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Exercise 1: Flux Balance Analysis and Flux Variability Analysis
Deadline: Tuesday, 17.05.2016, 08:00 a.m.

FBA
Write a program that:
  • reads in a metabolic network: a struct in a .mat file, which is called "network":
    • S: stoichiometric matrix
    • rev: reversibility-vector (rev(i) = 0: reaction i is not reversible, rev(i) = 1: reaction i is reversible)
    • rxns: names of the reactions
    • lb: lower bounds
    • ub: upper bounds
    • description: name of the network
  • reads in a second argument, which is either BIOMASS, the name of a reaction or BLOCKED
  • reads in a third argument, which is the name of the output file.
  • Depending on the second argument the program should do the following:
    • computes a flux distribution which maximises the biomass-production and fulfils the steady state assumption. The network contains at least one reaction which is called biomass or where the name contains the word biomass. If there are several reaction-names containing the word biomass the first one is chosen and the user receives a message that there are several biomass-reaction.
    • computes a flux distribution which maximises the flux through the given reaction and which fulfils the steady state assumption.
    • computes the blocked reactions
  • Output:
    • BIOMASS-mode:
      • A .txt file with to columns: the first column contains the reaction_id and the second column contains the corresponding rate
      • the first row contains the biomass-reaction. The remaining reactions are listed according to their indices.
    • Name of a reaction:
      similar to BIOMASS-mode, but the first row should contain the corresponding reaction.
    • BLOCKED-mode:
      • a vector which contains the names of the blocked reactions
      • these reactions are ordered according to their index.

FVA
Write a program that:
  • reads in a metabolic network: a struct in a .mat file, which is called "network":
    • S: stoichiometric matrix
    • rev: reversibility-vector (rev(i) = 0: reaction i is not reversible, rev(i) = 1: reaction i is reversible)
    • rxns: names of the reactions
    • lb: lower bounds
    • ub: upper bounds
    • description: name of the network
  • reads in a second argument, which is either BIOMASS or the name of a reaction
  • reads in a third argument, which is the name of the output file.
The program should compute the flux-variability for each reaction.
Output:
  • Three .txt Files which should have the name of the output file and as an addition _variable, _notvariable or _notused.
  • variable file should consists of three columns:
    • in the first column are the names of the reactions, ordered according to their index
    • in the second column is the maximum flux through the corresponding reaction
    • in the second column is the minimum flux through the corresponding reaction
  • The title of the columns are:
    • Name
    • Max Value
    • Min Value
  • The notvariable file should consists of two columns:
    • in the first column are the names of the reactions, ordered according to their index. In the first row is the biomass-reaction or the reaction which should be maximised
    • in the second column are the fluxes for the corresponding reactions
  • the notused file contains one column where the reaction names are listed (according to their indices) which never carry flux.


Please download these networks to test your programs.

Comments

 
Topic revision: r2 - 17 May 2016, AnnikaRoehl
 
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