Cell Maps

Cell Maps FAQ

The purpose of this FAQ is to provide a quick reference guide for researchers involved in any Cell Maps Initiative thus facilitating access to data, interaction and collaboration within the Network Data Exchange (NDEx) infrastructure.This FAQ can also be used as a reference by anyone interested in creating a collaborative project focused on generating networks from different data sources.

This figure below is a schematic representation of the Cancer Cell Maps Initiative (CCMI) architecture and workflow within NDEx.


FAQ

If you would like to recommend additions or changes to this document, please contact the NDEx Application Manager: rudi@ucsd.edu


1. I am a CCMI investigator… How do I get started?

  • First of all, you need to create your own personal NDEx account: visit the NDEx Public server and click "Login/Register" in the top right corner. If you already have a Google account, we recommend you choose the option to “Sign Up with Google”. Once your account is created, you can personalize it further. Please review THIS MANUAL for detailed info on how to create and use an NDEx account.
  • Then, search NDEx to find the group called "CCMI Project" and request access with "can read" permission. Please review THIS GUIDE for additional details on creating and using groups.

2. How can I load a network to NDEx?
Currently, there are 2 ways to load a network to your NDEx account

  • Through your favorite program/script - See this tutorial using our Python client
  • from Cytoscape
  • Detailed info, screenshots and link to tutorials and examples using the NDEx Python client are available in THIS PAGE

3. How do I make my networks pretty?

First of all, load your networks in cytoscape using the CyNDEx App and make them look good by applying your favorite layout and visual style. Once your networks are saved back NDEx (again using the CyNDEx App), edit the network "profiles" and "properties" in NDEx to add:

  • A meaningful name
  • A detailed description
  • A reference (if your network appears in a publication)
  • A version
  • Network properties: The disease property should be added to each network and its value set to the corresponding cancer type. The Tissue property should also be added to identify the type of cells used in the experiments. Other network properties can also be specified (organism, author, etc) so that your networks can be efficiently indexed by our SOLR server and therefore found in a search. Please refer to the Advanced Search Capabilities section of the Finding and Querying Networks manual to learn more about all available network properties 

4. How do I share a network with collaborators?

Select the network you want to share and click the “Share” button. You can then search for users or groups to share your network with and decide the level of access they are allowed (Read, Edit or Admin for networks and Member or Admin for groups). When done, click the green “Save Changes” button. You can also gain access to a network you are interested in by requesting permission to its Owner/Admin. Simply select the network you would like to gain access to and click the “Ask for Access” button. For more details, review THIS PAGE.

5. Are my networks safe in NDEx?

Yes! The NDEx server uses a bulletproof technology, the database is backed up once a day and you always control who has access to your networks:

  • by setting their privacy level (Public or Private)
  • by controlling access permissions (read, edit or admin) for individual users and groups

6.Can I create my own workgroup?

You can create as many workgroups as you want and invite other NDEx users to join them for collaboration. 

7. Can I shuttle my networks between NDEx and Cytoscape?

Yes, you can do this using the Cytoscape 3.7 or higher thanks to its built-in CyNDEx-2 core component. Please review THIS PAGE for a detailed guide and more info.

8. 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.

9. My networks are ready for public dissemination… What now?

Once your network is published in a peer-reviewed journal or is ready to be disseminated to the public, the only things left to do are:

  • Change the network's privacy to PUBLIC
  • Put a mark in the “Read-only” checkbox
  • Share your network with the CCMI Organization account granting it "read permission"

10. 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, make sure you check your publisher’s policy concerning the dissemination of data pre-publication.