Welcome to the Lectures Wiki
"Regulation and control of molecular networks" WS 2014/15

News

We will have a double lecture (10-12, 12-14) on December 12 and no lecture on December 19.

General information

SWS: 3, ECTS: 5

Lectures: Alexander Bockmayr / Heike Siebert
Exercises: Therese Lorenz

Language: English / German

Dates

Lecture:	Friday 10-12h	SR E.31/A7
Exercise (every two weeks):	Friday 12-14h	SR E.31/A7

Contents

We will focus on modeling and analysis of molecular networks, using continuous, discrete and hybrid discrete/continuous formalisms. Motivated by applications in systems medicine and biotechnology, we will discuss methods to uncover the relation between system design and function, e.g. using modularization approaches or optimisation principles. We also discuss possibilities for network control, e.g. via gene knock-outs.
This course is complementary to the seminar Molecular Networks.

Schedule (subject to change)

Date	Lecturer	Type	Topic	Material
17.10.2014	A. Bockmayr	Lecture	Chemical reaction networks	Sontag, Chap.1.6.1-1.6.2
24.10.2014	T. Lorenz A. Bockmayr	Exercises Lecture	Simple network examples Time-scale separation	Ingalls, Chap.2.1 Ingalls, Chap.2.2
31.10.2014	A. Bockmayr	Lecture	Michaelis-Menten kinetics Tikhonov's theorem	Ingalls, Chap.3.1 Sontag, Chap.1.6.8 Slides
07.11.2014	T. Lorenz A. Bockmayr	Exercises Lecture	Inhibition, Cooperativity	Sontag, Chap.1.6.9-1.7.2
14.11.2014	T. Lorenz	Lecture	Chemostat	Sontag, Chap.1.1.6-10, 1.2.4
21.11.2014	T. Lorenz A. Bockmayr	Exercises Lecture	Metabolic pathways	Ingalls, Chap.5.1-5-2
28.11.2014	A. Bockmayr	Lecture	Temporal gene expression	Article
05.12.2014	T. Lorenz A. Bockmayr	Exercises Lecture	Metabolism coupled to gene expression	Article
12.12.2014	Heike Siebert	Double Lecture	ODEs and PLDEs, phase space analysis	slides
19.12.2014	H. Siebert	no lecture
09.01.2015	T. Lorenz H. Siebert	Exercises Lecture	Logical modeling	exercise slides
16.01.2015	Heike Siebert T. Lorenz	Lecture Exercises	From logical to structure models	slides
23.01.2015	Heike Siebert	Lecture	Graph modules	slides
30.01.2015	Heike Siebert Therese Lorenz	Lecture Exercises	Statistical significance	slides
06.02.2015	Heike Siebert	Lecture	Dynamical modules	slides
13.02.2015	Heike Siebert Therese Lorenz	Lecture Exercises	Dynamical modules (cont.)	slides

Materials

Ingalls B. Mathematical Modeling in Systems Biology MIT Press, 2013

Sontag ED. Lecture Notes on Mathematical Systems Biology Rutgers Univ., Apr 2014

H. De Jong et al., Qualitative simulation of genetic regulatory networks using piecewise-linear models , Bull. Math. Biol., 2004

Concepts from graph theory for analysing biological networks are introduced here

Minimum requirements

Active and regular attendance at exercises, passing the final exam

Tutorial

Comments