File	Date	Author	Commit
.gitignore	2014-01-04	Arne Müller	[636a4d] gitignore file
README	2014-01-04	Arne Müller	[f89654] Initial commit
computeModules.m	2014-01-04	Arne Müller	[f89654] Initial commit
computeModulesOpt.m	2014-01-04	Arne Müller	[f89654] Initial commit
drawModule.m	2014-01-04	Arne Müller	[f89654] Initial commit
findCircuitBase.m	2014-01-04	Arne Müller	[f89654] Initial commit
findConnectedComponents.m	2014-01-04	Arne Müller	[f89654] Initial commit
gpl-3.0.txt	2014-01-04	Arne Müller	[f89654] Initial commit
interestingModules.m	2014-01-04	Arne Müller	[f89654] Initial commit
makeSummary.m	2014-01-04	Arne Müller	[f89654] Initial commit
visualizeModsSingle.m	2014-01-04	Arne Müller	[f89654] Initial commit

Read Me

= README: Fast Flux Module Computation =

The supplied code works with matlab in combination with the cobra toolbox. If you can get the cobra toolbox also to run with octave, the supllied code will also likely work with octave.

It follows a short overview of the supplied functions:

== 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 reproducability 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 summaryinformation


= Copyright =

Copyright (C) 2013  Arne Müller <arne.mueller@fu-berlin.de>

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.