MED 320 | Course Introduction and Application Information

Course Name
Basics of Clinical Bioinformatics
Code
Semester
Theory
(hour/week)
Application/Lab
(hour/week)
Local Credits
ECTS
MED 320
Fall/Spring
1
2
2
4

Prerequisites
None
Course Language
English
Course Type
Elective
Course Level
First Cycle
Mode of Delivery -
Teaching Methods and Techniques of the Course -
Course Coordinator
Course Lecturer(s)
Assistant(s) -
Course Objectives In this course, it is aimed to give the basic knowledge and practice in the field of bioinformatics for medical students who are enthusiastic about computer science and programming. Students will practice how to integrate skills in computer sciences in the field of medicine.
Learning Outcomes The students who succeeded in this course;
  • 1. Explain the purpose of next generation sequence analysis and clinical use of analysis data,
  • 2. Perform simple operations using basic commands in UNIX system,
  • 3. Use basic databases in genetics and bioinformatics,
  • 4. Run simple bioinformatics applications by using command line,
  • 5. Explain the concept of mutation and variant in clinical genetics and make basic variant prioritization,
  • 6. Explain the importance of clinical perspective in bioinformatics.
  • 7. Perform basic phylogenetic analysis
  • 8. Edit basic graphic images of molecules using RasMol program.
Course Description Bioinformatics, which is a multidisciplinary field consisting of genetics, statistics and computer sciences, is important to obtain accurate and qualified information from hundreds of gigabytes of data from next generation sequencing devices. \nIn this course; the fundamentals of bioinformatics that includes; clinical applications, next generation sequencing analysis, use of genetic and bioinformatics databases, basic phylogenetic analyzes and molecular graphical imaging will be explained both theoretically and practically to the students in order them to manage the growing data appropriately.

 



Course Category

Core Courses
Major Area Courses
Supportive Courses
X
Media and Management Skills Courses
Transferable Skill Courses

 

WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

Week Subjects Related Preparation
1 Introduction to genomic data science Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 1-2.
2 Next generation sequencing Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 3.
3 Genetic databases - 1 Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 5.
4 Genetic databases - 2 Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 5.
5 Basic commands in UNIX operating system William, E. (2019). Linux Command Line, 2nd Edition (pp. 1-37). No Starch Press, Incorporated.
6 Introduction to bioinformatics applications Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 4.
7 Mapping and alignment Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier, chapter 6.
8 Midterm
9 Raw data processing - Human genome Brown, S. M. (2013). Next-generation DNA sequencing informatics. 1st ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, chapter 8.
10 Evaluating processed data - Human genome Brown, S. M. (2013). Next-generation DNA sequencing informatics. 1st ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, chapter 8.
11 Metagenomics Brown, S. M. (2013). Next-generation DNA sequencing informatics. 1st ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press, chapter 11.
12 Basic Phylogenetic Analysis-1 (Data Preparation) Chapters 1,2,3, The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd Edition,2009.
13 Basic Phylogenetic Analysis-2 (Genetic distance and nucleotide substitution models, maximum likelihood methods) Chapters 4, 5, 6. The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, 2nd Edition,2009
14 Moleküler Grafik Görüntüleme-1 (RasMol) Power point presentations
15 Semester Review
16 Final Exam

 

Course Notes/Textbooks
  • The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis and Hypothesis Testing, Second Edition, Edited by Phillippe Lemey,Marco Salami and Anne-Mieke Vandamme, Cambridge University Press, UK, 2009. ISBN-13:978-0-511-71963-9 (E-Book), ISBN-13: 978-0-521-73071-6 (Paperback)
  • Choudhuri, S., & Kotewicz, M. (2014). Bioinformatics for beginners. London: Elsevier. ISBN-13: 978-0-12-410471-6.

 

  • William, E. (2019). Linux Command Line, 2nd Edition (pp. 1-37). No Starch Press, Incorporated. ISBN-13: 978-1-59327-952-3.

 

  • Brown, S. M. (2013). Next-generation DNA sequencing informatics. 1st ed. Cold Spring Harbor, New York: Cold Spring Harbor Laboratory Press. ISBN-13: 978-1936113873.
Suggested Readings/Materials

 

EVALUATION SYSTEM

Semester Activities Number Weigthing
Participation
Laboratory / Application
Field Work
Quizzes / Studio Critiques
Portfolio
Homework / Assignments
1
30
Presentation / Jury
Project
Seminar / Workshop
Oral Exams
Midterm
1
30
Final Exam
1
40
Total

Weighting of Semester Activities on the Final Grade
2
60
Weighting of End-of-Semester Activities on the Final Grade
1
40
Total

ECTS / WORKLOAD TABLE

Semester Activities Number Duration (Hours) Workload
Theoretical Course Hours
(Including exam week: 16 x total hours)
16
1
16
Laboratory / Application Hours
(Including exam week: '.16.' x total hours)
16
2
32
Study Hours Out of Class
0
Field Work
0
Quizzes / Studio Critiques
0
Portfolio
0
Homework / Assignments
1
10
10
Presentation / Jury
0
Project
0
Seminar / Workshop
0
Oral Exam
0
Midterms
1
20
20
Final Exam
1
30
30
    Total
108

 

COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

#
Program Competencies/Outcomes
* Contribution Level
1
2
3
4
5
1

Knowledge for Practice: Uses knowledge in biomedical, clinical, epidemiological, biostatistics, biomedical informatics, social and behavioral sciences for the prevention, diagnosis, treatment and management of medical problems.

X
2

Information Management and Research: Uses the information generated through research and accessed from different sources in evidence-based patient management processes

X
3

Patient management: Provides patient-centered, holistic, safe, reliable and evidence-based health care for common health problems in the community, prioritizing health protection and improvement*.

4

Patient and employee safety: Provides health services by considering the health and safety of patients and employees.

5

Protection and promotion of health: Prioritizes protecting and improving the health of individuals and society in the provision of health services under usual/unusual situations. Performs clinical and public health practices in a holistic and competent manner

6

Adherence to ethical principles: Fulfills the duties and obligations within the framework of ethical principles and, rights and legal responsibilities required by the profession.

7

Professional competence: Provides a high-quality healthcare service that prioritizes patient safety. While applying the profession, he/she knows his/her limits, evaluates his/her own performance, determines the aspects that need to be developed and improves them within a plan

X
8

Professional virtues: Avoid behaviors that will undermine the public's trust in medicine. S/he approaches her/his patients with compassion and care without discrimination, and puts their welfare ahead of her/his own interests

9

A healthy physician- a healthy society: Gives importance to his/her personal health, safety and appearance, sets an example for his/her colleagues and society by taking the necessary precautions.

X
10

Planetary health and healthy lifestyles: Considering the effects of the resources offered by our planet on individual and public health, he/she accepts promoting healthy lifestyles and eliminating the factors that negatively affect health his/her duty.

11

Protecting and improving health as a social responsibility: Accepts protection and improvement of public health as a social responsibility, identifies the primary health problems of the society served and produces solutions.

X
12

Health policies: Evaluates the impact of health policies on the health indicators of individuals and society, and advocates increasing the quality of health services.

13

Change management: Systematically identifies and manages the issues/processes and the necessary resources that require change in order to provide quality, safe and cost-effective health care.

X
14

Personal qualifications: Provides evidence exerting that he/she is equipped enough to lead changes to make healthcare more qualified, safe and cost-effective

15

Communication skills: Uses verbal and non-verbal communication effectively. Communicates with patients in a way that makes them feel understood, with active listening behaviors (eye contact, affirmation, summarizing, etc.)

16

Communication with patients and their relatives: Establishes supportive relationships with patients and their families that contribute positively to the treatment process

17

Communication for qualified and safe health care: Communicates with patients, their relatives, health workers, other professional groups, institutions and organizations in a clear, understandable and professional manner that will minimize patient safety risks and increase the quality of health care. Considers and protects patient privacy and data security in all communications.

18

Explains the place and importance of scientific research and evidence in providing qualified and safe health care. Analyzes the health problems in the society s/he serves with scientific methods. Reaches information to access evidence. Uses the information analyzed and the evidence accessed from the literature to provide more qualified and safer health care

19

Reflection: Using reflective approaches, he/she questions his/her professional performance, identifies areas that require improvement, and develops his/her professional knowledge and skills by identifying learning needs.

20

Stress management: Explains and applies strategies for coping with stress and preventing burnout

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest

 


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