License for Cytoscape Logo

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Mingxun Wang

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May 27, 2021, 6:56:24 PM5/27/21
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Hi,

We would like to use the Cytoscape logo in a figure for publication, but there is no explicit license for the image. Is there an official policy or approval process for this?

Thanks!

Ming

Alex Pico

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May 27, 2021, 7:09:44 PM5/27/21
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Go for it! We just ask that you use it appropriately, e.g., in reference to the Cytoscape software. And please cite https://www.ncbi.nlm.nih.gov/pubmed/14597658. 
 - Alex


Mingxun Wang

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May 27, 2021, 7:19:50 PM5/27/21
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Definitely! We are saying that we export graphml files and recommend users load it up in the desktop Cytoscape software and have the accompanying citation. 

Thanks Alex!

Ming

Dexter Pratt

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May 28, 2021, 1:27:37 PM5/28/21
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Hi Ming,

Did you know that you can also make your networks available online using NDEx (www.ndexbio.org), the Cytoscape network cloud storage and publication system?
You can reference those networks from your publication. We can even mint DOIs for them. NDEx is approved as an official repository for networks by Springer-Nature and PLoS.

Here are a couple of networks in NDEx supporting publications:

Combinatorial CRISPR-Cas9 screens for de novo mapping of genetic interactions.
Nat Methods. 2017 Jun;14(6):573-576

Huttlin et al.
Dual proteome-scale networks reveal cell-specific remodeling of the human interactome.
Cell (online, May 6th), (2021)

Dexter

Dexter Pratt

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May 28, 2021, 1:28:23 PM5/28/21
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Also, your readers will be able to download those networks to Cytoscape with a single click.

Mingxun Wang

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May 28, 2021, 1:44:06 PM5/28/21
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Hi Dexter,

I just discovered this a few weeks ago and I love it. I want to get GNPS to be using NDEx soon. We actually a few years ago created our own little graphml to Cytoscape export and visualization of networks in Cytoscape JS (for mass spectrometry centric applications) and I think there is a nice path to integration if we can upload to NDEx automatically. 


I think this sharing will be a great integration point especially so far people have created somewhere around 300K networks at GNPS!

I'll definitely reach out if I have any questions and about possible more heavy weight integration opportunities. Thanks to your whole team for making such great software, we love it. 

Best,

Ming

Dexter Pratt

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May 29, 2021, 5:04:48 PM5/29/21
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Hi Ming, 

GNPS looks awesome! We absolutely would like to support you in integration.

Here is a tutorial from a year ago that shows several aspects of NDEx-Cytoscape-R-Python intercommunication.
The javascript section demonstrates downloading a network into Cytoscape, loading and saving a network from/to NDEx, and displaying a network with Cytoscape visual styles.
That would be enough to add "open in Cytoscape" and "save to NDEx" to the GNPS downloader.
But definitely bring us in when you are ready to try things. We intend to upgrade our libraries and make this simpler, and it seems to me that your applications could be great driving cases.

Dexter
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