cyREST

Core App: Language-agnostic RESTful API
# *Core App*: cyREST __IMPORTANT: Now this app is now automatically delivered with Cytoscape v3.3 and later!__ You can update your CyREST to the latest version by using the _Check for Updates_ tab in Cytoscape's App Manager. ---- ## Summary CyREST is the technology that powers Cytoscape Automation, which enables you to create reproducible workflows executed entirely within Cytoscape or by external tools (e.g., Jupyter, R, GenomeSpace, etc). This enables Cytoscape to scale to large collections of datasets and larger more complex workflows than is practical via keyboard and mouse. ## With cyREST, you can... * Automate your data analysis and visualization workflows * Use Cytoscape from [python](https://www.python.org/), [Jupyter Notebook](http://jupyter.org/) or [RStudio](http://www.rstudio.com/) * Connect your services to Cytoscape with the programming language, and libraries of your choice -- such as: * Python + NumPy + SciPy for implementing layout algorithms * R + igraph for writing network analysis tools To learn more about Cytoscape Automation, visit our [Wiki](https://github.com/cytoscape/cytoscape-automation/wiki). ---- ## cyREST Paper Please cite our paper for project sustainability: __Ono, Keiichiro, et al. "[CyREST: Turbocharging Cytoscape Access for External Tools via a RESTful API](http://f1000research.com/articles/4-478/v1)." F1000Research 4 (2015).__ ---- ## REST API Documentation CyREST API docs are available within Cytoscape main menu through the __Help__ → __Automation__ sub-menu. ---- ## Related Packages, Apps and Modules * The Cytoscape Automation Wiki contains resources for scripters interested in using python or R to access CyREST [here](https://github.com/cytoscape/cytoscape-automation/tree/master/for-scripters), including wrapper libraries to ease access via CyREST and drastically reduce boilerplate code. * The [RCyjs package](http://www.bioconductor.org/packages/release/bioc/html/RCyjs.html) is a separate but related resource that can be used to display Cytoscape-like graphs in a web browser from within an R session. ---- ## Samples Generated with cyREST and R/Python ![](http://cl.ly/bfUV/structure-aware-layout.png) Figure 1: Graph structure-aware visualization with cyREST, igraph, and R. Code is available [here](https://github.com/idekerlab/cy-rest-R/blob/develop/workflow1_structure_based_visualization.R). ![](http://chianti.ucsd.edu/~kono/images/humannet_session2.png) Figure 2: Human interactome (HumanNet v1) to subgraphs using Chromosome names ---- ## News: * __6/9/2017__: Version 3.5.0 released. CyREST API documentation is now available in the Cytoscape Help menu. * __5/8/2016__: Version 3.4.0 released. Apps can now create REST endpoints. Examples can be found in the [Cytoscape Automation](https://github.com/cytoscape/cytoscape-automation/tree/master/for-app-developers) GitHub repository. * __9/13/2016__: Version 3.3.7 released. Critical bug found in 3.3.6 and this contains the fix for it. * __9/8/2016__: Version 3.3.6 released. Minor bug fix release. * __9/1/2016__: Version 3.3.5 released. Contains new _/collections_ API. * __6/22/2016__: Bugfix version released. You can simply press *Upgrade* button to install the new version. * __11/16/2015__: Migration to Core App. Now cyREST is a part of Cytoscape Core Distribution. If you are using Cytoscape 3.3 or later, you don't have to install this app. * __9/2/2015__: 2.0.2 released. Merged with Command REST module. Commands features are available under /v1/commands. This is just a straight port from existing core code base, and Commands APIs are not RESTful (yet). * __7/28/2015__: 1.1.1 released. Get network as file API added (and some bug fixes) * __6/26/2015: 1.1.0 released. SVG and PDF export functions are supported!__ * __6/14/2015__: 0.9.17 released. Layout attributes and local table columns are supported. * __6/9/2015__: 0.9.16 released. Now Layout parameters are accessible through API. * __6/5/2015__: Python wrapper (py2cytoscape) released.

3.8.0

Works with Cytoscape 3.7

Release Notes

* Updated to work with Cytoscape 3.7.0 * Improved error reporting * Added App endpoints * Upgraded JAX-RS support to version 2.1 * Fixed image export height and width issues.

3.7.0

Works with Cytoscape 3.6

Release Notes

* Added operation to list Apps exposing Automation. * Port setup (the port established through the -r setting) is available immediately in Java properties after CyREST starts, instead of asynchronously. * Reduced JAX-RS warnings in the Cytoscape framework log * Added operation to set visual properties for Networks * Improved Collections Swagger * Added support for list types in Table put statements. * Added get/set operations for the current network and current network view [GitHub Milestone](https://github.com/cytoscape/cyREST/milestone/1?closed=1)

3.6.1

Works with Cytoscape 3.6

Release Notes

* Improved CyREST Swagger for Functions * BugFixes

3.6.0

Works with Cytoscape 3.6

Apps that depend on this release

Release Notes

* Improved Cytoscape Command handling, including JSON output, JSON input, and expanded Swagger support. * Provides implementations for Cytoscape 3.6 Cyber Infrastructure and Cytoscape model to JSON handling.

3.5.1

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

Added BugFixes: * Returned column JSON was leaving out cells that contained nulls, reducing length and making column JSON hard to map to SUIDS. Now returns null for null entries. * More explicit handling of Command execution. Now execution waits for an allFinished call before returning anything.

3.5.0

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

* Added Help menu items to provide Swagger Documentation, and links to the Cytoscape Automation Repository. (available under Help > Automation) * Expanded Swagger documentation to surpass the coverage of old miredot docs. * Added new endpoints to support node and edge selection.

3.4.0

Works with Cytoscape 3.5

Apps that depend on this release

Release Notes

- Apps can now add their own REST resources via JAX-RS. - Swagger Annotations are available and supported for both CyREST and App resources

3.3.8

Works with Cytoscape 3.3


3.3.7

Works with Cytoscape 3.3

Release Notes

Bug fix version. CX Support is now an optional dependency.

3.3.6

Works with Cytoscape 3.3


3.3.5

Works with Cytoscape 3.3


3.3.4

Works with Cytoscape 3.3


3.3.3

Works with Cytoscape 3.3


3.3.2

Works with Cytoscape 3.3

Apps that depend on this release


3.3.1

Works with Cytoscape 3.3


3.3.0

Works with Cytoscape 3.3


2.0.2

Works with Cytoscape 3.2


1.1.1

Works with Cytoscape 3.2


1.1.0

Works with Cytoscape 3.2


0.9.17

Works with Cytoscape 3.2


0.9.16

Works with Cytoscape 3.2


0.9.15

Works with Cytoscape 3.2


0.9.14

Works with Cytoscape 3.1


0.9.13

Works with Cytoscape 3.1


0.9.12

Works with Cytoscape 3.1


0.9.11

Works with Cytoscape 3.1


0.9.10

Works with Cytoscape 3.1

Release Notes

This is a minor bug-fix version. * Fixed duplicate row problem in table column API.

0.9.9

Works with Cytoscape 3.1

Release Notes

This is a minor bug fix version. * Fixed group deletion problem * Updated API ducuments

0.9.8

Works with Cytoscape 3.1

Release Notes

* POSTing Edge List now respects collection name. * _title_ parameter added for POST method for network.

0.9.7

Works with Cytoscape 3.1

Release Notes

Accepts IP other than _localhost_.

0.9.6

Works with Cytoscape 3.1


0.9.5

Works with Cytoscape 3.1


0.9.3

Works with Cytoscape 3.1


0.9.0

Works with Cytoscape 3.1


CYTOSCAPE 3

Version 3.8.0

License Click here

Released 23 Oct 2018

Works with Cytoscape 3.7

Download Stats Click here