Analysis Workflow Tool
Gregory R. Warnes
University of Rochester Center for Biodefense Immune Modeling
2006-12-14
Workflow-based interface for gene expression studies
Goal: Improve the process of performing and analyzing immunology experiments.
Approach: Provide an integrated software tool that supports entire process of designing, running, collecting, processing, analyzing, visualizing, modeling, and presenting gene expression studies.
Principles:
Open Architecture “Permiable”- Allow data to be be easily moved
into/out of the system at any stage Collect data when it is first generated Allow users to ‘jump’ between stages Make it easy to do the ‘best’ thing
Mechanism:
Web-based UI Workflow stages are explicitly represented At each stage:
Collect data generated Perform computations needed
Integrate experimental design, data collection data processing, statistical analysis, data visualization
Previous Work - MiDAS
The next few slides show the 'MiDAS' “MIcroarray Data Analysis System” I developed at Pfizer for handling mRNA microarray experiments.
The web interface is based on RStatServer All computations are performed using “R” with
BioConductor libraries Calculations occur on a Linux cluster, ensuring
rapid completion