Welcome to the Lectures Wiki Metabolic Networks SS 2015

News

General information

SWS: 2+1, ECTS: 5

Lecturer: Alexander Bockmayr
Tutor: Therese Lorenz

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
16.04.2015	Lecture	Bockmayr	Introduction	Slides	Article
23.04.2015	Lecture Exercises	Bockmayr Lorenz	FBA, FVA, FCA	Slides	Article
30.04.2015	Lecture	Bockmayr	FCA	Slides	Article
07.05.2015	Lecture Exercises	Bockmayr Lorenz	EFMs	Slides	Article
14.05.2015	Holiday
21.05.2015	Lecture	Bockmayr	Targeted EFMs	Slides	Article
28.05.2015	Lecture Exercises	Bockmayr Lorenz	Targeted EFMs (ctd)
04.06.2015	Lecture	Bockmayr	Flux cone + MMBs	Slides
11.06.2015	Lecture Exercises	Bockmayr Lorenz	Sequential metabolic phases	Slides	Article
18.06.2015	Lecture	Bockmayr	Regulatory FBA (rFBA)	Slides	Article Article
25.06.2015	Lecture Exercises	Bockmayr Lorenz	Integrated FBA (iFBA)	Slides	Article Article
02.07.2015	Lecture	Bockmayr	Temporal gene expression	Slides	Article
09.07.2015	Exercises	Lorenz
16.07.2015	Lecture Lecture	Bockmayr Bockmayr	Dynamic enzyme-cost FBA (deFBA)	Slides	Article

Materials

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.

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

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

David L, Bockmayr A. Computing elementary flux modes involving a set of target reactions. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 11/6, 1099-1107, Nov/Dec 2014

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

Palinkas A, Bulik S, Bockmayr A, Holzhütter HG. Sequential Metabolic Phases as a Means to Optimize Cellular Output in a Constant Environment. PLoS ONE, 10(3): e0118347, Mar 2015

Covert MW, Schilling CH, Palsson B. Regulation of gene expression in flux balance models of metabolism. J Theor Biol. 2001 Nov 7;213(1):73-88

Covert MW, Xiao N, Chen TJ, Karr JR. Integrating metabolic, transcriptional regulatory and signal transduction models in Escherichia coli. Bioinformatics. 2008 Sep 15;24(18):2044-50

Klipp E, Heinrich R, Holzhütter HG. Prediction of temporal gene expression. Metabolic opimization by re-distribution of enzyme activities. Eur J Biochem. 2002 Nov;269(22):5406-13

Waldherr S, Oyarzún DA, Bockmayr A. Dynamic optimization of metabolic networks coupled with gene expression. Journal of Theoretical Biology, 365, 469-485, Jan 2015

Minimum requirements

Active and regular attendance at exercises

Tutorial

Please sign in for the mailinglist to get shortterm informations about the tutorials : https://lists.fu-berlin.de/listinfo/MetabolicNetworksSS15

Exercises:

Exercise sheet 1 (due 30.04.): MetabolicNetworks_Ex1.pdf. The testing examples can be downloaded here: MetabolicNetworks.zip

Exercise sheet 2 (due 14.05.): MetabolicNetworks_Ex2.pdf. The article needed for the last exercise is F2C2 Article.
Edited: In Exercise 4d the inference rules are the transitivity rules of the coupling relations.
Second chance: Due 04.06.

Exercise sheet 3 (due 18.06.): MetabolicNetworks_Ex3.pdf. The script of the tutorial: DeFig.pdf.
The small testing examples can be downloaded here: BeispielNetzwerke.zip, as more interesting examples use the examples of exercise 1.
Be careful: The small examples have individual names, instead of the standard name 'network', so your program may either accept a previously loaded struct as argument or determine the correct field name by using 'model = load('struct.mat'); names = fieldnames(model);'
Additional material : Computing the shortest elementary flux modes in genome-scale metabolic networks by Luis de Figueiredo et al.
Algorithm: shortestEFMs.m

Exercise sheet 4 : MetabolicNetworks_Ex4.pdf. For the next tutorial you should read the this Article and especially focus on your example (Ex. 1 - Marthe, Balduin; Ex. 2 - Marjan, Moritz; Ex. 3 - David, Pascal).

Comments

AdditionalMaterialMolnetz15

To get access to the additional material (including slides), please send an e-mail including your zedat-accountname to Therese Lorenz: therese.lorenz@fu-berlin.de