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Research Institutes Assess Impact of Coming End of ARRA Funding

By Alex Philippidis

NEW YORK (GenomeWeb News) – With the end of stimulus funding from the American Recovery and Reinvestment Act of 2009 rapidly approaching, it appears that research institutes are prepared to proceed without the additional money and believe other sources of funding will be found to support their work.

ARRA is the $814 billion measure signed into law by President Obama last year with the intent of stimulating the nation's economy. (The Congressional Budget Office last month revised the projected cost down from its previous estimate of $862 billion in January).

The National Institutes of Health was appropriated around $10 billion under the legislation, which requires all funds available to NIH to be committed or "obligated" by the agency to researchers or institutions by the end of this month.

In interviews this past week with GenomeWeb Daily News, officials at three research institutes said that the end of ARRA funding is not expected to hinder their research efforts. Of the three, only one received significant amounts from the stimulus act, and now says it will pursue funding from other government sources, especially NIH, as well as private sources.

ARRA money doesn't have to be in the hands of grant winners, generally, until Sept. 29, 2011. According to NIH, awards from stimulus funding are subject to the standard terms of award as indicated in the NIH Grants Policy Statement — including the authority to extend the final budget period of a previously approved project period for up to 12 months without additional funds.

No Worries

"The lost ARRA funding will be replaced with something else," Antony Peake, director of grants accounting for the Sanford-Burnham Medical Research Institute, told GWDN. Sanford-Burnham has campuses in La Jolla, Calif., and the Lake Nona community of Orlando, Fla.

"We have somebody in position here who is assigned that task of working with developing government relations to find other sources of funds. But NIH is still going to be our main source. We're looking at other options as well, as we continue to expand both at La Jolla and Lake Nona," Peake said.

Sanford-Burnham won just under $21 million in 55 grants for 34 projects funded by NIH and one funded by the National Science Foundation. Of the 34 projects, 20 received funds for both of ARRA's funding years. That funding helped propel Sanford-Burnham to its highest-ever annual amount of grant and contract funding — a total $105 million in the fiscal year that ended on June 30.

Peake said Sanford-Burnham expects to increase its grant funding in its current fiscal year. Researchers hired within the past two years are expected to generate new grants over the next couple of years, he said. Also, the institute is in the process of recruiting at least four, and possibly up to six, investigators for its La Jolla, Calif., campus, and another two or three investigators for its Lake Nona campus in Florida.

"We'll have new investigators that will be coming in here to our Cancer Center, one earmarked for neuroscience aging stem cell research, one for our Sanford Children's Health Research Center, and we just recruited one in August for our Infectious and Inflammatory Disease Center," Peake said.

In Florida, he added, investigators will be recruited for Sanford-Burnham's Diabetes and Obesity Research Center.

ARRA's impact can also be seen at The Jackson Laboratory's headquarters in Bar Harbor, Me., where administrators held a groundbreaking ceremony Aug. 20 to mark the start of work on an expansion of its bioinformatics facilities, funded through a $2.1 million grant by the National Center for Research Resources from stimulus funds.

The project — officially known as Bioinformatics Expansion Phase III — entails the construction and renovation of a computing infrastructure facility to house existing and anticipated additional computing hardware, as well as office and conference space for bioinformatics and computational biology faculty.

"Jackson plans to recruit four new faculty members over the next five years with expertise in applying computational approaches to solving biological problems," the laboratory stated in an abstract of the project available on ARRA's website.

"However, our three-floor BI/CB area is at capacity because of the rapid growth of existing programs," it said. "There is no space for new recruits or expected program expansions. In addition, there is insufficient space to house the expanding computing hardware necessary to meet the increased needs of the BI/CB programs and our wet-bench research programs, which are increasingly dependent on computation."

Jackson Lab won $12.4 million toward 25 projects, six of which were funded for two years.

Faring better through ARRA was the Broad Institute in Cambridge, Mass. The Broad won a total of $57.3 million to fund 19 projects — including six that received two years' worth of funds. A spokesman for the Broad, Fintan Steele, said the institute does not comment on funding of its projects.

By contrast, ARRA funded just three projects totaling almost $5.2 million at Seattle's Institute for Systems Biology. That's a small slice of ISB's revenue from grants and contracts, which ballooned from $27.9 million in 2008 to almost $35.2 million last year.

"It's not a big deal for us," ISB spokesman Todd Langton said.

IGS: A Stimulus Success

Researchers at the Institute for Genome Sciences at the University of Maryland School of Medicine were enthusiastic on Sept. 1, the day they released the new version of their CloVR virtual machine, which provides push-button pipelines for analysis of microbial genome sequences and runs on a desktop or a cloud.

The CloVR project was made possible through ARRA funding. It received an RC2, or Research and Research Infrastructure "Grand Opportunities" grant from the National Human Genome Research Institute of $674,786 for FY 2009, and $689,826 for FY 2010, as well as about $460,000 from the National Science Foundation.

The new release of the CloVR virtual machine includes an expanded 16S analysis pipeline with several tools popular in human microbiome projects, Florian Fricke, one of two PIs involved in the project, told GenomeWeb Daily News. The new release allows for the fully automated assembly, gene prediction, and annotation of Roche 454 and Illumina sequence reads from single microbial genome projects, he said.

Fricke said researchers have improved the CloVR virtual machine through expansion of its existing pipelines to accept more input file types and to include more analysis tools, as well as through expansion of its multi-platform support. "Significant efforts have been made to organize CloVR as a platform that allows easy integration of additional tools and pipelines by us and others in the future," Fricke said.

In total, IGS won $2.5 million in ARRA funds toward three projects, two of which were funded for two years — compared with the $71 million in total open grants and contracts won by the university. Since many of its grants and contracts are for multiple years, the institute estimates it generates a total $22 million to $23 million annually.

When ARRA funds run out, "that doesn't mean that they can't then use the data from that to generate different grant applications," Lori McKay, senior administrator for IGS, told GWDN.

"The hope was two-fold. Not only was it to create jobs, which we certainly did here, but it was also to create data that would allow you to apply for other funding," McKay said. "In some cases, we need to be able to continue the funds because they did bring in positions. We do have FTEs associated with these funds. But we knew coming into the picture that it was temporary funding."

ARRA also was the source of funding for an IGS project titled, "A Quality Assurance, Coordination and Analysis Center for HMP," carried out in two NIH contracts totaling almost $1.2 million. The funding helped IGS supplement earlier funding toward its work as the data analysis and coordination center, or DACC, for the Human Microbiome Project.

Creation of the DACC involved five research groups, one of which was led by IGS' Owen White. The other groups were led by Victor Markowitz and Gary Anderson, both of Lawrence Berkeley National Laboratory; Nikos Kyrpides of the DOE-Joint Genome Institute in Walnut Creek, Calif.; and Rob Knight of the Department of Chemistry and Biochemistry at the University of Colorado in Boulder.

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