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Revision as of 15:13, 14 February 2006

Overview

'(who uses this , why/ what for? background )

geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extendible collection of tools for the management, analysis, visualization and annotation of biomedical data.

Benefits include:

• Integrates with existing bioinformatics modules for analysis and visualization.
• Support for a variety of genomic data including microarrays, sequences, pathways, networks, alignments and phenotypes.
• Access to remote servers and clusters for the performance of computationally intensive calculations.
• Integration of analyses with biological annotations from the National Cancer Institute.
• Flexible import options: allows user to merge files from various sources.
• Community: decribe this aspect
• developer benefit

Intro graphic

Tutorials

The following { insert description)

Getting Started

• Starting the application
• GUI elements
  • Panels
  • Navigation

Loading Data

• Data formats

Working with Marker and Phenotype Panels

• Creating panels
• Visualizing

Visualize Gene Expression

Filter and Normalize Data

Clustering Gene Expression Data

• Hierarchical Clustering
• Self Organizing Map (SOM)

Differential Expression

• T Test
• Multi Test
  • Volcano Plot
  • Color Mosaic

Regulatory Network

• Reverse Engineering
• Cytoscape

Integrated Annotation Information

Enrichment Analysis

• Go Term
  • Go Miner

Sequence Analysis

• Sequence Retrieval
• Sequence Homology Analysis
  • Blast
  • Other

Pattern Discovery

• Position Histogram

Promoter Analysis