Bioinformatics and Genome Analysis, 7.5 credits

Contents

The course is an introduction to bioinformatics and provides fundamental skills in bioinformatics. The course covers basic information retrieval, common bioinformatics algorithms, the Linux command line, the use of Python for statistical analysis and visualization, analysis of bioinformatics and genomics data and tools for data integration.

The course consists of two modules: Theory (4.5 ECTS) and Group Project (3 ECTS). The theory module covers fundamental bioinformatics algorithms and resources, as well as their applications and the interpretation of results. The group project builds on the theory module and consists of a research project integrating protein bioinformatics and cancer genomics data. The group project also includes a written report and an oral presentation.

Expected learning outcomes

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

Knowledge and understanding:

• Demonstrate the ability to use common databases such as NCBI, UniProt, and PDB for biological data
• Demonstrate understanding of how different types of biological data are stored in computers
• Show knowledge of common tools used in bioinformatics and genomics
• Explain how fundamental bioinformatics algorithms work
• Describe 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
• Use Python for statistical analysis and data visualization
• Show awareness of which bioinformatics tools, data, and formats are required for common tasks
• Interpret and integrate different types of bioinformatics results in a biological context
• Perform sequence 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

Required Knowledge

30 ECTS credits from completed courses in chemistry, mathematics and mathematical statistics, including at least 5 ECTS credits each in biochemistry, linear algebra and mathematical statistics; 35 ECTS credits from completed courses in biology, including at least 15 ECTS credits in cell and molecular biology and at least 5 ECTS credits in molecular genetics; and 5 ECTS credits in programming (Python).

Form of instruction

The course includes both on-campus and recorded lectures. In addition to theoretical content, considerable emphasis is placed on practical training through individual assignments, group assignments, and interpretation of results within the theory module. Some of the learning takes place through group-based assignments in which students apply bioinformatics methods. The course also includes a larger group project in which students carry out a research project. The research project includes a literature review, report writing, and an oral presentation. Teacher-led sessions are offered, during which students can actively work on the assignments and the group project.

The language of instruction is English.

Examination modes

The course is assessed through an individual written on-campus examination and written and oral assessment of group work. The group work is examined as a group, but students are assessed individually. The written examination is graded Fail (U), Pass (G), or Pass with Distinction (VG). The group work is graded Fail (U) or Pass (G). A final grade for the course is awarded only after all assessed components have been completed and graded. To receive a Pass (G) for the course, all assessments must be awarded at least a Pass (G). To receive a Pass with Distinction (VG) for the course, the student must, in addition to passing the group work, receive a Pass with Distinction (VG) on the written examination.

In case of absence from a mandatory teaching session, the examiner will decide whether the student should complete a replacement assignment or retake the component at a later date.
To pass the course, all assignments must be completed in accordance with the specified requirements.

The course coordinator may decide that active participation in non-mandatory taskswill 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. Bonus points may be applied to the regular examination and to the two re-examination opportunities offered before the next time the course runs.

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.

For students who have been granted recommended support due to a disability, the examiner may decide to make exceptions to the form of assessment specified in the course syllabus. Individual adaptations of the assessment method should be considered based on the student's needs and the intended learning outcomes of the course. For further information, please refer to the Procedures for support for students with disabilities and the Rules for grades and examination at first- and second-cycle studies.

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).

The course cannot be included in a degree together with the course Introduction to Bioinformatics.

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.