DIGITAL GAME DESIGN
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	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 :	Assist. Prof. CEMALETTİN BEKPEN
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)	Comprehend the conceptual importance of the game in the field of communication, ability to implement the player centered application to provide design.
2)	Analyze, synthesize, and evaluate information and ideas from various perspectives.
3)	Analyze the key elements that make up specific game genres, forms of interactions, mode of narratives and understand how they are employed effectively to create a successful game.
4)	Understand game design theories and methods as well as implement them during game development; to make enjoyable, attractive, instructional and immersive according to the target audience.
5)	Understand the technology and computational principles involved in developing games and master the use of game engines.
6)	Understand the process of creation and use of 2D and 3D assets and animation for video games.
7)	Understand and master the theories and methodologies of understanding and measuring player experience and utilize them during game development process.
8)	Comprehend and master how ideas, concepts and topics are conveyed via games followed by the utilization of these aspects during the development process.
9)	Manage the game design and development process employing complete documentation; following the full game production pipeline via documentation.
10)	Understand and employ the structure and work modes of game development teams; comprehend the responsibilities of team members and collaborations between them while utilizing this knowledge in practice.
11)	Understand the process of game publishing within industry standards besides development and utilize this knowledge practice.
12)	Pitching a video game to developers, publishers, and players; mastering the art of effectively communicating and marketing the features and commercial potential of new ideas, concepts or games.