8. Extending Cytoscape Web

Apps and Service Apps are community built additions that add new functionality or extend existing capabilities of Cytoscape Web.

8.1. Apps

Creating an App (written in Typescript) gives the developer the most access to Cytoscape Web APIs to extend and augment both the user interface and analysis tools, but requires experience in web development.

To enable/disable Apps in Cytoscape Web, choose Apps -> Manage Apps in the main menu and check or uncheck the appropriate boxes. For example, checking the box next to Simple Menu App enables that example app.

To use the App, choose Apps -> Simple Dialog Example from the main menu. When you do so, a Hello Cytoscape World! window will pop up as shown below:

8.2. Service Apps

The Service Apps are more limited in accessibility, but are easier to implement and offer freedom of language.

To enable a Service App, paste its URL into the External Service URL field, and click Add.

For example, if you paste in this URL:

https://cd.ndexbio.org/cy/cytocontainer/v1/updatetablesexample

The Update tables example Service App will be enable in Cytoscape Web. To use it, choose Apps -> Example Service App -> Update tables example.

Additional example Service Apps are available to test and familiarize with this feature.

NOTE: *All active Apps and Service Apps will be cleared if you reset Cytoscape Web by using Data -> Clear Local Database. To preserve active Apps and Service Apps, please make sure to use Data -> Save Workspace As… to save a snapshot of your Cytoscape Web workspace to your NDEx account. For more details, please review the section on how to Save to NDEx.

8.3. Community Available Service Apps

Here are all the community available Service Apps that can be registered and used in Cytoscape Web. Please refer to the paragraph on Service Apps for detailed instructions.

1. g:profiler Enrichment

Analyze gene sets against biological databases to identify statistically significant pathways. Requires a network map with at least one data column (in the node table) containing a whitespace- or comma-separated list of gene symbols.

 https://cd.ndexbio.org/cy/cytocontainer/v1/gprofilerenrichment

2. IQuery Enrichment

Analyze gene sets against NDEx IQuery to retrieve pathways ranked by similarity-based matches. Requires a network map with at least one data column (in the node table) containing a whitespace- or comma-separated list of gene symbols.

    https://cd.ndexbio.org/cy/cytocontainer/v1/iqueryenrichment

The screenshot below shows the App Manager window with all Apps disabled and the 2 enrichment Service Apps enabled:

8.4. For Developers

Writing Apps

Documentation to build an App.

For integration of a custom App into Cytoscape Web please contact us.

Writing Service Apps

A Service App is a REST service that can be registered with Cytoscape Web to extend functionality. For more information about creating a Service App see: Cytoscape Web Service App REST service V1 specification.

Here are some example Service Apps to test or use as reference:

  1. Add Network

https://cd.ndexbio.org/cy/cytocontainer/v1/addnetworksexample

  1. Open URL

https://cd.ndexbio.org/cy/cytocontainer/v1/openurlexample

  1. Update Layout

https://cd.ndexbio.org/cy/cytocontainer/v1/updatelayoutsexample

  1. Update Network

https://cd.ndexbio.org/cy/cytocontainer/v1/updatenetworkexample

  1. Update Selection

https://cd.ndexbio.org/cy/cytocontainer/v1/updateselectionexample