Biana: a software framework for compiling biological interactions and analyzing networks

BMC Bioinformatics

Table 1 Comparison of network analysis platforms.

Feature	CY	GM	VA	OS	CD	AR	IN	GG	PI	PR	BL	PA	BI
Free for academic use	X	X	X	X	X				X	X	X	X	X
Free for commercial use	X	X	X		X				X	X	X		X
Open source	X	X							X	X	X		X
Curated pathway/network content		X		X		X	X	X
Standard file format support	X		X		X				X	X		X	X
User-defined networks/pathways	X	X	X	X	X	X	X	X	X	X	X	X	X
Functionality to infer new pathways	X		X			X		X	X				X
GO/pathway enrichment analysis	X	X	X				X	X					X
Automated graph layout	X		X	X	X	X	X	X		X	X	X	X
Complex criteria for visual properties		X				X	X	X		X	X	X
Multiple visual styles	X		X	X		X	X			X			X
Advanced node selection	X		X	X		X	X	X	X	X	X	X	X
Customizable gene/protein database		X	X			X		X	X				X
Rich graphical annotation		X	X				X	X				X	X
Statistical network analysis	X		X				X	X	X		X		X
Extensible functionality: plugins or API	X		X		X	X	X	X	X				X
Quantitative pathway simulation					X	X

BIANA has been compared with the same programs and using the same set of features as the ones presented in [21]. Compared software: CY, Cytoscape [55]; GM, GenMAPP [58]; VA, VisANT [59]; OS, Osprey [60]; CD, CellDesigner [61]; AR, Ariadne Genomics Pathway Studio [62]; IN, Ingenuity Pathways Analysis http://www.ingenuity.com; GG, GeneGO http://www.genego.com; PI, PIANA [13]; PR, ProViz [63]; BL, BioLayout [64]; PA, PATIKA [65]; BI, BIANA.

ISSN: 1471-2105