Flux Balance

This project hosts the SBW Flux Balance Module. The program supports the SBML Level 3 Flux Balance Proposal, and so is able to read SBML files.

The program uses LPsolve as solver, and can so solve reasonably sized problems without any issue.

With the latest SBW version installed, the program also allows to import Jarnac or COPASI files!

Download

Github no longer supports binary releases. So starting with 1.8 they will be available from SourceForge. The current version is:

• Version 1.9: http://sourceforge.net/projects/sbw/files/modules/FluxBalance/SetupFBA-1.9.exe/download (Corrected SBW export, added menu item, to allow to send L2 or L3 models to SBW).

• Version 1.8: http://sourceforge.net/projects/sbw/files/modules/FluxBalance/SetupFBA-1.8.exe/download (New is additional export of SBML Level 2 Models using either FBA or COBRA annotations).

Previous Versions

Version 1.7 import of COBRA annotations, re-designed LP generation, so it will work for large models. Version 1.5, fixed issues with L3 package annotations in L2 models.
The Version 1.4, fixed issues with import from L2 annotation of FAME!
Version 1.3, the first version from github is still available!
The first version of the tool is still available from my blog, but essentially superceded by this project.

License

This project is open source and freely available under the Simplified BSD license. Should that license not meet your needs, please contact me.

Copyright (c) 2013, Frank T. Bergmann
All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
   

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.