ARCHITECTURE
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 Fall	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)	Using the theoretical/conceptual and practical knowledge acquired for architectural design, design activities and research.
2)	Identifying, defining and effectively discussing aesthetic, functional and structural requirements for solving design problems using critical thinking methods.
3)	Being aware of the diversity of social patterns and user needs, values and behavioral norms, which are important inputs in the formation of the built environment, at local, regional, national and international scales.
4)	Gaining knowledge and skills about architectural design methods that are focused on people and society, sensitive to natural and built environment in the field of architecture.
5)	Gaining skills to understand the relationship between architecture and other disciplines, to be able to cooperate, to develop comprehensive projects; to take responsibility in independent studies and group work.
6)	Giving importance to the protection of natural and cultural values in the design of the built environment by being aware of the responsibilities in terms of human rights and social interests.
7)	Giving importance to sustainability in the solution of design problems and the use of natural and artificial resources by considering the social, cultural and environmental issues of architecture.
8)	Being able to convey and communicate all kinds of conceptual and practical thoughts related to the field of architecture by using written, verbal and visual media and information technologies.
9)	Gaining the ability to understand and use technical information about building technology such as structural systems, building materials, building service systems, construction systems, life safety.
10)	Being aware of legal and ethical responsibilities in design and application processes.