Use case

Micro array analysis

Reference	Userreq.MicroArray
High-level reqs	R TavernaGridService LongRunningWorkflows ApiSep BioConductor LargeData ExpressionProfiler
Proposed by	Misha Kapushesky
Champions	StianSoiland, Paul Fisher

	Taverna 1.3	Taverna 2.0
Priority

Overview

Provide methods for doing micro array analysis using Taverna, for instance by using methods from Expression Profiler and running R scripts using Bioconductor.

The micro array community also wants to be able to run Taverna as a Grid service or Web service, to be able to monitor and control progress programmatically.

Overall Goals

• Micro array analysis workflows could possibly take a long time to execute, and therefore some way of running a workflow detached is important, preferably as a web/grid service.
• R is used to a large extent in the community, so a R processor is important. However, R is usually only applied to run BioConductor services, and so what is really needed is to expose bio conductor services to Taverna
• The Expression Profiler provides many micro array analysis services. These services should be usable from Taverna, but this might be easiest to achieve if the EP people make a WSDL based web service of the EP.
• Micro array data can be huge, so Taverna must be able to handle this, preferably by some referencing or data caching scheme.
• When testing several T-test values, it would be useful to do a parallel iteration over the different values. Some way of "submitting" the job to a cluster of web services instead of a single web service.

Required services

• BioConductor
• Techreq.R
• ExpressionProfiler

Workflow outline

1. Data import of raw CEL files from the micro array chips
2. Quality Assurance
3. Normalisation (RMA)
4. Post-normalisation QA
5. Moderated T-test for different T values

Output of T-test, a gene list of statistically differentially expressed genes, will be further processed using several techniques:

• Reduce to Top 100 DOWN regulated
• Reduce to Top 100 UP regulated
• Retrieve annotations
• GO analysis
• Kegg analysis

Appendix

See the MicroArray integration page.