FIA Software, Version RC1
=========================

Overview
--------

Fluxomer Iterative Algorithm (FIA) is a novel approach for 
metabolic flux analysis (MFA) based upon 13C tracer experiments.

Detailed explanation can be found in 
 <ARTICLE CITE>  

The software is implemented in Python and the source code is available.

Prerequisites
-------------

* Python (preferably 2.6)
* NumPy
* SciPy 
* UMFPACK libraries

Installing the prerequisites (if not already available)
-------------------------------------------------------

Using Ubuntu:
	Invoke the following command:
		sudo apt-get install python-scipy python-tk

From scratch:
	1. Install Python
	   - Download from http://www.python.org/
	 
	   FIA was tested with Python 2.6.
	
	   - Unpack and install Python
	
	3. Install UMFPACK 
	
	   Best thing would be installing the binary package for your machine. 
	   If unavailable, compilation from sources is also possible.
	
	   - Download sources from http://www.cise.ufl.edu/research/sparse/umfpack/ 
	
	   - Follow the author's compilation instructions for the building procedures.

	2. Install Scientific Tools for Python 
	
	   - Download NumPy from http://www.numpy.org/ or http://www.scipy.org .
	
	   - Unpack and Install the NumPy package
	
	   - Download Scipy from http://www.scipy.org .
	
	   - Unpack and Install the SciPy package

Running FIA
-----------

Simply click the "fia_gui.py" and run it
OR
use the command line to invoke "python fia_gui.py" (make sure to run the command from the directory FIA was extracted to).
	
Documentation
-------------

User manual is available online and in PDF format.
Full API documentation is available online.

Acknowledgements
----------------

This work was done as part of the Masters thesis work at the

Technion, Israel Institute of Technology .

