geWorkbench Overview Support Team Molecular Analysis Tools Knowledge Center Columbia University and The 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 data  Access to multiple external data sources  Provide a gateway to a number of computational services

Operations on Microarray Data  Obtaining data from local or remote data sources  Filtering and normalization  Basic statistical analysis  Clustering (Hierarchical, SOM)  Gene Ontology analysis (coming soon!)  Visualization using many common tools, such as: Scatter Plot Volcano Plot Expression Profiles Expression Value Distribution Color Mosaic Dendrogram 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:  For more information on how to use geWorkbench, please visit NCI Knowledge Center, geWorkbench section at : kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench.geWorkbench section kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench  Have a geWorkbench related question? Find the answers in geWorkbench FAQ section at: kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench_FAQ.geWorkbench FAQ kc.nci.nih.gov/Molecular/KC/index.php/GeWorkbench_FAQ  New more helps? Post it in geWorkbench Forum at : kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3.geWorkbench Forum kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3