Table 1

Summary of tasks supported by VANTED
Task Sub-Tasks Implemented in
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
)

The first column comprises the task covered by the VANTED framework. The second column shortly summarizes sub-tasks. Underlined sub-tasks indicate new functionalities developed since the initial VANTED publication in 2006 [4]. The third column lists the modules of the VANTED framework (VANTED core, add-ons) that implement the described tasks.

Rohn et al.

Rohn et al. BMC Systems Biology 2012 6:139   doi:10.1186/1752-0509-6-139

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