The course provides an introduction to the field of bioinformatics including key concepts, algorithms, structures and databases, the development of the field historically, its applications and relevant developments in the field. The course covers the basics of bioinformatics sequence analysis and related tools and databases. Topics covered include pairwise alignment, score matrices, sequence database search, biological networks, network analysis and machine learning techniques, and visualization. The course also an overview of basics of molecular biology, including the concepts of genomes and genes and includes an introduction to genome browsers and central biological databases and knowledge-bases.
Course Content
This course contains; Introduction to the course material, what is bioinformatics, and why to study bioinformatics.,Building the background: Basic concepts in bioinformatics.,suffix trees and arrays,Sequence Alignment basics,pairwise sequence alignment,multiple sequence alignment,Databases and database search,Microarray data analysis,Presentations by students lecture/ articles / tools,Presentations by students lecture/ articles / tools-2,Machine learning, Network model and graph analysis,Phylogenetic Trees,Biological networks, visualization and analysis,Project Presentation.
Dersin Öğrenme Kazanımları
Teaching Methods
Assessment Methods
1. Recognize the central topics and concepts within the field of bioinformatics.
10, 14, 16, 9
A, E, F, G
2. Uses the dynamic programming algorithms for alignment of biological sequences.
10, 14, 16, 9
A, E, F, G
3. Compares the technical aspects of the pairwise local and global sequence alignment algorithm.
10, 14, 16, 9
A, E, F, G
4. Explain the fundamentals of molecular biology and evolution regarding sequence alignment.
10, 14, 16, 9
A, E, F, G
5. Compare technical aspects of pairwise local and global sequence alignment algorithm.
10, 14, 16, 9
A, E, F, G
5. Use biological databases and knowledgebases, machine learning and network analysis.
10, 14, 16, 9
A, E, F, G
7. Makes inferences about central topics and concepts in the field of bioinformatics
A: Traditional Written Exam, E: Homework, F: Project Task, G: Quiz
Course Outline
Order
Subjects
Preliminary Work
1
Introduction to the course material, what is bioinformatics, and why to study bioinformatics.
2
Building the background: Basic concepts in bioinformatics.
3
suffix trees and arrays
4
Sequence Alignment basics
5
pairwise sequence alignment
6
multiple sequence alignment
7
Databases and database search
8
Microarray data analysis
9
Presentations by students lecture/ articles / tools
10
Presentations by students lecture/ articles / tools-2
11
Machine learning, Network model and graph analysis
12
Phylogenetic Trees
13
Biological networks, visualization and analysis
14
Project Presentation
Resources
"No specific text book, notes will be made available, including in class notes, (sometimes) slides, research papers, book chapters, etc.
Recommendaed Reference: Understanding Bioinformatics Marketa Zvelebil & Jeremy O. Baum"
Course Contribution to Program Qualifications
Course Contribution to Program Qualifications
No
Program Qualification
Contribution Level
1
2
3
4
5
1
Develop and deepen knowledge in the same or in a different field to the proficiency level based on Bachelor level qualifications.
X
2
Conceive the interdisciplinary interaction which the field is related with.
X
3
Use of theoretical and practical knowledge within the field at a proficiency level and solve the problem faced related to the field by using research methods.
X
4
Interpret the knowledge about the field by integrating the information gathered from different disciplines and formulate new knowledge.
X
5
Independently conduct studies that require proficiency in the field.
X
6
Take responsibility and develop new strategic solutions as a team member in order to solve unexpected complex problems faced within the applications in the field.
7
Evaluate knowledge and skills acquired at proficiency level in the field with a critical approach and direct the learning.
X
8
Investigate, improve social connections and their conducting norms with a critical view and act to change them when necessary. Communicate with peers by using a foreign language at least at a level of European Language Portfolio B2 General Level.
X
9
Define the social and environmental aspects of engineering applications.
10
Audit the data gathering, interpretation, implementation and announcement stages by taking into consideration the cultural, scientific, and ethic values and teach these values.
X
Assessment Methods
Contribution Level
Absolute Evaluation
Rate of Midterm Exam to Success
50
Rate of Final Exam to Success
50
Total
100
ECTS / Workload Table
Activities
Number of
Duration(Hour)
Total Workload(Hour)
Course Hours
14
3
42
Guided Problem Solving
14
2
28
Resolution of Homework Problems and Submission as a Report
1
40
40
Term Project
0
0
0
Presentation of Project / Seminar
1
30
30
Quiz
5
1
5
Midterm Exam
1
40
40
General Exam
1
40
40
Performance Task, Maintenance Plan
0
0
0
Total Workload(Hour)
225
Dersin AKTS Kredisi = Toplam İş Yükü (Saat)/30*=(225/30)
8
ECTS of the course: 30 hours of work is counted as 1 ECTS credit.
Detail Informations of the Course
Course Description
Course
Code
Semester
T+P (Hour)
Credit
ECTS
APPLIED BIOINFORMATICS
BEBY1112978
Fall Semester
3+0
3
8
Course Program
Perşembe 16:30-17:15
Perşembe 17:30-18:15
Perşembe 18:30-19:15
Prerequisites Courses
Recommended Elective Courses
Language of Course
English
Course Level
Second Cycle (Master's Degree)
Course Type
Elective
Course Coordinator
Prof.Dr. Reda ALHAJJ
Name of Lecturer(s)
Prof.Dr. Reda ALHAJJ
Assistant(s)
Aim
The course provides an introduction to the field of bioinformatics including key concepts, algorithms, structures and databases, the development of the field historically, its applications and relevant developments in the field. The course covers the basics of bioinformatics sequence analysis and related tools and databases. Topics covered include pairwise alignment, score matrices, sequence database search, biological networks, network analysis and machine learning techniques, and visualization. The course also an overview of basics of molecular biology, including the concepts of genomes and genes and includes an introduction to genome browsers and central biological databases and knowledge-bases.
Course Content
This course contains; Introduction to the course material, what is bioinformatics, and why to study bioinformatics.,Building the background: Basic concepts in bioinformatics.,suffix trees and arrays,Sequence Alignment basics,pairwise sequence alignment,multiple sequence alignment,Databases and database search,Microarray data analysis,Presentations by students lecture/ articles / tools,Presentations by students lecture/ articles / tools-2,Machine learning, Network model and graph analysis,Phylogenetic Trees,Biological networks, visualization and analysis,Project Presentation.
Dersin Öğrenme Kazanımları
Teaching Methods
Assessment Methods
1. Recognize the central topics and concepts within the field of bioinformatics.
10, 14, 16, 9
A, E, F, G
2. Uses the dynamic programming algorithms for alignment of biological sequences.
10, 14, 16, 9
A, E, F, G
3. Compares the technical aspects of the pairwise local and global sequence alignment algorithm.
10, 14, 16, 9
A, E, F, G
4. Explain the fundamentals of molecular biology and evolution regarding sequence alignment.
10, 14, 16, 9
A, E, F, G
5. Compare technical aspects of pairwise local and global sequence alignment algorithm.
10, 14, 16, 9
A, E, F, G
5. Use biological databases and knowledgebases, machine learning and network analysis.
10, 14, 16, 9
A, E, F, G
7. Makes inferences about central topics and concepts in the field of bioinformatics
A: Traditional Written Exam, E: Homework, F: Project Task, G: Quiz
Course Outline
Order
Subjects
Preliminary Work
1
Introduction to the course material, what is bioinformatics, and why to study bioinformatics.
2
Building the background: Basic concepts in bioinformatics.
3
suffix trees and arrays
4
Sequence Alignment basics
5
pairwise sequence alignment
6
multiple sequence alignment
7
Databases and database search
8
Microarray data analysis
9
Presentations by students lecture/ articles / tools
10
Presentations by students lecture/ articles / tools-2
11
Machine learning, Network model and graph analysis
12
Phylogenetic Trees
13
Biological networks, visualization and analysis
14
Project Presentation
Resources
"No specific text book, notes will be made available, including in class notes, (sometimes) slides, research papers, book chapters, etc.
Recommendaed Reference: Understanding Bioinformatics Marketa Zvelebil & Jeremy O. Baum"
Course Contribution to Program Qualifications
Course Contribution to Program Qualifications
No
Program Qualification
Contribution Level
1
2
3
4
5
1
Develop and deepen knowledge in the same or in a different field to the proficiency level based on Bachelor level qualifications.
X
2
Conceive the interdisciplinary interaction which the field is related with.
X
3
Use of theoretical and practical knowledge within the field at a proficiency level and solve the problem faced related to the field by using research methods.
X
4
Interpret the knowledge about the field by integrating the information gathered from different disciplines and formulate new knowledge.
X
5
Independently conduct studies that require proficiency in the field.
X
6
Take responsibility and develop new strategic solutions as a team member in order to solve unexpected complex problems faced within the applications in the field.
7
Evaluate knowledge and skills acquired at proficiency level in the field with a critical approach and direct the learning.
X
8
Investigate, improve social connections and their conducting norms with a critical view and act to change them when necessary. Communicate with peers by using a foreign language at least at a level of European Language Portfolio B2 General Level.
X
9
Define the social and environmental aspects of engineering applications.
10
Audit the data gathering, interpretation, implementation and announcement stages by taking into consideration the cultural, scientific, and ethic values and teach these values.
