Omics - Analysis of Large-scale Biomolecular Datasets
Omik - analys av storskaliga biomolekylära dataset

KIMN20, 7.5 credits, A (Second Cycle)

Valid for: 2024/25
Faculty: Faculty of Engineering LTH
Decided by: PLED B/K
Date of Decision: 2024-04-17
Effective: 2024-05-08

General Information

Main field: Biotechnology Depth of study relative to the degree requirements: Second cycle, in-depth level of the course cannot be classified
Elective for: B5-mb, K5, MBIO2, MLAK2
Language of instruction: The course will be given in English

Aim

The aim of this course is to convey basic knowledge and a broad understanding of usage of different types of large scale parallel molecular analysis techniques, so called "omics" and the data that these techniques generate

Learning outcomes

Knowledge and understanding
For a passing grade the student must

• be able to describe the basic methods for genomics, transcriptomics, proteomics and metabolomics as well as methods for corresponding methods for analysis of single cells and analyses with spatial resolution.
• be able to describe how omics can be used within biological and medical applications.
• be able to describe possibilities and limitations of usage of omics methods.
• be able to describe how omics can be used to understand function of biological systems.
• be able to give an overview of the most common omics data formats.
• be able to describe possibilities and challenges regarding integration of data from multiple omics experiments.
• be able to describe qualitative aspects of omics methodology and how experimental setup and data analysis strategies can affect the outcome of analyses.

Competences and skills
For a passing grade the student must

• be able to perform basic analyses of omics data.
• be able to programmatically handle quantitative data matrices from omics experiments.
• be able to present quantitative omics analyses in a formally correct way in a report.

Judgement and approach
For a passing grade the student must

• be able to evaluate the possibilities of omics techniques to answer biological questions

Contents

The course will include lectures covering:

• Techniques for genomic, transcriptomic, proteomic and metabolomic analyses
• Handling and analysis of data from omics experiments
• Functional analyses and biomarker discovery
• Integration of omics data from different experiments
• Techniques for omics analysis of single cells and spatially resolved analyses

The course will also include:

• Study visit at infrastructure for omics analysis
• Computer laborations within processing and analysis of omics data
• An omics data analysis project

Examination details

Grading scale: TH - (U, 3, 4, 5) - (Fail, Three, Four, Five)
Assessment:

Attendance in compulsory lectures and active participation in compulsory laboratory moments and projects. Reporting of laboratory work and project. Ordinary examination is written. Re-examination is written or individual oral examination (as defined by the examiner). The final grade is based on the written or oral examination.

The examiner, in consultation with Disability Support Services, may deviate from the regular form of examination in order to provide a permanently disabled student with a form of examination equivalent to that of a student without a disability.

Modules
Code: 0124. Name: Practical.
Credits: 3.0. Grading scale: UG - (U, G). Assessment: Computer laboratory work and reporting thereof. Active participation in project sessions, including reporting. The module includes: Computer laboratory work and reporting thereof. The laboratory work will involve methods used for processing and analysis of omics data. Project work. The projects will involve analysis of omics data and literature.
Code: 0224. Name: Theory.
Credits: 4.5. Grading scale: TH - (U, 3, 4, 5). Assessment: Attendance at mandatory lectures and study visits. Written or oral examination. The module includes: Lectures and study visits about omics

Admission

Admission requirements:

• ((EXTA70 Biology of the Cell or KBK011 Biochemistry or KBKA05 Technical Biology or KBKA10 Biochemistry or KBKF05 Cell biology or KBKF15 Biochemistry or TEK295 Biology of the Cell) and EDAA70 Introduction to Programming Using Python) or KBTN20 Molecular Biotechnology

Reading list

• The course literature consists of lecture, exercise and computer laboratory materials that are updated yearly. There is also a collection of references and links to further reading that are freely available.

Contact

Course coordinator: Fredrik Levander, fredrik.levander@immun.lth.se
Teacher: Peter Spégel, peter.spegel@chem.lu.se
Examinator: Fredrik Levander, fredrik.levander@immun.lth.se
Director of studies: Kathrin Zeller, kathrin.zeller@immun.lth.se