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 202122 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:
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.
Date  Topic  Homework  Reading 
Week 1 18 Jan 
Introduction:

HW #1 (PDF) HW #1 (IPYNB) Out: 18 Jan 
week1_python_intro.ipynb week1_python_intro.pdf Review: Computational Biology 
Week 2 25 Jan 

HW #2 (PDF) HW #2 (IPYNB) Out: 25 Jan 
week2_data_analysis.ipynb week2_data_analysis.pdf BFS Section 1.2 Review: Synthetic Biology 
Week 3 1 Feb 
Core Biological Processes  I

HW #3 (PDF) HW #3 (IPYNB) Out: 1 Feb 
week3_intro_ode.ipynb week3_intro_ode.pdf BFS Section 2.2 PBoC Section 3.2.1: Timing the machines of the central dogma 
Week 4 8 Feb 
Core Biological Processes  II

HW #4 (PDF) HW #4 (IPYNB) Out: 8 Feb 
BFS Section 2.3
Alon Section 1.3 PBoC: Extracting gene expression from microscopy images week4_hill_functions.ipynb week4_hill_functions.pdf 
Week 5 15 Feb 
From Processes to Circuits  I

HW #5 (PDF) HW #5 (IPYNB) Out: 15 Feb 
Toggle Switch in E. coli
Repressilator in E. coli week5_feedback_systems.ipynb week5_feedback_systems.pdf PBoC Ch 19: Stability Analysis of the Genetic Switch 
Week 6 22 Feb 
From Processes to Circuits  II

HW #6 (PDF) HW #6 (IPYNB) Out: 22 Feb 
PBoC Chapter 19
Paper: Negative Autoregulation Paper: Eukaryotic Transcriptional Control week6_system_analysis.ipynb week6_system_analysis.pdf 
Week 7 1 Mar 
Dynamical System Tools for Biological Circuits

HW #7 (PDF) HW #7 (IPYNB) Out: 1 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 week7_stochastic_systems.ipynb week7_stochastic_systems.pdf 
Week 8 8 Mar 
Biological Circuit Motifs and Systems

No Homework: Spring Break 
Alon Ch. 3
week8_feedforward_loops.ipynb week8_feedforward_loops.pdf 
Week 9: Spring Break  
Week 10 22 Mar 
Modeling Biological Circuits

HW #8 Out: 22 Mar 

Week 11 29 Mar 
CRN Models for Biological Processes

HW #9 Out: 29 Mar 

Week 12 5 Apr 
Modeling and Analysis of Biological Motifs

HW #10 Out: 5 Apr 

Week 13 12 Apr 
Case Study 1

Project Discussions #1  
Week 14 19 Apr 
Case Study 2

Project Discussions #2  
Week 15 26 Apr 
Summary:

Final Project Reports Due 
The final grade will be based on homework sets and a final project:
The primary resources are the following two textbooks:
Additional References: