NDEx 2.1 Release Notes - Q2-2017 Update (v2.1)

June 30th, 2017

Overview

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.


New Features

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. ***

  • Search Term Expansion: when searching for genes and/or proteins, users can now decide to expand their search terms to all possible synonyms/aliases available. These feature makes searching networks easier and more efficient as networks in NDEx can be annotated using a number of different identifiers and nomenclature standards.
    Note: Search Term Expansion is only available for genes and proteins and is not compatible with the use of boolean operators or other Lucene Syntax.
    Please review the manual about Finding and Querying Networks for detailed information and examples about searching networks in NDEx.

  • Network Sets: users can now create and share Network Sets, "folders" where networks can be grouped and organized in collections.
    • Each Network Set can be assigned a specific name, description and reference in case its network content has been already published in a scientific journal.
    • Networks can be included in a Set regardless of their ownership and visibility, which means that "user A" can create a set that includes his own networks as well as networks owned by other NDEx users as long as he can access them.
    • Networks can easily be added or removed from a set at any time.
    • Sets can be "showcased" to control their visibility on the owner's page.
    • Sets can be "shared" using the new "Share URL" feature described below.
    • As of NDEx 2.1, Network Sets are not returned in the search results: so, in order to see a Network Set, users need to visit the Set's owner page.

  • Share URL: individual networks as well as Network Sets can now be shared easily with anyone. This feature works like the sharable URL in Google Docs or Dropbox: users can enable the Share URL for a certain network (or Set) and send it to any recipients by pasting in the body of an email or including it in a paper submission or grant proposal.
    • The Share URL feature is only available for PRIVATE networks; public networks are visible to anyone and can easily be shared by copying the URL displayed in the browser's address bar.
    • Users can disable the Share URL feature at any time if they wish to restrict access to a particular network (or Set).

  • Disk Space Quota: every user in NDEx has a generous 9.3 GB disk space allowance to store networks. The amount of disk spaced used is shown on the left hand side in the user's account page. If your account needs additional disk space, please contact us.

  • Clone: users can now create a personal copy of any NDEx network using the new Clone function. This feature is useful when users want to modify/update a network but cannot operate on the original one because it is a public reference network and therefore not editable.
    • Any networks can be cloned regardless of their visibility as long has you have access to them.
    • Cloning a network will affect your disk space allowance.
    • Cloning events are recorded in the network provenance history.

  • Consolidated Network Property Editor: all network properties, including "Visibility", are now grouped in the new Network Property Editor that can be accessed using the "Edit Properties" button in the network view page.
    The Network Property Editor also displays an "NDEx Score" for the network, that depends on its degree of annotation.

  • NDEx Score: the network score is a very important parameter as it determines how networks rank in the search results: if a network is very well annotated (i.e. NDEx Score = 80), it will be returned at the top of the search results while if it is poorly annotated (i.e NDEx Score = 10) it will be pushed down to the bottom.
    • The NDEx Score can range anywhere from "0" (Critical) to "115" (Top).
    • The more network properties are defined, the higher the score.
    • Custom properties can be added but their contribution to the overall NDEx Score is limited.

NDEx 2.1 Installation Bundle

The new NDEx 2.1 installation bundle is now available for DOWNLOAD from our FTP Server. The bundle includes:

  • NDEx 2.1 server
  • NDEx 2.1 WebApp
  • Combined Query Service
  • NDEx Sync 2.0 (copier program)

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.

NDEx R Client

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"!


Network Content

The Q2-2017 Update also provides access to updated pathways and networks: these include but are not limited to:

In addititon, new data driven networks are being generated and progressively loaded to NDEx: All new and updated networks provide direct links to relevant external databases and include custom visual styles and layouts.







NDEx 2.0 Release Notes - Q1-2017 Update (v2.0.1)

April 7th, 2017

Overview

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.


Web User Interface

These are the NDEx web UI changes introduced in the Q1-2017 Update:

  • Re-enabled and expanded "Network Property" editor: network properties for individual networks and Cytoscape collections with 1 subnetwork can now be edited again in the NDEx UI. Editing network properties for Cytoscape collections with more than 1 subnetwork is not supported in the NDEx UI: such collections should be edited directly in Cytoscape. In addition, the schema of available network properties that are indexed by our Solr server has been expanded. An updated table showing all indexed properties can be found in the user manual Finding and Querying Networks.
  • Re-enabled "Bulk Actions": Change description, Change reference and Change version can now be used again to set these properties on multiple networks simultaneously. As for the network properties mentioned above, bulk actions are not available to operate on Cytoscape collections that have more than 1 subnetwork.
  • Added logo and warnings for Cytoscape collections: the UI now displays a black Cytoscape icon in the network table to easily identify Cytoscape collections that have more than 1 subnetwork. Mouse-over or clicking the icon displays a warning message.
  • Re-enabled the "Advanced Query" feature: networks can now be queried not only by keywords but also by properties associated with their nodes and/or edges. This feature is handled by our new stand-alone combined query engine using the latest version of the NDEx Python library. The new service is plugged into the existing user interface and no major change will be experienced end users. !!! Important Note !!!: the combined query service is not available for Cytoscape collections with more than 1 subnetwork.

Supported Network File Formats

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.


NDEx 2.0 Installation Bundle

The new NDEx 2.0 installation bundle is now available for DOWNLOAD from our FTP Server. The bundle includes:

  • NDEx 2.0 server
  • NDEx 2.0 WebApp
  • Combined Query Service
  • NDEx Sync 2.0 (copier program)

Updated, detailed Installation Instructions can be found on this documentation website.


Compatibility Issues

  • The copier program (NDEx Sync 2.0) is not back compatible with prior NDEx releases and can only synchronize/update content between servers running NDEx 2.0. For more information, please review the technical document about Using the NDEx Sync Program.
  • Operations on Cytoscape collections with more than 1 subnetwork are limited to uploading (via CyNDEx), sharing and downloading.






NDEx 2.0 Release Notes

December 21st, 2016

Overview

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


Web User Interface

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.


Supported Network File Formats

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.


New Features

Neighborhood Query

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.

NDEx 2.0 API

For developers, the REST API has been streamlined and clarified. Please review the new NDEx 2.0 API documentation for details.

Full CyNDEx support

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.


Supported Web Browsers

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

  Safari


Compatibility Issues

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.