You are here: Wiki>AgMathLife Web>MolnetzASS14 (19 Apr 2016, AnnikaRoehl)Edit

Welcome to the Lectures Wiki Metabolic Networks SS 2014

News

General information

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

Please sign in for the mailinglist: 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)

Comments

AdditionalMaterialMolnetz

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
Topic revision: r35 - 19 Apr 2016, AnnikaRoehl
 
  • Printable version of this topic (p) Printable version of this topic (p)