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The oral exams will be held on Friday, 12 July 2013 (see schedule below).

For the first part, see the web page at MPI.

General Information

SWS/credit hrs: 2+2+2 , credits: 10 ECTS
Lecturer: Alexander Bockmayr, Julia Lasserre, Martin Vingron

Language: Englisch

Dates

  Time Location
Lecture Friday 10 - 12 Arnimallee 6 SR 025/026
Exercise Friday 12 - 14 Arnimallee 6 SR 025/026
Seminar Monday 10 - 12 Arnimallee 6 SR 025/026

Lecture Schedule

Date Topic Lecturer Material
6 May 2013 Introduction A. Bockmayr Slides Article
10 May 2013 Continuous modeling (Reaction networks, phase plane) A. Bockmayr Slides Software
13 May 2013 Continuous modeling (Stability) A. Bockmayr Slides
17 May 2013 Continuous modeling (Bifurcations) A. Bockmayr Slides Exercises
24 May 2013 Discrete modeling (Thomas formalism) A. Bockmayr Slides
27 May 2013 Discrete modeling (Discrete vs. continuous descriptions) A. Bockmayr Slides
31 May 2013 Discrete modeling (Illustrating example, model checking) A. Bockmayr Slides
3 June 2013 Continuous modeling (Seminar) D. von Meer Slides Software
Paper Video
7 June 2013 Discrete modeling (model checking ctd.) A. Bockmayr Slides Exercises
10 June 2013 Discrete modeling (Seminar) M. Jeschek Slides Software
Paper1 Paper2
14 June 2013 No lecture and exercises    
17 June 2013 Constraint-based modeling A. Bockmayr Slides
21 June 2013 Constraint-based modeling A. Bockmayr Slides
24 June 2013 Constraint-based modeling (Seminar) A. Grigore Slides Software
28 June 2013 No lecture/exercises    
1 July 2013 Network visualization (Seminar) H. Detering Slides Software
5 July 2013 Stochastic modeling A. Bockmayr Slides Slides
8 July 2013 Stochastic modeling (Seminar) J. Biedermann  
12 July 2013 Oral examinations J. Lasserre
A. Bockmayr
 

Oral Examinations

Date/location: Friday 12 July @ Arnimallee 6, 1st floor, r142 (office Alexander Bockmayr)
Please wait in hallway until you are called in.

Time Student
09.15 H. Detering
09.40 M. Jeschek
10.05 A. Grigore
10.30 L. Ly
10.55 A. Vowinkel
11.40 L. Sousa
12.05 J. Biedermann
12.30 D. von Meer
12.55 C. Matzig

Materials

Introduction

Continuous modeling

Discrete modeling

Constraint-based modeling

Stochastic modeling
  • Gillespie D. Numerical simulation for biochemical kinetics. In: Szallasi Z, Stelling J, Periwal V (Eds) System Modelling in Cellular Biology, Chapter 16, 2006 (Bibliothek)
  • Gillespie D. A rigorous derivation of the chemical master equation Physica A 1992; 188: 404-425

In der FB-Bibliothek

  • Szallasi Z, Stelling J, Periwal V (Eds) System Modelling in Cellular Biology. MIT Press, 2006
  • Braun M. Differential Equations and Their Applications. 4th ed, Springer, 1993.
  • Strogatz SH. Nonlinear Dynamics and Chaos, Westview Press, 2001.
Topic revision: r26 - 10 Mar 2014, EkaterinaEngel
 
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