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Table 1 Summary of tasks supported by VANTED

From: VANTED v2: a framework for systems biology applications

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)  
  1. 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.