GRADUATE SCHOOL
M.SC. in Bioengineering (With Thesis)
BEN 519 | Course Introduction and Application Information
| Course Name |
Advanced Bioinformatics
|
|
Code
|
Semester
|
Theory
(hour/week) |
Application/Lab
(hour/week) |
Local Credits
|
ECTS
|
|
BEN 519
|
Fall/Spring
|
3
|
0
|
3
|
7.5
|
| Prerequisites |
None
|
|||||
| Course Language |
English
|
|||||
| Course Type |
Elective
|
|||||
| Course Level |
Second Cycle
|
|||||
| Mode of Delivery | - | |||||
| Teaching Methods and Techniques of the Course | - | |||||
| Course Coordinator | ||||||
| Course Lecturer(s) | - | |||||
| Assistant(s) | - | |||||
| Course Objectives | The objective of the course is to provide a background in programming and teach the students computational techniques used for processing biological data in bioengineering. |
| Learning Outcomes |
The students who succeeded in this course;
|
| Course Description | The course contains introduction of usage of Python in bioinformatics applications. The course starts with fundamentals for programming with Python computer language. This part contains the Python syntax and processing of biological data. It will be proceeded with introduction of problems of bioinformatics such as next generation data analysis, evolutionary relationship analysis, detection of single-nucleotide and copy-number variations. |
|
|
Core Courses | |
| Major Area Courses |
X
|
|
| Supportive Courses | ||
| Media and Management Skills Courses | ||
| Transferable Skill Courses |
WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES
| Week | Subjects | Related Preparation |
| 1 | Introduction to bioinformatics | |
| 2 | Variables, data types, operators, return function, if/else block | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 1 |
| 3 | Importing modules, module functions, declerations | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 2 |
| 4 | List, Dict, Tuple types, comment block | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 3 |
| 5 | For and while loops, break, continue and iterators | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 4 |
| 6 | Time, sys, os modules, reading and writing to files | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 6 |
| 7 | Classes, regular expression and regex module | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 5 |
| 8 | Midterm | |
| 9 | Numpy, scipy and panda modules. Matrices and sparse matrices | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 10 |
| 10 | Matplotlib module, K-means clustering and hierarchical clustering | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 11 |
| 11 | Biopython module, pairwise alignment, communication with NCBI | Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Chapter 10 |
| 12 | Midterm II | |
| 13 | Introduction to NGS, Single-nucleotide and copy-number polymorphism | Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Chapter 22, 23 Bioinformatics and Functional Genomics, 3rd Edition, Jonathan Pevsner, Wiley. ISBN: 978-1-118-58178-0, Chapter 9 |
| 14 | Multi sequence alignment and construction of phylogenetical tree | Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Chapter 23 |
| 15 | Review of the semester | |
| 16 | Final Exam |
| Course Notes/Textbooks | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Bioinformatics and Functional Genomics, 3rd Edition, Jonathan Pevsner, Wiley. ISBN: 978-1-118-58178-0 |
| Suggested Readings/Materials |
EVALUATION SYSTEM
| Semester Activities | Number | Weigthing |
| Participation |
1
|
10
|
| Laboratory / Application | ||
| Field Work | ||
| Quizzes / Studio Critiques |
4
|
20
|
| Portfolio | ||
| Homework / Assignments | ||
| Presentation / Jury | ||
| Project | ||
| Seminar / Workshop | ||
| Oral Exams | ||
| Midterm |
2
|
30
|
| Final Exam |
1
|
40
|
| Total |
| Weighting of Semester Activities on the Final Grade |
7
|
60
|
| Weighting of End-of-Semester Activities on the Final Grade |
1
|
40
|
| Total |
ECTS / WORKLOAD TABLE
| Semester Activities | Number | Duration (Hours) | Workload |
|---|---|---|---|
| Theoretical Course Hours (Including exam week: 16 x total hours) |
16
|
3
|
48
|
| Laboratory / Application Hours (Including exam week: '.16.' x total hours) |
16
|
0
|
|
| Study Hours Out of Class |
15
|
7
|
105
|
| Field Work |
0
|
||
| Quizzes / Studio Critiques |
4
|
1
|
4
|
| Portfolio |
0
|
||
| Homework / Assignments |
0
|
||
| Presentation / Jury |
0
|
||
| Project |
0
|
||
| Seminar / Workshop |
0
|
||
| Oral Exam |
0
|
||
| Midterms |
2
|
18
|
36
|
| Final Exam |
1
|
32
|
32
|
| Total |
225
|
COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP
|
#
|
Program Competencies/Outcomes |
* Contribution Level
|
||||
|
1
|
2
|
3
|
4
|
5
|
||
| 1 | To be able to have adequate knowledge in Mathematics, Life Sciences and Bioengineering; to be able to use theoretical and applied information in these areas to model and solve Bioengineering problems. |
X | ||||
| 2 | To be able to use scientific methods to complete and apply information from uncertain, limited or incomplete data; to be able to combine and use information from related disciplines. |
X | ||||
| 3 | To be able to design and apply theoretical, experimental and model-based research; to be able to solve complex problems in such processes. |
X | ||||
| 4 | Being able to utilize Natural Sciences and Bioengineering principles to design systems, devices and processes. |
X | ||||
| 5 | To be able to follow and apply new developments and technologies in the field of Bioengineering. |
X | ||||
| 6 | To be able to work effectively in multi-disciplinary teams within the discipline of Bioengineering; to be able to exhibit individual work. |
X | ||||
| 7 | To be able to have the knowledge about the social, environmental, health, security and law implications of Bioengineering applications, to be able to have the knowledge to manage projects and business applications, and to be able to be aware of their limitations in professional life. |
X | ||||
| 8 | To be able to have the social, scientific and ethical values in the stages of collection, interpretation, dissemination and application of data related to the field of Bioengineering. |
X | ||||
| 9 | To be able to prepare an original thesis/term project in accordance with the criteria related to the field of Bioengineering. |
|||||
| 10 | To be able to follow information about Bioengineering in a foreign language and to be able to participate in discussions in academic environments. |
X | ||||
| 11 | To be able to improve the acquired knowledge, skills and qualifications for social and universal purposes regarding the studied area. |
X | ||||
| 12 | To be able to recognize regional and global issues/problems, and to be able to develop solutions based on research and scientific evidence related to Bioengineering. |
X | ||||
*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest