SSB-30306 Systems Biology: From Omics to Integrative Biological Networks
Code last year: (MIB-31806)
Course
Credits 6.00
Teaching method | Contact hours |
Lectures | 36 |
Literature study | 12 |
Practical intensively supervised | 76 |
Problem-based learning | 22 |
Self-study | 14 |
Course coordinator(s) | dr. PJ Schaap |
Lecturer(s) | dr. PJ Schaap |
prof. dr. D Weijers | |
prof. dr. SC de Vries | |
dr. ir. CA Maliepaard | |
Examiner(s) | prof. dr. SC de Vries |
prof. dr. VAP Martins dos Santos |
Language of instruction:
English
Assumed knowledge on:
Basic knowledge of statistics, Microbiology & Biochemistry or Gentechnology and Bioinformation Technology
Continuation courses:
-Toolbox Systems@work, Toolbox Molecular Biology
Contents:
Nowadays increasing numbers of complete genomic sequences are available and methods have been developed to study system wide gene expression, protein interaction and metabolite formation. Systems biology integrates the results of the different ~omics techniques in order to understand how they work together using special analysis and visualization techniques to extract relevant information for elucidating the function of genes, proteins and metabolites, the interactions between these molecules and the underlying regulatory mechanisms. The course is modular and focuses on data generation, mining, analysis and visualisation and data integration.
Learning outcomes:
Knowledge (of):
- micro array data handling specifically: Data Pre-processing, background subtraction, Log transformation;
- variation Control: Experimental design, Normalisation methods and Scaling;
- metabolomics data handling specifically: Sampling variation and biases and sampling methods GC-MS, LC-MS, NMR, FTIR;
- metabolomics data Output processing, Baseline correction, Peak assignment.
Skills:
- an ability to preproces and analyze microarray and metabolomics data;
- an ability to understand and interpret mass spectrometry datasets of proteins;
- an ability to synthesise 'omics' information with respect to the biological questions.
Activities:
Hands on course, lectures, training and study of relevant literature, programming in R.
Examination:
20%: Written reports on the results obtained from the exercises and 80%: Written examination (open book/internet).
Literature:
During the course, literature and exercises will be available at http://www.systemsbiology.nl.
Programme | Phase | Specialization | Period | ||
---|---|---|---|---|---|
Restricted Optional for: | MBF | Bioinformatics | MSc | 3WD |