ENGR 164: Introduction to Biological System Design.

Course Logistics

This is the course homepage for ENGR 164, listed as Introduction to Biomedical Engineering in the Engineering course catalog at Harvey Mudd College for Spring 2021-22 semester. The actual course title is Introduction to Biological System Design. This course is intended for juniors and seniors interested in the computationally exploring the design of natural and engineered biological systems. After completion of the course, students will be able to:

  1. understand the basics of biological systems design
  2. develop mathematical models for biological circuits
  3. use numerical approaches to understand and analyze biological data

Course Description

E164. Introduction to Biological System Design. Spring Semester at Harvey Mudd College.
Credits: 3 (2.5 hr lecture, 0 hr lab, 6 hr homework).
Prerequisites: CS5 and E79 or by instructor's permission.
Course Topics: Introduction to the broad fields of systems and synthetic biology by describing the basic biological processes, mechanisms, and components of biological designs. Particular topics include: gene regulatory networks, transcriptional and translational regulation, common motifs in biological circuit designs, chemical reaction network modeling for biological systems, mathematical analyses using differential equations, calculus, and algebra for biological models, and two case studies of biological systems. The course will be taught in Python language — so we will use programming in Python to numerically or analytically understand the topics.

Lecture Schedule

Date Topic Homework Reading
Week 1

18 Jan
20 Jan

  • Course logistics
  • Overview: Biological Systems Design
  • Introduction to Python
  • Introduction to Systems and Synthetic Biology
HW #1 (PDF)

Out: 18 Jan
Due: 25 Jan
HW #1 Solution PDF (HMC only)
HW #1 Solution IPYNB (HMC only)

Review: Computational Biology
Week 2

25 Jan
27 Jan

  • Biological Experiments and Data
  • Cell Growth Dynamics
HW #2 (PDF)

Out: 25 Jan
Due: 2 Feb
HW #2 Solution PDF (HMC only)
HW #2 Solution IPYNB (HMC only)

BFS Section 1.2
Review: Synthetic Biology
Week 3

1 Feb
3 Feb

Core Biological Processes - I
  • Transcription and Translation
  • Modeling Biological Processes
HW #3 (PDF)

Out: 1 Feb
Due: 8 Feb
HW #3 Solution PDF (HMC only)
HW #3 Solution IPYNB (HMC only)

BFS Section 2.2
PBoC Section 3.2.1: Timing the machines of the central dogma
Week 4

8 Feb
10 Feb

Core Biological Processes - II
  • Gene Regulation
  • Phenomenological Modeling of Biological Systems
HW #4 (PDF)

Out: 8 Feb
Due: 15 Feb
HW #4 Solution PDF (HMC only)
HW #4 Solution IPYNB (HMC only)

BFS Section 2.3
Alon Section 1.3
PBoC: Extracting gene expression from microscopy images
Week 5

15 Feb
17 Feb

From Processes to Circuits - I
  • Simple Biological Circuits
  • Introduction to Feedback Systems
  • Dynamical System Analysis
HW #5 (PDF)

Out: 15 Feb
Due: 22 Feb

Toggle Switch in E. coli
Repressilator in E. coli
PBoC Ch 19: Stability Analysis of the Genetic Switch
Week 6

22 Feb
24 Feb

From Processes to Circuits - II
  • Gene Regulatory Networks
  • Design Principles of Gene Regulation
HW #6 (PDF)

Out: 22 Feb
Due: 1 Mar

PBoC Chapter 19
Paper: Negative Autoregulation
Paper: Eukaryotic Transcriptional Control
Week 7

1 Mar
3 Mar

Dynamical System Tools for Biological Circuits
  • Introduction to Stochasticity in Biology
  • Simulation of Stochastic Systems
HW #7 (PDF)

Out: 1 Mar
Due: 8 Mar

BFS Ch. 4 Section 4.1 - CME and RRE
BFS Ch. 4 Section 4.2 - Simulation
Stability of NAR: Paper on stability of negative autoregulation
Gene Expression Noise: Paper on stochastic noise in gene expression
Week 8

8 Mar
10 Mar

Biological Circuit Motifs and Systems
  • Feedback Loops
  • Feedforward Loops
  • From circuit motifs to functions
No Homework: Spring Break

Alon Ch. 3
Week 9: Spring Break
Week 10

22 Mar
24 Mar

Modeling Biological Circuits
  • Review: Ordinary Differential Equations (ODEs)
  • Review: Chemical Reaction Networks (CRNs)
  • ODEs for CRNs
HW #8

Out: 22 Mar
Due: 29 Mar

Week 11

29 Mar
31 Mar

CRN Models for Biological Processes
  • Transcription and Translation
  • Gene Regulation
  • Model Reduction using QSSA and Conservation Laws
HW #9

Out: 29 Mar
Due: 5 Apr

Week 12

5 Apr
7 Apr

Modeling and Analysis of Biological Motifs
  • Logic Gates With Feedforward Loops
  • Robustness and Sensitivity Analysis
HW #10

Out: 5 Apr
Due: 12 Apr

Week 13

12 Apr
14 Apr

Case Study 1
  • Feedback Loops
  • Feedforward Loops
Project Discussions #1
Week 14

19 Apr
21 Apr

Case Study 2
  • Feedback Loops
  • Feedforward Loops
Project Discussions #2
Week 15

26 Apr
28 Apr

  • Class Review
  • Final Project Presentations
Final Project Reports Due


The final grade will be based on homework sets and a final project:

Course Resources

The primary resources are the following two textbooks:

Additional References:

  1. [CompSysBio] Kitano, Hiroaki. "Computational systems biology." Nature 420.6912 (2002): 206-210.
  2. [HistorySynBio] Cameron, D. Ewen, Caleb J. Bashor, and James J. Collins. "A brief history of synthetic biology." Nature Reviews Microbiology 12.5 (2014): 381-390.
  3. [Repressilator2000] Elowitz, Michael B., and Stanislas Leibler. "A synthetic oscillatory network of transcriptional regulators." Nature 403.6767 (2000): 335-338.
  4. [ToggleSwitch2000] Gardner, Timothy S., Charles R. Cantor, and James J. Collins. "Construction of a genetic toggle switch in Escherichia coli." Nature 403.6767 (2000): 339-342.
  5. [AutoRepression] Rosenfeld, Nitzan, Michael B. Elowitz, and Uri Alon. "Negative autoregulation speeds the response times of transcription networks." Journal of molecular biology 323.5 (2002): 785-793.
  6. [EukaryoticTranscription] Kornberg, Roger D. "Eukaryotic transcriptional control." Trends in biochemical sciences 24.12 (1999): M46-M49.
  7. [StabilityNAR] Becskei, Attila, and Luis Serrano. "Engineering stability in gene networks by autoregulation." Nature 405.6786 (2000): 590-593.
  8. [GeneExpressionNoise] Elowitz, Michael B., et al. "Stochastic gene expression in a single cell." Science 297.5584 (2002): 1183-1186.