Skip to main content
Premium Trial:

Request an Annual Quote

DOE Starts Systems Biology Knowledgebase Collaboration

By a GenomeWeb staff reporter

NEW YORK (GenomeWeb News) – The US Department of Energy has formed a collaboration of researchers that it has tasked with developing a systems biology database that will enable comparative genomics research for scientists studying plants, microbes, and the environment.

DOE's Office of Science said yesterday that the team, spread across eight institutions around the country, will work together to develop the Systems Biology Knowledgebase, which is designed to enhance collaborative computational research.

Initiated with $3 million in funding from the 2009 American Recovery and Reinvestment Act, the Knowledgebase project will provide new capabilities for researchers to evaluate data-driven theories of microbial and plant systems and to generate new data, protocols, algorithms, and testable models.

The first round of funding supported development of a mapping strategy, architecture, and pilot software projects for the database. The DOE's Office of Science 2012 budget request to Congress seeks $12 million to fund the build-out of the Knowledgebase, which will include extensive software development, data capture, and integration efforts.

"Hidden in the mountains of biology data we are accumulating today are the secrets of Nature's solutions to a broad range of challenges we face in energy and the environment," said Sharlene Weatherwax, DOE's associate director of science for biological and environmental research (BER). "The Knowledgebase will accelerate our ability to unlock those secrets and help take systems biology to a new level."

Funded through BER's Genomic Science division, the Knowledgebase will use capabilities and supercomputing facilities within the DOE's national lab complex including the Joint Genome Institute, the BioEnergy Scientific Computing Center at Lawrence Berkeley National Laboratory, the Magellan testbed, and other DOE facilities.

The Knowledgebase project will be led by principal investigator Adam Arkin, director of the Physical Biosciences Division of the Lawrence Berkeley National Lab.

The collaborators will include researchers at Argonne National Laboratory; Oak Ridge National Laboratory; Brookhaven National Laboratory; the University of California, Davis; Hope College; the University of Illinois at Urbana-Champaign; Cold Spring Harbor Laboratory; and Yale University.

The Scan

Suicidal Ideation-Linked Loci Identified Using Million Veteran Program Data

Researchers in PLOS Genetics identify risk variants within and across ancestry groups with a genome-wide association study involving veterans with or without a history of suicidal ideation.

Algorithm Teases Out Genetic Ancestry in Individuals at Biobank Scale

Researchers develop an algorithm known as Rye to tease apart ancestry fractions in admixed individuals at a biobank-scale, applying it to 488,221 UK Biobank participants in Nucleic Acids Research.

Multi-Ancestry Analysis Highlights Comparable Common Variants at Complex Trait-Linked Loci

Researchers in Nature Genetics examine common variants implicated in more than three dozen conditions, estimating genetic effect similarities across ancestry tracts in admixed individuals.

Sick Newborns Selected for WGS With Automated Pipeline

Researchers successfully prioritized infants with potential Mendelian conditions for whole-genome sequencing or rapid whole-genome sequencing, as they report in Genome Medicine.