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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
Data input template. Flux data input template specifying: (1) experimental metadata, (2) the conditions, (3) the time points/samples, (4) the substance weights, e. g. number of C-atoms, (5) the reaction-equations and (6) the flux values including quality information. The template shows data from the first use case described in the Results section.
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Figure 2: Data input template. Flux data input template specifying: (1) experimental metadata, (2) the conditions, (3) the time points/samples, (4) the substance weights, e. g. number of C-atoms, (5) the reaction-equations and (6) the flux values including quality information. The template shows data from the first use case described in the Results section.

Mentions: For the import of flux data, FluxMap makes use of a structured Excel template file (see Figure‚ÄČ2). In fields 1 and 2 the user is asked to specify experimental metadata such as experiment annotation and information about different conditions. Field 3 contains information about time points which have been considered in the course of the experiment. In case of the visualization of substance fluxes, the user needs to specify the substance weights (assigning atom numbers to metabolites) in field 4. For visualization of mass fluxes the atom number has to be set to 1 for each metabolite. Reaction formulas have to be defined in field 5 with the corresponding flux measurement values in field 6. The reaction formula consists of two arrow-separated lists of reactant and product substances. Stoichiometric factors are part of the reaction formula and are allowed to be non-integer numbers. Furthermore, the input template supports the assignment of quality parameters (e. g. confidence interval) to each flux measurement value. Taken together the template enables users to import and save the flux measurement data together with experiment metadata in a well-structured way.


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)

Data input template. Flux data input template specifying: (1) experimental metadata, (2) the conditions, (3) the time points/samples, (4) the substance weights, e. g. number of C-atoms, (5) the reaction-equations and (6) the flux values including quality information. The template shows data from the first use case described in the Results section.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 2: Data input template. Flux data input template specifying: (1) experimental metadata, (2) the conditions, (3) the time points/samples, (4) the substance weights, e. g. number of C-atoms, (5) the reaction-equations and (6) the flux values including quality information. The template shows data from the first use case described in the Results section.
Mentions: For the import of flux data, FluxMap makes use of a structured Excel template file (see Figure‚ÄČ2). In fields 1 and 2 the user is asked to specify experimental metadata such as experiment annotation and information about different conditions. Field 3 contains information about time points which have been considered in the course of the experiment. In case of the visualization of substance fluxes, the user needs to specify the substance weights (assigning atom numbers to metabolites) in field 4. For visualization of mass fluxes the atom number has to be set to 1 for each metabolite. Reaction formulas have to be defined in field 5 with the corresponding flux measurement values in field 6. The reaction formula consists of two arrow-separated lists of reactant and product substances. Stoichiometric factors are part of the reaction formula and are allowed to be non-integer numbers. Furthermore, the input template supports the assignment of quality parameters (e. g. confidence interval) to each flux measurement value. Taken together the template enables users to import and save the flux measurement data together with experiment metadata in a well-structured way.

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