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Syllabus ( BSB 511 )

   Basic information
Course title: Fundamentals of Bioinformatics
Course code: BSB 511
Lecturer: Assist. Prof. Onur SERÇİNOĞLU
ECTS credits: 7.5
GTU credits: 3 (3+0+0)
Year, Semester: 1/2, Spring
Level of course: Second Cycle (Master's)
Type of course: Compulsory
Language of instruction: English
Mode of delivery: Face to face , Lab work
Pre- and co-requisites: none
Professional practice: No
Purpose of the course: The purpose of the course is to provide students with following topics: Sequence Analysis, Genome Analysis, Protein Bioinformatics, Databases and Ontologies. Basics of post-sequencing bioinformatics will also be covered via the analysis of cellular networks.
   Learning outcomes Up

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

  1. Perform comparisons of DNA and protein sequences

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Grasp the importance of bioinformatics and systems biology based viewpoint in the analysis and interpretation of working principles of the cell.

    Method of assessment

    1. Written exam
    2. Homework assignment
  2. Analyze genomes by predicting and annotating genes using related algorithms

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Acquire scientific knowledge and work independently
    3. Develop an awareness of continuous learning in relation with modern technology

    Method of assessment

    1. Written exam
    2. Homework assignment
  3. Gain knowledge on the prediction, comparison and modeling of protein structures

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Identify the changes in cellular and molecular mechanisms in health and disease from the perspective of bioinformatics and systems biology.
    3. Find out new methods to improve his/her knowledge.
    4. Grasp the importance of bioinformatics and systems biology based viewpoint in the analysis and interpretation of working principles of the cell.

    Method of assessment

    1. Written exam
    2. Homework assignment
  4. Gain practical knowledge on the structures and usage of biological databases

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Develop an awareness of continuous learning in relation with modern technology

    Method of assessment

    1. Written exam
    2. Homework assignment
  5. Analyze cellular networks by using basic bioinformatic tools

    Contribution to Program Outcomes

    1. Define and manipulate basic and advanced concepts in the field of Bioinformatics and Systems Biology
    2. Apply modelling approaches to cellular networks.
    3. Formulate, code, solve and analyze problems on biomolecular interactions by using an engineering viewpoint.
    4. Grasp the importance of bioinformatics and systems biology based viewpoint in the analysis and interpretation of working principles of the cell.

    Method of assessment

    1. Written exam
    2. Homework assignment
   Contents Up
Week 1: Definition, history and significance of Bioinformatics
Introduction to biological databases and bioinformatics tools
Week 2: Databases and tools I: NCBI tools, EBI tools, Molecular interaction databases
Homework I
Week 3: Databases and tools II: Nucleic acid sequence databases, Genome databases, Protein sequence databases
Homework II
Week 4: Sequence Analysis I: Comparative genomics, Alignment, BLAST algorithm and derivatives
Week 5: Sequence Analysis II: Sequence search and Sequence motifs
Genome Analysis I: Genome sequencing
Homework III
Week 6: Genome Analysis II: Gene prediction and annotation
Homework IV
Week 7: Protein Bioinformatics I: PDB database, Protein structures, Prediction of secondary structures
Quiz I
Week 8: Protein Bioinformatics II: Protein domains and functional sites, Protein motifs, Protein structural alignment
Homework V
Week 9: Protein Bioinformatics III: Protein modeling methods (Homology modeling, Threading and Docking)
Homework VI
Week 10: Protein Bioinformatics IV: Drug discovery
Quiz II
Week 11: Databases and tools III: Transcriptome, Proteome, Metabolome databases
Week 12: Databases and tools IV: Gene Ontologies, KEGG, DAVID, BioCyc, ENTREZ, ExPASy
Homework VII
Week 13: Post-sequencing Bioinformatics I: Metabolic networks, Metabolic pathway alignment
Quiz III
Week 14: Post-sequencing Bioinformatics II: Gene regulatory networks, Protein networks
Homework VIII
Week 15*: General Overview
Week 16*: Final Exam
Textbooks and materials: 1. A. Lesk, "Introduction to Bioinformatics", Oxford University Press, 4th Edn., 2014

2. M. Zvelebil, J. O. Baum, "Understanding Bioinformatics" Garland Science, 2007
Recommended readings: 1. G.B. Singh, "Fundamentals of Bioinformatics and Computational Biology: Methods and Exercises in MATLAB", Springer, 2015

2. J. Ramsden, "Bioinformatics: An Introduction", Springer, 3rd Edn., 2015
  * 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: 2, 3, 5, 6, 8, 9, 12, 14 40
Quiz: 7, 10, 13 30
Final exam: 16 30
  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: 6 14
Practice, Recitation: 2 1
Homework: 5 8
Term project: 0 0
Term project presentation: 0 0
Quiz: 1 3
Own study for mid-term exam: 0 0
Mid-term: 0 0
Personal studies for final exam: 10 1
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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