Flux Visualization Using VANTED/FluxMap

Krach, Christian; Junker, Astrid; Rohn, Hendrik; Schreiber, Falk; Junker, Björn H.

doi:10.1007/978-1-4939-1170-7_14

Cited by 2 publications

(2 citation statements)

References 9 publications

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“…To visualize these flux data is also important to activation/deactivation of individual reactions. FluxMap [40,41] is one of the tools to incorporate such type of data. A recent review article [42] also lists such tools.…”

Section: Resultsmentioning

confidence: 99%

Metabolomic pathway visualization tool outsourcing editing function

Sugimoto

2015

2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

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Recent rapid improvements of measuring instrument enables us to perform various omics studies to simultaneous profile multiple molecules, which provides a holistic view of various molecular interactions, such as signal transaction, protein interactions, and metabolic pathways. Metabolomics is recently emerged omics that can identify and quantify low weight metabolites usually defined as organic molecules whose size is <; 1500 Da. In comparison to the other omics, the development of software tools to deal with metabolomic data is not matured. Conventional pathway drawing and visualization tool provide tool-specific unique functions, however, such user interface requires users to learn the usage and prevention for the use of these tools. Here, we developed a more generic pathway visualization tool. This tool incorporate pathway data yielded by common drawing tools, e.g. MS PowerPoint, and visualize the quantified values on the pathways. The statistical results also can be overlaid on each metabolite. The developed tools facilitate the interpreting metabolomic data in pathway forms.

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Section: Resultsmentioning

confidence: 99%

Metabolomic pathway visualization tool outsourcing editing function

Sugimoto

2015

2015 37th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC)

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“…Once constructed, the models can be used to simulate growth by, for example, flux balance analysis (FBA) and to determine the boundaries of fluxes by flux variability analysis (FVA). Tools for modelling are Pysces [ 28 ], the SEED [ 26 ] and VANTED [ 29 ]. 3 Microbiome analysis All microbes present in a particular niche are termed a microbiome.…”

Section: Introductionmentioning

confidence: 99%

Microbial bioinformatics for food safety and production

Alkema¹,

Boekhorst²,

Wels³

et al. 2015

Brief Bioinform

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In the production of fermented foods, microbes play an important role. Optimization of fermentation processes or starter culture production traditionally was a trial-and-error approach inspired by expert knowledge of the fermentation process. Current developments in high-throughput ‘omics’ technologies allow developing more rational approaches to improve fermentation processes both from the food functionality as well as from the food safety perspective. Here, the authors thematically review typical bioinformatics techniques and approaches to improve various aspects of the microbial production of fermented food products and food safety.

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Flux Visualization Using VANTED/FluxMap

Cited by 2 publications

References 9 publications

Metabolomic pathway visualization tool outsourcing editing function

Metabolomic pathway visualization tool outsourcing editing function

Microbial bioinformatics for food safety and production

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