tue 17 Apr

Due Challenge 4-3
Reading: §§ 18.3–18.7
Exercises 23 due: 18.3, 18.4, 18.8, 18.9, 18.10
Quiz 20
Topics:
- Work on Challenges
Optional: Challenge 6
Transcript of R session

Fri 20 Apr

Final deadline for all course work, 6:00pm

Mon 23 Apr

Deadline for instructor submission of final grades, 6:00pm

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