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New Center Sets Goal of Developing Network Biology Software on Par with Genome Sequencing Tools

By Alex Philippidis

NEW YORK (GenomeWeb News) — A new NIH-funded center aims to develop the sorts of tools for advanced studies of biological systems that now exist for genome sequencing, the center's principal investigator told GenomeWeb Daily News.

"The real goal of the center is to develop a suite of software which will be the next Blast, will be the next phylogenies software — all the tools you think about for sequencing, our intent is to put all of those types of tools in place for networks," said Trey Ideker, PI for the National Resource for Network Biology.

"Right now, we are as a community building up databases and protein interactions and other kinds of molecular interactions. There really are no tools for operating on those and analyzing those in any agreed-upon way" in network biology in the way that GenBank and Blast revolutionized genomic sequencing analysis, Ideker added.

Ideker who also is associate professor of bioengineering in UCSD's Jacobs School of Engineering, and chief of the Division of Genetics at UCSD's School of Medicine, said the new tools to be developed by NRNB will not supplant the main informatics tool developed by Ideker and his lab — Cytoscape, the online open-source platform available over the past eight years. Cytoscape describes and visualizes the molecular interactions within cells, allowing for modeling and analysis of biological networks.

Ideker said Cytoscape is going to be the basic platform of the center from which most of the tools will be developed, and for which more than 100 apps have been written, mostly by researchers outside the new NRNB.

NRNB — to be based at the University of California, San Diego School of Medicine — says it will maintain both a basic and a clinical focus. NRNB has said its studies will be designed to identify disease biomarkers and molecular targets for potential drugs, define genetic risk factors and decipher how individual or group lifestyles, such as social networks, affect the development and transmission of disease.

"Just because you know there's 25,000 or 35,000 genes doesn't mean you know anything about how they function. One of the first things you want to know when you study how genes function is, what's the wiring or pathway diagram connecting all their protein products together?" Ideker said.

According to Ideker, the new center will pursue research by its scientists and others that have suggested biomarkers should not be viewed as an individual gene, but as pathways of genes or complexes of genes. Any combination of a certain number of proteins, for example, could be associated with a disease.

"The rule I'm really trying to learn is that it's somehow some function of A, B, or C, or it's A, or B, or C, or some average of A, B, and C that I should be looking at, and that's the biomarker, based on these three proteins at once, not based on any one of them. That's just one example of where we think networks are really going to revolutionize clinical genomic medicine, and there are others," Ideker said.

NCNB is being funded through a five-year, $6.5 million grant from the NIH's National Center for Research Resources, announced earlier this week.

"What this big center award lets us really do is, it lets us consolidate all of that effort under one funding mechanism," Ideker said. "These NIH supported centers are nice because unlike an individual research grant, with a center grant you can run a 24/7 help desk. You can really invest money and time and resources into developing user tutorials and doing user outreach.

"We are going to continue to research new approaches to analyzing biological networks and using those in human disease. But we also are now going to have a lot of support for staff and user support," Ideker said. He added that the center plans to hire "two or three" support staffers.

NCNB's Executive Director is Alexander Pico, bioinformatic group leader at The Gladstone Institutes at UC San Francisco. Other researchers collaborating within the new center include James Fowler, a UCSD professor in the School of Medicine and Division of Social Sciences who specializes in social networks; Bruce Conklin of The Gladstone Institute of Cardiovascular Disease; Gary Bader of the University of Toronto; Chris Sander of Memorial Sloan-Kettering Cancer Center in New York; and Benno Schwikowski of France's Institut Pasteur.

Each researcher will oversee development and dissemination of the tools to be developed by NCNB, and the collaborations that will follow, in a given region. Ideker will work with researchers in southern California; Pico in northern California and the Pacific Northwest; Bader, the US Midwest; Sander, the East Coast; and Schwikowski, Europe.

"Most of these centers that have been funded in the past have been centered at one university, and so all the technology emanates from that one central location, and somehow has to make its way to the rest of the nation via different collaborations. For us, we're sort of the reverse model," Ideker said. "Rather than decentralized, we're federated. The hope is that that's going to really facilitate getting these tools out to the general public."

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