Molecular Data Science: from disease mechanisms to personalized medicine
Focus of the course: Molecular Epidemiology in Ageing research
Biomedical research increasingly involves the generation and analysis of very large data sets whether it is whole-genome DNA sequencing, gene expression, or magnetic resonance imaging data. In particular, large-scale data will be the cornerstone of personalized medicine. This course is aimed at biomedical students who not only want to be responsible for the generation of large-scale data in their future projects, but also want to be able to analyse and interpret their own data.
Literature and documents for study assignments will be handed out during the course.
Coordinators
Bas Heijmans, Molecular Epidemiology; 071-526 69785, b.t.heijmans@lumc.nl
Ingrid Meulenbelt, Molecular Epidemiology; 071-526 9734, i.meulenbelt@lumc.nl
Location
Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden: Room J1-84 at the main building.
For the practicals, computers in J1-84 will be used.
Storing valuables
Store valuables, especially during breaks, in one of
the lockers available for library users, located on the left of the
library entrance.
Assessment plan
- Handing in assignments (Pass/Fail, individually assessed).
- Contribute to interim evaluation of student participation and development during workgroups (0%).
- Fill out project proposal form as preparation for reflective assignment (0%).
- Presentation project proposal (background, hypothesis, pilot data, objectives, study design, workplan, expected outcomes; 45%, assessed in duos).
- Active and critical participation during discussion after project presentations of peers (15%, individually assessed).
- Reflective assignment that shows mastering key aspects of development of research proposal in molecular data science and addressing points raised during peer review (40%, individually assessed).
Overall the evaluation will be a score between 0-10 composed of a weighted average of the different modules.
Part 1: Acquiring Knowledge and Skills
Students will gain knowledge of the different study designs used in investigations, with a focus on complex diseases. In the practicals, students will acquire skills (bioinformatic and statistical tools) that will enable them to analyse large datasets of genetic, gene expression, and phenotypic data, to identify patterns in this data, and match results with existing biological information to form new hypotheses.
Week 1
Monday October 21 (Location J1-84/building 1, LUMC)
Tuesday October 22 (Location J1-84/building 1, LUMC)
Wednesday October 23 (Location J1-84/building 1, LUMC)
Thursday October 24 (Location J1-84/building 1, LUMC)
Friday October 25 (Location J1-84/building 1, LUMC)
Week 2
Monday October 28 (Location J1-84/building 1, LUMC)
Tuesday October 29 (Location J1-84/building 1, LUMC)
Wednesday October 30 (Location J1-84/building 1, LUMC)
Thursday October 31 (Location J1-84/building 1, LUMC)
Friday November 1 (Location J1-84/building 1, LUMC)
Week 3
Monday November 4 (Location J1-84/building 1, LUMC)
Tuesday November 5 (Location J1-84/building 1, LUMC)
When |
What: Databases and Reproducibility |
Who |
Where |
09.00-10.00 |
Lecture: Databases |
Bas Heijmans |
J1-84 |
10.00-10.15 |
Break |
|
|
10.15-12.30 |
Practical: Using Online Databases: Age and Methylation |
Bas Heijmans |
J1-84 |
12.30-13.30 |
Lunch |
|
|
When |
What: Animal models on ageing |
Who |
Where |
13.30-14.00 |
Lecture: Mouse model of Ageing |
Vered Raz |
J1-84 |
14.00-15.15 |
Self Study: Mouse model of Ageing |
Vered Raz |
J1-84 |
15.15-15.30 |
Break |
|
|
15.30-17.00 |
Mouse model of Ageing: Presentation and Discussion |
Vered Raz |
J1-84 |
Wednesday November 6 (Location J1-84/building 1, LUMC)
When |
What: Research Findings |
Who |
Where |
09.00-10.00 |
Free |
Self |
### |
10.00-10.15 |
Break |
|
|
10.15-12.30 |
Free |
Self |
### |
12.30-13.30 |
Lunch |
|
|
13.30-15.00 |
From Ideas to Study: Vandenbroucke and Pearce (2018) |
Suzanne Cannegieter |
V5-39 |
15.00-15.15 |
Break |
|
|
15.15-17.00 |
From Ideas to Study: Vandenbroucke and Pearce (2018) |
Suzanne Cannegieter |
V5-39 |
Part 2: Applying Acquired Knowledge and Skills to Ageing.
Students will apply newly acquired skills to write a research proposal that follows a data science approach. This proporal will focus on ageing as a key example of a complex human trait. Students will work on developing a project proposal in pairs. Generating pilot data to support hypotheses by analyzing available real -omics data sets will be an integral part of the project proposal. During the week, there will be regular moments of interaction with the module coordinators and the opportunity to contact other tutors of the course.
Thursday November 7 (Location J1-84/building 1, LUMC)
When |
What: Introduction to Developing Project Proposal |
Who |
Where |
09.00-10.00 |
Project Proposal: Where does Research Start. Part 1 |
Eline Slagboom |
J1-84 |
10.00-10.15 |
Break |
|
|
10.15-11.00 |
Project Proposal: Where does Research Start. Part 2 |
Eline Slagboom |
J1-84 |
11.00-12.00 |
Work on the Project Proposal: Formulation of Hypothesis |
Self |
J1-84 |
12.00-13.00 |
Lunch |
|
|
13.00-15.00 |
Work on the Project Proposal: Formulation of Objectives |
Self |
J1-84 |
15.00-15.15 |
Break |
|
|
15.15-17.00 |
Work on the Project Proposal: Formulation of Objectives |
Self |
J1-84 |
Friday November 8 (Location J1-84/building 1, LUMC)
When |
What: Final assignment |
Who |
Where |
09.00-17.00 |
Work on the Project Proposal |
Self |
J1-84 |
Monday November 11 (Location J1-84/building 1, LUMC)
When |
What: Final assignment |
Who |
Where |
09.00-17.00 |
Work on the Project Proposal |
Self |
J1-84 |
Tuesday November 12 (Location J1-84/building 1, LUMC)
When |
What: Final assignment |
Who |
Where |
09.00-17.00 |
Work on the Project Proposal |
Self |
J1-84 |
Wednesday November 13 (Location J1-84/building 1, LUMC)
Thursday November 14 (Location J1-84/building 1, LUMC)
When |
What: Final assignment |
Who |
Where |
09.00-12.30 |
Work on the Project Proposal |
Self |
J1-84 |
12.00-13.00 |
Lunch |
|
|
13.00-17.00 |
Oral Presentation and Defense of Project Proposal |
All |
V3-18/22 |
Friday November 15 (Location J1-84/building 1, LUMC)
When |
What Final assignment |
Who |
Where |
09.00-13.00 |
Self study |
Self |
J1-82 |
13.00-15.00 |
Reflective Assignment |
All |
J1-82 |
15:00 |
End of course |
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