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Welcome to FluxModules Wiki!

Here, you find a brief overview on the content of the project. This project contains essentially the supplementary material for a (not yet published) paper in the RECOMB 2014 proceedings (reference will follow as soon as available).

Source Code

You can find the code in the Git-Repository and in the Files.

It is currently a bunch of matlab scripts for module detection and visualization. This code depends on the openCOBRA-Toolbox.

Module Computation

• computeModulesOpt.m - computes the modules for the optimal flux space (w.r.t to the objective function of the model)
• computeModule.m - compute the modules for the full flux space (used by computeModulesOpt)
• findCircuitBase.m - compute the fundamental circuits (you'll probably not use this directly)
• findConnectedComponents.m - computes connected components of a bipartite graph (you'll probably not use this directly)

Module Vizualization

• drawModule.m - draws a single module
• visualizeModsSingle.m - draws the interactions between modules

General Summary Generation

For reproduceability we also supply the matlab code that we used to generate the results in the supplementary material.
It is not really intended for other uses.
* makeSummary.m - runs all the afore mentioned methods and creates a latex file with summary information

Mathematical Proofs

The proofs from the paper you can find in the files.

Examples

We also uploaded some examples so that you can see what kind of results can be obtained.
For each example network there is a .zip file, which contains

• the results in text-form,
  • flux.txt a feasible flux distribution (here, we only analyze the optimal flux space, so this is actually an optimal feasible flux distribution)
  • modules.txt the names of the reactions in the modules (one line for each module)
  • variability.txt minimal and maximal flux values (in the order as in the network)
• run time
  • time.txt runtime in seconds
• figures of the computed modules (unless the modules are too big), for example:
  
• a figure showing the interactions of the modules
  [Home/attachment/network.pdf]
• a pdf giving summary informtion on the modules. [Home/attachment/network_summary.pdf]

Metabolic Networks

SBML files of the metabolic networks used for the example computation can be found

• in the BiGG database
• Human Recon 2 at Biomodels Database
• E. coli iJO1366 at PMC

Project Members:

• arne (admin)