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'''Purpose:''' This step will give you an introduction to what Cytoscape is, how it is used, and an overview of technologies used. ==== What is Cytoscape? ==== ==== What is Cytoscape used for? ==== ==== The Cytoscape Community ==== ==== Cytoscape Architecture and Technologies ==== |
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==== The Relationship Between Cytoscape Core and 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. ==== Resources ==== |
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=== API and Javadocs === |
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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
Purpose: This step will give you an introduction to what Cytoscape is, how it is used, and an overview of technologies used.
What is Cytoscape?
What is Cytoscape used for?
The Cytoscape Community
Cytoscape Architecture and Technologies
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.
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
The Relationship Between Cytoscape Core and 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.