Bioinformatics and Genome Analysis, 7.5 credits

Contents

The course is an introduction to bioinformatics and provides basic skills in bioinformatics. The course covers basic information retrieval, introduction to R and the Linux command line, statistics and linear models, analysis of genomics data and common tools for data integration.

Expected learning outcomes

After completing the course, the student must be able to, with regard to:

Knowledge and understanding:

• Identify the most commonly used databases for biological data

• Demonstrate understanding of how typical types of biological data are stored in computers

• Show knowledge of the most common tools used in basic bioinformatics

• Explain how a design matrix can be used to model common biological problems

• Describe common distance metrics used for comparing biological data

Competence and Skills:

• Retrieve common biological data from online resources and use common online tools relevant to bioinformatics

• Use basic Linux commands for file management and software execution

• Create basic scripts in R using documentation on the Internet

• Solve basic statistical problems through programming

• Visualize data using standard tools and programmatically

• Apply linear models to solve common biological problems

• Perform basic NGS (Next-Generation Sequencing) analyses

• Compare large-scale datasets using standard methods

• Demonstrate proficiency in evaluating and interpreting sequence comparison results and the phylogenetic relationships derived from such comparisons

Judgement and approach:

• Assess when the FAIR principles should be applied

Form of instruction

The course includes recorded lectures covering both theoretical concepts and practical workflows, as well as individual assignments. Great emphasis is placed on hands-on practice through individual tasks with step-by-step instructions. A large portion of the course is delivered online via recorded lectures. Students may complete the individual exercises remotely, but teacher-led sessions are also offered where they can work on the assignments.

The language of instruction is English.

Examination modes

The course is assessed through an individual written exam conducted on campus, and the final grade is based on the evaluation of this exam. For students enrolled in engineering programmes, the grading scale is Fail (U), Pass (3), Pass with Merit (4), and Pass with Distinction (5). For other students, the grading scale is Fail (U), Pass (G), and Pass with Distinction (VG).

The course coordinator may decide that active participation in non-mandatory tasks, case studies, or discussion forums will award bonus points to be added to the exam score, not exceeding 10% of the total exam points. It is the responsibility of the course coordinator to inform students at the start of the course which activities offer bonus points and the criteria for earning them.

For students who have not been approved at the regular exam, a new exam will be arranged in accordance with Umeå University's Rules for grades and examinations at undergraduate and advanced level (FS 1.1-574-22). The first re-exam is offered no later than two months after the regular exam. In the cases where the regular exam takes place in May or June, a first re-examination is offered instead within three months of the regular exam. In addition, at least one further re-examination is offered within one year from the regular exam date. If the result is Fail, the student is then referred to the exam the next time the course/module is given.

A student who has failed two examinations for a course or part of a course without a passing result, has the right to have another examiner appointed, unless there are special reasons against it (HF ch. 6 § 22). The request for a new examiner is made to the Deputy Head of the Department of Molecular Biology.

Examiners may decide to deviate from the modes of assessment in the course syllabus. Individual adaption of modes of assessment must give due consideration to the student's needs. The adaption of modes of assessment must remain within the framework of the intended learning outcomes in the course syllabus. Students who require an adapted examination must submit a request to the department holding the course no later than 10 days before the examination. The examiner decides on the adaption of the examination, after which the student will be notified.

Other regulations

The student has the right to be tested if previous education or corresponding knowledge and skills acquired in professional activities can be credited for the corresponding education at Umeå University. The application for credit is sent to the Studentcentrum. More information about credit transfer can be found on Umeå University's student website and in the Higher Education Ordinance (ch. 6).

Transitional provisions

In the event that the syllabus ceases to apply or undergoes major changes, students are guaranteed at least three examinations (including the regular examination opportunity) according to the regulations in the syllabus that the student was originally registered on for a period of a maximum of two years from the time that the previous syllabus ceased to apply or that the course ended.