• Basic information
• Learning outcomes
• Contents
• Assessment
• Workload

Learning outcomes

Upon successful completion of this course, students will be able to:

1. Extract relevant information from biological databases

   Contribution to Program Outcomes

   1. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   2. Acquire knowledge for research methods which are required to develop novel application methods
   3. Apply mathematical analysis and modeling methods for bioengineering design and production processes.
   4. Conduct and develop bioengineering applications for relevant sectors such as health and agricultural industry.
   5. Design processes for the investigation of bioengineering problems, collect data, analyze and interpret the results.

   Method of assessment

   1. Homework assignment
   2. Term paper
2. Describe methods used in biological sequence and structure analysis.

   Contribution to Program Outcomes

   1. Acquire knowledge on biological, chemical, physical and mathematical principles which constitute the basis of bioengineering applications
   2. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects

   Method of assessment

   1. Written exam
3. Identify similarities between biological sequences by using sequence alignment algorithms

   Contribution to Program Outcomes

   1. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects
   2. Acquire knowledge for research methods which are required to develop novel application methods
   3. Convert biological, chemical, physical and mathematical principles into novel applications for the benefit of society,
   4. Apply mathematical analysis and modeling methods for bioengineering design and production processes.
   5. Conduct and develop bioengineering applications for relevant sectors such as health and agricultural industry.
   6. Design processes for the investigation of bioengineering problems, collect data, analyze and interpret the results.

   Method of assessment

   1. Homework assignment
   2. Term paper
4. Describe algorithms used in databases scanning for detection of homologous proteins

   Contribution to Program Outcomes

   1. Acquire knowledge on biological, chemical, physical and mathematical principles which constitute the basis of bioengineering applications
   2. Acquire knowledge on current bioengineering applications from the industrial and scientific aspects

   Method of assessment

   1. Written exam
5. Perform molecular docking simulations to identify interactions between small molecules and their target proteins

   Contribution to Program Outcomes

   1. Convert biological, chemical, physical and mathematical principles into novel applications for the benefit of society,
   2. Apply mathematical analysis and modeling methods for bioengineering design and production processes.
   3. Conduct and develop bioengineering applications for relevant sectors such as health and agricultural industry.
   4. Design processes for the investigation of bioengineering problems, collect data, analyze and interpret the results.
   5. Work effectively in multi-disciplinary research teams
   6. Combine and effectively integrate knowledge acquired from different disciplines.
   7. Develop an awareness of continuous learning in relation with modern technology.
   8. Demonstrate sufficiency in English to follow literature, present technical projects and write articles

   Method of assessment

   1. Homework assignment
   2. Term paper

Contents
Week 1:	Introduction to Molecular Biology and Bioinformatics: DNA, RNA, and Protein Synthesis
Week 2:	Scientific Publications and Archives in Life Sciences
Week 3:	Biological Databases
Week 4:	Global Pairwise Sequence Alignment: Needleman-Wunsch Algorithm
Week 5:	Local Pairwise Sequence Alignment: Smith-Waterman Algorithm
Week 6:	Multiple Sequence Alignment Methods
Week 7:	Molecular Evolution and Phylogenetic Trees
Week 8:	Detection of Homologous Proteins: BLAST and FASTA algorithms
Week 9:	Protein Structure and Functions
Week 10:	Structural Bioinformatics
Week 11:	Protein Structure Prediction
Week 12:	Protein-Ligand Interactions and Molecular Docking
Week 13:	Protein Dynamics
Week 14:	Project presentations
Week 15*:	-
Week 16*:	Final Exam
Textbooks and materials:	Bioinformatics and Functional Genomics (3rd ed.). J. Pevsner. Wiley-Blackwell, 2015. Understanding Bioinformatics. M. Zvelebil, J. Baum. Garland Science. 2007. Bioinformatics (4th ed.). Baxevanis, A. D., Bader, G. D., & Wishart, D. S. (Eds.). Wiley. 2020. Introduction to Bioinformatics (5th Ed.). A. Lesk. OUP. 2019
Recommended readings:	Bioinformatics: An Introduction (3rd ed.). J. Ramsden. Springer. 2015.
	* Between 15th and 16th weeks is there a free week for students to prepare for final exam.

Assessment
Method of assessment	Week number	Weight (%)
Mid-terms:		0
Other in-term studies:		0
Project:	14	30
Homework:	4, 7, 12	30
Quiz:		0
Final exam:	16	40
	Total weight:	(%)

Workload
Activity	Duration (Hours per week)	Total number of weeks	Total hours in term
Courses (Face-to-face teaching):	3	14
Own studies outside class:	3	13
Practice, Recitation:	0	0
Homework:	4	3
Term project:	4	5
Term project presentation:	1	1
Quiz:	0	0
Own study for mid-term exam:	0	0
Mid-term:	0	0
Personal studies for final exam:	4	2
Final exam:	3	1
		Total workload:
		Total ECTS credits:	*
	* ECTS credit is calculated by dividing total workload by 25. (1 ECTS = 25 work hours)