Introduction to Bioinformatics (SE446) Course Detail

Course Name	Course Code	Season	Lecture Hours	Application Hours	Lab Hours	Credit	ECTS
Introduction to Bioinformatics	SE446	Area Elective	3	0	0	3	5

Pre-requisite Course(s)
N/A

Course Language	English
Course Type	Elective Courses
Course Level	Bachelor’s Degree (First Cycle)
Mode of Delivery	Face To Face
Learning and Teaching Strategies	Lecture.
Course Coordinator
Course Lecturer(s)
Course Assistants
Course Objectives	The objective of the course is to provide necessary knowledge and skills related to computational techniques for mining the large amount of biological data. In this course the applications of the computational techniques in bioinformatics will be introduced.
Course Learning Outcomes	The students who succeeded in this course; Apply DNA and protein sequence alignment techniques Build phylogenetic trees Apply techniques to predict protein structure Gain skills for clustering methods used in bioinformatics Analyze gene/protein networks
Course Content	DNA and protein sequence alignment, phylogenetic trees, protein structure prediction, motive findin, microarray data analysis, gene/protein networks.

Weekly Subjects and Releated Preparation Studies

Week	Subjects	Preparation
1	Introduction	Chapters 1,2,3 (main text)
2	Producing and Analyzing Sequence Alignments	Chapter 4
3	Pairwise Sequence Alignment and Database Searching	Chapter 5
4	Pairwise Sequence Alignment and Database Searching	Chapter 5
5	Patterns, Profiles, and Multiple Alignments	Chapter 6
6	Patterns, Profiles, and Multiple Alignments	Chapter 6
7	Recovering Evolutionary History	Chapter 7
8	Building Phylogenetic Trees	Chapter 8
9	Obtaining Secondary Structure from Sequence	Chapter 11
10	Predicting Secondary Structures	Chapter 12
11	Modeling Protein Structure	Chapter 13
12	Clustering Methods and Statistics	Chapter 16
13	Clustering Methods and Statistics	Chapter 16
14	Clustering Methods and Statistics	Chapter 17
15	Final Examination Period	Review of topics
16	Final Examination Period	Review of topics

Sources

Course Book	1. M. Zvelebil and J. O. Baum, Understanding Bioinformatics, Garland Science, 2008
Other Sources	2. N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004
	3. A. M. Lesk, Introduction to Bioinformatics, Oxford University Press, 2002
	4. D. Mount, Bioinformatics: Sequence and genome analysis, Cold Spring Harbor Laboratory Press, 2001
	5. T. Jiang, Y. Xu, and M. Zhang, eds. Current Topics in Computational Molecular Biology, MIT press, 2002

Evaluation System

Requirements	Number	Percentage of Grade
Attendance/Participation	-	-
Laboratory	-	-
Application	-	-
Field Work	-	-
Special Course Internship	-	-
Quizzes/Studio Critics	-	-
Homework Assignments	1	20
Presentation	-	-
Project	1	30
Report	-	-
Seminar	-	-
Midterms Exams/Midterms Jury	1	20
Final Exam/Final Jury	1	30
Toplam	4	100

Percentage of Semester Work	70
Percentage of Final Work	30
Total	100

Course Category

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

The Relation Between Course Learning Competencies and Program Qualifications

#	Program Qualifications / Competencies	Level of Contribution
#	Program Qualifications / Competencies	1	2	3	4	5
1	Possesses sufficient knowledge in mathematics, natural sciences, and discipline-specific topics in Electrical and Electronics Engineering; uses this theoretical and practical knowledge to solve complex engineering problems.			X
2	Identifies, defines, formulates, and solves complex engineering problems; selects and applies appropriate analytical and modeling methods for this purpose.			X
3	Designs complex systems, processes, devices, or products under realistic constraints and conditions to meet specific requirements; applies modern design methods for this purpose. (Realistic constraints and conditions may include factors such as economy, environmental issues, sustainability, manufacturability, ethics, health, safety, social and political issues, depending on the nature of the design.)			X
4	Selects and uses modern techniques and tools necessary for the analysis and solution of complex problems encountered in engineering applications; effectively uses information technologies.
5	Designs experiments, conducts tests, collects data, analyzes, and interprets results to investigate complex engineering problems or discipline-specific research topics.
6	Works effectively in disciplinary and interdisciplinary teams; develops the ability to work independently.					X
7	Communicates effectively in both written and verbal forms; possesses proficiency in at least one foreign language; writes effective reports, understands written reports, prepares design and production reports, delivers effective presentations, and gives and receives clear instructions.
8	Recognizes the need for lifelong learning; accesses information, follows developments in science and technology, and continuously renews oneself.
9	Acts in accordance with ethical principles, assumes professional and ethical responsibility, and possesses knowledge about the standards used in engineering practices.
10	Possesses knowledge about professional practices such as project management, risk management, and change management; gains awareness of entrepreneurship and innovation; understands the principles of sustainable development.
11	Understands the universal and societal impacts of engineering practices on health, environment, and safety; recognizes the contemporary issues reflected in the field of engineering and understands the legal implications of engineering solutions.

ECTS/Workload Table

Activities	Number	Duration (Hours)	Total Workload
Course Hours (Including Exam Week: 16 x Total Hours)	16	3	48
Laboratory
Application
Special Course Internship
Field Work
Study Hours Out of Class	16	2	32
Presentation/Seminar Prepration
Project
Report
Homework Assignments	3	5	15
Quizzes/Studio Critics
Prepration of Midterm Exams/Midterm Jury	2	10	20
Prepration of Final Exams/Final Jury	1	15	15
Total Workload			130