Uploading and Saving Networks

Last updated: September 27th, 2017

There are several ways to upload a network to NDEx: users can upload directly from Cytoscape, can use a programmatic approach or simply upload a file through the web user interface. This guide describes how to load a network to NDEx using the web user interface.

IMPORTANT NOTE: The screenshots in all our user manuals are for training purposes and might be different from the actual screen output you will obtain when working on the current NDEx version deployed to our public server.

Uploading Networks

  • At this time, the NDEx web UI only allows the upload of networks in CX format.
  • In your MyAccount page, Click the Upload Networks option.

  • Select the file to upload by using the Choose file button in the upper left corner

  • Click on the green Upload button to begin the process.
  • Alternatively, select multiple files and upload them at once by clicking Upload all.

  • Once the process is complete, a new task will be created. The task is a pending action that the NDEx system will resolve.
  • You can view a network loading task at the bottom of the screen.

  • You can also view the status of a task in the Tasks & Notifications tab of your ‘My Account" page.

  • The status will change during the upload process. When the task is done, you will see the status change to completed. At this point, the network will be in the system and appear at the top of the list in the Networks tab of your " My Account" page.

Saving a Subnetwork

  • A subnetwork (or neighborhood) is the result of a specific query on a larger network. In this example, we select the BEL Small Corpus Document and run a query for "akt1": the system will return a subnetwork consisting of 79 nodes and 79 edges related to the term akt1.
  • The query result can be saved as a new network using the Save Query Result function (red arrow).

  • The new network is now visible at the top of the list in the on the user's "My Account" page.

Editing the Network Profile

  • As an admin of the new network you just saved, the signed-in user can modify the network profile information. To do so, click the new subnetwork you just saved and select the "Edit Network Profile" function.

  • Besides changing the network name, adding a description, a publication reference and a version number, you can also control the visibility and accessibility of a network that you administrate.
  • By default, your new subnetwork will be PRIVATE: this means you are the only one who can see it and the network will not be displayed when any other user runs a search.
  • You can change the visibility to PUBLIC if you want the network to be readable by anyone, even anonymous users (users that are not logged in to an NDEx account.)