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Syllabus ( BENG 451 )


   Basic information
Course title: Introduction to Bioinformatics
Course code: BENG 451
Lecturer: Assist. Prof. Onur SERÇİNOĞLU
ECTS credits: 5
GTU credits: 3 ()
Year, Semester: 3/5, Fall
Level of course: First Cycle (Undergraduate)
Type of course: Departmental Elective
Language of instruction: English
Mode of delivery: Face to face
Pre- and co-requisites: None
Professional practice: No
Purpose of the course: The purpose of this course is to provide students with a comprehensive understanding of molecular biology and bioinformatics, covering key concepts from DNA, RNA, and protein synthesis to advanced topics in protein dynamics, as well as practical skills in sequence alignment, protein modeling, and in silico approaches to drug discovery.
   Learning outcomes Up

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. 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. Utilize pairwise sequence alignment algorithms to align biological sequences

    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.

    Method of assessment

    1. Homework assignment
  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
   Contents Up
Week 1: Introduction to Molecular Biology and Bioinformatics: DNA, RNA, and Protein Synthesis
Week 2: Biological Databases: Primary and Secondary Databases
Week 3: Sequence Alignment: Introduction to Pairwise Sequence Alignment
Week 4: Global Sequence Alignment: Needleman-Wunsch Algorithm
Homework I
Week 5: Local Sequence Alignment: Smith-Waterman Algorithm
Week 6: Detection of Homologous Proteins: BLAST and FASTA
Week 7: Multiple Sequence Alignment: Methods and Tools
Homework II
Week 8: Protein Structures: Primary, Secondary, Tertiary and Quaternary Structures
Week 9: Structural Bioinformatics: Analysis of Protein Structures
Week 10: Computational Protein Modeling: Protein Structure Prediction
Homework III

Week 11: Protein-ligand Interactions and Molecular Docking
Homework IV
Week 12: Drug Discovery: In Silico Approaches
Week 13: Protein Dynamics: Molecular Dynamics Simulations
Homework V

Week 14: Advanced Topics in Protein Dynamics
Week 15*: -
Week 16*: Final Exam
Textbooks and materials: Pevsner, J. (2015). Bioinformatics and Functional Genomics (3rd ed.). Wiley-Blackwell.
Recommended readings: Zvelebil, M., & Baum, J. O. (2007). Understanding Bioinformatics. Garland Science.

Ramsden, J. (2015). Bioinformatics: An Introduction (3rd ed.). Springer.

Baxevanis, A. D., Bader, G. D., & Wishart, D. S. (Eds.). (2020). Bioinformatics (4th ed.). Wiley.

  * Between 15th and 16th weeks is there a free week for students to prepare for final exam.
Assessment Up
Method of assessment Week number Weight (%)
Mid-terms: 0
Other in-term studies: 0
Project: 0
Homework: 4, 7, 10, 11, 14 50
Quiz: 0
Final exam: 16 50
  Total weight:
(%)
   Workload Up
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 14
Practice, Recitation: 2 1
Homework: 4 8
Term project: 0 0
Term project presentation: 0 0
Quiz: 0 0
Own study for mid-term exam: 0 0
Mid-term: 0 0
Personal studies for final exam: 5 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)
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