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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].