===== Metabolic network analysis =====

Leonid Chindelvitch\\
//School of Computing Science,//
//Simon Fraser University, Burnaby, BC, Canada//

==== Room and times ====
18.-21.4.2017\\
10-12, room U10-146 (theory)\\
13-14, room V6-116  (hands-on: **Bring your laptops, please.**)\\
[[https://ekvv.uni-bielefeld.de/kvv_publ/publ/vd?id=92130672|(Link to eKVV)]]

==== Objectives ====
This short course will provide an overview of metabolic network analysis, a topic at the intersection of computational biology, systems biology and mathematical modelling. It will go into detail into the modeling and analysis of metabolic networks in the constraint-based formalism, which complement metabolomics data analysis. By the end of the course the students will have an appreciation for the advantages and shortcomings of metabolic network models, the tools used for their analysis, and the open problems currently facing the field. They will also learn the use of Mongoose, an open-source metabolic network analysis platform ([[http://cb.csail.mit.edu/cb/mongoose/|mongoose.csail.mit.edu]]).

==== Schedule ====

=== Day 1: Metabolic network analysis formalisms ===
  * topological analysis and deficiency zero theorem
  * biochemical systems analysis and control theory
  * constraint-based formalism and flux balance analysis

=== Day 2: Structural analysis of metabolic network models ===
  * blocked reactions classification
  * enzyme and isozyme subsets
  * redundant constraint identification

=== Day 3: Troubleshooting metabolic network models ===
  * unblocking blocked reactions
  * identifying and correcting “free lunches”
  * network reconciliation and refinement

=== Day 4: Extensions ===
  * inclusion of thermodynamic constraints
  * metabolic engineering applications
  * enumeration of elementary modes and minimal cut sets

==== Materials and References ====

=== Day 1 ===

  * {{mongoose-rational-arithmetic.pdf}}
  * [[https://www.seas.upenn.edu/~jadbabai/ESE680/Fei87a.pdf|Feinberg, 1986]]
  * [[https://www.ncbi.nlm.nih.gov/pubmed/5387046|Savageau, 1996]]

=== Day 2 ===

  * {{Day2.pptx}}
  * [[https://academic.oup.com/bioinformatics/article/20/2/226/204870/Minimal-cut-sets-in-biochemical-reaction-networks | Klamt and Gilles, 2004]]
  * [[https://www.nature.com/articles/ncomms5893|Chindelevitch et al., 2014]]

=== Day 3 ===

  * [[https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-5-175|Gagneur and Klampt, 2004]]
  * [[https://www.ncbi.nlm.nih.gov/pubmed/19962421|Acuna et al., 2009]]

=== Day 4 ===

  * [[http://projects.csail.mit.edu/wiki/pub/Evodesign/MetabolicNetworks/Beard-etal-2004-j-theo-biology.pdf|Beard et. al, 2004]]
  * [[http://maranas.che.psu.edu/pub/burgard-etal03a.pdf|Burgard et al., 2003]]