Run Workflows inside Bioclipse

From BioclipseWiki

Contents 1 Introduction 2 Workflow engines 3 Implementation 4 Prototype 5 Responsible

Introduction

This project aims at providing execution of workflows from inside Bioclipse. Design will probably be done in respecive workflow engine's designer.

Workflow engines

The engines we will start with are:

• Taverna
• Knime
• ActiveBpel

Implementation

• Set up T2 as an application server [DONE], see http://ws1.bmc.uu.se:8080/taverna-server-0.2.1/home.html)
• Call the T2 app server from Java code [DONE] (proof-of-concept)
• Create plugins for Bioclipse [Started]
• Integrate Taverna datatypes with Bioclipse (right-click a sequence in Navigator, execute workflow X)
• Run and execute T2 workflows locally
• Visualize T2 workflows in a Bioclipse editor (use Dot or Zest)
• Improve data type integration
• and so on...

Prototype

Sample screenshot from the prototype showing a Taverna workflow inside a TavernaEditor.

Responsible

Ola Spjuth, --Ola 11:58, 25 January 2008 (CET)