Recent changes to Home

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 15:33:20 -0000

--- v6
+++ v7
@@ -3,7 +3,10 @@

 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](http://dx.doi.org/10.1093/bioinformatics/btt059) for algorithmic details.

-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](http://scip.zib.de).
+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](http://scip.zib.de). 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).

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 15:31:20 -0000

--- v5
+++ v6
@@ -26,8 +26,6 @@

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

-[[download_button]]

-
 Installation
 ------------

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 15:31:01 -0000

--- v4
+++ v5
@@ -26,7 +26,7 @@

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

-[[download_button]]
+[[download_button]]


 Installation
 ------------

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 15:30:37 -0000

--- v3
+++ v4
@@ -21,13 +21,12 @@

 Download
 --------
-[[download_button]]
-
 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.

+[[download_button]]

 Installation
 ------------

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 15:28:25 -0000

--- v2
+++ v3
@@ -1,8 +1,45 @@
-Welcome to the Metaopt Wiki!
+Metaopt (fast-tFVA)
+===================

-This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].
+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](http://dx.doi.org/10.1093/bioinformatics/btt059) for algorithmic details.

-The wiki uses [Markdown](/p/metaopt/wiki/markdown_syntax/) syntax.
+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](http://scip.zib.de).
+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).

-[[project_admins]]
+
+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
+--------
 [[download_button]]
+
+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]]

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 13:12:27 -0000

--- v1
+++ v2
@@ -1,4 +1,4 @@
-Welcome to your wiki!
+Welcome to the Metaopt Wiki!

 This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

Discussion for Home page

arne — Mon, 11 Feb 2013 13:07:16 -0000

Metaopt

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.

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.
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 cna be so configured to build the toolbox without Matlab.

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

WikiPage Home modified by arne

arne — Mon, 11 Feb 2013 09:55:22 -0000

Welcome to your wiki!

This is the default page, edit it as you see fit. To add a new page simply reference it within brackets, e.g.: [SamplePage].

The wiki uses Markdown syntax.

arne