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= 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. * [[http://neilbartlett.name/blog/osgibook/|OSGi in Practice]] * [[http://www.osgi.org/Main/HomePage|OSGi Alliance]] * [[http://felix.apache.org/site/index.html|Apache Felix]]: Although OSGi is implementation-independent, this implementation will be used as standard development/testing tool. * [[http://wiki.ops4j.org|OPS4J]] Products: This project has a lot of usuful scripts to develop OSGi bundles * [[http://www.springsource.com/repository/app/|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. * [[http://code.google.com/p/google-guice/|Google Guice]]: Currently focused on DI only. * [[http://springframework.org/about|Spring Framework]]: De facto standard framework for DI and AOP. * [[http://springframework.org/osgi|Spring-DM]]: Integration of Spring Framework and OSGi * [[http://maven.apache.org/|Apache Maven]]: 3.0 project will be moved from Ant to Maven. * [[http://www.sonatype.com/book/|Maven: The Definitive Guide]] * [[http://m2eclipse.codehaus.org/|Maven integration for Eclipse]] * [[http://mvnrepository.com/|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. * [[http://incubator.apache.org/tuscany/|Apache Tuscany]]: An open-source implementation of Service Component Architecture. * [[http://www.springsource.com/products/suite/applicationplatform|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. * [[http://jruby.codehaus.org/|JRuby]]: Ruby scripting language running on JVM. Actively developed by Sun. * [[http://www.mozilla.org/rhino/|Rhino]]: JavaScript. Bundled with Java SE 6. * [[http://www.jython.org/Project/|Jython]]: Python implementation. * [[http://openjdk.java.net/projects/mlvm/|Da Vinci Machine Project]] == Developer's Tutorials and References == === For Eclipse Users === ==== Basic Tutorial ==== * {*} [[Cytoscape_3.0/Eclipse|Developing Cytoscape 3 Core with Eclipse and its Plugins]] ==== Optional ==== * [[Cytoscape_3.0/Spring|How to use Spring Framework in Cytoscape 3]] * [[Cytoscape_3.0/Maven|Create Cytoscape 3 plugin from Maven Archetype]] (incomplete) === For Netbeans Users === * {*} [[Cytoscape_3.0/Netbeans|Setting Netbeans 6.1 or 6.5 for building and running or debugging Cytoscape 3]] === Other OSGi Tools and Technical Notes === * [[Cytoscape_3.0/PAX|How to build bundles with Pax-Construct]] * [[Cytoscape_3.0/AOP|How to use AOP on Spring + OSGi environments]] |
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.
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 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.
Developer's Tutorials and References
For Eclipse Users
Basic Tutorial
Optional
Create Cytoscape 3 plugin from Maven Archetype (incomplete)
For Netbeans Users