MetaBoFlux

 Amine Ghozlane, Frederic Bringaud, Fabien Jourdan and Patricia Thébault

  Please see the file ChangeLog for a log of recent changes in MetaBoFlux

        More information about MetaBoFlux is available online at
           	 http://www.cbib.u-bordeaux2.fr/metaboflux/

       Please report problems with MetaBoFlux using the tracker at
          http://sourceforge.net/projects/metaboflux/support

  Mailing lists and online web forums for discussing MeTaBoFlux are at
          http://sourceforge.net/projects/metaboflux/forums

    To contact MetaBoFlux developer directly, send email to
                       amine.ghozlane@labri.fr

   ,----------------------------------------------------------------.
  | Table of contents                                               |
  | 1. Quick start                                                  |
  | 2. Reporting bugs and other problems                            |
  | 4. Mailing lists                                                |
  | 4. Licensing and distribution                                   |
  | 5. Acknowledgments                                              |
   `----------------------------------------------------------------'
         Date of last update to this file: 2011-01-12 18:00:00

================
=1. QUICK START=
================

==================
1.1. Requirements
==================

  - CMake >= 2.6
  - Gcc >= 3.4.0
  - Python >= 2.6 with package python-dev
  - LibXmL2 with package libxml2-dev
  -	R >= 2.10.0+ (http://www.r-project.org/) with packages gplots (http://cran.r-project.org/web/packages/gplots/) and XML (http://cran.r-project.org/web/packages/XML/)
  - GSL >= 1.14 (http://www.gnu.org/software/gsl/)
  - MPI v2: openmpi (http://www.open-mpi.org/) or mpich2 (http://www.mcs.anl.gov/research/projects/mpich2/)
  - LibSBML - v4.2.0 with python option (http://sbml.org/Software/libSBML)
  


==================
1.2. Installation
==================

To install MetaBoFlux, run :
	
	./MetaBoFlux_install.sh -I

MetaBoFlux is now available in MetaBoFlux-<version>/bin repertory.

=====================
1.3. Compile the Api
=====================

To compile the documentation API be sure that you have install :

  - Doxygen (www.doxygen.org/)
  
Then run :

	./MetaBoFlux_install.sh -D

The Api documentation is now available in MetaBoFlux-<version>/doc repertory.

======================
1.4. Start MetaboFlux
======================

The first step is to load SBML library package for python :

	export PYTHONPATH=DIR/lib/version/site-packages/libsbml:DIR/lib/version/site-packages

Verification :

	python
	>>>import(libsbml)
	>>>

The complete list of command is obtain by :

	./bin/MetaBoFlux.py -h

Example :

	./bin/MetaBoFlux.py -smr --par ./examples/parametre_glycosome.xml --sbml ./examples/modele_glycosome.xml  --sim_out ./temp/ --min_out ./temp/ --stat_out ./temp/

Running options :

Option          Case            Filename        Type    Description
-------------------------------------------------------------------
-s              no              no              no      Simulated annealing
-m              no              no              no      Minimization
-r              no              no              no      Statistic representation
-t              -s -t           no              no      Number of thread to launch
-p              -s -t           no              Out     Connect port
--debug         -s -m           no              Output  Debug file output
--sbml          -s -m           sbml.xml        Input   SBML file
--par           -s -m -r        parameter.xml   Input   Parameter file
--sim_out       -s -m           Repertory/      In/Out  Simulation out repertory
--min_out       -m -r           Repertory/      In/Out  Minimization out file
--stat_out      -r              Repertory/      Output  Statistic out repertory

======================================
=2. Reporting bugs and other problems= 
======================================

We invite you to report bugs and other problems using the issue
tracker for MetaBoFlux on SourceForge.  The following URL will take you
there directly:

  http://sourceforge.net/projects/metaboflux/support

You can also ask questions on the 'metaboflux-support@lists.sourceforge.net' mailing
list, either over email or using the web forum interface (see below).

==================
=3. MAILING LISTS=
==================

=======================
Discussion lists
=======================

All discussion lists, their web interfaces and their RSS feeds are at

         http://sourceforge.net/projects/metaboflux/forums

If you use MetaBoFLux, we encourage you to subscribe to 
'metaboflux-support@lists.sourceforge.net' mailing
list, where people discuss the development, use, and interoperability 
of the software.

If you are interested in helping to modify MetaBoFlux, or just want to
know about deeper issues and technical topics, you are welcome to
subscribe to the 'metaboflux-development@lists.sourceforge.net' mailing list.  
Being a member of metaboflux-development will enable you to keep in touch with the
latest developments in MetaBoFlux as well as to ask questions and share
your experiences with fellow developers and users of MetaBoFlux.

===============================
=4. LICENSING AND DISTRIBUTION=
===============================
Licensing and Distribution Terms for MetaBoFlux:

Copyright (C) 2010 Amine Ghozlane from LaBRI and University of Bordeaux 1   
                                                                            
MetaBoFlux is free software: you can redistribute it and/or modify          
it under the terms of the GNU Lesser General Public License as published by        
the Free Software Foundation, either version 3 of the License, or           
(at your option) any later version.                                         
                                                                            
MetaBoFlux 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 Lesser General Public License           
along with this program name "COPYING".  If not, see <http://www.gnu.org/licenses/>.

====================
=5. Acknowledgments= 
====================

This work is supported by the Agence Nationale de la Recherche
(ANR) program METABOTRYP of the ANR-MIME and
SYSTRYP of the ANR-BBSRC call and the CBiB.

-----------------------------------------------
File author: A. Ghozlane
Last Modified: $Date: 2011-01-12 18:00:00 $
Last Modified By: $Author: Ghozlane $
-----------------------------------------------

# The following is for [X]Emacs users.  Please leave in place.
# Local Variables:
# fill-column: 70
# End: