Welcome to the Lectures Wiki Netzwerkanalyse SS 2017

News

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.

Topics:

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

Dates

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	Slides
08.05.2017	Bockmayr	Lecture	Continuous modeling: bifurcation analysis	Slides
	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
		Seminar
20/21.07.2017	Oral exams

Materials

Systems biology

• Kitano H. Systems biology: a brief overview Science. 2002 Mar 1;295(5560):1662-4
• Walhout M, Vidal M, Dekker J. Handbook of Systems Biology, Elsevier, 2013

Continuous modeling

• Sontag ED. Lecture Notes on Mathematical Systems Biology Rutgers Univ., Mar 2015
• Ingalls B. Mathematical Modeling in Systems Biology MIT Press, 2013
• Tyson JJ, Chen K, Novak B. Network dynamics and cell physiology Nat Rev Mol Cell Biol. 2001 Dec;2(12):908-916

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

• 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 pdf
• Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol. 2010 Mar;28(3):245-8.
• Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol. 2012 10(4):291-305.
• Steuer R. CyanoGrowth - die architektur des phototrophen wachstums. Von der Systembiologie zur biotechnologischen Anwendung systembiologie.de, 2015 May;9:48-52.

Stochastic modeling

• Gillespie DT, Hellander A, Petzold LR. Perspective: Stochastic algorithms for chemical kinetics J Chem Phys. 2013 May 7;138(17):170901.

Exercises

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)