|
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
|
•
| ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ |
- 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].
