Syllabus for Introduction to Bioinformatics

Introduktion till bioinformatik

Syllabus

  • 10 credits
  • Course code: 1MB438
  • Education cycle: Second cycle
  • Main field(s) of study and in-depth level: Bioinformatics A1N

    Explanation of codes

    The code indicates the education cycle and in-depth level of the course in relation to other courses within the same main field of study according to the requirements for general degrees:

    First cycle
    G1N: has only upper-secondary level entry requirements
    G1F: has less than 60 credits in first-cycle course/s as entry requirements
    G1E: contains specially designed degree project for Higher Education Diploma
    G2F: has at least 60 credits in first-cycle course/s as entry requirements
    G2E: has at least 60 credits in first-cycle course/s as entry requirements, contains degree project for Bachelor of Arts/Bachelor of Science
    GXX: in-depth level of the course cannot be classified.

    Second cycle
    A1N: has only first-cycle course/s as entry requirements
    A1F: has second-cycle course/s as entry requirements
    A1E: contains degree project for Master of Arts/Master of Science (60 credits)
    A2E: contains degree project for Master of Arts/Master of Science (120 credits)
    AXX: in-depth level of the course cannot be classified.

  • Grading system: Fail (U), Pass (G)
  • Established: 2018-03-06
  • Established by:
  • Revised: 2019-02-08
  • Revised by: The Faculty Board of Science and Technology
  • Applies from: week 28, 2019
  • Entry requirements: A Bachelor's degree including: Alternative 1) 15 credits mathematics or statistics, and 45 credits biology including 30 hp in molecular biology, cell biology, evolution or genetics; Alternative 2) 30 credits mathematics and 30 credits computer science including 5 credits in database design .
  • Responsible department: Biology Education Centre

Learning outcomes

On completion of the course, the student should be able to:

  • account for and use methods in sequence bioinformatics such as sequence alignment, phylogenetic analysis and pattern recognition
  • account for and use methods in structural bioinformatics such as classification of protein structures, structure prediction, simulations and structure based drug design
  • analyse and compile results of bioinformatic analyses critically
  • solve given biological problems by using appropriate bioinformatic methods and databases
  • use and design simple scripts in R.
In the course, an introduction to master studies is included. After passing this module, the student should be able to:
  • show awareness of ethical aspects on research and development including plagiarism issues and equal opportunities/equal treatment
  • demonstrate an understanding of the possibilities of the bioinformatics, limitations and role in society
  • make an individual study plan.

Content

Basic sequence and structural bioinformatics as well as introduction to bioinformatic algorithms. Pairwise and multiple sequence alignment. Methods for phylogenetic analysis and pattern recognition. Bioinformatic databases and servers. Classification and comparison of protein structures. Prediction of secondary and tertiary structure from sequence and homology modelling of the three-dimensional structure of proteins. Molecular dynamics simulations and molecular docking with applications to drug design. Applications of bioinformatic research. Computer exercises in bioinformatic scientific environment. Introduction to basic programming in R. Ethical aspects in education, research and development. Bioinformatics in Society.

Instruction

Lectures, seminars and computer exercises.

Assessment

Introduction to master's studies (2 credits) active participation in seminars, written report and completed study plan.
Sequence bioinformatics: written examination (2.5 credits) and laboratory reports (1 credit).
Structural bioinformatics: (2.5 credits) written examination and laboratory reports (1 credit).
Introduction to programming in R (1 credit) laboratory reports.

If there are special reasons for doing so, an examiner may make an exception from the method of assessment indicated and allow a student to be assessed by another method. An example of special reasons might be a certificate regarding special pedagogical support from the disability coordinator of the university.

Reading list

Reading list

Applies from: week 28, 2019

  • Zvelebil, Marketa J.; Baum, Jeremy O. Understanding bioinformatics

    New York: Garland Science, c2008

    Find in the library