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Cytoscape 3.0 App Development

Introduction

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.

API and Javadocs

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.

There's a lot to learn about OSGi and Maven. We don't expect everyone to have the time to learn about them. So we have two types of apps, simple and bundle.

Simple Apps don't require any understanding of OSGi or Maven. They are single jars, like Cytoscape 2.x plugins except for the 3.0 API. They can't take full advantage of the Cytoscape 3.0 architecture. Here's how to create a simple app.

Bundle Apps are OSGi bundles that have all the benefits of the Cytoscape 3.0 architecture. With bundle apps, you can reference third-party jars in a consistent way and avoid the library clashes which were common in 2.x. We will host third-party jars to support your apps, if they are not already hosted by maven central or our nexus repository. Here's how to create a bundle app using the command line or using Eclipse.

To help app developers to develop their own app, the Cytoscape developer team developed a cookbook, a collection of small apps.

Cytoscape 3 App Cookbook

Getting Started

Here are some guides to setting up your development environment for Cytoscape 3.0 apps.

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-There are two kinds of apps. ''Simple Apps'' are single jar files without dependencies on third-party jars. If you are developing an app with basic functionality that doesn't rely on other libraries, then you can skip some of the new technologies as build a Simple App.  ''Bundle Apps'' are OSGi bundles that take full advantage of the new 3.0 architecture and technologies. With Bundle Apps, you can reference third-party jars in a consistent way and avoid the library clashes which were common in 2.x. We will host third-party jars to support your apps, if they are not already hosted by maven central or our nexus repository. If your app will depend on other libraries, then we recommend that you look into writing a Bundle App.

 * [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_a_Simple_Cytoscape_3_App|Create a Simple App]]

 * [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_an_OSGi_Bundle_Cytoscape_3_App|Create a Bundle App Using Command Line]]

 * [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Create_a_Bundle_App_Using_IDE|Create a Bundle App Using IDE]]
+There's a lot to learn about OSGi and Maven. We don't expect everyone to have the time to learn about them. So we have two types of apps, ''simple'' and ''bundle''.



''Simple Apps'' don't require any understanding of OSGi or Maven. They are single jars, like Cytoscape 2.x plugins except for the 3.0 API. They can't take full advantage of the  Cytoscape 3.0 architecture. [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_a_Simple_Cytoscape_3_App|Here's how to create a simple app]].



''Bundle Apps'' are OSGi bundles that have all the benefits of the Cytoscape 3.0 architecture. With bundle apps, you can reference third-party jars in a consistent way and avoid the library clashes which were common in 2.x. We will host third-party jars to support your apps, if they are not already hosted by maven central or our nexus repository. Here's how to create a bundle app [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Creating_an_OSGi_Bundle_Cytoscape_3_App|using the command line]] or [[http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:Create_a_Bundle_App_Using_IDE|using Eclipse]].