Welcome to the Lectures Wiki Metabolic Networks SS 2014

News

General information

SWS: 3, ECTS: 5

Lecturer: Alexander Bockmayr / Annika Röhl

Language: English / German

Dates

Lecture:	Thursday 14-16h	Arnimallee 6 SR 025/026
Exercise (every two weeks):	Thursday 16-18h	Arnimallee 6 SR 025/026

Contents

The goal of this course is to give an introduction to the most important mathematical and algorithmic ideas underlying the constraint-based analysis of genome-scale metabolic networks, with applications to systems biology and biotechnology.

We will discuss the steady-state flux cone, flux balance analysis (FBA), flux variability analysis (FVA), flux coupling analysis (FCA), elementary flux modes (EFMs), thermodynamic constraints, and metabolic regulation. On the algorithmic side, the focus will be on linear and mixed-integer optimisation methods.

Schedule (subject to change)

Date	Type	Lecturer	Topic	Lecture Material	Additional Material
17 April 2014, 14-16	Lecture	Bockmayr	Introduction	Slides	Article
24 April 2014, 14-16 24 April 2014, 16-18	Lecture Exercise	Bockmayr Röhl	FBA, FVA	Slides Exercise	Article
01 May 2014	Holiday
08 May 2014, 14-16	Lecture	Bockmayr	FCA	Slides	F2C2 Article
15 May 2014, 14-16 15 May 2014, 16-18	Lecture Exercise	Bockmayr Röhl	EFMs	Slides Article
22 May 2014, 14-16	Lecture	Bockmayr	Targeted EFMs	Slides	Report
29 May 2014	Holiday
05 June 2014, 14-16 05 June 2014, 16-18	Lecture Exercise	Bockmayr Röhl	Flux cone descriptions	Slides Exercise 4	Article
12 June 2014, 14-16	Lecture	Bockmayr	MMBs	Slides	Article 1 Article 2
19 June 2014, 14-16 19 June 2014, 16-18	Lecture Exercise	Bockmayr Röhl	Metabolic alterations	Slides Article
26 June 2014, 14-16	Exercise	Röhl		Exercise
03 July 2014, 14-16 03 July 2014, 16-18	Lecture Lecture	Bockmayr Bockmayr	Regulatory FBA	Slides	Article 1 Article 2
10 July 2014, 14-16	Exercise	Röhl
17 July 2014, 14-16 17 July 2014, 16-18	Lecture Lecture	Bockmayr Bockmayr	Dynamic optimisation	Slides

Materials

David L, Bockmayr A. Computing elementary flux modes involving a set of target reactions. Matheon Preprint #1045, Nov 2013

Lewis NE, Nagarajan H, Palsson BO. Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods. Nat Rev Microbiol., 10(4):291-305, 2012.

Larhlimi A, David L, Selbig J, Bockmayr A. F2C2: a fast tool for the computation of flux coupling in genome-scale metabolic networks. BMC Bioinformatics 13:57, 2012

Rezola A, de Figueiredo LF, Brock M, Pey J, Podhorski A, Wittmann C, Schuster S, Bockmayr A, Planes FJ Exploring metabolic pathways in genome-scale networks via generating flux modes. Bioinformatics, 27/4, 534-540, 2011

Orth JD, Thiele I, Palsson BØ. What is flux balance analysis? Nat Biotechnol., 28(3):245-8, 2010.

Larhlimi A, Bockmayr A. On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network. Computational Methods in Systems Biology, CMSB 2008, Rostock. Springer, LNBI 5307, 308-327, 2008

Larhlimi A, Bockmayr A. A new constraint-based description of the steady-state flux cone of metabolic networks. Discrete Applied Mathematics, 157, 2257-2266, 2009

Minimum requirements

Active and regular attendance at exercises, passing the final exam

Tutorial

Please sign in for the mailinglist: https://lists.fu-berlin.de/listinfo/listMetalbolischeNetzwerke14

First Exercise: Exercise 1.

Second Exercise: Write in MATLAB an FBA and an FVA: Exercise 2. Output: one vector with maximal values and one with minimal values for every network you got the data from me (Ecoli_Textbook, Hpylori_iIT341, Mtuberculosis_iNJ661, Saureus_iSB619, Scerevisiae_iND750).

Send me please your m-file and the output files.

Third Exercise: Write in MATLAB an EFM-Finding Algorithm based on the idea in this Article.

Fourth Exercise: Exercise 4. A detailed explanation for the GFM finding algorithm can be find in this Article.

Fifth Exercise: Write in MATLAB a rank test to test if a flux is an EFM. Send me the m-file. Detailed explanation can be found in this Article.

Sixth Exercise: Exercise 6.

Points:

1 point: program contains critical errors

2 points: program contains small errors

3 points: program runs without errors

4 points: program runs without errors and you send me some extra explanation (what is the program good for)

For Aktive Teilnahme it is necessary to visit the tutorial and to do the homework (50% of the points in the end)

Comments

AdditionalMaterialMolnetz

Hier findet ihr zusätzliches Material. Solltet ihr keinen Zugriff haben (auch auf die Slides), schreibt einfach eine Email an Annika: annika.roehl@fu-berlin.de