VANTED v2: a framework for systems biology applications

BMC Systems Biology

Table 2 Comparison of non-commercial tools for the network-centered visualization and analysis of biological data

Tasks	Vanted	Cytoscape	Ondex	Omix	Cell	PathVisio	BioUML	VisAnt	Pathway	BiNA	MapMan
		[[12]]	[[54]]	[[55]]	Designer	[[57]]	[[58]]	[[59]]	Projector	[[61]]	[[62]]
					[[56]]				[[60]]
Import
networks	+	+	+	+	+	(+)	+	(+)	+	+	-
experimental data	+	+	+	+	(+)	+	+	-	+	(+)	+
connection to experiment database	+	+	+	-	(+)	-	-	-	-	+	-
connection to network databases	+	+	+	-	(+)	-	+	+	(+)	+	+
Visualization
charts on nodes and edges	+	-	-	+	-	-	-	-	+	-	+
automatic network layouts	+	+	+	+	+	-	+	+	-	+	-
SBGN support	+	+	-	-	(+)	+	+	-	-	-	-
flux data support	+	+	-	+	+	-	-	-	(+)	+	-
3D visualization	+	(+)	-	+	-	-	-	-	-	-	-
Integration
mapping of numerical or	+	+	+	+	+	+	-	-	+	+	+
multimodal data
mapping tables, identifier mapping	+	+	+	-	-	(+)	+	-	+	(+)	-
linking other resources	+	+	+	+	+	+	+	+	+	-	+
Simulation
constraint-based analysis	+	(+)	-	+	(+)	-	-	-	-	-	-
Petri net analysis	+	-	-	-	(+)	-	-	-	-	-	-
Exploration and interaction
panning, zooming, collapsing,	+	+	+	+	(+)	(+)	+	+	+	+	(+)
search and selection
network exploration	+	+	+	-	-	(+)	+	+	+	+	+
brushing, image exploration	+	-	-	-	-	-	-	-	-	-	-
Analysis
networks	+	+	+	-	(+)	-	+	+	-	(+)	-
statistics	+	+	+	-	-	+	-	-	-	(+)	+
enrichment analysis	+	+	-	-	-	+	+	+	-	+	+
Export
raster graphics, vector graphics	+	+	+	+	+	+	+	+	-	+	(+)
interactive websites	+	-	-	-	-	(+)	+	+	+	-	-
experimental data	+	+	-	-	+	-	+	-	+	+	-
networks	+	+	+	+	+	+	+	(+)	-	+	-

The first column comprises the sub-tasks of Table 1, which are covered by the respective tool. Please note that also add-ons and plugins of the respective system were evaluated. “-” no or inadequate support, “(+)” = partial support, “+” good support of the sub-task.

ISSN: 1752-0509