Table 1 Summary of tasks supported by VANTED

Import

∙ networks (GML, GraphML, SBML, KGML, SIF,

DOT, BioPAX, SBGN-ML, PNML)

core, MetaCrop add-on, DBE² add-on

∙ experimental data (XLS, XLSX^∗, CSV)

∙ connection to experiment database DBE²

∙ connection to network databases

(MetaCrop, KEGG, RIMAS)

Visualization

∙ charts (line, bar, pie, heat maps) on nodes and edges

core, SBGN-ED add-on,

HIVE add-on, FluxMap

add-on

∙ automatic network layouts (e. g., Graphviz,

force-directed, tree layout)

∙SBGN support

∙flux data support

∙3D visualization of networks and multimodal data

Integration

∙mapping of numerical or multimodal data

∙mapping tables, identifier mapping

∙ linking other resources

core, HIVE add-on

Simulation

∙constraint-based analysis

FBA-SimVis add-on,

∙Petri net analysis

Petrinet add-on

Exploration and interaction

∙ panning, zooming, collapsing, search, selection

∙network exploration

∙brushing, image exploration

core, GLIEP add-on, HIVE add-on

Analysis

∙ networks (centralities, shortest path, cycle detection, motifs)

core, Centilib add-on

∙ statistics (correlation, clustering, t-test)

∙enrichment analysis

Export

∙ raster graphics (PNG, JPG), vector graphics

(SVG, PDF, PPT, SBGN-ML)

core, DBE² add-on

∙interactive websites

∙ experimental data (XLS, XML, DBE²)

∙ networks (GML, GraphML, DAT (Metatool),

SBML, SBGN-ML, PNML)