Feature - Hammering out cures at the genome workbench

Using a connection to Cancer Bioinformatics Infrastructure Objects (caBIO), a repository of molecular biology data, inter-cellular pathway diagrams can be retrieved and displayed in geWorkbench.
Image courtesy of the geWorkbench project.

As biomedical research becomes a more collaborative effort, scientists need a quick and easy way to share information and analysis tools as they work to better understand diseases and search for cures. In the past, most biomedical researchers developed their applications independently, and in consequence, these tools have varied greatly. Research could progress much faster with a more unified approach.

To address this problem, the National Center for Multiscale Analysis of Genomic and Cellular Networks (MAGnet), hosted at the Center for Computational Biology and Bioinformatics at Columbia University, has developed geWorkbench (genomics Workbench), a framework for application development and dissemination. It brings together many of the most valuable graphical biomedical analysis and visualization applications into one unified interface.

GeWorkbench is the only genomic analysis platform that integrates conventional and highly functional tools for gene expression and sequence analysis, more advanced cellular network tools, and powerful visualization and analysis tools, according to Andrea Califano, associate director for bioinformatics at the Herbert Irving Comprehensive Cancer Center.

Currently, more than 50 analysis applications are available on geWorkbench. Developers add between five and ten new ones each year and expend much effort in maintaining upgraded versions of the older ones. If researchers need an application that geWorkbench itself doesn’t provide, the interface lets them extend their search to caGrid. CaGrid is the grid infrastructure underlying the caBIG (the Cancer Biomedical Informatics Grid) information network. It offers many tools as grid services that users can connect to online and utilize remotely.

A dendrogram is a tree diagram frequently used in computational biology to illustrate the clustering of genes. This geWorkbench screenshot displays a dendogram of the results of an analysis using a hierarchical clustering algorithm.

Image courtesy of the geWorkbench project.

Accessing grid services from within the geWorkbench interface hides the complexities of the grid from users. Researchers can seamlessly switch between geWorkbench applications and grid services without having to keep track of where each one comes from or where it’s running.

If researchers cannot find the tool they need on either geWorkbench or caGrid, they can use geWorkbench to easily develop their own tools with minimum programming.

“GeWorkbench provides a user-friendly interface where researchers can collect the information and applications they need, search for and use a grid service when necessary, and quickly get results,” said Aris Floratos, of the Center for Computational Biology and Bioinformatics.

—Amelia Williamson, for iSGTW