AMEBA: Advanced MEtabolic Branchpoint Analysis
Copyright 2012 Rene Rex (r.rex@tu-bs.de)
Licensed under the terms of the GNU General Public License 

Installation
------------

 1. Install the following packages using the package manager of your
    distribution - e.g. under Debian/Ubuntu:
    sudo apt-get install gcc python2.7 python2.7-dev python-pip python-numpy libgraphviz-dev graphviz
    
    Please note that AMEBA requires at least Python in version 2.7 to work properly.

 2. Download (http://metano.tu-bs.de) and install metano:
    sudo pip install metano-*.tar.gz
    Note: If you intend to use all features of metano (e.g. flux balance
    analysis), you need to follow the installation instructions of metano.

 3. Download (http://metano.tu-bs.de/ameba) and install AMEBA:
    sudo pip install ameba-*.tar.gz


Usage
-----

For an explanation of all command line options type:
ameba -h

A working example can be found in the ameba example folder in the dist-packages
location of your python installation. In the case of Ubuntu 12.04 this is:

/usr/local/lib/python2.7/dist-packages/ameba/example/

Alternatively, you can find the examples in the ameba archive file (under
src/example).

The example folder contains the reaction file (rea_Ecoli_iAF1260_bigg.txt) of
the iAF1260 model of E. coli (Feist et al, 2007) and the corresponding parameter
file for an aerobic glucose scenario (para_Ecoli_iAF1260_bigg.txt) in the metano
format. Furthermore, we provide a precomputed solution calculated by the FBA
implementation of metano (flux__Ecoli_iAF1260_bigg.txt). The file bpa.ini
contains display options for ameba, which you may want to adjusted to your
needs. After changing to the example folder AMEBA can be started at the node of
the metabolite chorismate by typing:

ameba -r rea_Ecoli_iAF1260_bigg.txt -s flux__Ecoli_iAF1260_bigg.txt -c bpa.ini -n chorismate[C_c]

Now, you can navigate through the metabolic network by clicking on any node in the GUI.

