Course syllabus for Bioinformatics

Bioinformatik

Specific entry requirements

A Bachelor's degree or a professional degree worth at least 180 credits in biomedicine, biotechnology, cellular and molecular biology, medicine, or the equivalent. Proficiency in English equivalent to the Swedish upper secondary school course English 6/English B.

Outcomes

On completion of the course, the student should be able to:

Knowledge and understanding:
- Demonstrate knowledge and understanding of the scope of the field of bioinformatics
- Describe research questions and problems in biomedicine where bioinformatics analyses are employed, and how bioinformatics tools can contribute to the general knowledge of biological systems
- Explain the theoretical background and the rationale underlying basic bioinformatics methods
- Relate bioinformatics analysis to a systems biology approach to biomedical research questions
- Describe basic principles in good research practice and Health Data Management

Competence and skills
- Define biomedical research questions involving the use of bioinformatics data, and design a bioinformatics based approach for data collection and analysis
- Critically assess and evaluate different approaches and methods employed inbioinformatics analyses of data
- Plan experimental designs and critically evaluate the appropriateness of the different methods and technologies (such as different sequencing methods for nucleic acids) for collecting data for bioinformatics analysis
- Apply and integrate bioinformatics resources and tools to answer a biomedical question
- Apply basic programming skills in analysing datasets

Judgement and approach
- Critically reflect on the opportunities, limitations and ethical challenges posed by advances in bioinformatics as part of health data science
- Demonstrate knowledge of the emerging challenges and opportunities of bioinformatics in a societal context, for example in a global health or sustainable development perspective

Content

This course covers central knowledge and skills in bioinformatics used in biomedical research, including critical analysis and application of different approaches and tools to collection and data analysis. Bioinformatics is discussed as a field that combines a broad set of knowledge and tools from different disciplines, with the aim of understanding complex biological and biomedical systems by analysing and understanding different types of data produced in biological and biomedical research. The focus is very much on the basic practical tools for analysis of sequence and gene expression data including basic programming skills, genomics and general bioinformatics-based structure and structural and functional analysis of biomolecules. Biomedical applications include simulated DNA- and RNA-sequencing processes and simulated design and analysis of CRISPR-modified organisms. Definition of research problems and evaluation of different research methods and approaches are studied in the context of research ethics, GDPR, good scientific practice, scientific communication and public and global health perspecties. Basic concepts of teamwork and project membership and management are integrated in the Team Based Learning parts of the course.

Teaching methods

The learning and teaching activities include hybrid learning activities and Team Based Learning activities, including small and large group sessions. There are lectures, lessions, demonstrations, data practicals, writtten and oral communication excercises. The parts of the course with Team Based Learning include peer learning and team work elements.

Examination

The examination consists of three parts:

- individual ethical reflection, written assignment
- individual analysis of unknown sequence data, "Mystery DNA sequence", written assignment
- individual written exam, summative examination

To pass the whole course all three parts must have been passed. All three parts contribute to the course grade, graded Fail/Pass/Pass with distinction.

Compulsory participation
Participation in data practicals and TBL modules is obligatory.

The examiner assesses if and, in that case, how absence from compulsory components can be compensated. The student must participate in all compulsory parts or compensate for absence in accordance with the examiner's instructions, in order to pass the course. Absence from a compulsory activity may result in the student not being able to compensate the absence until the next time the course is given.

Limited to the number of examinations sessions
A student who does not pass an examination at their first attempt is entitled to participate in five additional examination sessions. If the student does not pass after four examinations, he/she is recommended to retake the course at the next regular course occasion, and may, after that, participate in two more examination sessions. If the student has failed six examinations, no additional examination sessions are provided.

Physically attending or otherwise commencing an examination is regarded as an examination session. Handing in a blank exam is considered taking part in an examination session. An examination, for which the student registered but did not participate, is not counted as an examination session.

Adaption of examination
If there are special grounds, or a need for adaptation for a student with a disability, the examiner may decide to deviate from the syllabus's regulations on the examination form, the number of examination opportunities, the possibility of supplementation or exemptions from the compulsory section/s of the course etc. Content and learning outcomes as well as the level of expected skills, knowledge and abilities may not be changed, removed or reduced.

Other directives

The course is given in English, and examination is in English.

Course evaluation will be carried out in accordance with the guidelines established by the Committee for Education.