91̽»¨

This course is part of the Master’s program in Bioinformatics. The course can also be taken as a freestanding course.

For admission to the course, at least 120 credits (or equivalent) in any of the following fields: natural sciences (including mathematics), medicine or pharmacy.

It is required to have a basic coding proficiency (recommended: Python) such as from the course BIO511 (or equivalent).

Further, the course BIO512 (or equivalent) is recommended.

In addition, English proficiency is required to the level of English 6/English Course B from Swedish Upper Secondary School, or be certified by an internationally recognized test, for example TOEFL or IELTS or equivalent.

The course offers an in-depth exploration of Systems Biology, focusing on various 'omics' technologies, such as proteomics, that rely on mass spectrometry to measure and quantify biomolecules, and their applications in biological systems, such as in studying cancer. Mass spectrometry is an advanced analytical technique that helps scientists measure and identify molecules with incredible precision. Throughout the course, you will learn how these mass spectrometry data are generated and analyzed, particularly in areas such as metabolomics (measuring all small molecules in a sample), glycomics (measuring all complex carbohydrates in a sample), or proteomics (measuring all proteins in a sample), as well as learning about newer methods such as single-cell mass spectrometry and machine learning approaches.

The course covers theoretical and practical knowledge in topics ranging from differential abundance analyses (comparing amounts of molecules between different conditions), compositional data analysis (understanding relative proportions of molecules and how these shift in disease), to combining different types of 'omics data. You will also discover how machine learning can help understand biological interactions in practical projects where you will train and use your own models. The knowledge acquired in this course is utilized across the fields of molecular biology, bioinformatics, and systems biology, and holds significant applications in understanding complex biological processes, disease mechanisms, and potential therapeutic interventions. Practical components include hands-on experience with systems biology data analysis, for instance to find out which molecules change abundance between conditions, providing you with essential skills for modern biological research.

The course is divided in sub-courses.

Sub-course 1; Systems biology theory, 7,5 credits

Sub-course 2; Systems biology practical data analysis, 7,5 credits

On successful completion of the course the student will be able to:

Knowledge and understanding

• Describe how mass spectrometry data are generated, processed, and analyzed
• Name and explain bioinformatics approaches used in the analysis of systems biology data
• Integrate ‘omics data to model biological systems
• Explain characteristics of mass spectrometry-driven systems biology data (e.g., proteomics, glycomics, metabolomics)

Competence and skills

• Summarize and present scientific papers
• Analyze systems biology data
• Integrate ‘omics data to model biological systems
• Apply appropriate statistical methodology to answer research questions in systems biology
• Modify common bioinformatic workflows in systems biology to suit specific cases
• Write and utilize Python code to analyze systems biology data
• Apply machine learning/AI to predict biological interactions

Judgement and approach

• Describe different measurement and analyses techniques used in systems biology and assess their strengths and weaknesses
• Assess the quality of a mass spectrometry-derived systems biology dataset
• Devise appropriate analysis workflows to analyze and visualize systems biology data
• Evaluate the significance of scientific results in systems biology

Sub-course 1; This sub-course is based on lectures and seminars to present and discuss literature.

Compulsory parts in the course are the seminars, as shown in the course schedule.

Sub-course 2; This sub-course is based on practical sessions to explore and analyze systems biology data.

Compulsory parts in the course are the practical sessions, as shown in the course schedule.

Sub-course 1; The sub-course ends with a written exam covering the full course. In addition, literature seminars that include presentations and active participation.

Sub-course 2; A report submission (including code) of the practical session

If a student who has been failed twice for the same examination element wishes to change examiner before the next examination session, such a request is to be granted unless there are specific reasons to the contrary (Chapter 6 Section 22 HF).

If a student has received a certificate of disability study support from the University 91̽»¨ with a recommendation of adapted examination and/or adapted forms of assessment, an examiner may decide, if this is consistent with the course’s intended learning outcomes and provided that no unreasonable resources would be needed, to grant the student adapted examination and/or adapted forms of assessment.

If a course has been discontinued or undergone major changes, the student must be offered at least two examination sessions in addition to ordinary examination sessions. These sessions are to be spread over a period of at least one year but no more than two years after the course has been discontinued/changed. The same applies to placement and internship (VFU) except that this is restricted to only one further examination session.

If a student has been notified that they fulfil the requirements for being a student at Riksidrottsuniversitetet (RIU student), to combine elite sports activities with studies, the examiner is entitled to decide on adaptation of examinations if this is done in accordance with the Local rules regarding RIU students at the University 91̽»¨.

Sub-course 1; The grading scale comprises: Pass with Distinction (VG), Pass (G), and Fail (U).

Requirements for Pass (G) is 60% of total points and for Pass with distinction (VG) 85 % of total points for the written exam. In addition, the literature seminars must have pass (G).

Sub-course 2; Requirements for Pass (G) is 60% of total points on the submitted report.

Final grade; To pass the course, 60% of the total points for the theoretical exam is required. For the grade Pass with distinction, 85% of the theoretical part must be correct. In addition, the grade G is required on the literature seminars and sub-course 2 for the final grade.

The results of and possible changes to the course will be shared with students who participated in the evaluation and students who are starting the course.