Wordprocessing

Fluxviz - cytoscape plug-in for visualization of flux distributions in networks

Abstract:

Motivation: Methods like FBA and kinetic modeling are widely used to calculate fluxes in metabolic networks. For the analysis and understanding of simulation results and experimentally measured fluxes visualization software within the network context is indispensable. Results: We present Flux Viz, an open-source Cytoscape plug-in for the visualization of flux distributions in molecular interaction networks. FluxViz supports (i) import of networks in a variety of formats (SBML, GML, XGMML, SIF, BioPAX, PSI-MI) (ii) import of flux distributions as CSV, Cytoscape attributes or VAL files (iii) limitation of views to flux carrying reactions (flux subnetwork) or network attributes like localization (iv) export of generated views (SVG, EPS, PDF, BMP, PNG). Though FluxViz was primarily developed as tool for the visualization of fluxes in metabolic networks and the analysis of simulation results from FASIMU, a flexible software for batch flux-balance computation in large metabolic networks, it is not limited to biochemical reaction networks and FBA but can be applied to the visualization of arbitrary fluxes in arbitrary graphs. Availability: The platform-independent program is an open-source project, freely available at http://sourceforge.net/projects/fluxvizplugin/ under GNU public license, including manual, tutorial and examples.

22081592

Projects: No Projects

Genome Inform
Genome Inform 24(1): 96-103
1st Jul 2010

Matthias König, Hermann-Georg Holzhütter

help Authors

[Matthias König] [Hermann-Georg Holzhütter]

help Attributions

None

help Scales


Not Specified
Views: 1381
  • Created: 4th Jan 2013 at 11:14
  • Last updated: 24th Oct 2013 at 16:20

Related items

Ajax-loader-large

Log in / Register

Need an account?
Sign up

Forgotten password?

Front Page

Virtual Liver Network

(v.0.22.0)

Related Projects and friends


Imprint Taverna workflow workbench myExperiment JWS Online ISATAB myGrid Sabio-RK BioPortal Semantic SBML

Powered by:

Ror-logo-32

Icons:
Silk icons 1.3
Crystal Clear icons