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FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks.

Rohn H, Hartmann A, Junker A, Junker BH, Schreiber F - BMC Syst Biol (2012)

Bottom Line: Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists.Various visualization options enable the user to adapt layout and network representation according to individual purposes.The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research, IPK, Molecular Genetics, Corrensstr 3, Gatersleben 06466, Germany. rohn@ipk-gatersleben.de

ABSTRACT

Background: The quantification of metabolic fluxes is gaining increasing importance in the analysis of the metabolic behavior of biological systems such as organisms, tissues or cells. Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists. The visualization of flux distributions is a necessary prerequisite for intuitive flux data exploration in the context of metabolic networks.

Results: We present FluxMap, a tool for the advanced visualization and exploration of flux data in the context of metabolic networks. The template-based flux data import assigns flux values and optional quality parameters (e. g. the confidence interval) to biochemical reactions. It supports the discrimination between mass and substance fluxes, such as C- or N-fluxes. After import, flux data mapping and network-based visualization allow the interactive exploration of the dataset. Various visualization options enable the user to adapt layout and network representation according to individual purposes.

Conclusions: The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks. It is available as a Java open source tool from http://www.vanted.org/fluxmap.

Show MeSH
Schematic workflow of FluxMap. FluxMap requires the import of structured flux data and metabolic networks (SBML, KGML or GML). The flux measurement values are mapped to the metabolic network and validation can be performed. In case of invalid flux distributions, the imported data should be re-checked. The visualization of a valid flux distribution can be adapted to individual purposes and exported in several file formats. Various interaction options enable the visual and comparative exploration of flux distributions in the context of biologicalnetworks.
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Figure 1: Schematic workflow of FluxMap. FluxMap requires the import of structured flux data and metabolic networks (SBML, KGML or GML). The flux measurement values are mapped to the metabolic network and validation can be performed. In case of invalid flux distributions, the imported data should be re-checked. The visualization of a valid flux distribution can be adapted to individual purposes and exported in several file formats. Various interaction options enable the visual and comparative exploration of flux distributions in the context of biologicalnetworks.

Mentions: Here we present FluxMap, a Vanted [3] add-on specialized on the visualization and exploration of flux distributions, supporting all above mentioned requirements. The FluxMap workflow schema depicted in Figure‚ÄČ1 and an example shown in detail in Additional file 1.


FluxMap: a VANTED add-on for the visual exploration of flux distributions in biological networks.

Rohn H, Hartmann A, Junker A, Junker BH, Schreiber F - BMC Syst Biol (2012)

Schematic workflow of FluxMap. FluxMap requires the import of structured flux data and metabolic networks (SBML, KGML or GML). The flux measurement values are mapped to the metabolic network and validation can be performed. In case of invalid flux distributions, the imported data should be re-checked. The visualization of a valid flux distribution can be adapted to individual purposes and exported in several file formats. Various interaction options enable the visual and comparative exploration of flux distributions in the context of biologicalnetworks.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3403919&req=5

Figure 1: Schematic workflow of FluxMap. FluxMap requires the import of structured flux data and metabolic networks (SBML, KGML or GML). The flux measurement values are mapped to the metabolic network and validation can be performed. In case of invalid flux distributions, the imported data should be re-checked. The visualization of a valid flux distribution can be adapted to individual purposes and exported in several file formats. Various interaction options enable the visual and comparative exploration of flux distributions in the context of biologicalnetworks.
Mentions: Here we present FluxMap, a Vanted [3] add-on specialized on the visualization and exploration of flux distributions, supporting all above mentioned requirements. The FluxMap workflow schema depicted in Figure‚ÄČ1 and an example shown in detail in Additional file 1.

Bottom Line: Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists.Various visualization options enable the user to adapt layout and network representation according to individual purposes.The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks.

View Article: PubMed Central - HTML - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research, IPK, Molecular Genetics, Corrensstr 3, Gatersleben 06466, Germany. rohn@ipk-gatersleben.de

ABSTRACT

Background: The quantification of metabolic fluxes is gaining increasing importance in the analysis of the metabolic behavior of biological systems such as organisms, tissues or cells. Various methodologies (wetlab or drylab) result in sets of fluxes which require an appropriate visualization for interpretation by scientists. The visualization of flux distributions is a necessary prerequisite for intuitive flux data exploration in the context of metabolic networks.

Results: We present FluxMap, a tool for the advanced visualization and exploration of flux data in the context of metabolic networks. The template-based flux data import assigns flux values and optional quality parameters (e. g. the confidence interval) to biochemical reactions. It supports the discrimination between mass and substance fluxes, such as C- or N-fluxes. After import, flux data mapping and network-based visualization allow the interactive exploration of the dataset. Various visualization options enable the user to adapt layout and network representation according to individual purposes.

Conclusions: The Vanted add-on FluxMap comprises a comprehensive set of functionalities for visualization and advanced visual exploration of flux distributions in biological networks. It is available as a Java open source tool from http://www.vanted.org/fluxmap.

Show MeSH