News
SWS: 3, ECTS: 5
Lecturer: Alexander Bockmayr / 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 |
17 April 2014, 14-16 |
Lecture |
Bockmayr |
Introduction |
Slides |
Article |
24 April 2014, 14-16 24 April 2014, 16-18 |
Lecture Exercise |
Bockmayr Röhl |
FBA, FVA |
Slides Exercise |
Article |
01 May 2014 |
Holiday |
|
|
|
|
08 May 2014, 14-16 |
Lecture |
Bockmayr |
FCA |
Slides |
F2C2 Article |
15 May 2014, 14-16 15 May 2014, 16-18 |
Lecture Exercise |
Bockmayr Röhl |
EFMs |
Slides Article |
|
22 May 2014, 14-16 |
Lecture |
Bockmayr |
Targeted EFMs |
Slides |
Report |
29 May 2014 |
Holiday |
|
|
|
|
05 June 2014, 14-16 05 June 2014, 16-18 |
Lecture Exercise |
Bockmayr Röhl |
Flux cone descriptions |
Slides Exercise 4 |
Article |
12 June 2014, 14-16 |
Lecture |
Bockmayr |
MMBs |
Slides |
Article 1 Article 2 |
19 June 2014, 14-16 19 June 2014, 16-18 |
Lecture Exercise |
Bockmayr Röhl |
Metabolic alterations |
Slides Article |
|
26 June 2014, 14-16 |
Exercise |
Röhl |
|
Exercise |
|
03 July 2014, 14-16 03 July 2014, 16-18 |
Lecture Lecture |
Bockmayr Bockmayr |
Regulatory FBA |
Slides |
Article 1 Article 2 |
10 July 2014, 14-16 |
Exercise |
Röhl |
|
|
|
17 July 2014, 14-16 17 July 2014, 16-18 |
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 genotype-phenotype relationship using a phylogeny of in silico methods.
Nat Rev Microbiol., 10(4):291-305, 2012.
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
Orth JD, Thiele I, Palsson BØ.
What is flux balance analysis? Nat Biotechnol., 28(3):245-8, 2010.
Larhlimi A, Bockmayr A.
On Inner and Outer Descriptions of the Steady-State Flux Cone of a Metabolic Network. Computational Methods in Systems Biology, CMSB 2008, Rostock. Springer, LNBI 5307, 308-327, 2008
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
Minimum requirements
Active and regular attendance at exercises, passing the final exam
Tutorial
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https://lists.fu-berlin.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 m-file and the output files.
Third Exercise: Write in MATLAB an EFM-Finding 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 m-file. 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@fu-berlin.de