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Publication for FBA-SimVis
Using Bioconductor Package BiGGR for Metabolic Flux Estimation Based on Gene Expression Changes in Brain
[…] 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 […]
Improving Collaboration by Standardization Efforts in Systems Biology
[…] 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., ). […]
Computational Approaches for Microalgal Biofuel Optimization: A Review
[…] 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 […]
Genome Scale Modeling in Systems Biology: Algorithms and Resources
[…] 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 […]
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