Cytoscape 3 Developer's Guide

Related Frameworks and Technologies

From 3.0, new technologies/frameworks will be used for implementation. The following is the list of links to documents related to those frameworks/technologies.

• OSGi - Cytoscape will be modularized by following this standard.

  • OSGi in Practice

  • OSGi Alliance

  • Apache Felix: Although OSGi is implementation-independent, this implementation will be used as standard development/testing tool.

  • OPS4J Products: This project has a lot of usuful scripts to develop OSGi bundles

  • SpringSource Bundle Repository: To use existing plain JAR libraries in an OSGi environment, we need to add metadata to it. This repository is a collection of OSGi-ed popular libraries, i.e., repository of OSGi bundles managed by Spring Source.

• Dependency Injection Frameworks - One of the scopes of 3.0 is modulalization and make Cytoscape usable as a part of other programs, including server-side application or command -line tools. The following DI frameworks are POJO-base and popular among server-side application developers.

  • Google Guice: Currently focused on DI only.

  • Spring Framework: De facto standard framework for DI and AOP.

    • Spring-DM: Integration of Spring Framework and OSGi

• Apache Maven: 3.0 project will be moved from Ant to Maven.

  • Maven: The Definitive Guide

  • Maven integration for Eclipse

  • Maven Repository Search - Note: Cytoscape cannot use most of these libraries directly. To use these, they should be re-packed as an OSGi bundle.

• Server-Side / SCA - Once Cytoscape is modulalized based on OSGi, we can use Cytoscape bundles and these frameworks to build server-side applications or web services.

  • Apache Tuscany: An open-source implementation of Service Component Architecture.

  • SpringSource Application Platform: OSGi-Spring powered application server.

• Scripting Language Support - There are several implementations of scripting languages running on JVM. These will be used to implement scripting feature in Cytoscape.

  • JRuby: Ruby scripting language running on JVM. Actively developed by Sun.

  • Rhino: JavaScript. Bundled with Java SE 6.

  • Jython: Python implementation.

  • Da Vinci Machine Project

Developer's Tutorials and References

For Eclipse Users

Basic Tutorial

• Developing Cytoscape 3 Core with Eclipse and its Plugins

Optional

• How to use Spring Framework in Cytoscape 3

• Create Cytoscape 3 plugin from Maven Archetype (incomplete)

For Netbeans Users

• Setting Netbeans 6.1 or 6.5 for building and running or debugging Cytoscape 3

Other OSGi Tools and Technical Notes

• How to build bundles with Pax-Construct

• How to use AOP on Spring + OSGi environments