Department of Biomedical Engineering National Taiwan University

Syllabus

Information and Syllabuses of (Only those offered in English are listed.)

Feng-Huei Lin

Course Information
Course Name ADVANCED BIOCHEMISTRY
Semester 105-1
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor FENG-HUEI LIN
Course No. Biomed 5002
Class COLLEGE OF ENGINEERING BLDG.209
Credits 3
Full/Half Yr. Half
Required/ Elective Elective
Time Monday 789
Remarks Max. students allowed: 30
Course Website https://ceiba.ntu.edu.tw/1041Biomed5002_
Course Syllabus
Course Description  Topics:
“Bio-molecules” is a multidisciplinary science; the first task in presenting it to students of widely varying backgrounds is to put it in the class. Part one provides the necessary background and connects bio-molecules to the other sciences. Part two focuses on the structure and dynamics of important cellular components. Molecular biology is covered in Part three. The final part of the class is devoted to intermediary metabolism. Some topics are discussed several times, such as control of carbohydrate metabolism. Subsequently discussions make use of and build on information students have already learned. It is particularly useful to return a topic after students have had time to assimilate and reflect. The class gives an overview of important topics of interest to biomaterials scientists and shows how the remarkable recent progress of bio-molecules impinges on other sciences. The length is intended to provide students with a choice of favorite topic without being overwhelming for the limited amount of time available in one semester.
Course Objective The class is intended for students in any field of science or engineering who want to go further on biochemistry. The main goal of the class is to make biochemistry as clear and as interesting as possible and to familiarize all science students with the major aspects of biochemistry.
Course Requirement Students who is going to join the class should have the level at least one year general chemistry.
Office Hours 08:00-12:00 Saturday
References
  1. Biochemistry
  2. 5th Edition, 2005
  3. Mary K. Champbell

Chung-Ming Chen

Course Information
Course Name FUNDAMENTALS OF BIOMEDICAL IMAGE PROCESSING
Semester 105-1
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor CHUNG-MING CHEN 
Course No. Biomed 7016
Class UNION EDUCATION BLDG. ROOM 211
Credits 3
Full/Half Yr. Half
Required/ Elective Elective
Time Monday 234
Remarks Max. students allowed: 20
Course Website https://ceiba.ntu.edu.tw/1041Biomed7016_
Course Syllabus
Course Description

Image processing is a basic tool for biomedical image analysis. Ranging from contrast enhancement to stereotatic surgery, image processing provides various levels of assistance to the biomedical researches and clinical applications. As an introductory course to the biomedical image processing, the aim of this course is to offer the entry-level graduate students the fundamental image processing techniques. The scope of this course will cover the basic transformation techniques, properties of various medical images, image acquisition, processing and rendering. In addition to the regular lectures, the students are required to exploit advanced techniques independently to reinforce learning. It will include one term project and a couple of paper studies. 
Actual implementation of the image processing algorithms on the biomedical images will be emphasized in this course. Although it is not a pre-requisite, the students need to use Matlab as the programming tool for the homeworks. There will be about five homeworks for practice. One exam will be given toward the end of the class. The students will be asked to demonstrate the result of the term project by an oral presentation and a written report.

Topics
  • Basic Transformation Techniques
  • Basics of Medical Images
  • Image Acquisition, Sampling, and Quantization
  • Image Enhancement
  • Image Segmentation
  • Image Compression
  • Volumetric Image Analysis
  • Rendering Techniques
Course Objective Getting acquainted with the fundamental image processing techniques for medical images
Course Requirement Calculus, matrix computation, Matlab
Office Hours To be determined
References
  • Digital Image Processing, 3rd Ed., R. C. Gonzalez & R. E. Woods
  • Fundamentals of Digital Image Processing, A. J. Jain

I-Jen Chiang

Course Information
Course Name MEDICAL DATABASE SYSTEMS
Semester 105-1
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor I Jen Chiang
Course No. Biomed 7021
Class UNION EDUCATION BLDG. ROOM 211
Credits 3
Full/Half Yr. Half
Required/ Elective Elective
Time Wednesday 234
Remarks Max. students allowed: 20.
Course Website https://ceiba.ntu.edu.tw/1041Biomed7021_
Course Syllabus
Course Description 　This course relies on primary readings from the database community to introduce graduate students to the medical database systems, focusing on two parts: 1) Basics such as the relational algebra and data model, schema normalization, query optimization, and transactions. 2) State of the art NoSQL databases for Big Data Processing, such as key-valued based, column-based, document-based, and graph-based.
Course Objective 　Students should be able to: 1) Distinguish between flat file, relational databases, and NoSQL databases. 2) Understand the fundament (algebra and calculus) of databases. 3) Describe the means after normalization. 4) Use entity relation modelling to describe applications. 5) Use SQL efficiently. 6) Design a simple application by using database management systems.
Course Requirement 　
Office Hours 　5:30~7:00 Tuesday.
References Elmasri, Ramez and Shamkant B. Navathe, Fundaments of Database Systems, 6th Edition, Addison-Wesley, 2011.　

Jaw-Lin Wang

Course Information
Course Name Special Topics on Innovative Medical Device Development and Regulation
Semester 105-1
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor Jaw-Lin Wang
Course No.
Class COLLEGE OF ENGINEERING BLDG 215
Credits 1
Full/Half Yr. Half
Required/ Elective Elective
Time Saturday 1
Remarks Max. students allowed: 70.
Course Website https://ceiba.ntu.edu.tw/1051Biomed7116_
Course Syllabus
Course Description 　The purpose of this course is to understand the Global medical device regulatory (ex. EU, USA, Japan, Korea, Singapore, Hong Kong, Taiwan, India, China system). The medical device regulatory challenge in different countries and how they handle it. Senior lectures from Singapore and Taiwan from area of academia, industry and regulatory department will give lectures in this course. To enhancing students' professional knowledge and expand their worldview.
Course Objective 　To introduce the Global and Asia regulatory of innovative medical devices
Course Requirement 　
Office Hours No
References No　

IBME Course of 2nd Semester

Jaw-Lin Wang

Course Information
Course title Development Procedure of Innovative Medical Device  
Semester 104-2
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor Jaw-Lin Wang
Administrative Curriculum Number 545 M1810
Teaching Curriculum Number Biomed 7115
Class Normal Classroom301
Credits 1
Full/Half Yr. Half
Required/ Elective Elective
Time Monday 1 
Remarks Max Students allowed: 80
Ceiba Web Server https://ceiba.ntu.edu.tw/1042Biomed7115_
Course Syllabus
Course Description The purpose of this course is to understand the development procedure of innovative medical devices. Senior lectures from Japan, Singapore, and Taiwan from area of academia, industry and regulatory department will give lectures in this course. Student group report from Taiwan and Japan will also present their research and invention in this course. Field trip to regulatory and certification company, and related testing laboratories will be held in the end of class.
Course Objective To introduce the development procedure of innovative medical devices
Course Requirement No
Office Hours No
References
No

Tung-Wu Lu

Course Information
Course title OPTIMIZATION IN BIOMECHANICAL ENGINEERING  
Semester 104-2
Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
Instructor TUNG-WU LU
Administrative Curriculum Number 548EM0910
Teaching Curriculum Number Biomed7054
Class Common Subjects Classroom Building Rm.402(共402)
Credits 3
Full/Half Yr. Half
Required/ Elective Elective
Time Wednesday 234 
Remarks The upper limit of the number of students:15
Ceiba Web Server https://ceiba.ntu.edu.tw/1032Biomed7054_
Course Syllabus
Course Description Many features of the form and function of the human body suggest that the evolution of the human body is a process of optimization of certain criteria. Based on this observation, optimization techniques have played an important role in the study of the body parts and the design and development of their replacements, as well as relevant biomechanical systems. This course aims to provide a systematic introduction to the optimization of biomechanical systems including the human body. Apart from lectures, the students will work in groups to finish a term project under the supervision of the lecturer. The students will learn to convert statements of a physical problem to a mathematical one, and then solve the problem using optimization techniques covered in the class with the assistance of a commercial software package. The interpretation of the results of an optimization problem will also be emphasized.
Course Objective After the completion of the class, the students should have a complete knowledge of the basic theory of optimization and its relevant biomechanical applications.
Course Requirement No
Office Hours No
References
  1. Arora, J.S., Introduction to Optiumum Design, John Wiley & Son Ltd, 1998.
  2. Mow, V.C. and Hayes, W.C. Basic Orthopaedic Biomechanics, 2nd Edition, Lippincott-Raven, New York, 1997.
  3. Haug, E.J. and Arora, J.S., Applied Optimal Design: Mechanical and Structural Systems, John Wiley and Sons, New York, 1979.  
  4. Pennycuick, C.J., Newton rules biology: a physical approach to biological problems, Oxford University Press, 1992.
Grading
  • Homework 30%
  • Midterm Exam 30%
  • Final Project 40%
    		•

    Feng-Huei Lin

    Course Information
    Course title TISSUE ENGINEERING
    Semester 104-2
    Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
    Instructor FENG-HUEI LIN 
    Administrative Curriculum Number 548EM0150
    Teaching Curriculum Number Biomed7010
    Class COLLEGE OF ENGINEERING BLDG.B04(工綜B04)　
    Credits 3
    Full/Half Yr. Half
    Required/ Elective Elective
    Time Monday 789  
    Remarks The upper limit of the number of students: 40
    Ceiba Web Server https://ceiba.ntu.edu.tw/1042Biomed7010_
    Table of Core Capabilities and Curriculum Planning Students Should Have the Following Core Capabilities by the Time They Graduation:
    • Independent and Innovative Thinking
    • Integration and Collaboration
    • Expertise of engineering technology, clinical medicine, life sciences and knowledge management.
    • Motivation for Lifelong Learning
    Course Syllabus
    Course Description
      Topic/Hours
    1. Why Tissue Engineering/3
    2. Introduction (What is tissue engineering?)/3
    3. Stem cells (幹細胞及其應用)/3
    4. Cell signaling (細胞訊息傳遞)/3
    5. Cell junction/3
    6. Cell adhesion (細胞貼附)/3
    7. Extra-cellular matrix (細胞外基質)/6
    8. Biopolymer (生物高分子)/6
    9. Scaffold (支架)/3
    10. Surface modification & bio-molecules immobilization/6
    11. Bioreactor (生物反應器)/3
      This course is intended to provide you with an introduction to recent biomedical research activities in the area of tissue engineering. The term "tissue engineering" has been coined to describe the interdisciplinary field concerned with the study of generation or regeneration of tissues. Researchers in this area utilize knowledge of the molecular basis of cellular function and interactions, in combination with fundamental engineering principles, to gain insights into tissue structure and function, with the purpose of developing bioartificial tissues or enhancing native tissue function.
    Course Objective Tissue engineering will ultimately have a more profound impact than we can appreciate. It not only will modify the practice of medicine and help elucidate mechanisms of developmental biology, but also the potential to influence economic development in the industry of biotechnology more than any single advance in science or medicine during the last decades. A challenge to the large-scale development and application of tissue engineering is the immunological barrier. Improvements in the understanding of immunology and the ability to trick the host into thinking foreign cells are “self” may ultimately allow for implantation of allograft or even xenograft cells to generate functional tissue. The class is going to give a basic principle to the students in cell sources, cell-cell communications, stem cells, material for scaffold, extracellular matrix for tissue engineering. This class is intended not only as a class for engineering students and students in cell biology, biotechnology, and medical courses at advanced graduate level, but also as a reference tool for research and clinical laboratories. I believe the students can have the knowledge of tissue engineering after the class finished.
    Course Requirement No
    Office Hours 08:00-12:00 Saturday
    References "Tissue Engineering" by Palsson and Bhattia ("P&B"), Pearson Prentice Hall Publishers (ISBN: 0-13-041696-7)
    Grading
  • Midterm Exam 50%
  • Final Project 50%
    		•

    Chii-Wann Lin

    Course Information
    Course Title NANO/MICRO ENGINEERING IN BIOMEDICINE 
    Semester 104-2
    Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
    Instructor CHII-WANN LIN 
    Administrative Curriculum Number 548 M0650 
    Teaching Curriculum Number Biomed7038
    Class YONG-LIN BLDG. ROOM NO.414(永齡館414)　
    Credits 3
    Full/Half Yr. Half
    Required/Elective Elective
    Time Friday 234
    Remarks The upper limit of the number of students: 10
    Ceiba Web Server https://ceiba.ntu.edu.tw/1032Biomed7038_
    Table of Core Capabilities and Curriculum Planning Graduate Institute PHD
    • Independent and Innovative Thinking
    • Expertise of engineering, science and technology, clinical medicine, life sciences and knowledge management
    Graduate Institute
    • Independent and Innovative Thinking
    • Expertise of engineering, science and technology, clinical medicine, life sciences and knowledge management
    Course Syllabus
    Course Description Nano/micro engineering technology has increasing impacts in biomedical research. The manipulation and measurement of this scale, ie,several hundred nanometers down to atomic resolution, is closely related to the dimension of many important biomolecules and the sampling of the volume down to this size has significant biomedical implications.The full understanding of a biological system is the first step of being able to control or even manipulate it in the future. In this course, we will introduce some basic nano/micro engineering techniques used at our lab for the biosensing, analysis, and manipulation at molecular, cellular and tissue levels. In previous years, the course is undergone by a weekly class with half part in literature discussion and the other half for technique introduction. In this year, we have made some changes by decreasing the literature discussion with most literature discussion dedicated on the identification of a biomedical issue; on the other hand, the related nano/micro techniques are introduced in more details and accompanied by approperiate demonstration. The choice of a term project has been changed from technique-based to biomedical issue-oriented.Instead of picking a technique and finding a biomedical application, the students have to identify a central question in biomedical research or come up with a device design to facilitate biomedical test, and then find the appropriate techniques to answer or fullfil the purpose and intention raised in their project. This will help students to pick up all the nano/micro engineering techniques which meet the biomedical research requirement. And with the guidance of the need in biomedical research, students will be able to foresee the future direction of technology advancement in assisting the biomedical research and practice.
    Course Objective
    • 1. Encourage the interdisiplinary discussion and enlarge the understanding of the core biomedical issues from a multidisciplinary view.
    • 2. Gaining in-depth experience from a hands-on project
    Course Requirement For every class, there will be a given article to read and discuss during the first hour of class. Students will be divided into three groups to take turn for presentation of
    • 1. Review papers: a.highlights (backgrounds), b. state of arts, c. what are missing
    • 2. Technical papers: a.highlights (backgrounds), b. Results (materials & methods, data), and c. Discussions and future works. All three groups should upload the ppt file to CEIBA before class. I will grade according to your contributions (on time, details of contents, interesting ideas etc.) with A. B. C. for all three groups
    • 3. This semester will have no written exam. However, we will have two presentations and written report, one for midterm and one for final. In the mid term, each groups will need to choose a suitable title with background introduction of problems in mind and literature review. This will lead to the experimetnal design and expected results for final presentation by the end of this semester.
    • 4. The tentative topic(s) should be biomedical related and better for potetnial clinical applicaitons in mind.
    Office Hours Tuesdays 09:00~12:00
    References 1.Bionanotechnology Lessons from nature, David S. Goodsell, Wiley-Liss, 2004
    2.Nanomedicine vol: 1 Basic capabilities, Robert A. Freitas, Landes Bioscience, 1999
    3.Nanophotonics, Paras N. Prasad, Wiley Interscience, 2004
    4.Surface plasmon resonance on smooth, roughness, and corrogated surface,
    5.Surface plasmon resonance based sensors, J. Homola, Springer series on Chemcial Sensors and Biosensors vol.4, O.S. Wolfbeis, Springer, 2006
    6.http://www.cnst.ntu.edu.tw
    7.http://www.nanofilm.com
    8.http://www.nanoink.net
    9.http://www.zess.de/micro
    10.http://www.gwctechnologies.com
    11. Introduction to BioMEMS, Albert Folch, CRC Press, 2013
    Grading
  • Paper discussion 30% For the discussion of assigned paper, the grade will be given based on 1. Participation in the discussion 2. Proper summary of the highlights fo assigned paper 3. Concise and Clearness of the presentation 4. Comments and feedbacks
  • Final report 40% Oral presentation 20%, Writeen Report 20% All students in the groups need to submit his/her report onto CEIBA homework section with highlight of his/her contribution in the joined report.
  • Mid term report 30% Oral presentation 15%, Writeen Report 15% All students in the groups need to submit his/her report onto CEIBA homework section with highlight of his/her contribution in the joined report.

    • I Jen Chiang

    Course Information
    Course title Biomedical Big Data Processing and Analytics
    Semester 104-2
    Department COLLEGE OF ENGINEERING GRADUATE INSTITUTE OF BIOMEDICAL ENGINEERING
    Instructor I Jen Chiang
    Administrative Curriculum Number 548 M0390
    Teaching Curriculum Number Biomed7114
    Class BASIC MEDICAL BLDG.ROOM NO.505(基醫505)
    Credits 3
    Full/Half Yr. Half
    Required/ Elective Elective
    Time Tuesday 234 
    Remarks The upper limit of the number of students:30 
    Ceiba Web Server https://ceiba.ntu.edu.tw/1042Biomed7114
    Course Syllabus
    Course Description
    1. Big Data Concept 
    2. Cloud Computing and Big Data Processing 
    3. Asynchronization and Coroutine 
    4. MapReduce, Hadoop and Spark 
    5. NoSQL & HDFS 
    6. Big Data Clustering Schemes 
    7. Big Data Classification Schemes 
    8. Unstructured Data Analyses 
    9. Decision trees and lazy learning 
    10. Visualization 
    11. Dimension Reductions and Curse of Dimensionality 
    12. Nonstationary environment 
    13. Artificial neural networks and Deep Learning 
    14. Streaming Analyses 
    15. Social Analyses 
    16. Boosting, stacking, and bagging 
    17. Computational learning theory  
    18. Temporal sequent analysis 
    19. IoE and Big Data 
    Course Objective The key objectives of this course are thtree-fold: (1) to teach the fundamental concepts of Big Data processing and techniques; (2) to teach the Big Data analytics and mining schemes; and (3) to provide extensive hands-on experience in applying the concepts to real-world applications from UCI machine learning repositories or public domain by using statistic R and Spark. The core topics to be covered in this course include classification, clustering, association analysis, temporal/sequence analysis, and cloud data analysis. 　
    Course Requirement 　
    Office Hours Tuesdays: 4:30-7:30 pm in BME biomedical informatics lab.　
    References Hastie, Tibshirani, Friedman, “The Elements of Statistical Learning” 
    J. Han and M. Kamber, “Data Mining: Concepts and Techniques”, 3rd. 
    T. Mitchell, “Machine Learning”
    Grading
  • Homework 20%
  • Midterm #1 30%
  • Final report 50%
    		•