Welcome to the Lectures Wiki Metabolic Networks SS 2016

News

General information

SWS: 2+1, ECTS: 5

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

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

Tutorial

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

Exercises:

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

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). 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)

Comments

AdditionalMaterialMolnetz16

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