INTERNATIONAL BURCH UNIVERSITY
Faculty of Engineering and Natural Sciences
Department of Genetics and Bioengineering
2016-2017

SYLLABUS
Code Name Level Year Semester
GBE 307 Bionformatics Undergraduate 3 Fall
Status Number of ECTS Credits Class Hours Per Week Total Hours Per Semester Language
Compulsory 5 2 + 2 94

Instructor Assistant Coordinator
Şenol Doğan, Assist. Prof. Dr. Senol Dogan Serkan DOĞAN, Assist. Prof. Dr.
[email protected] [email protected] no email

The aim of the course is to establish a basic background in the significant and more emerging field of bioinformatics. Its main subjects are PubMed and Medline databases, DNA- and protein-based bioinformatics tools, as well as several new and emerging information tools. Students are expected to have a working knowledge of genetics and molecular biology concepts in order to fully benefit from utilization of available information sources. The course is organized concurrently with a laboratory course in which students are applying bioinformatics in practice in order to analyze DNA, RNA, and protein sequences, as well as to study phylogeny.

COURSE OBJECTIVE
The cognitive, affective and behavioral objectives of this course are following:  Showing the importance of bioinformatics as a method to overcome modern biomedical research problems.  Enabling skill development in software using, critical evaluation of the results and their interpretation.  Illustrating how to work with DNA sequences.  Explaining how to work with protein sequences.  Illustrating how to construct phylogenetic trees.
Course

COURSE CONTENT
Week
Topic
  1. Introduction to bioinformatics
  2. Pubmed
  3. Using nucleotide sequence databases
  4. Using protein and specialized sequence databases
  5. Working with a single DNA sequence
  6. Working with a single nucleotide sequence
  7. Similarity searches on sequence databases
  8. MID-TERM EXAM WEEK
  9. Comparing two sequences
  10. Building a multiple sequence alignment
  11. Editing and publishing alignments
  12. Working with protein 3D structures
  13. Working with RNA
  14. Building phylogenetic trees: NJ method
  15. Building phylogenetic trees: UPGMA method

LABORATORY/PRACTICE PLAN
Week
Topic
  1. Beginning of classes
  2. Pubmed
  3. Using nucleotide sequence databases
  4. Using protein and specialized sequence databases
  5. Working with a single DNA sequence
  6. Working with a single nucleotide sequence

  1. Similarity searches on sequence databases
  2. MID-TERM EXAM WEEK
  3. Comparing two sequences
  4. Building a multiple sequence alignment
  5. Editing and publishing alignments
  6. Working with protein 3D structures
  7. Working with RNA
  8. Building phylogenetic trees: NJ method
  9. Building phylogenetic trees: UPGMA method

TEACHING/ASSESSMENT
Description
  • Interactive Lectures
  • Practical Sessions
  • Excersises
  • Presentation
Description (%)
Method Quantity Percentage (%)
Midterm Exam(s)120
Presentation110
Lab/Practical Exam(s)120
Attendance110
Final Exam140
Total: 100
Learning outcomes
  • Showing the importance of bioinformatics as a method to overcome modern biomedical research problems.
  • Showing the importance of bioinformatics as a method to overcome modern biomedical research problems.
  • Illustrating how to work with DNA sequences
  • Explaining how to work with protein sequences.
  • Illustrating how to construct phylogenetic trees.
  • Operate single DNA sequences
  • Perform multiple sequence alignments
  • Perform multiple sequence alignments
TEXTBOOK(S)

    ECTS (Allocated based on student) WORKLOAD
    Activities Quantity Duration (Hour) Total Work Load
    Lecture (14 weeks x Lecture hours per week)15230
    Laboratory / Practice (14 weeks x Laboratory/Practice hours per week)15230
    Midterm Examination (1 week)122
    Final Examination(1 week)122
    Preparation for Midterm Examination11515
    Preparation for Final Examination11515
    Assignment / Homework/ Project 130
    Seminar / Presentation 180
    Total Workload: 94
    ECTS Credit (Total workload/25): 4