(Under Construction!)

Cytoscape IDE for Eclipse

Introduction

The purpose of this project is minimize plugin developer's setup time for developing Cytoscape 3 plugins. For Cytoscape 3, we are going to use several new technologies including OSGi, Spring, scripting, etc. Developers have to spend some time to setup their environment to use those new technologies for Cytoscape 3. To avoid the overhead for using them, I'll introduce a new plugin for Eclipse, tentatively named Cytoscape IDE.

The goal of this Eclipse plugin is the following:

1. Install all required Eclipse plugins for Cytoscape 3 development.
2. Provide templates for Cytoscape 3 plugin projects.
3. Integration to Eclipse PDE (Plugin Development Environment)

Development Plan

Phase 1: Develop the mechanism to install all required plugins for Cytoscape 3 core/plugin development Phase 2: Provide template for Cytoscape 3 plugin project using Maven archetype Phase 3: Provide wizard to publish the plugin (optional)

Design

Target Platform

This SDK is for Eclipse 3.4 (Ganymede) or later. Assume Eclipse is installed with PDE.

Required Plugins

To develop Cytoscape 3 code, developers should install the following plugins for Eclipse:

Required for All Developers

• Subclipse - Client for our source code management system
• Maven Integration for Eclipse - For Maven projects
• Spring IDE - For Spring DM
• PAX Coursor - Run OSGi bundles on Felix
• Jalopy - Code fomatter.

Optional Plugins

• FindBugs - Find potentical cause of bugs in source code

• Checkstyle - Coding style cheker

Cytospcae IDE should install these automatically from an Update Site

How it works?

• Automatically install all required plugins from Cytoscape project's update site (maybe on chianti.ucsd.edu). Our server hosts only the Cytoscape IDE plugin. All dependencies will be imported from other project's update site.
• Develop maven archetypes for the following projects:
  • Cytoscape 3 plugin
  • Cytoscape 3 Plugin with Spring-DM support
  • Cytoscape 3 Script Project

• Manage maven archetypes using Nexus

• Add Cytoscape Plugin Project to the File-->New menu on Eclipse workbench.

• Setup perspective

Status

• Version 0.0.1 - Install all required plugins above.

Tutorial