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[[../../ | Introduction to Cytoscape App development]] === Introduction to Cytoscape 3.0 App Development ===

Cytoscape 3.0 has a clearly defined, simplified API. API jars are strictly separate from the implementation jars. We believe that [[/LessonsFrom2x|we’ve learned our lessons with 2.x]] and have greatly improved the usability of the API to benefit our active developer community. The API is versioned using the [[http://www.semver.org|Semantic Versioning standard]]. This means that the API won't change throughout 3.x, so an app designed to work with an early version of 3.x will be guaranteed to work up to version 4.0 of Cytoscape. Our commitment to supporting app developers is stated in an explicit '''''backwards compatibility contract''''' found in each class in the public API so that both core developers and app writers will understand how a class might change.

=== Architecture and Technologies ===
Cytoscape 3.0 strives for a modular architecture where the application consists of a set of jar files where each jar contributes a well defined subset of functionality to the application. The design is oriented around the OSGi service model (i.e. micro service) with API and implementation separated into different jar files. We’ve introduced the use of OSGi as a way to create and enforce a modular, sustainable code base. We’ve also introduced Maven as a build system to help manage the many jar files created. Read more about these

 * [[../CoreDevelopment/Architecture|Cytoscape Architecture]]
 * [[../CoreDevelopment/Architecture#OSGi_Basics|Introduction to OSGi]]
 * [[../CoreDevelopment/Architecture#Maven_Basics|Introduction to Maven]]

=== API and Javadocs ===
 * [[../CoreDevelopment/APIOverview|API overview]]
 * [[http://code.cytoscape.org/jenkins/job/cytoscape-3-javadoc/javadoc/|Javadocs]]

TO DO: Remove this section?
=== Plugins, Simple Apps and Bundle Apps ===
If you've developed Cytoscape plugins before, then you will notice quite a few changes in developing for Cytoscape 3.0. These changes cover both core and plugin architectures. To highlight the differences and added benefits of developing on the Cytoscape 3.0 platform, we're now calling them ''apps''. So, consider porting your 2.x plugins to 3.0 apps. And if you are new to Cytoscape development, you can pretty much ignore plugins and focus on the app developer documentation.

Introduction to Cytoscape 3.0 App Development

Cytoscape 3.0 has a clearly defined, simplified API. API jars are strictly separate from the implementation jars. We believe that we’ve learned our lessons with 2.x and have greatly improved the usability of the API to benefit our active developer community. The API is versioned using the Semantic Versioning standard. This means that the API won't change throughout 3.x, so an app designed to work with an early version of 3.x will be guaranteed to work up to version 4.0 of Cytoscape. Our commitment to supporting app developers is stated in an explicit backwards compatibility contract found in each class in the public API so that both core developers and app writers will understand how a class might change.

Architecture and Technologies

Cytoscape 3.0 strives for a modular architecture where the application consists of a set of jar files where each jar contributes a well defined subset of functionality to the application. The design is oriented around the OSGi service model (i.e. micro service) with API and implementation separated into different jar files. We’ve introduced the use of OSGi as a way to create and enforce a modular, sustainable code base. We’ve also introduced Maven as a build system to help manage the many jar files created. Read more about these

API and Javadocs

TO DO: Remove this section?

Plugins, Simple Apps and Bundle Apps

If you've developed Cytoscape plugins before, then you will notice quite a few changes in developing for Cytoscape 3.0. These changes cover both core and plugin architectures. To highlight the differences and added benefits of developing on the Cytoscape 3.0 platform, we're now calling them apps. So, consider porting your 2.x plugins to 3.0 apps. And if you are new to Cytoscape development, you can pretty much ignore plugins and focus on the app developer documentation.

Cytoscape_3/AppDeveloper/Cytoscape_App_Ladder/Intro_to_Cytoscape (last edited 2017-05-29 18:21:32 by AlexPico)

Funding for Cytoscape is provided by a federal grant from the U.S. National Institute of General Medical Sciences (NIGMS) of the Na tional Institutes of Health (NIH) under award number GM070743-01. Corporate funding is provided through a contract from Unilever PLC.

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