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Table 1 Overview of the different features present in DynOVis, Cytoscape and the different Cytoscape applications

From: DynOVis: a web tool to study dynamic perturbations for capturing dose-over-time effects in biological networks

Tools

DynOVis

Cytoscape

DyNet

CyAnimator

DyNetViewer

Platform

web

Standalone Java application

Cytoscape plugin

Cytoscape plugin

Cytoscape plugin

Input Network

List of interactions, Adjacency matrix, .sif file

List of interactions, Adjacency matrix, .sif file, URL or database

Cytoscape input types + 2 equal networks

Cytoscape input

Cytoscape input

Input data

Text file, CSV file, excel workbook

Text file, CSV file, Excel workbook, URL or database

Text file, CSV file, Excel workbook, URL or database

Text file, CSV file, Excel workbook, URL or database

Text file

Built-in database

Yes

No

No

No

No

Network layout

Force directed layout

Multiple different layouts

Cytoscape Layouts

Cytoscape Layouts

Cytoscape Layouts

Weighted edge visualization

No

Yes

Yes

Yes (from Cytoscape Core function)

No

Dynamic node expression

Yes

No

Yes

Yes

No

Dynamic node interactions

Yes

No

Yes

No

Yes

3D visualization

Yes

No

No

No

No

2D Line graph expression values

Yes

No

No

No

No

Pathway histogram

Yes

No

No

No

No