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Table 1 Comparison of BiNoM functionalities with other software tools

From: BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats

Function BiNoM CellDesigner BioPAX2SBML SyBiL SBFC Biographer CySBML ShortestPath Glay MCode Moduland ClusterMaker NeMo
Standalone application ∘ • • • • • ∘ ∘ ∘ ∘ ∘ ∘ ∘
Cytoscape plugin • ∘ ∘ ∘ ∘ ∘ • • • • • • •
BioPAX import • • • • • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
BioPAX visualization • • ∘ • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
BioPAX properties editor • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
BioPAX queries • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
BioPAX export • ∘ ∘ • • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
SBML import • • ∘ • • • • ∘ ∘ ∘ ∘ ∘ ∘
SBML visualization • • ∘ • ∘ • • ∘ ∘ ∘ ∘ ∘ ∘
SBML validation ∘ ∘ ∘ ∘ • ∘ • ∘ ∘ ∘ ∘ ∘ ∘
SBML layout and              
qualitative support ∘ ∘ • ∘ ∘ ∘ • ∘ ∘ ∘ ∘ ∘ ∘
CellDesigner import,              
visualization and export • • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
CSML import • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
CSML visualization • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Cytoscape extra              
utilities • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Get connected              
network components • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ • ∘ • •
Semantic clustering • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Community structure              
clustering ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ • ∘ ∘ ∘ ∘
Hierarchical modules              
clustering ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ • ∘ ∘
Multiple standard              
clustering methods ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ • ∘
Network decomposition • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Get shortest paths • ∘ ∘ ∘ ∘ ∘ ∘ • ∘ ∘ ∘ ∘ ∘
Get optimal and suboptimal              
shortest paths • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Get all non              
self-intersecting paths • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Path influence quantification • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
Module manager • ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘ ∘
  1. The table is comparing the main functions in BiNoM with other visualization and network analysis tools. The symbol • indicates that the function is available within the tool, while ∘ indicates that the function is not available. The references for the software tools are: CellDesigner [20, 23], BioPAX2SBML [24], SyBiL [25], SBFC (Systems Biology File Converter (http://www.ebi.ac.uk/compneur-srv/sbml/converters/SBMLtoBioPax.html), biographer (http://code.google.com/p/biographer/), cySBML [26], ShortestPath (http://csresources.sourceforge.net/ShortestPath/), Glay [27], MCode [28], ModuLand [29], clusterMaker [30], NeMo [31].
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BMC Systems Biology

ISSN: 1752-0509

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