June 30th, 2017
The NDEx Q2-2017 Update adds new functionalities focused on the NDEx Project's mission to enhance collaboration while facilitatating publication and dissemination of biological networks. All new features and improvements are deployed to the NDEx Public Server as well as available in the NDEx 2.1 Installation Bundle that can be downloaded from our FTP Server.
This section lists all the new features introduced with this Q2-2017 Update: some of the features have limitations that will be addressed in future releases as we gather more feedback and usage statistics.
*** Note to developers: please review the NDEx API Documentation for more information about new functions related to the New Features listed below. ***
The new NDEx 2.1 installation bundle is now available for DOWNLOAD from our FTP Server. The bundle includes:
Updated, detailed Installation Instructions can be found on this documentation website. Please review the NDEx v2.1 installation instructions carefully even if you have already successfully performed a de novo> NDEx installation in the past.
The NDEx R Client (ndexR) is a module that simplifies access to the NDEx Server API and provides convenience methods for common operations on networks. It was developed by the Kramer Lab at the Univeristy of Goettingen, Germany and is available as a Bioconductor Package. Please review the NDEx R Client doc for additional info and a useful "ndexR cheat sheet"!
The Q2-2017 Update also provides access to updated pathways and networks: these include but are not limited to:
April 7th, 2017
Besides bug fixes and general improvements, the Q1-2017 Update restores a numberof functionalities that had been temporarily disabled in the NDEx 2.0 official release back in December 2016. In addition, the NDEx 2.0 installation bundle is now available for download from our FTP server.
These are the NDEx web UI changes introduced in the Q1-2017 Update:
The Q1-2017 Update introduces the "GSEA Gen Set" export format; this feature generates a text file (.grp) containing unique human gene symbols that can be used for enrichment analysis. Additional export formats will be added in future updates.
The new NDEx 2.0 installation bundle is now available for DOWNLOAD from our FTP Server. The bundle includes:
Updated, detailed Installation Instructions can be found on this documentation website.
December 21st, 2016
The NDEx v2.0 release provides a major improvement in performance, scalability and reliability. Our new, streamlined NDEx 2.0 server and API bring you faster upload/download speeds to handle larger networks, support a larger user-base and heavier traffic loads. Features such as our “Neighborhood Query” have been decoupled from the core server and deployed as stand alone services thus creating a more flexible infrastructure. Improvements in the web UI simplify the end user experience and full support for CyNDEx 3.3.0 strengthen the already tight bond between NDEx and Cytoscape.
Some features of NDEx have been temporarily deactivated in v2.0; we will be adding back these features following a modular, short-cycle release strategy. A few features have been permanently removed for clarity, stability or simply lack of use. Please take a moment to carefully review this document before using NDEx 2.0.
!!! NDEx 2.0 is currently available ONLY on the NDEx Public server: an installation bundle, relative installation instructions and the new copier program (ndex-sync 2.0) will be released later in Q1 2017 !!!
Thanks for using NDEx and please contact us with bugs, suggestions, and requests. We would especially like to hear about the ways in which you would like to use biological networks, either as an end user or application developer: this will help us plan the next phases of NDEx development.
The NDEx Team
These are some of the web UI changes we have introduced in NDEx 2.0:
Redesign of main NDEx landing page: new “Featured Collections” help you get started using NDEx.
Improved NDEx network viewer: result of a neighborhood query now retain the graphic style of the parent network.
Improved search results table: we added a quick download icon to easily retrieve any network in CX format; we also added a Reference column, Status column as well as Disease and Tissue. The new “Showcase” feature allows you to control which networks are publicly displayed in your user account page. Finally, we removed the Format column.
Added e-mail verification: in NDEx 2.0, you need to verify your e-mail address when creating a new account. After signing up, the UI enables you to view and update your email address.
Removed “Archive” and “Download” features for BEL Namespace files: this feature will be replaced as part of the upcoming release of the new BEL Uploader
Temporarily disabled the “Network Property” editor: although NDEx 2.0 allows Cytoscape users to save and access “collections” containing multiple sub-networks, it currently cannot handle editing of network properties for individual sub-networks. Therefore, we have temporarily disabled the “Network Property” editor for Cytoscape collections that have more than 1 subnetwork.
Added “Bulk Action”:the “read-only” flag can now be set/unset for multiple networks at the same time.
Disabled some “Bulk Actions”: Change description, change reference and change version are temporarily unavailable for any networks.
Improved “Neighborhood Query” feature: this feature is now deployed as a stand alone service using the latest version of the NDEx Python client. Nothing changed in the user interface. More info about this feature are available below.
Temporarily disabled the “Advanced Query” feature: the advanced query feature is currently in development and will be restored in Q1 2017.
In NDEx 2.0, the web UI only allows the direct UPLOAD of networks in CX (.cx) format.
!!! IMPORTANT NOTICE !!!
Other network formats, including but not limited to BioPAX Level 3 (.owl), XGMML (.xgmml) and SIF/Extended Binary SIF (.sif), can be loaded to NDEx directly from Cytoscape using the CyNDEx App available in the Cytoscape App Store. Please refer to the CyNDEx tutorial for additional info.
NDEx 2.0 allows to DOWNLOAD networks only as CX (.cx) files through the new “Quick Download” icon in the NDEx UI.
Additional planned EXPORT formats include SIF, Microsoft Excel, TSV, GSEA and will be added later in Q1 2017.
The NDEx 2.0 Network Query is a fast, convenient way to view a subset of your network. Query performance is increased by 30% for networks with up to 10,000 edges; in addition, the Query service is now deployed as a stand-alone component and completely decoupled from the core NDEx server, thus allowing the release of improvements and new features independently of server updates. No changes were made in the web UI Query controls.
For developers, the REST API has been streamlined and clarified. Please review the new NDEx 2.0 API documentation for details.
Cytoscape and NDEx are the two main components of the new service-oriented “Cytoscape Cyberinfrastructure”. NDEx 2.0 therefore fully supports the previously released Cytoscape API. You can keep using CyNDEx v3.3.0 with your favorite Cytoscape version (3.3 or higher) and save your networks to either an NDEx v1.3 server or the new NDEx 2.0 Public server.
We recommend that you always update your preferred web browser to the latest version whenever possible. NDEx fully supports the following browsers:
– Google Chrome
– Mozilla Firefox
The copier program (NDEx Sync v1.3.3) is not compatible with the new NDEx 2.0. We will release a new copier program later in Q1 2017.