Question: Cytoscape Or Gephi?
gravatar for lkmklsmn
6.7 years ago by
United States
lkmklsmn930 wrote:

I am vaguely familiar with the network visualization softwares cytoscape and gephi.
Before I go more into depth with one of them I would like to hear about pros and cons of each. Any comments?

visualization cytoscape • 14k views
ADD COMMENTlink modified 6.5 years ago by Woa2.8k • written 6.7 years ago by lkmklsmn930
gravatar for Istvan Albert
6.7 years ago by
Istvan Albert ♦♦ 84k
University Park, USA
Istvan Albert ♦♦ 84k wrote:

Cytoscape has biology awareness, recognizes formats such as SMBL and knows about gene ontology formats and data. The apps developed for Cytoscale are mostly systems biology oriented.

Gephi is a more generic network visualizer that is not targeting any specific use case.

ADD COMMENTlink written 6.7 years ago by Istvan Albert ♦♦ 84k

This is exactly my impression. One thing to add: Gephi is a smaller, simpler, perhaps less "mature" project than Cytoscape. Therefore, if you just want a quick and dirty network visualizer to get a feel for the basics, Gephi may be a good place to start, because it is less complicated and not as confusing the first time you use it. For actual, real world research involving biological networks, Cytoscape will probably be necessary to use, however.

ADD REPLYlink written 6.7 years ago by Superbest120
gravatar for keiono
6.5 years ago by
keiono50 wrote:

Disclosure: I'm a core developer of Cytoscape

Cytoscape is a de-facto standard in life science research, mainly because of large user community and its Apps. Of course, Gephi has some advantages over Cytoscape, such as nice presets and built-in statistical analysis module and we, Cytoscape core team, is learning from them. If you have feature request which is available in Gephi but not in Cytoscape, please let us know :)

ADD COMMENTlink written 6.5 years ago by keiono50
gravatar for dcolinmorgan
6.7 years ago by
SciLifeLab, Stockholm
dcolinmorgan100 wrote:

I would highly recommend Cytoscape 3 - it has a much more polished, refined UI, and the new "app store" continues this trend by facilitating simple plugin installation - however, not all plugins are supported by version 3; version 2.8 is still very usable and supports the majority of plugins out there. However, many large datasets I had trouble loading into version 3 were tackled by version 2.8 no problem, I suspect due to visualization improvement requirements.

I have only played around with gephi, and my impressions are exactly what Istvan noted - its intended use for a broader audience makes its use not as straightforward regarding biological data

ADD COMMENTlink written 6.7 years ago by dcolinmorgan100
gravatar for clementlevallois
6.3 years ago by
clementlevallois20 wrote:

Disclosure: I am a member of the Gephi community support team.

I agree with what Istvan Albert and keiono have shared. Cytoscape has a much broader ecology of plugins for biological research, for example. One strength of Gephi is that it handles well the visualization of very large, dynamic networks.

Both software keep evolving, so it is worth re-checking their features periodically. If you have any question or feature request for Gephi please use the forum of Gephi, post on the Facebook group or give a shout to @gephi on Twitter.

ADD COMMENTlink modified 7 months ago by RamRS28k • written 6.3 years ago by clementlevallois20
gravatar for Woa
6.5 years ago by
United States
Woa2.8k wrote:

Check some cytoscape generated images:

ADD COMMENTlink written 6.5 years ago by Woa2.8k
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