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fast-tfva 2.0
=============
fast-tfva is a tool for fast thermodynamic constrained flux-variability analysis. It is written as a C++ plugin script for Matlab.
Copyright (C) 2012  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/>.


A Remark on Version 2.0
=======================
fast-tfva 2.0 is a complete rewrite. It is
* does not necessarily depend on libSBML
* easier to install
* easier to extend
  * constraints on metabolite concentrations are supported
  * additional constraints can easily be added when using the C++ library

Installation of fast-tfva
=========================
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! 
This instruction is designed for Linux and may also work for other UNIX-type systems. For Windows you will probably have to adjust some configura
tions. (If you have an install instruction for Windows, please send them to me!)
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Fast-tfva 2.0 uses:
* SCIP Optimization Suite - http://scip.zib.de

Optionally you can link in
* libSBML - http://sbml.org/Software/libSBML
* Matlab

Without SCIP, you won't be able to run fast-tfva. SCIP is open-source. See its webpage for lincensing-details.

On university computers it is usually the case that the user does not have root access. Hence, the installation procedure is designed to work also with non-root access.

After you have installed all the third-party dependencies (see third_party/README for instructions), you simply have to call make to build the fast tfva.

If you have no matlab dependencies installed, call
make MATLAB=off

If you have no sbml dependencies installed, call
make SBML=off

Those two options can also be intercombined. Per default, usage of Matlab and SBML is activated.


Testing of fast-tfva
====================

If you compiled fast-tfva with Matlab support, you can run a test case (tfva on E coli iAF1260) by calling

make test

======================
DONE - CONGRATULATIONS
======================

If you have problems with installing fast-tfva, you can send me an email: arne.mueller[at]fu-berlin.de
Source: README, updated 2013-02-11