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FBA-SimVis specifications

Information


Unique identifier OMICS_05186
Name FBA-SimVis
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Windows
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Publication for FBA-SimVis

FBA-SimVis citations

 (4)
library_books

Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain

2015
PLoS One
PMCID: 4373785
PMID: 25806817
DOI: 10.1371/journal.pone.0119016

[…] tware packages are currently available (see [] for an overview), each having a different scope and flavor. Most of the tools are based on MATLAB, such as the COBRA Toolbox 2.0 [], CellNetAnalyzer [], FBA-SimVis [] or the RAVEN toolbox []. Other tools are stand-alone software, for instance SurreyFBA [] or OptFlux []. FAME is the first web-based approach to stoichiometric flux analysis [].BiGGR prov […]

library_books

Improving Collaboration by Standardization Efforts in Systems Biology

2014
Front Bioeng Biotechnol
PMCID: 4259112
PMID: 25538939
DOI: 10.3389/fbioe.2014.00061

[…] ate solutions for complex enzyme reactions and even solve ODE and DAE systems with delays and events. Further important tools for FBA are FASIMU (Hoppe et al., ), the VANTED (Junker et al., ) plug-in FBA-SimVis (Grafahrend-Belau et al., ), and PySCeS (Olivier et al., ). […]

library_books

Computational Approaches for Microalgal Biofuel Optimization: A Review

2014
Biomed Res Int
PMCID: 4189764
PMID: 25309916
DOI: 10.1155/2014/649453

[…] in to visualize flux distribution in the molecular interaction network. VANTED [, ] is another data visualization and data integration tool which can be utilized as a stand-alone tool. FluxMap [] and FBA-SimVis [] are VANTED plug-in for visualization of metabolic flux after FBA analysis. In addition, Paint4net [] is a tool to automatically generate maps of reaction fluxes in conjunction with COBRA […]

library_books

Genome Scale Modeling in Systems Biology: Algorithms and Resources

2014
Curr Genomics
PMCID: 4009841
PMID: 24822031
DOI: 10.2174/1389202915666140319002221

[…] ich additionally contains example pathways and measurement datasets. VANTED contains some Add-ons for demonstration and analysis of biological networks in which we will describe them in the summary. FBA-SimVis: The constraint-based analysis of metabolic models. FluxMap: advanced visualization of simulated or measured flux data in biological networks. PetriNet: handle discrete and continuous pla […]

Citations

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FBA-SimVis institution(s)
Leibniz-Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben and Institute of Computer Science, Martin-Luther-University Halle-Wittenberg, Germany

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