FACULTY OF ENGINEERING

Department of Software Engineering

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 Work
Problem Solving
Lecture / 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;
  • will be able to define the bioinformatics problems,
  • will be able to explain biological databases as well as the data formats,
  • will be able to discuss the famous bioinformatics algorithms,
  • will be able to classify statistical analysis techniques of genomic information,
  • will be able to write Python codes using bioinformatics algorithms.
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.

 



Course Category

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, Computer Science and Software Engineering; 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 Software Engineering problems; to be able to select and apply proper analysis and modeling methods for this purpose.

X
3

To be able to design, implement, verify, validate, document, measure and maintain a complex software system, process, or product under realistic constraints and conditions, in such a way as to meet the requirements; ability to apply modern 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 software engineering 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 Software Engineering problems.

6

To be able to work effectively in Software Engineering 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 be able to present effectively, to be able to give and receive clear and comprehensible instructions.

8

To have knowledge about global and social impact of engineering practices and software applications on health, environment, and safety; to have knowledge about contemporary issues as they pertain to engineering; to be aware of the legal ramifications of Engineering and Software Engineering solutions.

9

To be aware of ethical behavior, professional and ethical responsibility; to have knowledge about standards utilized in engineering applications.

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 Software Engineering, and to be able to communicate with colleagues in a foreign language. ("European Language Portfolio Global Scale", Level B1)

12

To be able to speak a second foreign language at a medium level of fluency efficiently.

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 Software Engineering.

*1 Lowest, 2 Low, 3 Average, 4 High, 5 Highest

 


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