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Table 4 Comparison of tools considering compatible network file formats importing.

From: Visualization of protein interaction networks: problems and solutions

File Format

Tools

 

Arena3D

AVIS

BioLayout3D

Cytoscape

Medusa

NAViGaTOR

ONDEX

Osprey

Pajek

PIVOT

ProViz

SBML

-

-

-

-

-

?

?

BioPAX

-

-

-

-

-

-

?

?

PSI-MI

-

-

-

-

?

?

graphml

-

-

-

-

-

-

-

?

?

oxl

-

-

-

-

-

-

-

-

?

?

mepn

-

-

-

-

-

-

-

-

?

?

xml

-

-

-

-

-

-

?

?

xls

-

-

-

-

-

-

-

-

?

?

XGMML

-

-

-

-

-

-

-

-

?

?

layout

-

-

-

-

-

-

-

-

?

?

gml

-

-

-

-

-

-

-

?

?

txt

-

-

-

?

?

SIF

-

-

-

-

-

-

-

?

?

net

-

-

-

-

-

-

?

?

sig

-

-

-

-

-

-

-

-

?

?

avis

-

-

-

-

-

-

-

-

?

?

nwb

-

-

-

-

-

-

-

-

?

?

expression

-

-

-

-

-

-

-

-

?

?

paj

-

-

-

-

-

-

-

-

?

?

osp

-

-

-

-

-

-

-

?

?

dat

-

-

-

-

-

-

-

?

?

gl

-

-

-

-

-

-

-

?

?

  1. The table lists the network file formats that each tool can read in order to display it. Each file format allows to store additional information about network layout and allows network data exchange with the compatible programs and data sources. More information on functions load/import can be found in the tool's website, cited in the previous section. The ? means that it was not possible to establish the feature for the tool.
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BMC Bioinformatics

ISSN: 1471-2105

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