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    Bmed 3510 Syllabus s15

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    Sulaiman Somani
    This document provides information about the BMED 3510 Biomedical Systems and Modeling course, including its credit hours, prerequisites, schedule, objectives, outcomes, evaluation criteria, textbook, instructional format, and topical outline. The course is a 3-2-4 credit junior level spring/fall course that introduces students to computational systems biology and biomathematical modeling. It covers modeling frameworks, steady state analysis, parameter estimation, and simulating biomedical scenarios. The course aims to equip students with skills in quantitative modeling of biomedical systems.

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    Bmed 3510 Syllabus s15

    Uploaded by

    Sulaiman Somani
    113 views4 pages
    This document provides information about the BMED 3510 Biomedical Systems and Modeling course, including its credit hours, prerequisites, schedule, objectives, outcomes, evaluation criteria, textbook, instructional format, and topical outline. The course is a 3-2-4 credit junior level spring/fall course that introduces students to computational systems biology and biomathematical modeling. It covers modeling frameworks, steady state analysis, parameter estimation, and simulating biomedical scenarios. The course aims to equip students with skills in quantitative modeling of biomedical systems.

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    This document provides information about the BMED 3510 Biomedical Systems and Modeling course, including its credit hours, prerequisites, schedule, objectives, outcomes, evaluation criteria, textbook, instructional format, and topical outline. The course is a 3-2-4 credit junior level spring/fall course that introduces students to computational systems biology and biomathematical modeling. It covers modeling frameworks, steady state analysis, parameter estimation, and simulating biomedical scenarios. The course aims to equip students with skills in quantitative modeling of biomedical systems.

    Copyright:

    © All Rights Reserved
    Download as PDF, TXT or read online from Scribd
    Download as pdf or txt
    113 views4 pages

    Bmed 3510 Syllabus s15

    Uploaded by

    Sulaiman Somani
    This document provides information about the BMED 3510 Biomedical Systems and Modeling course, including its credit hours, prerequisites, schedule, objectives, outcomes, evaluation criteria, textbook, instructional format, and topical outline. The course is a 3-2-4 credit junior level spring/fall course that introduces students to computational systems biology and biomathematical modeling. It covers modeling frameworks, steady state analysis, parameter estimation, and simulating biomedical scenarios. The course aims to equip students with skills in quantitative modeling of biomedical systems.

    Copyright:

    © All Rights Reserved
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    of 4

    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)

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