TU BRAUNSCHWEIG BI-BC-BS

AMEBA: Advanced MEtabolic Branchpoint Analysis

AMEBA screenshot

AMEBA is released under the terms of the GNU General Public License version 3.


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 python-gi
    Please note that AMEBA requires at least Python in version 2.7 to work properly.
  2. Download 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 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.


Reference

If you use AMEBA for your own published work, we kindly ask that you cite the following publication:

Riemer SA, Rex R, Schomburg D. A metabolite-centric view on flux distributions in genome-scale metabolic models. BMC Syst Biol, 7:33 (2013). Free full text


Contact

AMEBA was developed by René Rex in the Department of Bioinformatics and Biochemistry at Braunschweig University of Technology. For any questions please contact:

Alexander Riemer
Technische Universität Carolo-Wilhelmina zu Braunschweig
Department of Bioinformatics and Biochemistry
Langer Kamp 19b
38106 Braunschweig, Germany
E-mail: myemail
Phone: +49 531 391-8306

The website of our department can be found here.


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