Bioinformatics and System Biology Methods, 7.5 credits

Learning outcomes

Knowledge and comprehension
After completing the course, the student shall have knowledge of

• different OMICs platforms,
• bioinformatic tools, systems and databases,
• biomarker screening based on molecular profiles,
• problems that arises from multiple testing when working with "high-throughput screening" methods,
• validation of biomarker candidates, and
• basic systems biology.

Competence and Skills
After completed the course, the student shall be able to

• perform basic programming for biomarker screening analysis using the program R,
• use molecular databases,
• present findings in written reports, and
• critically review and discuss relevant results in relation to scientific studies within the area.

Judgement and Approach
After completing the course, the student shall have an

• understanding of the ethical considerations regard to the use of molecular and genetic markers in biology.

Content

The course deals with different methods of analysis of molecular OMICs profiles (transcriptomics/microarray, next-generation sequencing (NGS), metabolomics, gas chromatography-mass spectrometry (GC-MS), proteomics, MS- and antibody mediated techniques). The course includes programming (programming with R and statistical analysis) for various applications (univariate and multivariate) in biomarker analysis. The results are analysed using information from different databases in molecular biology. Several statistical concepts, such as statistical testing, multiple testing, and other concepts within statistical analysis will be presented. In addition, principles of systems biology and basic methods will be presented.

Examinations and grades

Theory, Part 1 of 2, 3 credits (Code: A001)
Grades used are Fail (F), Sufficient (E), Satisfactory (D), Good (C), Very Good (B) or Excellent (A).

Theory, Part 2 of 2, 2.5 credits (Code: A002)
Grades used are Fail (U) or Pass (G).

Seminars and Tasks, 2 credits (Code: A003)
Grades used are Fail (U) or Pass (G).

According to the Higher Education Ordinance, Chapter 6, Section 18, a grade is to be awarded on the completion of a course, unless otherwise prescribed by the university. The university may determine which grading system is to be used. The grade must be determined by a teacher specifically nominated by the university (the examiner).

In accordance with university regulations on grading systems for first and second-cycle courses and study programmes (Vice-Chancellor’s decision ORU 2018/00929), one of the following grades is to be used: fail (U), pass (G) or pass with distinction (VG). For courses included in an international master’s programme (60 or 120 credits) or offered to the university’s incoming exchange students, the A to F grading scale is to be used. The vice-chancellor, or a person appointed by them, may decide on exceptions from this provision for a specific course, if there are special grounds for doing so.

The grades used on this course are Fail (F), Sufficient (E), Satisfactory (D), Good (C), Very Good (B) or Excellent (A).

Modes of assessment

• Theory, Part 1 of 2 (code A001): Written exam
• Theory, Part 2 of 2 (code A002): Written assignment
• Seminars and Tasks (code A003): Oral examination and practical examination

If a student is absent from a mandatory course component, the examiner determines if the student will be able to make up for the component during another scheduled class of the same kind. Otherwise, the student is referred to the next time the course is offered. As an exception the examiner may decide on substitute assignments. These shall then be carried out before or shortly after the end of the course.

For students with a documented disability, the university may approve applications for adapted or other modes of assessment.

For further information, see the university's local examination regulations.

Specific entry requirements

Molecular Biology and Genetics 7.5 credits

For further information, see the university's admission regulations.

Other provisions

Language of instruction: Swedish and English. The course is given in English if there are exchange students registered.

Students who have been admitted to and registered on a course have the right to receive tuition and/or supervision for the duration of the time period specified for the particular course to which they were accepted (see, the university's admission regulations (in Swedish)). After that, the right to receive tuition and/or supervision expires.

Reading list and other learning resources

Required Reading

Required literature is provided.

Additions and Comments on the Reading List
Literature and other copied material will be added.