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The table below puts ViaComplex in context with other related softwares according to five features:

 

  • Visualization of network topology and/or interaction maps: Here are listed softwares able to visualize the network structure, whether in details or not.
  • Layout algorithms and/or network manipulation: softwares able to change the network structure, whether via algorithmic methods or via user interactive manipulation.
  • 3D representations: Here we list softwares able to show gene networks in both 2D and 3D representations. A pseudo-3D classification is indicated according to Pavlopoulos et al (BioData Mining, 1:12, 2008).
  • Node-based visualization of high-throughput data: softwares able to integrate high-throughput data into network nodes (i.e. able to plot quantitative data in network vertices only). This feature is mainly associated to the analysis of large scale gene expression datasets.
  • Landscape visualization of high-throughput data: Here we consider an essential classification to contrast ViaComplex with other softwares, that is, the ability to project high-throughput data onto gene network graphs. This feature differs from the node-based visualization, since it deals with the entire network topology plotting quantitative data as a third axis of the network coordinates, which is able to create gene expression landscapes.

 

Table 2. Comparative table among ViaComplex and several related softwares*.

Package

Accessibility

Visualization of network topology and/or interaction maps

Layout algorithms and/or network manipulation

3D representations

Node-based visualization of high-throughput data

Landscape visualization of high-throughput data

ViaComplex

Open source

X

-

X

-

X

Biotapestry

Open source

X

X

-

-

-

CellDesigner

Open source

X

X

-

-

-

Cytoscape

Open source

X

X

-

X

-

Pajek

Free for noncom. use

X

X

Pseudo-3D

-

-

tYNA

Open source

X

X

-

X

-

Medusa

Open source

X

X

-

-

-

BioLayout Express 3D

Open source

X

X

X

X

-

Osprey

Free for noncom. use

X

X

-

-

-

ProViz

Open source

X

X

Pseudo-3D

-

-

Ondex

Open source

X

X

-

X

-

PATIKA

Free for noncom. use

X

X

-

X

-

PIVOT

Free for noncom. use

X

X

-

-

-

Pathway Studio

Commercial

X

X

-

X

-

InterViewer

Free for noncom. use

X

X

-

-

-

VisANT

Free for noncom. use

X

X

-

X

-

Biological Networks

Free for academic use

X

X

-

X

-

Ingenuity Pathways

Commercial

X

X

-

X

-

biocGraph

Open source**

X

X

-

-

-

graph

Open source**

X

X

-

-

-

GraphAlignment

Open source**

X

X

-

-

-

hypergraph

Open source**

X

X

-

-

-

minet

Open source**

X

X

-

-

-

ontoTools

Open source**

X

X

-

-

-

pathRender

Open source**

X

X

-

X

-

RBGL

Open source**

X

X

-

-

-

Rgraphviz

Open source**

X

X

-

-

-

 

*This review is focused in general aspects necessary to delineate common features among all softwares or in those aspects necessary do evaluate ViaComplex. Therefore, please observe that these softwares can provide some specific functions not listed above. For example: “Build developmental gene-regulatory network models”, “Simulate and analyze network behavior”, “Visualize process diagrams”, “Conduct graph theoretical analysis”, “Integrate data from different sources”, etc.

**Related softwares available as R/Bioconductor package at ComputationalDomains, GraphsAndNetworks

 

 

 

Present

 

Partially present

 

Absent

 

 

 

 

 

 

Reviews:

  1. Joyce, AR; Palsson, B. The model organism as a system: integrating ‘omics’ data sets. Nat Rev. Mol. Cell Biol. 198(7):1998-210, 2006.
  2. Suderman, M; Hallett, M. Tools for visually exploring biological networks. Bioinformatics, 23(20): 2651–2659, 2007.
  3. Pavlopoulos, GA; Wegener A; Schneider R. A survey of visualization tools for biological network analysis. BioData Mining, 1:12, 2008.