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Course module: 8CM00
8CM00
Systems biology
Course info
Course module8CM00
Credits (ECTS)5
Category-
Course typeGraduate School
Language of instructionEnglish
Offered byEindhoven University of Technology; Biomedical Engineering; Computational Biology;
Is part of
Systems and Control
Contact personprof.dr.ir. N.A.W. van Riel
Telephone5506
E-mailn.a.w.v.riel@tue.nl
Lecturer(s)
Co-lecturer
dr.ir. H.M.M. ten Eikelder
Other course modules lecturer
Co-lecturer
prof.dr. P.A.J. Hilbers
Other course modules lecturer
Subject matter expert
prof.dr.ir. N.A.W. van Riel
Other course modules lecturer
Contactperson for the course
prof.dr.ir. N.A.W. van Riel
Other course modules lecturer
Responsible lecturer
prof.dr.ir. N.A.W. van Riel
Feedback and reachability
Other course modules lecturer
Academic year2017
Period
GS1  (04/09/2017 to 12/11/2017)
Starting block
GS1
TimeslotD: D - We 5-8, Th 9-10, Fr 1-4
Course mode
Fulltime
Remarks-
Registration openfrom 15/06/2017 up to and including 27/08/2017
Application procedureYou apply via OSIRIS Student
Explanation-
Registration using OSIRISYes
Registration open for students from other department(s)Yes
Pre-registrationNo
Waiting listNo
Number of insufficient tests-
Number of groups of preference0
Learning objectives
Insight in typical properties of complex, biochemical networks, like robustness.
  1. Static representation and analysis of biological pathways as graphs (degree distribution, hubs, distance metrics, cluster coefficient).
  2. Analysis and prediction of the influence of network structure (topology, modularity, feedback) and kinetic parameters on system dynamics. Estimation of model parameters from experimental data (inverse problem) and how experiments can be designed to yield (optimally) informative data.
  3. Stochastic models; understanding the difference with deterministic descriptions; modeling and simulation.

The methods will be applied to examples from ongoing research related to metabolic networks and signal transduction pathways. In particular, type 2 diabetes will be discussed.
Content
Sequence alignment, Hidden Markov Models, graph theory.

State space models (system of coupled differential equations) of biochemical networks: modeling with enzyme kinetics, implementation and simulation in Matlab. Parameter sensitivity analysis, including global sensitivity analysis. Parameter estimation and uncertainty analysis

Stochastic models: master equation, Gillespie simulation algorithm.
Entrance requirements
You must have completed the final examination bsc program exam
Entrance requirements tests
-
Assumed previous knowledge
• 8CA00 - Bio informatics
• 8CB10 - Simulation of biochemical systems
• 8CB20 - Synthetic and systems biology
Previous knowledge can be gained by
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Resources for self study
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Bachelor College or Graduate School
Graduate School
Required materials
-
Recommended materials
Cytoscape - Provided during course.
Matlab 2013 / 2014 a en 2014b
Matlab (optimization toolbox)
Instructional modes
Guided selfstudy

General
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Remark
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Lecture

General
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Remark
-
Tests
Assignment
Test weight100
Minimum grade6
Test type-
Number of opportunities1
OpportunitiesBlock GS1
Test duration in minutes-

Assessment
-

Remark
-

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