Table 1 Comparison of BiNoM functionalities with other software tools
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 | • | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ | ∘ |