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Table 1 Comparison of network analysis platforms.

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

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        
  1. 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.