NDEx Release Notes - Q4-2018 Update (v2.4.0)

December 20th, 2018

Overview

The Q4-2018 Update includes new features and improvements in the NDEx server, API, web application and documentation. All features in NDEx v2.4.0 are deployed and available on the NDEx Public Server.


New Features and Improvements

This section provides information about new features and improvements introduced with the Q4-2018 Update. Please review this document carefully prior to using NDEx 2.4.0 for your work.


New Landing Page - The NDEx landing page was completely redesigned and now provides more information about NDEx and how scientist can use it in their everyday research. The NDEx Twitter Feed keeps you informed on interesting topics related to network biology and the Featured Content panel provides quick access to network collections, new publications and upcoming conferences. The Top Menu bar grants easy access to our documentation, contact and Bug Report forms, while up-to-date Release Notes can be accessed by clicking the version number right next to the NDEx logo.
Note: if you encounter any page visualization issues, please clear your browser's cache and reload the page.


Google Sign Up - Creating an account in NDEx 2.4.0 is easier than ever; users have now the option to Register with Google, provided that they already have an active Google account. This new feature makes creating an account as easy as 2 clicks and will associate your Gmail address to your account, so you'll also be able to seamlessly Log in to NDEx with Google in the future. After you succesfully Sign Up with Google, our system will send you an email with your log in credentials that you can use if you are interested in using your NDEX account programmatically via custom scripts or applications. For additional details and step by step instructions with screenshots, please refer to the user manual Creating and Using an NDEx Account.


Neighborhood Query - In NDEx 2.4.0, the Neighborhood Query feature was improved and simplified. Users can now choose among 4 different types of query using a dropup menu: Neighborhood, Adjacent, Direct and Interconnect. In addition, when performing a Neighborhood or Adjacent query, the "Depth" can also be specified. Embedded documentation explains in detail the available query types and can be accessed by clicking the small "info" icon next to the query type drop up menu. Additional info and screenshots can be found in the manual on Finding and Querying Networks in NDEx.
Note: the Advanced Query feature is still in development and will be available later in 2019.


GraphML Exporter - In addition to exporting networks as GSEA Gene Sets, NDEx 2.4.0 also lets users export networks as GraphML objects. To export a network, click the More button in the network view page and select "Export" in the dropup menu; then choose the export format you want and click the Export Network button. Your export request will be qued as a task by the NDEx server. To check its status and download the exported file, please visit the "My Tasks & Notifications" tab in your NDEx account page.
Additional exporters are currently under development and will become available in 2019. These include an Excel Spreadsheet exporter, a tabular file exporter (csv and Tab-delimited text) and a CytoscapeJS exporter.


Cancel DOI Request - The request DOI feature was improved by adding the option to Cancel a DOI Request once it has been submitted. This improvement is particularly useful when users realize they have not included all information in the network before submitting their request. Cancelling a submitted DOI request makes the network editable again so that missing/incorrect information can be modified. If a DOI request is cancelled, users must submit a new request if they want a DOI assigned to their networks. For more information, please review the manual on Publishing in NDEx.


Account Management - Improvements in the account management logic now allow users to reset the password of their NDEx account using either their account name or e-mail address. In addition, whenever users change the email address associated to their account, the systems sends an email notification to the old address, just in case the change is unauthorized or executed by mistake.


CX Optimization - The CX format was simplified and made more efficient through a number of changes that are described in more detail in the CX Data Model document. The changes in NDEx v2.4.0 include but are not limited to:

  • Deprecating @context aspect. Use of ‘@context’ network attribute is recommended.
  • Deprecating the Numeric Range Precondition Element in CX format.
  • Deprecating the Provenance aspect.
  • The provenance tab was removed from the network view page in the NDEx web UI to simplify provenance handling.
  • The NDEx server no longer generates the ndexStatus aspect in networks.

cx2js Library - The code that managed CX JSON to Cytoscape.js JSON conversion was refactored into a general purpose npm package, allowing its re-use in other projects. Example use cases were included for package consumers, and unit tests were introduced to increase reliability and prevent regression. The font handling of the library was updated, fixing several bugs, including the handling of Java Logical Fonts and label positions. The cx2js GitHub repo is available HERE.


Improved Documentation - The documentation for NDEx v2.4.0 was revised and improved. All manuals are brand new and include up-to-date screenshots of the v2.4.0 web UI. All technical docs were updated to reflect the latest changes in the data model, CX format and API functions. A new Developing in NDEx - README!!! page was created to centralize all developer's related info and links to code repositories. Finally, more embedded documentation was added to the web UI in the form of tooltips and info modal windows. If you are new to NDEx, we recommend you beging with the updated Quick Start Guide and then explore the other manuals and documents using the blue Doc Navigation Menu.


Cytoscape Apps

The integration between NDEx and Cytoscape keeps improving and the CyNDEx-2 module is a core component in Cytoscape 3.7. We strongly recommend you download the latest Cytoscape version available and then update the CyNDEx-2 core component directly from the Cytoscape App manager if necessary.

All users relying on older Cytoscape versions can still take full advantage of the NDEx-Cytoscape integration thanks to the CyNDEx (v4.0.3) app! This is the first, original NDEx Cytoscape app and can be used with Cytoscape v3.3 or higher. There are no new features in this version of the CynDEx app; click the version number to access the app's store page and review the details about bug fixes and other improvements.
If you need help with the CyNDEx app, please review our updated CyNDEx Tutorial.


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

While we encourage the use of alternative web browsers, we cannot guarantee that all features will be available and functioning as intended.







NDEx Release Notes - Q3-2018 Update (v2.3.1)

July 25th, 2018

Overview

The Q3-2018 Update brings new features to the NDEx web application and improvements in Cytoscape integration. All features in NDEx v2.3.1 are deployed and available on the NDEx Public Server.

NDEx v2.3.1 is also available as an installation bundle for deploying private instances of the NDEx server. For more information and to download, please refere to the NDEx Installation Instructions.


New Features and Web User Interface Improvements

This section provides information about new features and improvements introduced with the Q3-2018 Update. Please review this document carefully prior to using NDEx 2.3.1 for your work.

Export Query Result - In NDEx 2.3.1, Neighborhood Query results can be exported in tabular format (tab-delimited text) directly by using the new Download Result button available in the Query result page. This new feature is available to all users, both anonymous and logged-in. For a detailed guide on using the Neighborhood Query, please refer to the user manual Finding and Querying Networks in NDEx.
Note: the Advanced Query feature is still in development and will be available later in 2018.

Google Sign-In for Safari - Existing initialization issues have been resolved and the convenient Google authentication feature can now be used with the Safari web browser.

Partial Support for Cytoscape Collections - NDEx v2.3.1 allows users to set the "Read-only" flag for Cytoscape collections either as a bulk action or directly in the network view page.
In addition, users can now also change the "Visibility" of a Cytoscape collection; however, at this time the feature is only available as a bulk action from your "My Account" page.

Display Networks in External Applications - This feature is tailored to developers and allows networks to be displayed in any application via the NDEx viewer and seamlessly opened in Cytoscape if desired, regardless whether networks are stored in NDEx or not. This feature is currently being used by some of our collaborators within the ITCR projects portfolio. If you are interested in displaying networks in your application and don't want to re-invent the wheel, Contact Us and we'll be happy to help!

Open in Cytoscape - The existing feature has been improved as part of the ongoing effort to better integrate NDEx and Cytoscape. Private networks can now be opened in Cytoscape along with unsaved "Neighborhood Query" results
Note: in order to use this feature, Cytoscape 3.6.0 or later must be running on your machine, the latest CyNDEx-2 App (v2.2.3) installed and the CyREST service listening on its default port (1234).

Network Table Customization - The network table in your "My Account" page has been improved to preserve user-defined sorting, filtering, multiple selection, and paging. Navigation has also been improved: users can now use the browser Back and Forward buttons to navigate to previously-visited network pages.

Visual Style Mappings - The NDEx network viewer has been improved to better translate visual style mappings between the Cytoscape desktop application and Cytoscape.js on the web. Pie Charts created in Cytoscape can now be rendered in NDEx; in addition, the following mappings are also rendered correctly in v2.3.1: Node Border Line Types, Node Label Position, Node Shape, Edge Line Type, Edge Source/Target Arrow Shape, Node and Edge Label Font Face, Node Label Position.

Remove Shared Networks - In NDExv2.3.1, users can reduce clutter in their accounts by removing networks that other users have previously shared with them. The "Remove From My Networks" feature is available both for individual networks in the network view page (click "More" and choose "Remove From My Networks") or as a bulk action directly in your "My Account" page.

Custom Network Sample - For large networks, the NDEx network viewer displays a randomly generated 300 edges sample to present a visually interpretable subset of the data. In NDEx v2.3.1, users have two methods to specify a custom sample to be displayed therefore improving the presentation of a large network:

  • Run a neighborhood query on a large network and use the "Set Sample" button to set the result to be the displayed sample.
  • Click the "More" button in the network view page and choose "Set Network Sample" to specify the UUID of another network to use as sample

For more details, please review the user manual Finding and Querying Networks in NDEx.


Cytoscape Apps

The integration between NDEx and Cytoscape keeps improving: the CyNDEx-2 (v2.2.3) app has just been released that includes bug fixes and new features as already described earlier in this document. We strongly recommend users download the latest Cytoscape version available and then update the CyNDEx-2 core component directly from the Cytoscape App manager.

All users relying on older Cytoscape versions can still take full advantage of the NDEx-Cytoscape integration thanks to the CyNDEx (v4.0.3) app! This is the first, original NDEx Cytoscape app and can be used with Cytoscape v3.3 or higher. There are no new features in this version of the CynDEx app; click the version number to access the app's store page and review the details about bug fixes and other improvements.
If you need help with the CyNDEx app, please review our updated CyNDEx Tutorial.


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

While we encourage the use of alternative web browsers, we cannot guarantee that all features will be available and functioning as intended.







NDEx Release Notes - Q2-2018 Update (v2.3.0)

April 5th, 2018

Overview

The NDEx Q2-2018 Update provides major improvements to the end-user experience while optimizing performance and scalability. All features in NDEx v2.3.0 are deployed and available only on the NDEx Public Server. No new installation bundle will be released in Q2-2018.


New Features

This section provides information about the new features introduced with the Q2-2018 Update. Please review this document carefully prior to using NDEx 2.3.0 for your work.

Neighborhood Query - In NDEx 2.3.0, the Neighborhood Query has been refactored to optimize performance as well as simplify and improve the end-user experience.
Note: the Advanced Query feature has been temporarily disabled to allow improving its performance, scalability and user experience. The new Advanced Query feature will be available later in 2018.
Details about new features and improvements in the Neighborhood Query are listed below and additional info and screenshots are available in the updated guide focused on Finding and Querying Networks in NDEx.
  • Interconnect Query
    A new query option, “Interconnect”, has been added to the query menu on network pages. An Interconnect returns only short paths between the nodes selected by the query string. The resulting subnetwork attempts to answer the question “How are these related to each other?”. It therefore is only appropriate for queries selecting 2 or more nodes. Query nodes for which no short paths are found to any other query node will appear as “orphans”, nodes that have no edges.
  • Improved Performance
    The Neighborhood Query now supports networks of any size and always returns a result up to 50,000 edges. Smaller query results will be presented in graphic form while larger results will only be shown in tabular form to avoid long delays.
  • Autosave Feature
    If the query result is larger than 50,000 thus exceeding the web browser's capability, the new Autosave feature will offer to automatically save the query result to the user's account. This feature is only available to logged in users; anonymous users will be prompted to log in and will need to re-run the query in order to have the result automatically saved.
  • Download Result
    Query results up to 50,000 edges can now be downloaded as tab-delimited text files (TSV). This feature is available both to anonymous and logged-in users and can be accessed using the new "Download Result" button available in the query result page.

Web User Interface Improvements

In NDEx 2.3.0, we have improved network visualization, especially for all those networks that have been styled and layed out using Cytoscape. To achieve this, we have:

  • updated our network visualizer to use the latest cytoscape js version available (v3.2.9)
  • fine-tuned its parameter to obtain a fast and smooth graphic rendering
  • changed sampling logic; when a network exported from Cytoscape is saved in NDEx, our visualizer now displays it in full if the network has up to 12,000 edges! For larger networks, a 300 edges sample view is generated instead.

Cytoscape Apps

The connection between NDEx and Cytoscape has now reached full integration: the CyNDEx-2 (v2.2.2) app has become a "core" Cytoscape component in the recently released Cytoscape v3.6.1. An NDEx sample session is also available to get new users started immediately with NDEx. Click the link above to access the app's store page for a more info and a brief tutorial. Additional information can be found in the Cytoscape online manual.

All users relying on older Cytoscape versions can still take full advantage of the NDEx-Cytoscape integration thanks to the CyNDEx (v4.0.3) app! This is the first, original NDEx Cytoscape app and can be used with Cytoscape v3.3 or higher. There are no new features in this version of the CynDEx app; click the version number to access the app's store page and review the details about bug fixes and other improvements.
If you need help with the CyNDEx app, please review our updated CyNDEx Tutorial.


Technical Documentation

New features and other improvements in NDEx 2.3.0 required changes in the REST API; please review carefully the NDEx API Documentation prior to using it for your work.


Network Content

NDEx 2.3.0 brings plenty of new, high quality up-to-date content for users to browse, download and re-use. We now have automated pipelines to regularly update all manually curated pathways available in the SIGNOR Database; also available are protein-protein interaction networks for several species, generated from the BioGRID and STRING current release data.







NDEx Release Notes - Q1-2018 Update (v2.2.1)

February 1st, 2018

Overview

The NDEx Q1-2018 Update brings changes and new features to improve the end-user experience while optimizing performance and scalability. All new features and improvements in NDEx v2.2.1 are deployed and available only on the NDEx Public Server. No new installation bundle will be released in Q1-2018.


New Features

This section provides information about the new features introduced with the Q1-2018 Update. Please review this document carefully prior to using NDEx 2.2.1 for your work.

  1. Open in Cytoscape - Beginning with v2.2.1, users can open an NDEx network in Cytoscape directly from the NDEx web User Interface. This feature is triggered by a new "Cytoscape button" available in the network view page. Due to technical limitations, right now this feature can only be used if the following conditions are met:
    • Cytoscape 3.6.0 or higher must be installed and running on your computer and have the CyNDEx-2 app installed *** Note: starting with Cytoscape 3.6.1, CyNDEx-2 will become a pre-installed, core app. ***
    • The network to be opened in Cytoscape must be either Public or Private and have the Sharable URL enabled

  2. @context Editor - NDEx 2.2.1 brings back the possibility to control the namespaces associated to any network. The @context Editor can be accessed from the network page and dinamically adapts to the user's privilege level for that specific network. Namespaces can always be viewed but can be added or modified only if the user has "Edit" or "Admin" privileges on the network. Defining namespaces using the @context Editor (or other method) is important as it will make possible for the NDEx UI to use the identifiers specified in the network (represents, alias and other network attributes) and automatically generate URL to point to relevant external resources. Defining namespaces for a network is not mandatory but highly recommended.

  3. Expanded Network Indexing Policy - In NDEx v2.2.1, the SOLR indexing policy has been modified to optimize server performance, relevance of search results and system scalability. There are now 3 tiers of indexing complexity the users can choose from:
    • Tier 0 (T0)
      • This is the default indexing behavior and applies to all PRIVATE and PUBLIC networks written to NDEx regardless of their origin (file loading, script, cytoscape)
      • T0 corresponds to the PRIVATE (Not Searchable) or PUBLIC (Not Searchable) visibility options currently available in the NDEx UI
      • Under T0, the only parameter that is indexed is the network's UUID
    • Tier 1 (T1)
      • This is the extended indexing behavior and can be applied to any PRIVATE or PUBLIC networks already existing in NDEx
      • T1 corresponds to the PRIVATE or PUBLIC visibility options currently available in the NDEx UI
      • T1 can only be selected manually in the NDEx UI, either on a per-network basis or as a bulk action
      • Under T1, the following network attributes are indexed for search: UUID, name, description, reference, disease, author, labels, tissue, methods, rightsHolder, rights, organism, networkType
      • Under T1, a new add-on option will become available via a selectable checkbox in the network property editor to optionally add "full node indexing". If selected, the network will be indexed according to the Tier 2 specs listed below.
    • Tier 2 (T2)
      • This is the most comprehensive indexing tier
      • Full indexing is only available on a per-network basis via a selectable checkbox in the network property editor; this option is not available as a bulk action
      • By default, the "Full Index" checkbox is NOT selected
      • When selected, in addition to the network attributes indexed under T1, the following node attributes will also be indexed for search: nodeName, represents, alias
      • This feature uses a lot of resources and should be used sparingly
      • "Certified" and "Pre-certified" networks are automatically indexed under T2

Web User Interface Improvements

In NDEx 2.2.1, the web UI includes several improvements to the general look and feel; the landing page has been decluttered to focus on the most important components: the search bar and featured collections. In addition, the landing page also shows the current NDEx version and provides direct access to the latest Release Notes.

The network view page has new embedded documentation in the form of tooltips that can be activated by hovering on buttons and other UI elements. Tooltips also provide explanatory messages in cases where a certain function is not available to the user.

Finally, the network viewer has been tweaked to render Cytoscape visual styles with higher fidelity when using discrete mappings, continous mappings and features like node and edge transparency.


Cytoscape Apps

The tight connection between NDEx and Cytoscape is now stronger than ever: with NDEx 2.2.1, user can choose between 2 different apps to round trip networks between NDEx and Cytoscape.

  1. CyNDEx v4.0.3
    This is the original NDEx Cytoscape app and can be used with Cytoscape v3.3 or higher. There are no new features in this version of the CynDEx app; click the version number to access the app's store page and review the details about bug fixes and other improvements.
    If you need help with the CyNDEx app, please review our updated CyNDEx Tutorial.

  2. CyNDEx-2 v2.2.1
    CyNDEx-2 is the latest NDEx Cytoscape app and can only be used with Cytoscape v3.6 or higher. CyNDEx-2 relies on the REACT framework, uses JX Browser and will become a "core app" in the upcoming Cytoscape v3.6.1 release.
    CyNDEx-2 has an improved user interface that makes it easier to browse, import, annotate and export networks. In addition, it makes possible to use the new "open in Cytoscape" feature described above in this document.
    If you work with Cytoscape v3.6 or higher, we recommend using CyNDEx-2 to take full advantage of allsnew features and improvements.
    For instructions about the app and its use, click the version number above to access the app's store page.

  3. NOTE: all Cytoscape collections are displayed in the NDEx UI with the a black Cytoscape icon. Any single-subnetwork 
    collection can be converted to single network simply by importing it into Cytoscape with CyNDEx-2 and re-exporting it to
    NDEx as network; we also recommend you uncheck the option to "Save as New Network" in order to update the existing copy of the network.

Technical Documentation

NDEx 2.2.1 brings a number of important back-end changes that are documented in our Technical Literature. Please review the Network Data Model document for updates in the CX specification and server changes.

New features and other improvements in NDEx 2.2.1 also required changes in the REST API; please review carefully the NDEx API Documentation prior to using it for your work.