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      FACULTY OF ENGINEERING

      Department of Biomedical Engineering

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      BME 311 | Course Introduction and Application Information

      Course Name
      Computational Bioinformatics
      Code
      Semester
      Theory
      (hour/week)
      Application/Lab
      (hour/week)
      Local Credits
      ECTS
      BME 311
      Fall/Spring
      2
      2
      3
      6

      Prerequisites
        SE 113 To succeed (To get a grade of at least DD)
      or SE 115 To succeed (To get a grade of at least DD)
      Course Language
      English
      Course Type
      Elective
      Course Level
      First Cycle
      Mode of Delivery face to face
      Teaching Methods and Techniques of the Course Discussion
      Group Work
      Problem Solving
      Application: Experiment / Laboratory / Workshop
      Lecture / Presentation
      National Occupation Classification -
      Course Coordinator
      • Doç. Dr. Osman DOLUCA
      Course Lecturer(s)
      • Doç. Dr. Osman DOLUCA
      Assistant(s)
      • Araş. Gör. Duygu GEÇKİN
      Course Objectives This course aims to teach the algorithms used for analysis of biological data and file formats that these biological data are stored in online databases.
      Learning Outcomes
      #
      Content
      PC Sub
      * Contribution Level
      1
      2
      3
      4
      5
      1Define the bioinformatics problems
      2Explain biological data formats and online databases
      3Discuss the algorithms used for different bioinformatics problems
      4Apply algorithms to solve a given bioinformatics problem
      5Apply simple programming skills for solving bioinformatics problems.
      Course Description The course covers algorithms used for sequence alignment, motif discovery in DNA and protein sequences, clustering protein networks, protein complex discovery using interaction networks, phylogenetic tree construction and next generation sequencing.
      Related Sustainable Development Goals

       



      Course Category

      Core Courses
      Major Area Courses
      X
      Supportive Courses
      Media and Management Skills Courses
      Transferable Skill Courses

       

      WEEKLY SUBJECTS AND RELATED PREPARATION STUDIES

      Week Subjects Related Preparation Learning Outcome
      1 Introduction to Python Chapter 2, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      2 Variables, if/else blocks, importing modules Chapter 1, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102 Chapter 3, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780124105102
      3 Functions and modules Chapter 5, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      4 Collections and comprehensions Chapter 5, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      5 Reading from FASTA and Genbank files Chapter 7, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      6 Using K-mer to find repeats in DNA sequences. Chapter 7, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      7 Using RegEx to find motifs Chapter 4, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      8 Clustering biological data using K-means Chapter 10, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      9 Protein complex discovery in interaction networks. Chapter 8, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      10 Sequence alignment using Biopython Chapter 6, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      11 Affine gap cost in sequence alignment. Chapter 6, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      12 Midterm I
      13 Algorithms used in next generation sequencing analysis and multiple sequence alignment. Chapter 7, Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      14 UPMGA and Neighbor-joining tree construction algorithms. Chapter 10, N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      15 Review of the Semester
      16 Final Exam

       

      Course Notes/Textbooks
      • Bioinformatics for beginners, Genes, Genomes, Molecular Evolution, Databases and Analytical Tools. Supratim Choudhuri. Elservier, 2014, ISBN: 9780124105102
      • N. C. Jones and P. A. Pevzner, An Introduction to Bioinformatics Algorithms, MIT press, 2004, ISBN: 9780262101066
      Suggested Readings/Materials

       

      EVALUATION SYSTEM

      Semester Activities Number Weigthing LO 1 LO 2 LO 3 LO 4 LO 5
      Participation
      Laboratory / Application
      Field Work
      Quizzes / Studio Critiques
      Portfolio
      Homework / Assignments
      1
      10
      Presentation / Jury
      Project
      1
      20
      Seminar / Workshop
      Oral Exams
      Midterm
      1
      30
      Final Exam
      1
      40
      Total

      Weighting of Semester Activities on the Final Grade
      4
      60
      Weighting of End-of-Semester Activities on the Final Grade
      1
      40
      Total

      ECTS / WORKLOAD TABLE

      Semester Activities Number Duration (Hours) Workload
      Theoretical Course Hours
      (Including exam week: 16 x total hours)
      16
      2
      32
      Laboratory / Application Hours
      (Including exam week: '.16.' x total hours)
      16
      2
      32
      Study Hours Out of Class
      14
      3
      42
      Field Work
      0
      Quizzes / Studio Critiques
      0
      Portfolio
      0
      Homework / Assignments
      1
      14
      14
      Presentation / Jury
      0
      Project
      1
      16
      16
      Seminar / Workshop
      0
      Oral Exam
      0
      Midterms
      1
      20
      20
      Final Exam
      1
      24
      24
          Total
      180

       

      COURSE LEARNING OUTCOMES AND PROGRAM QUALIFICATIONS RELATIONSHIP

      #
      PC Sub Program Competencies/Outcomes
      * Contribution Level
      1
      2
      3
      4
      5
      1

      To have adequate knowledge in Mathematics, Science and Biomedical 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 Biomedical Engineering problems; to be able to select and apply proper analysis and modeling methods for this purpose.

      X
      -
      -
      -
      -
      3

      To be able to design a complex system, process, device or product under realistic constraints and conditions, in such a way as to meet the requirements; to be able to apply modern design methods for this purpose.

      -
      X
      -
      -
      -
      4

      To be able to devise, select, and use modern techniques and tools needed for analysis and solution of complex problems in Biomedical Engineering applications.

      -
      -
      -
      X
      -
      5

      To be able to design and conduct experiments, gather data, analyze and interpret results for investigating complex engineering problems or Biomedical Engineering research topics.

      -
      -
      X
      -
      -
      6

      To be able to work efficiently in Biomedical Engineering disciplinary and multi-disciplinary teams; to be able to work individually.

      X
      -
      -
      -
      -
      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 present effectively, to be able to give and receive clear and comprehensible instructions.

      -
      -
      -
      -
      -
      8

      To have knowledge about global and social impact of Biomedical Engineering practices 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 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 Biomedical Engineering, and to be able to communicate with colleagues in a foreign language.

      -
      -
      -
      -
      -
      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 Biomedical Engineering.

      -
      -
      -
      -
      -

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


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