geWorkbench Overview

Support TeamMolecular Analysis Tools Knowledge

Center Columbia University

andThe Broad Institute of MIT and Harvard

geWorkbench Overview

geWorkbench – a platform for tool and data integration

geWorkbench is an open-source bioinformatics platform that provides an extensive collection of tools for the management, analysis, visualization and annotation of biomedical data.

geWorkbench has been designed with a plug-in framework. As new techniques are developed and implemented, they can be added to geWorkbench.

geWorkbench aims to allow different tools to easily work together, such as using microarray analysis to obtain a list of interesting genes, and then retrieving their coding or upstream sequences and using these in BLAST, pattern discovery, or transcription factor binding motif searches.

Scopes of geWorkbench

Perform extensive work with microarray data Analyze both genomic and protein sequence dataAccess to multiple external data sourcesProvide a gateway to a number of computational

services

Operations on Microarray Data

Obtaining data from local or remote data sources Filtering and normalizationBasic statistical analysisClustering (Hierarchical, SOM)Gene Ontology analysis (coming soon!)Visualization using many common tools, such as:

Scatter PlotVolcano PlotExpression ProfilesExpression Value DistributionColor MosaicDendrogram

geWorkbench supports many kinds of operations on microarray data:

Working with Sequence

geWorkbench also provides capabilities for working with sequence data:

BLAST

Pattern Discovery

Transcription Factor Mapping

Access to External Data Services

There are many biomedical data sources and computational services available through the internet. geWorkbench strives to make remote data and services directly available on the desktop, integrated with its own local tools.

External sources provide expression data, sequences and annotation: Microarray gene expression repositories (caArray) DNA sequence retrieval (UC Santa Cruz) Pathway diagrams (BioCarta via caBIO database at NCI) Curated cancer gene annotations (Cancer gene index at NCI)

External Computational Services

geWorkbench also provides a gateway to several computational services, including some hosted on Columbia servers and clusters.

BLAST – search for sequences similar to a query sequence via the NCBI BLAST service.

Pattern Discovery – find repeated patterns in a group of sequences.

Through the caGRID project, additional remote services are being added:

Hierarchical clustering – tree-like grouping by expression similarity.

SOM (Self-Organizing Maps) – divide expression profiles into a limited number of bins.

ARACNE – regulatory network reverse engineering.

Need More Information?

NCI is developing an extensive knowledge base to support various NCI molecular analysis tools. Visit us at NCI’s Molecular Analysis Tool Knowledge center at: https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Main_Page.

For more information on how to use geWorkbench, please visit NCI Knowledge Center, geWorkbench section at : https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench .

Have a geWorkbench related question? Find the answers in geWorkbench FAQ section at: https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench_FAQ.

New more helps? Post it in geWorkbench Forum at : https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3 .