BMED

3510 Biomedical Systems and Modeling

Credit: 3-2-4 (3rd year Spring/Fall)

Prerequisites: BMED 3100, BMED 2210, MATH 2403

Overview:


Jan 5: First day of classes

Jan 19: holiday

Mar 16-20: Spring break

April 20-24: dead week (no exams; projects)

Apr 24: last day of classes

Apr 27-May 1: Final exams

May 5: grades due

10 weeks before Spring break
5 weeks after Spring break

BMED 3510 Biomedical Systems and Modeling

Credit: 3-2-4
Prerequisite(s): BMED 3100, BMED 2210, MATH 2403

Catalog Description
The course introduces juniors in BME to the field of computational systems biology. It covers all typical
aspects of biomathematical modeling, including: the choice of a modeling framework from among alternative
approaches; the design of interaction diagrams; the identification of variables and processes; the design of
systems models; standard methods of parameter estimation; the analysis of steady states, stability,
sensitivity and gains; numerical evaluations of transients; phase-plane analysis; and the simulation of
representative biomedical scenarios. All theoretical concepts are exemplified with applications.

Objectives
This course introduces the student to the emerging field of systems biology. It will consist of a weekly
overview lecture, a problem solving session, and a homework discussion and recitation session. The
overarching objective is to equip students with solid basic knowledge of different types of mathematical and
computational modeling approaches and their applications to solving biomedical problems.

Expected Outcomes
By the end of the course the students should:
1. Understand the basic strengths and limitations of quantitative modeling
2. Have acquired a basic skill set for designing and implementing quantitative models of biomedical systems
3. Have mastered standard techniques of steady-state and dynamical analysis
4. Understand how to apply different modeling tools to the analysis of dynamical systems in biomedicine

Text
Voit, E.O.: A First Course in Systems Biology. Garland Science, New York, NY, 2012

Instructional Format
Four hours each week are scheduled for the class. The weekly one-hour overview lecture on Monday
presents a high-level discussion of the topics to be studied during the week. The session on Tuesday begins
with a brief question-and-answer period followed by hands-on projects and team-based problem solving.
The session on Thursday reviews and explains details of the topics to be learned during the week in a
question-and-answer manner and includes, if desired, a discussion of homework problems. The primary
weekly assignment is the reading and understanding of selected text from the book. Secondary assignments
consist of exercises from the book or uploaded to T-square.

Homework may be done and submitted in groups of up to four individuals. Three semester exams
and one final exam assess each students mastery of the materials discussed in class.


Evaluation
Weekly assignments and quizzes
15%
Three exams


20% each
Final exam



25%

Topical Outline

Date Class
1/5
Lecture
1/6
Review
1/8
Review
1/12 Lecture
1/13 Probl. Solv.
1/15 HW, Recit.
1/19 Holiday
1/20 Probl. Solv.
1/22 HW, Recit.
1/26 Lecture
1/27 Probl. Solv.
1/29 Exam 1
2/2
Lecture
2/3
Probl. Solv.
2/5
HW, Recit.
2/9
Lecture
2/10 Review
2/12 Exam 1

Instructor
Voit


Qiu





Qiu


Qiu


Qiu

2/16
2/17
2/19
2/23

Lecture
Probl. Solv.
HW, Recit.
Lecture

Qiu


Qiu

2/24
2/26
3/2
3/3
3/5
3/9

Probl. Solv.
HW, Recit.
Lecture
Probl. Solv.
HW, Recit.
Lecture

Fonseca


Fonseca

3/10
3/12

Review
Exam 2

3/16
3/17
3/29
3/23
3/24
3/26
3/30
3/31
4/2

Spring Break
Spring Break
Spring Break
Lecture
Probl. Solv.
HW, Recit.
Lecture
Probl. Solv.
HW, Recit.

Fonseca


Voit

Topic
Why modeling?
Crash course: functions, derivatives
Crash course: vectors and matrices
Types of models
Chapters 1, 2 (pp. 1-34)

Chapter 2 (pp. 35-48)
Static network models
Chapter 3 (pp. 51-74)
Discrete models (linear, nonlinear)
Chapter 4 (pp. 83-106)
Continuous models
Chapters 1-4
Focus: Chapters 1-4
(pp. 83-90 and 95-97)
Standard methods of analysis
Chapter 4 (pp. 107-118)
Parameter estimation
Chapter 5 (pp. 123-141)
Gene and protein networks
Chapter 6 (pp. 157-178)
Chapter 7 (pp. 189-213)
Metabolic systems

Assignment
Chapters 1, 2 (pp. 1-34)
HW1
HW2
Chapter 2 (pp. 35-48)
HW3


Chapter 3 (pp. 51-74)
HW4
Chapter 4 (pp. 83-90; 95-97)
HW5

Chapter 4 (pp. 90-95; 97-106)
HW6

Chapter 4 (pp. 107-118)


Chapter 5 (pp. 123-141)
HW7

Chapter 6 (pp. 157-178)
Chapter 7 (pp. 189-213)
HW8

Chapter 8 (pp. 219-239)
HW9

Chapter 9 (pp. 243-249;
253-258)

Chapters 4-7
Focus: Chap. 4 (from p. 91)
to Chap. 7






Bistability, hysteresis, MAPK cascade Chapter 10 (pp. 261-275)
Chapter 9 (pp. 243-249;
HW10
253-258)

Population models
Chapter 13 (pp. 347-368)
HW11
Chapter 10 (pp. 261-275)

4/6

Lecture

Voit

4/7
4/9
4/13
4/14
4/16
4/20

Probl. Solv.
HW, Recit.
Lecture
Review
Exam 3
Lecture

Voit


Voit

4/21
4/23
4/27
4/??
5/4

Probl. Solv.
Review
-
Final

Personalized medicine and

drug development
Chapter 13 (pp. 347-368)
Synthetic biology
Chapters 10, 13, 14
Focus: Chapters 10, 13, 14
Models of the heart;
Frontiers of systems biology
Chapter 12 (pp. 307-335)

Cumulative Exam
Grades due

Chapter 14 (pp. 373-393)

HW12

Chapter 12 (pp. 307-335)