FluxViz/CyFluxViz 1.00 – Cytoscape Plugin for Flux Visualization

FluxViz/CyFluxViz 1.00

:: DESCRIPTION

FluxViz is an open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks.FluxViz was used for the visualization and analysis of the metabolic network of the human hepatocyte

::DEVELOPER

Matthias König

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

FluxViz

:: MORE INFORMATION

Citation:

Genome Inform. 2010 Jul;24(1):96-103.
Fluxviz – cytoscape plug-in for visualization of flux distributions in networks.
König M, Holzhütter HG.

regEfmtool 3.3 – Regulatory Elementary Flux Mode Tool

regEfmtool 3.3

:: DESCRIPTION

regEfmtool is a computational tool that combines the calculation of elementary flux modes in metabolic networks with transcriptional regulatory networks. regEfmtool is based on the open source software efmtool 

::DEVELOPER

regEfmtool team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 regEfmtool

:: MORE INFORMATION

Citation

regEfmtool: speeding up elementary flux mode calculation using transcriptional regulatory rules in the form of three-state logic.
Jungreuthmayer C, Ruckerbauer DE, Zanghellini J.
Biosystems. 2013 Jul;113(1):37-9. doi: 10.1016/j.biosystems.2013.04.002.

FluxModeCalculator – Large-scale Flux mode Computation

FluxModeCalculator

:: DESCRIPTION

FluxModeCalculator is a MATLAB toolbox for computing the elementary flux modes, extreme pathways or minimal generating sets in stoichiometric models

::DEVELOPER

Jan Bert van Klinken

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • MatLab

:: DOWNLOAD

 FluxModeCalculator

:: MORE INFORMATION

Citation

FluxModeCalculator: an efficient tool for large-scale flux mode computation.
van Klinken JB, Willems van Dijk K.
Bioinformatics. 2015 Dec 18. pii: btv742.

FFCA 1.01 – Feasibility-based Flux Coupling Analysis of Metabolic Networks

FFCA 1.01

:: DESCRIPTION

FFCA is a Matlab based tool for flux coupling analysis. An LP solver should be installed separately and made “visible” from within Matlab. FFCA currently supports the usage of Linprog, Clp, Lindo and Glpk.

::DEVELOPER

Prof. Dr. Alexander Bockmayr

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Linux

:: DOWNLOAD

 FFCA

:: MORE INFORMATION

Citation

L. David, S.-A. Marashi, A.Larhlimi, B. Mieth, A. Bockmayr.
FFCA: a feasibility-based method for flux coupling analysis of metabolic networks“,
BMC Bioinformatics 2011, 12:236.