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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
Interaction. Part of a flux map, in which the nodes of the widely distributed substance “ATP_c” (brown nodes) were temporarily and interactively connected (green node and edges) in order to support tracking of main flux directions in large maps. Gray nodes indicate transport reactions to or from other compartments.
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Figure 4: Interaction. Part of a flux map, in which the nodes of the widely distributed substance “ATP_c” (brown nodes) were temporarily and interactively connected (green node and edges) in order to support tracking of main flux directions in large maps. Gray nodes indicate transport reactions to or from other compartments.

Mentions: FluxMap offers a simple dialog which can be used to parameterize the visualization of the flux distribution according to individual needs (see Figure 3). The multiplicator parameter adapts the global edge thickness of all fluxes (Figure 3, field 2). The arrowhead/-tail ratio might be varied in order to emphasize the edge direction rather than the edge thickness (field 2). Different reaction node visualization styles can be chosen, e. g. invisible, small, rounded or normal nodes with or without labels (field 3). It is additionally possible to visualize the quality parameters using a configurable color graduation, thereby highlighting potential measurement errors (field 4; compare also Figures 4 and 5, red saturation). Each of these parameter modifications triggers an instant redraw of t he flux map. Instead of the representation of flux values as edge thickness, flux data might also be visualized using charts, e. g. bar- or line-charts which are assigned to edges or the reaction nodes. General network editing functionalities (node and edge coloring, node size, node shape) are implemented in Vanted and accessible through FluxMap.


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)

Interaction. Part of a flux map, in which the nodes of the widely distributed substance “ATP_c” (brown nodes) were temporarily and interactively connected (green node and edges) in order to support tracking of main flux directions in large maps. Gray nodes indicate transport reactions to or from other compartments.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 4: Interaction. Part of a flux map, in which the nodes of the widely distributed substance “ATP_c” (brown nodes) were temporarily and interactively connected (green node and edges) in order to support tracking of main flux directions in large maps. Gray nodes indicate transport reactions to or from other compartments.
Mentions: FluxMap offers a simple dialog which can be used to parameterize the visualization of the flux distribution according to individual needs (see Figure 3). The multiplicator parameter adapts the global edge thickness of all fluxes (Figure 3, field 2). The arrowhead/-tail ratio might be varied in order to emphasize the edge direction rather than the edge thickness (field 2). Different reaction node visualization styles can be chosen, e. g. invisible, small, rounded or normal nodes with or without labels (field 3). It is additionally possible to visualize the quality parameters using a configurable color graduation, thereby highlighting potential measurement errors (field 4; compare also Figures 4 and 5, red saturation). Each of these parameter modifications triggers an instant redraw of t he flux map. Instead of the representation of flux values as edge thickness, flux data might also be visualized using charts, e. g. bar- or line-charts which are assigned to edges or the reaction nodes. General network editing functionalities (node and edge coloring, node size, node shape) are implemented in Vanted and accessible through FluxMap.

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