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) |