Genetics and Bioengineering
Bachelor	TR-NQF-HE: Level 6	QF-EHEA: First Cycle	EQF-LLL: Level 6

General course introduction information

Course Code:

GBM305

Course Name:

Bioinformatics

Course Semester:

Fall

Course Credits:

Theoretical	Practical	Credit	ECTS
2	2	3	8

Language of instruction:

Course Requisites:

Does the Course Require Work Experience?:

Type of course:

Compulsory

Course Level:

Bachelor

TR-NQF-HE:6. Master`s Degree

QF-EHEA:First Cycle

EQF-LLL:6. Master`s Degree

Mode of Delivery:

Face to face

Course Coordinator :

Dr.Öğr.Üyesi METİN YAZAR

Course Lecturer(s):

Dr.Öğr.Üyesi METİN YAZAR

Course Assistants:

Course Objective and Content

Course Objectives:

The course is designed to provide knowledge to bioengineers to solve the biological questions using bioinformatics and learn to use several databases. Students use online tools to analyze DNA, RNA and protein as well as learn how to use publicly available databases.

At the end of this course students will be able to:
• Use various publically available databases
• Use various bioinformatics tools
• Describe different Next generation sequencing methods
• Select necessary tools to analyze next generation sequencing data
• Run bioinformatic analysis for various biological questions

Course Content:

• Introduction of bioinformatics
• Introduction, Access to Information
• Align and compare two DNA/protein sequence
• Pairwise Alignment
• BLAST
• Multiple Sequence Alignment
• Molecular Phylogeny and Evolution – I
• Molecular Phylogeny and Evolution – II
• Eukaryotic Chromosomes and DNA analysis
• Bioinformatic Approaches to RNA and RNA Analysis
• Protein Structure and Proteomics – I
• Protein Structure and Proteomics – II
• Functional Genomics
• The Human Genome
• Human Disease

Learning Outcomes

The students who have succeeded in this course;

Learning Outcomes

1 - Knowledge
Theoretical - Conceptual
2 - Skills
Cognitive - Practical
3 - Competences
Communication and Social Competence
Learning Competence
Field Specific Competence
1) At the end of this course students will be able to run bioinformatic analysis for various biological questions
Competence to Work Independently and Take Responsibility

Lesson Plan

Week	Subject	Related Preparation
1)	• Syllabus • Introduction of bioinformatics
2)	• Introduction, Access to Information
3)	• Pairwise Alignment
4)	• BLAST
5)	• Multiple Sequence Alignment
6)	• Molecular Phylogeny and Evolution – I
7)	• Molecular Phylogeny and Evolution – II
8)	• Eukaryotic Chromosomes and DNA analysis
9)	• Bioinformatic Approaches to RNA and RNA Analysis
10)	• Protein Structure and Proteomics – I
11)	• Protein Structure and Proteomics – II
12)	• Functional Genomics
13)	The Human Genome
14)	• Human Disease
15)	• Final exam

Sources

Course Notes / Textbooks:	Bioinformatics & Functional Genomics 3rd Edition, Jonathan Pevsner (ISBN: 978-1-118-58178-0)
References:	Bioinformatics & Functional Genomics 3rd Edition, Jonathan Pevsner (ISBN: 978-1-118-58178-0)

Course-Program Learning Outcome Relationship

Learning Outcomes	1
Program Outcomes
1) Sufficient knowledge in mathematics, science and engineering related to their branches; and the ability to apply theoretical and practical knowledge in these areas to model and solve engineering problems.
2) The ability to identify, formulate, and solve complex engineering problems; selecting and applying appropriate analysis and modeling methods for this purpose.
3) The ability to design a complex system, process, device or product under realistic constraints and conditions to meet specific requirements; the ability to apply modern design methods for this purpose. (Realistic constraints and conditions include such issues as economy, environmental issues, sustainability, manufacturability, ethics, health, safety, social and political issues, according to the nature of design.)
4) Ability to develop, select and use modern techniques and tools necessary for engineering applications; ability to use information technologies effectively.
5) Ability to design experiments, conduct experiments, collect data, analyze and interpret results to examine engineering problems or discipline-specific research topics.
6) The ability to work effectively in disciplinary and multidisciplinary teams; individual work skill.
7) Effective communication skills in Turkish oral and written communication; at least one foreign language knowledge; ability to write effective reports and understand written reports, to prepare design and production reports, to make effective presentations, to give and receive clear and understandable instructions.
8) Awareness of the need for lifelong learning; access to knowledge, ability to follow developments in science and technology, and constant self-renewal.
9) Conform to ethical principles, and standards of professional and ethical responsibility; be informed about the standards used in engineering applications.
10) Awareness of applications in business, such as project management, risk management and change management; awareness of entrepreneurship, and innovation; information about sustainable development.
11) Information about the universal and social health, environmental and safety effects of engineering applications and the ways in which contemporary problems are reflected in the engineering field; awareness of the legal consequences of engineering solutions.

Course - Learning Outcome Relationship

No Effect	1 Lowest	2 Low	3 Average	4 High	5 Highest

	Program Outcomes	Level of Contribution
1)	Sufficient knowledge in mathematics, science and engineering related to their branches; and the ability to apply theoretical and practical knowledge in these areas to model and solve engineering problems.	2
2)	The ability to identify, formulate, and solve complex engineering problems; selecting and applying appropriate analysis and modeling methods for this purpose.	1
3)	The ability to design a complex system, process, device or product under realistic constraints and conditions to meet specific requirements; the ability to apply modern design methods for this purpose. (Realistic constraints and conditions include such issues as economy, environmental issues, sustainability, manufacturability, ethics, health, safety, social and political issues, according to the nature of design.)	1
4)	Ability to develop, select and use modern techniques and tools necessary for engineering applications; ability to use information technologies effectively.	2
5)	Ability to design experiments, conduct experiments, collect data, analyze and interpret results to examine engineering problems or discipline-specific research topics.
6)	The ability to work effectively in disciplinary and multidisciplinary teams; individual work skill.
7)	Effective communication skills in Turkish oral and written communication; at least one foreign language knowledge; ability to write effective reports and understand written reports, to prepare design and production reports, to make effective presentations, to give and receive clear and understandable instructions.	1
8)	Awareness of the need for lifelong learning; access to knowledge, ability to follow developments in science and technology, and constant self-renewal.
9)	Conform to ethical principles, and standards of professional and ethical responsibility; be informed about the standards used in engineering applications.
10)	Awareness of applications in business, such as project management, risk management and change management; awareness of entrepreneurship, and innovation; information about sustainable development.
11)	Information about the universal and social health, environmental and safety effects of engineering applications and the ways in which contemporary problems are reflected in the engineering field; awareness of the legal consequences of engineering solutions.

Learning Activity and Teaching Methods

Expression
Brainstorming/ Six tihnking hats
Individual study and homework
Group study and homework
Lab
Application (Modelling, Design, Model, Simulation, Experiment etc.)
Web Based Learning

Assessment & Grading Methods and Criteria

Written Exam (Open-ended questions, multiple choice, true-false, matching, fill in the blanks, sequencing)
Homework
Application

Assessment & Grading

Semester Requirements	Number of Activities	Level of Contribution
Attendance	1	% 5
Homework Assignments	6	% 5
Midterms	1	% 40
Final	1	% 50
total		% 100
PERCENTAGE OF SEMESTER WORK		% 50
PERCENTAGE OF FINAL WORK		% 50
total		% 100

Workload and ECTS Credit Grading

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	15	2	30
Laboratory	15	2	30
Homework Assignments	5	4	20
Final	1	2	2
Total Workload			82