MBG1002 Introduction to BioinformaticsBahçeşehir UniversityDegree Programs PHYSIOTHERAPY AND REHABILITATION (TURKISH)General Information For StudentsDiploma SupplementErasmus Policy StatementNational QualificationsBologna Commission
PHYSIOTHERAPY AND REHABILITATION (TURKISH)
Bachelor TR-NQF-HE: Level 6 QF-EHEA: First Cycle EQF-LLL: Level 6

Course Introduction and Application Information

Course Code Course Name Semester Theoretical Practical Credit ECTS
MBG1002 Introduction to Bioinformatics Spring 3 0 3 5
This catalog is for information purposes. Course status is determined by the relevant department at the beginning of semester.

Basic information

Language of instruction: English
Type of course: Non-Departmental Elective
Course Level: Bachelor’s Degree (First Cycle)
Mode of Delivery: Face to face
Course Coordinator : Dr. Öğr. Üyesi ELIZABETH HEMOND
Course Lecturer(s): Prof. Dr. SÜREYYA AKYÜZ
Dr. Öğr. Üyesi SERKAN AYVAZ
Recommended Optional Program Components: There is none.
Course Objectives: This course aims to prepare the students to work in the interdisciplinary area, bioinformatics that marry the advances in high-performance computing with the exploiting information resources of the human genome and related data.

Learning Outcomes

The students who have succeeded in this course;
1. Recognize the working in interdisciplinary teams of biologists, biochemists, medical researchers, geneticists, and computer engineers.
2. Perform sophisticated searches over enormous databases, and to interpret results.
3. Perform genomic comparisons, display genes and large genomic regions in Genome Browsers.
4. Recognize the basic bioinformatics problems and their solutions, including: fragment assembly, gene finding, protein folding and microarray studies.
5. Anayze the results in probabilistic terms using statistical significance.
6. Recognize the sequencing techniques, inherent computational problems, possible solutions.
7. Define Markov Model building and its usage for gene prediction.
8. Define computational methods for analysis of microarray data, and discuss the interpretations of gene expression from this data.
9. Discuss ethical, legal, and social issues associated with the Human Genome Project and its outcomes.

Course Content

Bioinformatics is a rapidly growing field that integrates molecular biology, statistics, and computer science. This course is devoted to the mathematical models and computer algorithms of DNA and protein sequence analysis. In this course, the students will learn many of the popular tools for performing bioinformatics analysis and you will be introduced to the thinking that drives these algorithms. Various existing bioinformatics methods will be critically described and the strengths and limitations of each will be discussed.

Weekly Detailed Course Contents

Week Subject Related Preparation
1) Introduction: Probability and statistics in a nut shell.
2) Analysis of nucleic acid and protein sequences.
3) Molecular Biology Databases on the Web.
4) Bioinformatics softwares on the internet
5) How the Genome is Studied, Maps and Sequences, The Human Genome Project
6) Sequencing: Next Gen, Exome, Shotgun
7) Fragment Assembly Problem; Sequence Alignment Models: Shortest Common Superstring, Reconstruction, Multicontig, Graph Model
8) Restriction mapping: a) Double Digest Problem, b) Partial Digest Problem
9) Computational Gene Hunting, Gene finding methods; sequence patterns, Hidden Markov Models.
10) Bioinformatics approaches to gene expression
11) Protein folding problem
12) Genome Rearrangements
13) Suffix trees I
14) Suffix trees II

Sources

Course Notes / Textbooks: Biyoinformatik ders notları haftalık olarak verilecektir.
Course material will be supplied weekly.
References: 1) Pevsner J., Bioinformatics and Functional Genomics, Wiley-Liss, 2009
2) Mount D.W., Bioinformatics: Sequence and Genome Analysis (2nd edition), Cold Spring Harbor Laboratory Press, 2004
3) Krane D.E., Raymer M.L., Fundamental Concepts of Bioinformatics, Benjamin Cummings, 2003
4) Setubal C., Meidanis J., Introduction to Computational Molecular Biology, PWS Publishing, 1997"

Evaluation System

Semester Requirements Number of Activities Level of Contribution
Homework Assignments 2 % 15
Project 1 % 20
Midterms 1 % 25
Final 1 % 40
Total % 100
PERCENTAGE OF SEMESTER WORK % 40
PERCENTAGE OF FINAL WORK % 60
Total % 100

ECTS / Workload Table

Activities Number of Activities Duration (Hours) Workload
Course Hours 14 3 42
Study Hours Out of Class 14 5 70
Project 1 10 10
Midterms 1 2 2
Final 1 2 2
Total Workload 126

Contribution of Learning Outcomes to Programme Outcomes

No Effect 1 Lowest 2 Low 3 Average 4 High 5 Highest
           
Program Outcomes Level of Contribution
1) To have theoretical and practical knowledge required to fulfill professional roles and functions of Physiotherapy and Rehabilitation field. 2
2) To act in accordance with ethical principles and values in professional practice. 1
3) To use life-long learning, problem-solving and critical thinking skills. 4
4) To define evidence-based practices and determine problem solving methods in Physiotherapy and Rehabilitation practices, using theories in health promotion, protection and care. 1
5) To take part in research, projects and activities within sense of social responsibility and interdisciplinary approach. 3
6) To have skills for training and consulting according to health education needs of individual, family and the community. 1
7) To be sensitive to health problems of the community and to be able to offer solutions. 3
8) To be able to use skills for effective communication. 5
9) To be able to select and use modern tools, techniques and modalities in Physiotherapy and Rehabilitation practices; to be able to use health information technologies effectively. 1
10) To be able to search for literature in health sciences databases and information sources to access to information and use the information effectively. 1
11) To be able to monitor occupational information using at least one foreign language, to collaborate and communicate with colleagues at international level. 1
12) To be a role model with contemporary and professional identity. 4