PERFORMING ARTS
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
MBG4059	Computational Methods in Bioinformatics	Spring Fall	3	0	3	6

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 Objectives:	The goal of this course is to provide an understanding of the fundamental computational methods used in bioinformatics and the set of algorithms that have important applications both inside and outside of the bioinformatics field.

Learning Outcomes

The students who have succeeded in this course;
1. Recognize the fundamental models of computation useful in modeling nucleic acid and protein sequences.
2. Design and implement algorithms useful for analyzing various molecular biology data.
3. Discuss Genetic Algorithm and its applications in bioinformatics.
4. Discuss Greedy Algorithms and its applications in bioinformatics.
5. Discuss Gibbs sampling and its applications in bioinformatics.
6. Recognize Expectation Maximization and its applications in bioinformatics.
7. Recognize Hidden Markov models and its applications in bioinformatics.
8. Define Bayesian networks and its applications in bioinformatics.
9. Define graphs and its applications in bioinformatics.

Course Content

This course will provide a broad and thorough background in computational methods and algorithms that are widely used in bioinformatics applications. Various existing methods will be critically described and the strengths and limitations of each will be discussed.

Weekly Detailed Course Contents

Week	Subject	Related Preparation
1)	A brief introduction to computational complexity and algorithm design techniques
2)	Exact sequence search algorithms
3)	Rabin-Karp algorithm, pattern matching, suffix trees
4)	Elements of dynamic programming, Manhattan tourist problem, k-band algorithm
5)	Approximate string matching, divide and conquer algorithms
6)	Branch and bound search
7)	Genetic Algorithm
8)	Greedy Algorithms
9)	Gibbs sampling
10)	Expectation Maximization
11)	Hidden Markov models
12)	Bayesian networks
13)	Graphs
14)	Review

Sources

Course Notes / Textbooks:	Haftalık ders notları iletilecektir. Weekly course notes will be provided.
References:	An Introduction to Bioinformatics Algorithms (Computational Molecular Biology), Neil Jones and Pavel Pevzner, MIT Press, 2004.

Evaluation System

Semester Requirements	Number of Activities	Level of Contribution
Homework Assignments	2	% 10
Project	1	% 15
Midterms	1	% 25
Final	1	% 50
Total		% 100
PERCENTAGE OF SEMESTER WORK		% 35
PERCENTAGE OF FINAL WORK		% 65
Total		% 100

ECTS / Workload Table

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	14	3	42
Study Hours Out of Class	14	6	84
Presentations / Seminar	5	4	20
Midterms	1	2	2
Final	1	2	2
Total Workload			150

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)	They acquire theoretical, historical and aesthetic knowledge specific to their field by using methods and techniques related to performing arts (acting, dance, music, etc.).	2
2)	They have knowledge about art culture and aesthetics and they provide the unity of theory and practice in their field.	2
3)	They are aware of national and international values in performing arts.	2
4)	Abstract and concrete concepts of performing arts; can transform it into creative thinking, innovative and original works.	1
5)	They have the sensitivity to run a business successfully in their field.	3
6)	Develops the ability to perceive, think, design and implement multidimensional from local to universal.	3
7)	They have knowledge about the disciplines that the performing arts field is related to and can evaluate the interaction of the sub-disciplines within their field.	2
8)	They develop the ability to perceive, design, and apply multidimensionality by having knowledge about artistic criticism methods.	3
9)	They can share original works related to their field with the society and evaluate their results and question their own work by using critical methods.	1
10)	They follow English language resources related to their field and can communicate with foreign colleagues in their field.	1
11)	By becoming aware of national and international values in the field of performing arts, they can transform abstract and concrete concepts into creative thinking, innovative and original works.	3
12)	They can produce original works within the framework of an interdisciplinary understanding of art.	2
13)	Within the framework of the Performing Arts Program and the units within it, they become individuals who are equipped to take part in the universal platform in their field.	3
14)	Within the Performing Arts Program, according to the field of study; have competent technical knowledge in the field of acting and musical theater.	2
15)	They use information and communication technologies together with computer software that is at least at the Advanced Level of the European Computer Use License as required by the field.	3