NDEx - Frequently Asked Questions


What is NDEx?

NDEx is a software infrastructure that allows to store, access, manage and visualize different types of network models. NDEx is fully integrated with the Cytoscape desktop application, can be used via its intuitive web user-interface and, although it is heavily committed to biological networks, it can accomodate any type of network models.

How do I cite NDEx?

If you use NDEx in your work, please cite the following publications:

Is NDEx free to use?

Absolutely YES! NDEx is an academic project, not-for-profit, open source and 100% FREE. In addition, if you create an NDEx account, you will receive 10 GB of FREE cloud storage for your networks!

Do I need to create an account in order to use NDEx?

No, you can always search, query and download public networks in NDEx. However, with an NDEx account you will also be able to save networks and query results, upload your own data as well as use several other features like requesting DOIs or sharing networks with collaborators...
Did we mention you also get 10 GB of FREE cloud storage when you create an NDEx account?!!!

How do I search for networks in NDEx?

Finding networks in NDEx is easy... Just use the Search Panel available at the top of the NDEx landing page! The Search Panel also provides quick access to a number of high quality networks and search examples. Additional information on searching in NDEx is available in THIS MANUAL.

How do I create an NDEx account?

Easy! Visit the NDEx Public Server and click the blue "Login/Register" button in the top right corner of the page. If you already have a Google account, we recommend you choose to Sign Up with Google and your account will be created in a few seconds in just 1 click. For a step by step guide with screenshots and additional details, CLICK HERE.

How can I load my network(s) to NDEx?

You can load networks to NDEx in several different ways and to do this you must have an NDEx account. The simplest way is through Cytoscape, if you can open your network in Cytoscape, you can easily save it to NDEx. Alternatively, you can load networks to NDEx using your custom program/script. Finally, you can load networks to NDEx via the web user interface if they are in CX format. Please refer to THIS GUIDE for additional information.

Is my data safe in NDEx?

We take security and privacy very seriously; the NDEx Public Server is hosted by Amazon Web Services (AWS), the database is backed up daily to minimize the detrimental effects in the remote eventuality of data loss/corruption, and you always control who has access to your networks:
  • by setting their privacy level (Public or Private)
  • by managing access permissions (read, edit or admin) for other NDEx users and groups

Can I share my network(s) with collaborators?

Yes! You can share your NDEx networks either internally (i.e. with other NDEx users and groups) or externally by using the network's Sharable URL feature, like you do in Dropbox or Google Drive. For a detailed guide with screenshots, visit THIS PAGE.

Can I create my own workgroups?

Yes, you can create as many workgroups as you want and invite other NDEx users to join in for collaboration. More information on Groups management in NDEx is available HERE.

Can I control who is allowed to edit my networks?

Yes, you decide who has permission to edit your networks and can always revoke permissions if you want to. For more details, please refer to THIS GUIDE.

Will my networks display the same in NDEx and in Cytoscape?

Yes, in 99% of the cases your networks will look the same both in NDEx and Cytoscape. In some rare cases, there could be slight differences and we are actively working to achieve 100% mapping fidelity. If you experience differences in the way your networks are displayed in NDEx vs Cytoscape, please Contact Us.

Can I have an account for my analysis pipelines to use?

Yes, you can create an account and access it programmaticaly from your favorite scripts and applications using the available client libraries. Please visit our Developer's README page for more information.

How many networks can I have in my account?

Anywhere from a few networks to tens of thousands depending on the size and complexity of your networks. The larger and the more annonated the networks are, the fewer you'll be able to store in your 10 GB of allotted space. If you need more storage space, Contact Us and we'll be happy to help!

Can I request a Digital Object Identifier (DOI) for my network(s)?

Yes, you can request DOIs for your networks to use in peer-reviewed publications, grant proposals, presentations, etc. Requesting a DOI is 100% FREE.
More info on DOI requests and other "publishing-focused" features can be found in THIS GUIDE.

My networks are ready for public distribution… What now?

Once your network is accepted for publication in a peer-reviewed journal or is ready to be distributed to the public, you want to make sure that:
  • It is well annotated, with a meaningful title, a clear description and the full reference of the article where it is described
  • Its visibility is set to PUBLIC
  • The "Read-only" checkbox is marked to prevent accidental changes in the future

Do I need to wait that my networks are published in a peer-reviewed scientific journal prior to public dissemination via NDEx?

That is up to you! However, we recommend you double check your publisher’s policy concerning the dissemination of data pre-publication.

Is NDEx recommended by publishers?

Yes, NDEx is officially recommended by Springer Nature, Scientific Data and the PLOS family of journals. We are constantly working with scientific publishers to simplify the submission and review processes and improve access and re-use of data.
NDEx complies with FAIR principles and is registered on FAIRsharing.org.