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Education

Systems Biology education is currently integrated into three Bachelor’s and two Master’s courses. PhD students and post-docs may attend the Master’s courses. Links to further information are given below.

The Bachelor’s course "Aspects of Molecular Life Sciences" provides students with a first introduction of how mathematical computer models can be used to understand complex dynamic non-linear systems. The focus lies on practical model-construction and simulation of key biological systems like oscillatory intracellular calcium signaling, protein phosphorylation and dephosphorylation and exocytosis.
The Bachelor’s course "Biochemistry inside the living cell" provides students with the key concepts of cellular energy homeostasis (glycolysis, TCA cycle, oxidative phosphorylation). Next, the basic principles of fluorescence, live cell microscopy and fluorescent reporter molecules are introduced. The obtained knowledge is then applied in practical experiments using live-cell microscopy and bioluminescence of healthy cells and cells from patients and mice with a mitochondrial disorder.
The Bachelor’s course "Comparative genomics" focuses on how genomic information can be used to gain a better understanding of biological processes and/or provide predictions concerning protein function. This includes the relevance of protein interaction data in the prediction of which proteins are involved in diseases.

At the Master’s level, two courses are taught: "Cellular imaging in four dimensions" and "Principles of Systems Biology" (the latter starts in January 2011).

In "Cellular imaging in four dimensions" students are taught the fundamentals and applications of advanced cellular imaging techniques in biomedical research and provides the students with practical examples of ongoing research. Topics include: introduction to microscopy, advanced microscopy techniques, protein-based reporter molecules, chemical reporter molecules, image processing and quantification, analysis of molecular complexes in cellular signal transduction, imaging of intracellular protein routing in health and disease, mitochondrial shape and function in metabolic disease, dynamic imaging of cancer, analysis of cellular import and residence time and breakdown of potential therapeutic molecules.
In "Principles of Systems Biology" students obtain insight into the fundamental concepts and applications of Systems Biology at the theoretical and practical level, with emphasis on human metabolism. Lectures will be given by core members of the Centre for Systems Biology and Bioenergetics and invited (external) lecturers. The biological focus will be on how systems biology approaches can help to understand human metabolism in health and disease. The course is divided in four main parts: biological systems, model types, modeling skills, and 'special topics'. This includes lectures about: metabolism, signal transduction, many particle models, kinetic models, dynamical systems, optimization and control theory, structural and stoichiometric models, deterministic kinetic and spatial models, stochastic dynamics, model building, model reduction and combination, data collection and statistical analysis, parameter selection and optimization, model testing and selection, local sensitivity/control theory and global sensitivity/uncertainty analysis, optimal control, spectral unmixing, machine learning and pattern recognition, nutraceuticals, drug discovery, adverse drug effects, and mitochondrial medicine.


A. Bachelor’s level

(I) "Aspects of Molecular Life Sciences"
Dr. P.H.G.M. Willems, Dept. of Biochemistry (286) NCMLS, RUNMC.
Dr. W.J.H. Koopman, Dept. of Biochemistry (286) NCMLS, RUNMC.

(II) "Biochemistry inside the living cell"
Dr. P.H.G.M. Willems, Dept. of Biochemistry (286) NCMLS, RUNMC.
Dr. W.J.H. Koopman, Dept. of Biochemistry (286) NCMLS, RUNMC.
 
(III) "Comparative genomics"
Prof. Dr. M.A. Huynen, Centre for Molecular and Biomolecular Informatics, Radboud University.

B. Master’s level

(I) "Cellular imaging in four dimensions"
Dr. P.H.G.M. Willems, Dept. of Biochemistry (286) NCMLS, RUNMC.
Dr. W.J.H. Koopman, Dept. of Biochemistry (286) NCMLS, RUNMC.
Dr. J.A.M. Fransen, Dept. of Cell Biology NCMLS, RUNMC.
 
(II) "Principles of Systems Biology"

Dr. W.J.H. Koopman, Dept. of Biochemistry (286) NCMLS, RUNMC
Prof. Dr. L.M.C. Buydens, Dept. of Analytical Chemistry IMM, Radboud University.