Advanced Bioinformatics, 7.5 credits

Contents

The course is given in the form of a “case study”. After a presentation of the cases, the students should work independently, with access to supervision. Implementation of solutions should be made according to modern methods and workflows that applied within the field of bioinformatics. Teaching material for learning these methods will be made available, but also methods from prerequisite courses will be used. The course places heavy emphasis on how the problem is solved as a means of teaching a professional problem-solving approach. The solutions will be presented at the end of the course.

Expected learning outcomes

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

Knowledge and understanding:
• Demonstrate understanding of the principles and practices involved in planning, executing, and evaluating advanced bioinformatics projects.

Competence and Skills:
• plan and execute an advanced bioinformatics project and critically evaluate the quality of the result
• use version control to manage the development process and collaborate with other bioinformaticians
• present results for users through interactive visual tools
• manage intellectual property rights and apply common licenses
• document bioinformatic code using standardized methods
• produce code following accepted guidelines, and with high modularity
• integrate large-scale datasets to draw conclusions about biology
• construct and use a database for bioinformatic problem solving
• present the project orally and written, in English
• critically evaluate, motivate and argue for solutions in own code and other groups projects, in English

Judgement and approach:
• identify one's own learning needs and take responsibility for one's own learning

Required Knowledge

90 ECTS from completed courses including at least 15 ECTS from a combination of courses in programming and bioinformatics, out of which 7.5 ECTS must be programming.

Form of instruction

The course is given in the form of a case study where students work in groups to solve a larger biological problem with the use of bioinformatics. The study materials primarily consist of scientific articles, tutorials, and pre-recorded lectures. Students have access to supervision throughout the course. The course is taught in English but may be taught in Swedish if there’s no need for English.

Participants are expected have access to their own computer with a Unix-like operating system (e.g., OSX, Linux, or Ubuntu-in-windows).

Examination modes

Students work and are assessed in groups, but with individual evaluation. The course is examined through an oral presentation and continuous monitoring of the group’s progress, where individual contributions are tracked using version control systems.

All expected learning outcomes are assessed during the oral presentation, which is graded as either Pass (G) or Fail (U). The practical work is assessed based on specified evaluation criteria provided at the beginning of the course. Active group members are awarded points according to these criteria, and final grades are determined based on the total number of points accumulated by the end of the course. To receive a passing grade for the course (3 or G), the oral presentation must be approved. To achieve a grade of Pass with Distinction (5), students must obtain at least 90% of the total points; for Pass with Merit (4), at least 70%; and for Pass (3), at least 50%. In the alternative grading scale, Pass with Distinction (VG) requires 80%, and Pass (G) requires 50%. If groups of deviating sizes are formed, adjusted point thresholds will be established at the beginning of the course.

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.