NEW YORK (GenomeWeb News) – The US Department of Energy Joint Genome Institute is in the process of hiring about 20 new staffers who will help analyze the growing amount of data it is generating through its sequencing activities.
JGI, which is headquartered in Walnut Creek, Calif., says some of the new staffers will hold positions within its separate plant, fungi, and metagenome programs, and others in the informatics department that offers support across all three.
"We're hiring both within the programs and within informatics," Jim Bristow, JGI's deputy director of programs, told GenomeWeb Daily News. "Broadly speaking, I would say that informatics support, in response to the dramatic increases in sequencing output, is where that hiring is going."
The new staffers — who join a workforce of about 250 full-time equivalent staffers — account for much of the budget increase proposed for JGI in the fiscal year that started Oct. 1 by the US Department of Energy, whose Office of Science funds the institute. While the energy department's FY '10 budget is still being reviewed by Congress, JGI isn't waiting to expand its workforce.
"It's a good time to hire people, particularly in informatics," said Bristow. "It's nice to have money in hard economic times. There are good people out there to be had."
The hiring of new staffers comes as JGI steps up its ability to carry out more complex sequencing projects, with production approaching the terabase range of base-pairs sequenced. To get started, the institute is taking what Bristow termed the "baby steps" of three ongoing pilot sequencing programs in the 100-gigabase scale:
• A Brassica plant genome project led by JGI computational genomics group leader Dan Rokhsar and Joseph Ecker of the Salk Institute.
• A prairie soil metagenome project that Jim Tiedje of Michigan State University is leading with Janet Jansson of Lawrence Berkeley National Laboratory.
• An Arabidopsis rhizosphere project led by JGI microbial ecology group leader Phil Hugenholtz and Jeff Dangl of the University of North Carolina at Chapel Hill.
During the fiscal year that ended Sept. 30, 2009, the institute projects it will have sequenced more than 750 gigabases, compared with just over 100 gigabases in FY '08, and 36 gigabases a year earlier as a Sanger-only institute.
Gigabase production during FY 2010 will rise "significantly," Bristow said, though he could not furnish a figure.
"The sequencing is so cheap, the non-sequencing parts of a genome project really become limiting — the analysis, getting the DNA in the door, keeping track of the projects, the upfront molecular biology," Bristow added. "The sequencing is actually the easiest part. It's the project management of really large projects, and the data analysis that's really going to be the sticking points. So we'd like to be … in a position to be able to lead in that particular area."
The Joint BioEnergy Institute accounted for 20 percent of JGI's sequencing and analysis activities in FY '09 — a share expected to grow to between 30 percent and 35 percent in FY 2010, he said.
The leaps in production output reflect the introduction of the Roche 454 and Illumina next-generation sequencing systems during FY 2008, and their expanded use in FY '09. JGI currently has 15 ABI 3730 capillary instruments — down from more than 100 two years ago — as well as eight Roche 454 systems and seven Illumina systems at the Walnut Creek headquarters. The institute also plans to buy additional 454 and Illumina systems, though the specific numbers of those have yet to be decided.
JGI is relying on 454 and Illumina technologies in the 71 new genomic sequencing projects that comprise the institute's 2010 Community Sequencing Program, according to an article in GWDN sister publication In Sequence.
JGI still uses Sanger equipment, however, for de novo genome sequencing, since the long range pairing information available through that platform "is incredibly useful, particularly in more complex eukaryotic genomes, where polymorphism and repeat content are significant hurdles to genome assembly," Bristow said.
JGI has begun using $11.1 million of $13.1 million received in August under the American Recovery and Reinvestment Act to upgrade its IT infrastructure, doubling its data storage capacity and tripling the computational capacity of its central computing cluster. Bristow said some of those stimulus funds are being used for "some reagent support for preliminary sequencing of switchgrass and miscanthus," both feedstocks used in the production of bioenergy.
JGI's stimulus funding is part of a larger $37.8 million set aside for the Lawrence Berkeley National Laboratory, one of six partner institutions whose genomic capabilities are coordinated through the institute.
A spokeswoman for the US House of Representatives Committee on Science and Technology told GenomeWeb Daily News no activity has taken place on the FY '10 budget since the committee's Subcommittee on Energy and Environment held a hearing Sept. 10.
During the hearing, the director of the Biological and Environmental Research program in DOE's Office of Science discussed JGI and other components of the program and sought to justify higher federal spending
"Vast amounts of data on the composition, physiology, and function of complex biological systems and their natural environments are emerging from new analytical technologies," Anna Palmisano, associate director of science for biological and environmental research, said in her testimony before the panel. "Effectively exploiting these data requires developing a new generation of capabilities for analyzing, mining, and managing the information."
According to the energy department's FY 2010 Congressional Budget Request, prepared in May, JGI would receive $69 million in FY '10 from BER, up 6 percent from $65 million in FY '09. "Funding is increased to focus on metagenome expression and sequencing of environmental microbial communities or the plant-microbe rhizosphere, as well as improved genome annotation and functional analysis and verification of genome-scale models," the budget request said.