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Welcome to the Lectures Wiki Netzwerkanalyse SS 2017


The oral exams will take place on Thursday, 20 July 2017, and Friday, 21 July 2017 in room 142, Arnimallee 6.

There is a doodle poll for scheduling the time slots. You may contact Prof. Bockmayr for getting the link.

The course has been rescheduled: Mon 10h15 - 13h45, Friday 9h00 - 10h30

General Information

SWS: 2+2+2 hours, Credits: 10 ECTS

Lecturers: Alexander Bockmayr, Martin Vingron

Tutor: Annika Röhl, Alena van Bömmel

Language: English

Goals: Students acquire a deepened understanding of the basic mathematical and algorithmic concepts in the domain of modeling, simulation, and analysis of molecular networks, in connection with current research problems in systems biology and biotechnology. The students know the basic methods for modeling molecular networks. They are able to analyse a given biological or biomedical question, to choose a suitable modeling approach, to develop their own problem solution, and to analyse and communicate the results.

  • Modeling of biochemical networks with ordinary differential equations
  • Discrete modeling of regulatory networks
  • Constraint-based modeling of metabolic networks
  • Stochastic and hybrid modeling


Time Location
Monday 10h15 - 13h45 Arnimallee 6 SR 025/026
Friday 9h00 - 10h30 Arnimallee 6 SR 025/026

Preliminary Schedule

Date Lecturer Type Topic Material Additional Material
21.04.2017 Bockmayr Lecture Introduction to systems biology Slides Article
  Bockmayr Lecture Continuous modeling:
reaction networks
24.04.2017 Bockmayr Lecture Continuous modeling:
phase plane analysis
Slides Sontag, Chap.2.4+2.6
  Bockmayr Lecture Continuous modeling:
stability analysis
Slides XPP Software
XPP Example
28.04.2017 Röhl Exercises Continuous modeling Exercise 1 COPASI Software
05.05.2017 Bockmayr Lecture Continuous modeling:
stability analysis 2
08.05.2017 Bockmayr Lecture Continuous modeling:
bifurcation analysis
  Röhl Exercises Continuous modeling Exercise 2  
12.05.2017 Szengel,
Gomezgil Yaspik
Seminar Continuous modeling Article1 Article2 Cell Cycle Page
15.05.2017 Bockmayr Lecture Discrete modeling: Slides Article
  Bockmayr Lecture Thomas formalism    
19.05.2017 Röhl Exercises Discrete modeling Exercise 3  
22.05.2017 Bockmayr Lecture Discrete modeling: Slides  
  Bockmayr Lecture Model checking    
26.05.2017 Röhl Exercises Discrete modeling Exercise 4  
29.05.2017 Larina Seminar Discrete modeling Article1 Article2 GINSIM Software
  Bockmayr Lecture Constraint-based modeling Slides Article
02.06.2017 Röhl Exercises Constraint-based modeling Exercise 5 Networks
09.06.2017 Bockmayr Lecture Constraint-based modeling Slides  
12.06.2017 Röhl Exercises Constraint-based modeling Exercise 6  
  Buntrock, Seeler Seminar Constraint-based modeling Article1 Article2 CellNetAnalyzer Software
16.06.2017 Bockmayr Lecture Stochastic modeling Slides1 Slides2 Article Online Lecture
19.06.2017 Vingron Lecture Biological Networks, Correlation, Probability distribution Slides 1  
  Vingron Lecture Information theory    
23.06.2017 Vingron Lecture Partial Correlation Slides 2  
26.06.2017 van Bömmel Exercises   Assignment1
  Bleich, Lüttringhaus Seminar Mutual Information Article
30.06.2017 Novikov, Sarfert Seminar Stochastic modeling Article1 Article2 StochPy Software
03.07.2017 Vingron Lecture   Slides 3  
  Vingron Lecture      
07.07.2017 van Bömmel Exercises   Assignment2
10.07.2017 Vingron Lecture   Slides 4 "Causation, Prediction, and Search" by Spirtes, Glymour and Scheines
  van Bömmel Exercises   Assignment3_final  
14.07.2017 van Bömmel Lecture    
17.07.2017   Seminar      
20/21.07.2017 Oral exams      


Systems biology

Continuous modeling

Discrete modeling

Constraint-based modeling

Stochastic modeling


Für die aktive Teilnahme gilt: Anwesenheit in den Übungen und die regelmäßige Abgabe der Hausaufgaben (50% der Gesamtpunkte in BEIDEN Teilen des Kurses)

For aktive Teilnahme: Being present in the tutorials and hand in the solutions of the exercises (you need to reach at least 50% of the points in BOTH parts of the course)
Topic attachments
I Attachment Action Size Date Who Comment
Assignment1.pdfpdf Assignment1.pdf manage 194.9 K 20 Jun 2017 - 09:41 AlenaVanBMmel  
Assignment2.pdfpdf Assignment2.pdf manage 235.8 K 30 Jun 2017 - 09:14 AlenaVanBMmel  
Assignment3_final.pdfpdf Assignment3_final.pdf manage 247.1 K 10 Jul 2017 - 12:04 AlenaVanBMmel  
Seminar_Mutual_Information.pdfpdf Seminar_Mutual_Information.pdf manage 514.0 K 28 Jun 2017 - 11:56 AlenaVanBMmel  
networks-lecture1.pdfpdf networks-lecture1.pdf manage 297.5 K 20 Jun 2017 - 09:45 AlenaVanBMmel  
networks-lecture2.pdfpdf networks-lecture2.pdf manage 199.3 K 28 Jun 2017 - 11:52 AlenaVanBMmel  
networks-lecture3.pdfpdf networks-lecture3.pdf manage 2389.9 K 06 Jul 2017 - 16:48 AlenaVanBMmel  
networks-lecture4.pdfpdf networks-lecture4.pdf manage 1723.7 K 13 Jul 2017 - 09:58 AlenaVanBMmel  
Topic revision: r46 - 13 Jul 2017, AlenaVanBMmel
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