High Level Requirement Specification

Bio conductor service

Reference	Techreq.BioConductor
Referenced Use-cases	MicroArray
Dependencies	R
Champion
Status	ASSESSED

	Taverna 1.3	Taverna 2.0
Priority		5
Rough estimate	MONTH	WEEK

Overview

Accessing Bio Conductor services from within Taverna. A new branch in the Available Services panel with the different Bio Conductor services listed and described. Bioconductor is a software project for the analysis and comprehension of genomic data, accessed through R.

Overall Goals

• Browse described Bio Conductor services (ie. functions), categorized
• Run Bio Conductor tools without the user needing to know R or to call R functions, with parameters described as normal input ports.

Assessment

This is a requirement to create a new service. This shouldn't really be done by the mygrid project team if we take a pure view on how this should work.

Affected Components

Key Tasks

1. Get to know BioConductor and R (two days)
2. Investigate widgetInvoke() (a function that describes all other services as an XML) (two days)
3. Build service panel plugin and processor plugin using widgetInvoke XML() and Rshell for invocation. (three days)
4. Require local R or can this be exposed as web services, like ExpressionProfiler? Investigate. (two days)
5. Build and deploy public web service that exposes BioConductor functions in a Taverna friendly way (two weeks)

Appendix

• Mygrid.MicroArray
• http://www.bioconductor.org/