FACULTY OF ENGINEERING
Department of Genetics and Bioengineering
CE 405 | Course Introduction and Application Information
| Course Name |
Programming for Bioinformatics
|
|
Code
|
Semester
|
Theory
(hour/week) |
Application/Lab
(hour/week) |
Local Credits
|
ECTS
|
|
CE 405
|
Fall/Spring
|
3
|
0
|
3
|
5
|
| Prerequisites |
None
|
|||||
| Course Language |
English
|
|||||
| Course Type |
Elective
|
|||||
| Course Level |
First Cycle
|
|||||
| Mode of Delivery | - | |||||
| Teaching Methods and Techniques of the Course | Group WorkProblem SolvingLecture / Presentation | |||||
| Course Coordinator | ||||||
| Course Lecturer(s) | ||||||
| Assistant(s) | - | |||||
| Course Objectives | Following the dissemination of the first results of the Human Genome Project in 2004 life sciences researchers have access to genome related information (DNA sequence, protein sequence etc.) that would revolutionize the clinical practice as we know it. However this information is kept in various databases and in various formats so that one has to employ special algorithms and tools for the analysis. This course aims to provide an introduction to the terminology, problems, algorithms and tools related to bioinformatics, which is one of the hottest research topics of computer science recently. |
| Learning Outcomes |
The students who succeeded in this course;
|
| Course Description | The course covers bioinformatics tools/software related to biological sequence (DNA, RNA, protein) analysis, molecular structure prediction, functional genomics, pharmacogenomics and proteomics, biological pathway analysis. |
|
|
Core Courses | |
| Major Area Courses | ||
| Supportive Courses | ||
| Media and Management Skills Courses | ||
| Transferable Skill Courses |
WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES
| Week | Subjects | Related Preparation |
| 1 | Introduction to Bioinformatics | Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elsevier, 2014 Chp. 1 |
| 2 | Basic biology information, Central dogma, DNA and RNA structure, gene, and proteins. Hairpins, loops, alpha helix and beta sheet. | Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014 Chp. 1 N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004 Ch.3 |
| 3 | Variables, data types, operators, return, if/else block. Importing modules, imported functions, declarations | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 1,2 |
| 4 | Lists, dictionaries, tuples, interactive user input, comment blocks, for, while loops, break and continue, iterators, Time, sys, os modules, file reading and writing | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 3,4 |
| 5 | Classes. Regular expressions and regex module. Biopython module, pairwise alignment. Accessing ncbi. FASTA and Genbank file formats | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 5 |
| 6 | Midterm | |
| 7 | Finding k-mers in in DNA sequences | Data Algorithms, Mahmoud Parsian, O’Reilly, ISBN: 9781491906187, Chapter 17 |
| 8 | Numpy, scipy and matplotlib modules. Matrices and sparse matrices. | Bioinformatics Programming Using Python: Practical Programming for Biological Data, Mitchell L Model, O’Reilly, 2009. ISBN: 9781449382902. Chapter 10 |
| 9 | Needleman-Wunsch, Waterman-Smith-Bayer, and other sequence alignment algorithms | Multiple Biological Sequence Alignment: Scoring Functions, Algorithms and Evaluation, Ken Nguyen, Xuan Guo, Yi Pan, ISBN: 978-1-118-22904-0, Chapter 2 |
| 10 | Gotoh alignment and affine gap cost algorithm | Multiple Biological Sequence Alignment: Scoring Functions, Algorithms and Evaluation, Ken Nguyen, Xuan Guo, Yi Pan, ISBN: 978-1-118-22904-0, Chapter 3 |
| 11 | K-means clustering and Hierarchical clustering | Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Chapter 10 |
| 12 | Midterm II | |
| 13 | RNA folding and motif analysis | Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elsevier, 2014 Chapter 7 |
| 14 | Multi sequence alignment and phylogenetic tree construction | Python for Bioinformatics, Sebastian Bass, CRC Press, 2016. ISBN: 9781584889304. Chapter 23 |
| 15 | Semester Review | |
| 16 | Final Exam |
| Course Notes/Textbooks | Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elsevier, 2014 |
| Suggested Readings/Materials | N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004 J. Xiong, Essential Bioinformatics, Cambridge University Press, 2006. S. Bassi, Python for Bioinformatics, CRC Press , 2010. Multiple Biological Sequence Alignment: Scoring Functions, Algorithms and Evaluation, Ken Nguyen, Xuan Guo, Yi Pan, ISBN: 978-1-118-22904-0 Data Algorithms, Mahmoud Parsian, O’Reilly, ISBN: 9781491906187 |
EVALUATION SYSTEM
| Semester Activities | Number | Weigthing |
| Participation |
1
|
10
|
| Laboratory / Application | ||
| Field Work | ||
| Quizzes / Studio Critiques | ||
| Portfolio | ||
| Homework / Assignments |
4
|
10
|
| Presentation / Jury | ||
| Project |
1
|
30
|
| Seminar / Workshop | ||
| Oral Exams | ||
| Midterm |
2
|
30
|
| Final Exam |
1
|
20
|
| Total |
| Weighting of Semester Activities on the Final Grade |
8
|
80
|
| Weighting of End-of-Semester Activities on the Final Grade |
1
|
20
|
| 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 |
14
|
1
|
14
|
| Field Work |
0
|
||
| Quizzes / Studio Critiques |
0
|
||
| Portfolio |
0
|
||
| Homework / Assignments |
4
|
2
|
8
|
| Presentation / Jury |
0
|
||
| Project |
1
|
25
|
25
|
| Seminar / Workshop |
0
|
||
| Oral Exam |
0
|
||
| Midterms |
2
|
18
|
36
|
| Final Exam |
1
|
19
|
19
|
| Total |
150
|
COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP
|
#
|
Program Competencies/Outcomes |
* Contribution Level
|
||||
|
1
|
2
|
3
|
4
|
5
|
||
| 1 | To have adequate knowledge in Mathematics, Science and Genetics and Bioengineering; to be able to use theoretical and applied information in these areas on complex engineering problems. |
X | ||||
| 2 | To be able to identify, define, formulate, and solve complex Genetics and Bioengineering problems; to be able to select and apply proper analysis and modeling methods for this purpose. |
X | ||||
| 3 | To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose. |
|||||
| 4 | To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Genetics and Bioengineering applications; to be able to use information technologies effectively. |
X | ||||
| 5 | To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Genetics and Bioengineering research topics. |
|||||
| 6 | To be able to work efficiently in Genetics and Bioengineering disciplinary and multi-disciplinary teams; to be able to work individually. |
|||||
| 7 | To be able to communicate effectively in Turkish, both orally and in writing; to be able to author and comprehend written reports, to be able to prepare design and implementation reports, to present effectively, to be able to give and receive clear and comprehensible instructions. |
|||||
| 8 | To have knowledge about global and social impact of Genetics and Bioengineering practices on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Genetics and Bioengineering solutions. |
|||||
| 9 | To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in Genetics and Bioengineering applications. |
X | ||||
| 10 | To have knowledge about industrial practices such as project management, risk management, and change management; to have awareness of entrepreneurship and innovation; to have knowledge about sustainable development. |
|||||
| 11 | To be able to collect data in the area of Genetics and Bioengineering, and to be able to communicate with colleagues in a foreign language. |
|||||
| 12 | To be able to speak a second foreign language at a medium level of fluency efficiently. |
X | ||||
| 13 | To recognize the need for lifelong learning; to be able to access information, to be able to stay current with developments in science and technology; to be able to relate the knowledge accumulated throughout the human history to Genetics and Bioengineering. |
|||||
*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest
NEWS |ALL NEWS
Elderly’s quality of life will increase
4 scientists from Izmir University of Economics (IUE) have begun work on developing a drug aimed at treating osteoarthritis, a disease mostly
Germany chose Ezgi
Ezgi Kaya, who graduated from Izmir University of Economics (IUE) Department of Genetics and Bioengineering this year, was accepted to the world-famous
Geneticists’ success in ‘Germany’
Nine newly graduated students from Izmir University of Economics (IUE) Department of Genetics and Bioengineering achieved great success by being accepted to
'Sustainable energy' ideas from students
Izmir University of Economics (IUE) organized a workshop on biohydrogen, which is used in many fields from industry to transportation and stands
Discovery in thermal spring
Asst. Prof. Dr. Mine Güngörmüşler from Izmir University of Economics (IUE), Department of Genetics and Bioengineering, and two graduate students examined the
Arda ranked among 7 people in the world
Arda Kıpçak, who graduated from Department of Genetics and Bioengineering, Izmir University of Economics (IUE) this year, was accepted to the world-renowned
'Smart cabinet' against the virus
Assoc. Prof. Dr. Osman Doluca and his 4 students from Izmir University of Economics (IUE) developed a 'PCR cabinet' that allows samples