Welcome to the Lectures Wiki Metabolic Networks SS 2016


General information

SWS: 2+1, ECTS: 5

Lecturer: Alexander Bockmayr
Tutor: Annika Röhl

Language: English / German


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


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
21.04.2016 Lecture Bockmayr Introduction Slides Article
28.04.2016 Lecture
FBA, FVA Slides
05.05.2016 Holiday        
12.05.2016 Lecture Bockmayr FCA Slides Article
19.05.2016 Lecture
EFMs Slides
26.05.2016 Lecture Bockmayr EFMs (ctd) Slides Article
02.06.2016 Lecture
Targeted EFMs Slides Article
09.06.2016 Exercises Röhl      
16.06.2016 Lecture
Flux cone Slides Article
23.06.2016 Lecture
Article Article
30.06.2016 Exercises Röhl      
07.07.2016 Lecture Bockmayr Sequential phases Slides Article
14.07.2016 Lecture
Sequential activation Slides Article
21.07.2016 Lecture Bockmayr Dynamic enzyme-cost FBA Slides Article


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

de Figueiredo LF, Podhorski A, Rubio A, Kaleta C, Beasley JE, Schuster S, Planes FJ. Computing the shortest elementary flux modes in genome-scale metabolic networks. Bioinformatics. 2009 Dec 1;25(23):3158-65

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

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

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

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 participation at the exercises


Please sign in for the mailing list to get short term informations about the tutorials : https://lists.fu-berlin.de/listinfo/MetabolicNetworksSS16


Find the first programming exercise here. Deadline: Tuesday, 17.05.2016, 08:00 a.m.

Find the second programming exercise here. Deadline: Tuesday, 31.05.2016, 08:00 a.m.

Find the third programming exercise here. Deadline: Tuesday, 14.06.2016, 08:00 a.m.

Find the fourth programming exercise here. Deadline: Tuesday, 28.06.2016, 08:00 a.m.

Find the fifth programming exercise here. Deadline: Tuesday, 12.07.2016, 08:00 a.m.

Sixth exercise: read the article and focus on one example. Explain this example in the tutorial (Thursday 14.07.2016).
Example 2: Stefan, Sara, Svenja
Example 3: Hamid, Mathis, Arsene
Example 4: Parnika, Javier, Dennis


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). Not for every program.

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



To get access to the additional material (including slides), please send an e-mail including your zedat-accountname to Annika Röhl: annika.roehl@fu-berlin.de
Topic revision: r27 - 20 Jul 2016, AlexanderBockmayr
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