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

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Select/Create Study

Describe Experiment (blank)

Describe Experiment (filled)

Upload Analysis Files

Edit Treatment Information (blank)

Edit Treatment Information (filled)

Treatment Information in MS-Excel (blank)

Treatment Information in MS-Excel (filled)

Focus Gene List (blank)

Normalization (before run)

Normalization (running)

Normalization (complete)

Diagnostic Plots (pre-run)

Diagnostic Plots (complete)

Notify Statistician (blank)

Notify Statistican (filled)

Notify Statistican (sent)

Define Model to be Fit (Blank)

Define Model to be Fit (Filled)

Fit Summary File (Server-side)

Model Fitting (Before run)

Model Fitting (After run)

View Analysis Results (Main Directory)

View Analysis Results (Plot Subdirectory)

One Result Plot

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