SCIENCE & ENGINEERING NEWS
Columbus, OH, and McLean, VA — The Ohio State University (OSU), Ohio Supercomputer Center (OSC), and LabBook, Inc. announce that they have formed a partnership to provide life science researchers with an annotated map of the human genome. The project combines OSU’s annotated human genome database, backed by OSC’s computational power, with the powerful visualization and analysis capabilities of LabBook’s personal discovery space. The partnership allows scientists the most sophisticated view of the human genome to date.
In June 2000, the international consortium of the Human Genome Project announced that they had completed a map of the human genome sequence. However, this important milestone is just the first step in identifying the genes hidden in the sequence and understanding their function — a process known as annotation. Through a novel combination of data resources, and with computational power provided by OSC, researchers at OSU have identified thousands of genes and obtained clues to their function. LabBook’s genomic discovery system displays this information in a highly intuitive and interactive environment, enabling the researcher to extract meaning from the sequence.
The annotation project at OSU was directed by Dr. Bo Yuan, Head of Bioinformatics in the Human Genetics Cancer Program. “We have combined accurate, non-fragmented and non-redundant whole genome mapping of expressed genes with comprehensive annotation,” said Dr. Yuan. “Now we can truly perform hypothesis driven queries of the human genome, which was not previously possible.”
“Annotation is what makes the genome useful,” agreed Dr. Fred Wright of Human Cancer Genetics, “and we have drawn on several unique resources to discover the genes and how they work. The OSC contribution was critical, as this work would have literally taken years without their computing power while LabBook’s discovery system enables researchers to visualize this information in a beautifully integrated environment.” Dr. Wright expects that the LabBook software will accelerate efforts underway at OSU to identify genes involved in numerous diseases.
The process of annotation is extremely computationally-intensive, involving millions of automated searches and comparisons along the 3-billion letter code of the human DNA sequence. The necessary hardware is beyond the capabilities of most university or industry laboratories. The supercomputing cluster machines at OSC proved ideal for the job. “The generation of this database required a tremendous amount of computer power,” said Al Stutz of OSC. “We were fortunate to have the Silicon Graphics 1400 cluster that provided us with this capability.”
While genomic annotation provides a solid basis for genetic research, its usefulness remains limited without powerful software to perform queries and visualize the results. Moreover, the human genome project has been accompanied by an explosion of information on human genes, along with modern high-throughput technologies for analyzing their functions. This expanding collection of information for drug discovery holds the key to treatments for a broad range of human diseases, but the data sources are dispersed and of limited use to biologists who are not trained in bioinformatics. Utilizing the data effectively requires integrating these disparate data types in a unified Web environment. To solve this problem, OSU, LabBook and OSC are providing the OSU Human Genome Database within LabBook’s genomic discovery space.
“The OSU Human Genome Database and the way we deliver it to the scientist represent an important advance in extracting meaningful information from human genome data,” said Dr. Shawn Green, CEO of LabBook. “This meticulously assembled, comprehensively analyzed, extensively annotated, and carefully integrated research platform enables utilization of human genomic data in ways that have not been possible until now.”
LabBook’s genomic discovery space derives its power from the synthesis of four complementary information technologies: an exhaustively analyzed, and comprehensively annotated human gene database; a uniquely effective and discovery-based query engine; a dynamic XML-based data visualization interface through LabBook’s Genomic XML Browser(TM); and a functionally integrated Web- based information management system, the eLabBook(TM). The browser maximizes the value of bioinformatics data by delivering it as “live”, reusable documents in a highly visual and interactive discovery environment. The combination of an open XML standard for bioinformatics with a biology-smart browser creates the ideal bioinformatics ‘front end’ that enables dynamic integration and annotation of diverse data.
“To fully exploit the data derived from the sequencing of the human genome for advancing drug discovery it has to be accessible to virtually all biologists and not just the bioinformatics specialist,” said Dr. Adel Mikhail, LabBook’s Vice President of Corporate Development. “Our approach is to integrate and simplify bioinformatic information so that all interested biologists can effectively utilize this information.”
OSU’s Human Genome DataBase will be made available later this year at http://www.labbook.com .
The Ohio State University is a comprehensive land-grant teaching and research institution enrolling about 55,000 students system-wide annually, including 48,000 on its main Columbus campus. Operating on a $2.1 billion budget, which includes an academic Medical Center and one of the nation’s few free-standing cancer hospitals, the university attracted more than $228 million in external research funding last fiscal year. Ohio State offers 177 undergraduate majors, 120 master’s degree programs and 94 doctoral programs, with some 4,000 faculty teaching approximately 10,500 courses each year.
About LabBook, Inc.
LabBook, Inc. is an XML powered life science informatics and information provider for the biotechnology, pharmaceutical, and academic life science researcher. LabBook’s enabling software, such as the LabBook Genomic XML Browser(TM) queries, manages, and visualizes heterogeneous genomic data types while retaining their underlying associations, and then intelligently communicates targeted information to the researcher. LabBook’s open XML format and unique browser capabilities deliver genomic data as “live” reusable documents that integrate underlying bioinformatic content. LabBook’s mission is to solve the life science industry’s need for rapid access to targeted information and new discoveries. LabBook, Inc. offices are located in McLean, Virginia and Columbus, Ohio. To learn more contact LabBook, Inc. at http://www.labbook.com .
Ohio Supercomputer Center (OSC), a state-supported resource, provides a reliable high performance computing and communications infrastructure for a diverse, statewide/regional community of education, academic research, industry, and state government users. As a shared resource, OSC accelerates the use of information technologies to strengthen the state’s attractiveness and global competitiveness.
Web site: http://www.labbook.com