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

Materials

Introduction

• Kitano H. Systems biology: a brief overview Science. 2002 Mar 1;295(5560):1662-4

Continuous modeling

• Sontag ED. Lecture Notes on Mathematical Systems Biology Rutgers Univ., Mar 2013
• Tyson JJ, Chen K, Novak B. Network dynamics and cell physiology Nat Rev Mol Cell Biol. 2001 Dec;2(12):908-916
• Tyson JJ, Novak B. Irreversible Transitions, Bistability and Checkpoint Controls in the Eukaryotic Cell Cycle: A Systems-Level Understanding Handbook of Systems Biology, 2013, Chapter 14, Pages 265–285

Discrete modeling

• Thomas R, Kaufman M. Multistationarity, the basis of cell differentiation and memory. II. Logical analysis of regulatory networks in terms of feedback circuits Chaos. 2001 Mar;11(1):180-195
• Thomas R, D'Ari R. Biological Feedback. CRC Press, 1990. Online version

Constraint-based modeling

• Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol. 2010 Mar;28(3):245-8.
• Terzer M, Maynard ND, Covert MW, Stelling J. Genome-scale metabolic networks Wiley Interdiscip Rev Syst Biol Med. 2009 Nov-Dec;1(3):285-97

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.