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Metaopt (fast-tFVA)

The Metaopt Toolbox is a general framework for flux balance analysis with thermodynamic constraints. It was developed for a fast implementation of thermodynamically constrained flux variability analysis (tFVA). See the Article published in Bioinformatics for algorithmic details.

Even large networks like the E. coli iAF1260 model with more than 2000 reactions can be analyzed in a few minutes.

However, the toolbox is not only restricted to tFVA, but also contains other algorithms that may be useful for other purposes. In general, it is designed around one optimization framework implemented using SCIP. It uses libSBML to load models from SBML files. It is written in such a way that it can be called from Matlab using COBRA models.

Next to the ordinary constraints encountered in metabolic network analysis arbitrary additional constraints can be added.
In particular, it also offers the integration on bounds of metabolite potentials.
However, most additional constraints are likely to cancel the speedups that are obtainable for the default case (FBA + thermodynamic constraints).

Structure

The project is structured into two subprojects.

There is a pure C++ implementation of the metaopt library. This offers all the features of the toolbox to C++ developers.

There is a Matlab wrapper that allows matlab users to acces the most basic tools like FBA, tFBA, FVA and tFVA.

Download

The bundled packages contain both parts (C++ library and Matlab binding) together with a make file to build everything. It is recommended to obtain the latest version as a bundled package (see Files).
The makefile can be so configured to build the toolbox without Matlab.

The git repositories separately store the C++ library and the matlab binding.

Installation

Please see the [Installation] page for details.

Changelog

Please see the [Changelog] page for details.

Contact

Admins of this project are

Project Admins:

• arne