SOFTWARE ENGINEERING
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
MBG4057	Special Topics in Bioinformatics	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:	This course aims to discuss technical papers from the recent bioinformatics literature, examine their algorithms and conduct an intensive study on a specific bioinformatics problem.

Learning Outcomes

The students who have succeeded in this course;
1. Define the open research questions in bioinformatics.
2. Discuss current solutions to tackle bioinformatics problems.
3. Develop an ability to discuss open research issues in computational biology.
4. Acquire an understanding of existing bioinformatics solutions for genomics.
5. Acquire an understanding of existing bioinformatics solutions for proteomics.
6. Develop an ability to focus on several bioinformatics articles and present their findings.
7. Obtain a familiarity with emerging topics in bioinformatics.
8. Obtain a familiarity with emerging topics in computational biology.
9. Develop an ability to find, read and discuss scientific articles published in the bioinformatics field.

Course Content

This discussion-based bioinformatics course will expose students to the latest developments in bioinformatics analyses and algorithms.

Weekly Detailed Course Contents

Week	Subject	Related Preparation
1)	Genomics (genome sequencing, storage and study of genome information, genome databases)
2)	Genomics (polymorphism in the human genome and association with diseases)
3)	Comparative genomics (genome subtraction method, whole-genome alignment methods, genome-context methods, gene-fusion method)
4)	Structural genomics (the scientific program of structural genomics, target selection in structural genomics)
5)	Functional genomics (integration of experimental and computational methods)
6)	Functional genomics (gene-expression data and DNA micro-arrays)
7)	Functional genomics (regulatory networks, protein-protein interaction networks)
8)	Proteomics, Protein folding and fold recognition
9)	Epigenomics
10)	Cancer informatics
11)	Non-coding RNA identification and search
12)	Emerging topics in bioinformatics
13)	Emerging topics in computational biology
14)	Presentations

Sources

Course Notes / Textbooks:	Haftalık ders notları iletilecektir. Course notes will be supplied.
References:	Articles from the primary literature (scientific journals, e.g. Nature Reviews Genetics, Nature, Science, Genome Research, Nature Genetics, Nature Methods, Bioinformatics, Molecular Systems Biology etc.)

Evaluation System

Semester Requirements	Number of Activities	Level of Contribution
Homework Assignments	2	% 15
Project	1	% 25
Midterms	1	% 10
Final	1	% 50
Total		% 100
PERCENTAGE OF SEMESTER WORK		% 25
PERCENTAGE OF FINAL WORK		% 75
Total		% 100

ECTS / Workload Table

Activities	Number of Activities	Duration (Hours)	Workload
Course Hours	14	3	42
Study Hours Out of Class	14	8	112
Midterms	1	2	2
Final	1	2	2
Total Workload			158

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)	Be able to specify functional and non-functional attributes of software projects, processes and products.
2)	Be able to design software architecture, components, interfaces and subcomponents of a system for complex engineering problems.
3)	Be able to develop a complex software system with in terms of code development, verification, testing and debugging.
4)	Be able to verify software by testing its program behavior through expected results for a complex engineering problem.
5)	Be able to maintain a complex software system due to working environment changes, new user demands and software errors that occur during operation.
6)	Be able to monitor and control changes in the complex software system, to integrate the software with other systems, and to plan and manage new releases systematically.
7)	Be able to identify, evaluate, measure, manage and apply complex software system life cycle processes in software development by working within and interdisciplinary teams.
8)	Be able to use various tools and methods to collect software requirements, design, develop, test and maintain software under realistic constraints and conditions in complex engineering problems.
9)	Be able to define basic quality metrics, apply software life cycle processes, measure software quality, identify quality model characteristics, apply standards and be able to use them to analyze, design, develop, verify and test complex software system.
10)	Be able to gain technical information about other disciplines such as sustainable development that have common boundaries with software engineering such as mathematics, science, computer engineering, industrial engineering, systems engineering, economics, management and be able to create innovative ideas in entrepreneurship activities.
11)	Be able to grasp software engineering culture and concept of ethics and have the basic information of applying them in the software engineering and learn and successfully apply necessary technical skills through professional life.
12)	Be able to write active reports using foreign languages and Turkish, understand written reports, prepare design and production reports, make effective presentations, give clear and understandable instructions.
13)	Be able to have knowledge about the effects of engineering applications on health, environment and security in universal and societal dimensions and the problems of engineering in the era and the legal consequences of engineering solutions.