News
SWS: 3, ECTS: 5
Lecturer: Alexander Bockmayr / Annika Röhl
Language: English / German
Dates
Lecture: 
Thursday 1416h 
Arnimallee 6 SR 025/026 
Exercise (every two weeks): 
Thursday 1618h 
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 constraintbased analysis of genomescale metabolic networks, with applications to systems biology and biotechnology.
We will discuss the steadystate 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 mixedinteger optimisation methods.
Schedule (subject to change)
Date 
Type 
Lecturer 
Topic 
Lecture Material 
Additional Material 
17 April 2014, 1416 
Lecture 
Bockmayr 
Introduction 
Slides 
Article 
24 April 2014, 1416 24 April 2014, 1618 
Lecture Exercise 
Bockmayr Röhl 
FBA, FVA 
Slides Exercise 
Article 
01 May 2014 
Holiday 




08 May 2014, 1416 
Lecture 
Bockmayr 
FCA 
Slides 
F2C2 Article 
15 May 2014, 1416 15 May 2014, 1618 
Lecture Exercise 
Bockmayr Röhl 
EFMs 
Slides Article 

22 May 2014, 1416 
Lecture 
Bockmayr 
Targeted EFMs 
Slides 
Report 
29 May 2014 
Holiday 




05 June 2014, 1416 05 June 2014, 1618 
Lecture Exercise 
Bockmayr Röhl 
Flux cone descriptions 
Slides Exercise 4 
Article 
12 June 2014, 1416 
Lecture 
Bockmayr 
MMBs 
Slides 
Article 1 Article 2 
19 June 2014, 1416 19 June 2014, 1618 
Lecture Exercise 
Bockmayr Röhl 
Metabolic alterations 
Slides Article 

26 June 2014, 1416 
Exercise 
Röhl 

Exercise 

03 July 2014, 1416 03 July 2014, 1618 
Lecture Lecture 
Bockmayr Bockmayr 
Regulatory FBA 
Slides 
Article 1 Article 2 
10 July 2014, 1416 
Exercise 
Röhl 



17 July 2014, 1416 17 July 2014, 1618 
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 genotypephenotype relationship using a phylogeny of in silico methods.
Nat Rev Microbiol., 10(4):291305, 2012.
Larhlimi A, David L, Selbig J, Bockmayr A.
F2C2: a fast tool for the computation of flux coupling in genomescale 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 genomescale networks via generating flux modes. Bioinformatics, 27/4, 534540, 2011
Orth JD, Thiele I, Palsson BØ.
What is flux balance analysis? Nat Biotechnol., 28(3):2458, 2010.
Larhlimi A, Bockmayr A.
On Inner and Outer Descriptions of the SteadyState Flux Cone of a Metabolic Network. Computational Methods in Systems Biology, CMSB 2008, Rostock. Springer, LNBI 5307, 308327, 2008
Larhlimi A, Bockmayr A.
A new constraintbased description of the steadystate flux cone of metabolic networks. Discrete Applied Mathematics, 157, 22572266, 2009
Minimum requirements
Active and regular attendance at exercises, passing the final exam
Tutorial
Please sign in for the mailinglist:
https://lists.fuberlin.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 mfile and the output files.
Third Exercise: Write in MATLAB an EFMFinding 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 mfile. 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)
Hier findet ihr zusätzliches Material.
Solltet ihr keinen Zugriff haben (auch auf die Slides), schreibt einfach eine Email an Annika:
annika.roehl@fuberlin.de