Admission requirements
Core course in MSc Bioinformatics and MSc Life Science and Technology, elective course MSc Chemistry
Assumed/Recommended prior knowledge
Students should be familiar with fundamental concepts in molecular biology. Programming experience is useful, but not required.
Description
The course will cover the methods, algorithms and practical aspects of bioinformatics for omics data analysis, with a particular focus on human health and disease. The following topics will be covered:
a) bioinformatics data resources (global and FAIR data sharing for omics data)
b) computational analyses of genomic data (genome sequencing approaches, genome assembly, de novo sequencing, resequencing and variation analysis),
c) computational analyses of RNA and protein data (RNA-Seq and microarray analyses, RNOmics, pathway analysis, functional enrichment/over-representation and protein-protein interaction networks)
d) medical informatics (computational analyses of omics data in rare and complex disease studies, principles and problems for managing and sharing patient data)
Course objectives
At the end of the course, students will be able to:
- Make use of global public bioinformatics data resources, identifying and linking data to answer biomedical research questions
- Explain the FAIR data principles (i.e. that data should be Findable, Accessible, Interoperable and Reusable) and the role FAIR plays in data reuse and reproducibility
- Discriminate between different approaches to analysing genomic and transcriptomics data (in the context of the data and research question)
- Discriminate between different approaches to “downstream analyses” – using structured knowledge resources, such as ontologies and biological pathway databases, to interpret omics results
- Explain the consequence and significance of the genomic revolution on biomedical research and human health
- Design and execute a bioinformatics workflow to analyse and evaluate the consequences of genomic variants from an individual
- Critically assess published peer-reviewed research by reanalysing and evaluating results against the original outcomes
Timetable
The most recent timetable can be found at the Computer Science (MSc) student website.
In MyTimetable, you can find all course and programme schedules, allowing you to create your personal timetable. Activities for which you have enrolled via MyStudyMap will automatically appear in your timetable.
Additionally, you can easily link MyTimetable to a calendar app on your phone, and schedule changes will be automatically updated in your calendar. You can also choose to receive email notifications about schedule changes. You can enable notifications in Settings after logging in.
Questions? Watch the video, read the instructions, or contact the ISSC helpdesk.
Note: Joint Degree students from Leiden/Delft need to combine information from both the Leiden and Delft MyTimetables to see a complete schedule. This video explains how to do it.
Mode of instruction
Lectures, practical classes, research paper seminars and assignments.
Assessment method
The course will be assessed by written examination (50%) and two practical assignments (25% each).
The examination contains material from the lectures, practical classes and seminars. It will assess objectives 2-5.
Assignment 1: Development of a scientific workflow to analyse, prioritise and interpret variant data from an individual human genome (25%). This assignment will assess the course objectives 1, 3, 6 and 7
Assignment 2: Reanalysing published omics data (25%). This assignment will assess objectives 1, 2, and 7. You will need to critically assess your results against those published, to determine your confidence in the original findings and limitations in the study design, reproducibility and FAIRness.
In order to pass the course, marks for the exam and combined assignments must be at least 5.5.
Students will be permitted to retake one of the two assignments during the exam retake period if they do not receive a passing grade during the course.
Reading list
- Current bioinformatics literature referenced in the lectures and practical sessions
Registration
As a student, you are responsible for enrolling on time through MyStudyMap.
In this short video, you can see step-by-step how to enrol for courses in MyStudyMap.
Extensive information about the operation of MyStudyMap can be found here.
There are two enrolment periods per year:
Enrolment for the fall opens in July
Enrolment for the spring opens in December
See this page for more information about deadlines and enrolling for courses and exams.
Note:
It is mandatory to enrol for all activities of a course that you are going to follow.
Your enrolment is only complete when you submit your course planning in the ‘Ready for enrolment’ tab by clicking ‘Send’.
Not being enrolled for an exam/resit means that you are not allowed to participate in the exam/resit.
Contact
Remarks
Software
Starting from the 2024/2025 academic year, the Faculty of Science will use the software distribution platform Academic Software. Through this platform, you can access the software needed for specific courses in your studies. For some software, your laptop must meet certain system requirements, which will be specified with the software. It is important to install the software before the start of the course. More information about the laptop requirements can be found on the student website.