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 TypeSorted ascending Lecturer Topic Lecture Material Additional Material
09.07.2015 Exercises Lorenz
14.05.2015 Holiday
16.04.2015 Lecture Bockmayr Introduction Slides Article
30.04.2015 Lecture Bockmayr FCA Slides Article
21.05.2015 Lecture Bockmayr Targeted EFMs Slides Article
04.06.2015 Lecture Bockmayr Flux cone + MMBs Slides
18.06.2015 Lecture Bockmayr Regulatory FBA (rFBA) Slides Article Article
02.07.2015 Lecture Bockmayr Temporal gene expression Slides Article
23.04.2015 Lecture
Exercises
Bockmayr
Lorenz
FBA, FVA, FCA Slides Article
07.05.2015 Lecture
Exercises
Bockmayr
Lorenz
EFMs Slides Article
28.05.2015 Lecture
Exercises
Bockmayr
Lorenz
Targeted EFMs (ctd)
11.06.2015 Lecture
Exercises
Bockmayr
Lorenz
Sequential metabolic phases Slides Article
25.06.2015 Lecture
Exercises
Bockmayr
Lorenz
Integrated FBA (iFBA) Slides Article Article
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
Topic revision: r37 - 16 Jul 2015, AlexanderBockmayr
 
  • Printable version of this topic (p) Printable version of this topic (p)