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DNA Blueprints Guide The Construction Of Specific Human Structures
Chad Mirkin discusses using DNA to build a three-dimensional structure out of gold, likening the process to building a house. Starting with basic materials such as bricks, wood, siding, stone and shingles, a construction team can build many different types of houses out of the same building blocks.
The article includes an audio recording of the full interview. Photo courtesy of the UCSD School of Medicine.
| Next Generation Data Visualization Tool For Exploring The Genome |
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| Science - Genetics & Genome | |||
| TS-Si News Service | |||
| Monday, 04 August 2008 17:00 | |||
Cambridge, MA, USA. The genome contains a lot of data that has to be collected, cleaned, normalized, processed, and analyzed in a manner. This has to be done in a manner that enhances understanding and can lead to new insights. With increasing computer power available, data visualization has come into its own.
Scientists and others have communicated using visual media since the dawn of humanity. However, the advent of serious attention to the genome has resulted in the collection of and vast quantities of new data. Researchers collect vast amounts of diverse genomic data with ever-increasing speed, but effective ways to visualize these data in an integrated manner have lagged behind the ability to generate them.
Integrative Genomics Viewer (IGV). Computer software (2008). The Broad Institute of MIT and Harvard. Cambridge, MA, USA. [ Quick Start PDF ] [ User Guide PDF ]
[ Sample Research PDF ] [ Sample Data ZIP ]
Scientists in laboratories across the US and around the world are working on ways to address this growing need. In an important development, researchers at the Broad Institute of MIT and Harvard have developed the Integrative Genomics Viewer (IGV). [N1] The Integrative Genomics Viewer (IGV) is freely available to researchers worldwide and can be accessed at the IGV website. [N1]
The IGV is a visualization tool that helps users simultaneously integrate and analyze different types of genomic data and rapidly view them at any level of resolution. A researcher has the flexibility to zoom in on a specific genomic region of interest or to pan out for a broad, whole genome view.
 Jill Mesirov, Chief Informatics Officer and Director of Computational Biology and Bioinformatics at the Broad Institute.
"This new tool offers a Google Maps®-like view of integrative genomic data," Mesirov says. "It brings together different kinds of genomic data into a single, holistic view."
"I'm incredibly proud of our computational scientists for responding so rapidly and effectively to the critical needs of the growing genomics research community."
"Other tools offer detailed, localized views of genomic data, and a few tools are equipped to provide a whole genome view," said Senior Software Engineer Jim Robinson, one of the program's creators. "IGV was designed to integrate both and to provide smooth zooming and panning across all resolution scales." [N2]
Broad Associate Member John Rinn, an assistant professor at Harvard University and Beth Israel Deaconess Medical Center (Boston), has used a variety of visualization tools to sift through different types of genomic data. "Before I was introduced to IGV, I had to use three different programs to visually integrate my data," Rinn said. "But now this one, universal browser allows me to rapidly scan the entire genome and identify promising regions, which has revolutionized my work."
 With IGV, researchers can still choose a Google Maps®-like "street view" of the As, Cs, Ts, and Gs that make up the genome, but they can also simultaneously visualize additional layers of complex information about gene expression as well as sequence alterations, or mutations, in the genetic code.
Other genomic details, such as copy number variation, chromatin immunoprecipation data, and epigenetic modifications, can also be viewed in IGV.
Moreover, all these data types can be overlaid or superimposed to determine how changes at one level will affect another. Users can choose from a variety of display options, viewing their data as a heat map, histogram, scatter plot, or other formats of their choice. This new visualization tool is free and publicly available to researchers via the web.
"Most visualization tools are limited in their ability to handle multiple types of genomic data and are typically 'retrofitted' to accommodate new data types as they have arisen," said Michael Reich, Director of Cancer Informatics Development at the Broad Institute. "IGV was designed from the ground up to integrate all of these data, and to provide a strong platform for future growth and refinement."
IGV promises to increase the flow of discovery in many areas of biomedical research. "This tool is designed to enable researchers to view many types of genomic data, especially those relevant to human disease," said Reich. "We're particularly excited about its already groundbreaking use in ongoing studies of the cancer genome."
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| Last Updated on Monday, 04 August 2008 10:30 |
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