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Facing Bioinformatics Funding Crunch, NCGR Lays Off Programmers, Focuses on Sequencing

The National Center for Genome Resources, founded in 1994 to develop informatics tools for the Human Genome Project when it was still managed by the Department of Energy, is turning its back on bioinformatics in the face of a funding crisis.
Two weeks ago, NCGR laid off around one-third of its staff — all but two of whom are software engineers — as part of an effort to cut costs as it shifts its focus to DNA sequencing.
BioInform sibling publication GenomeWeb Daily News reported last week that NCGR’s remaining staffers are all business-operation employees and a handful of informatics researchers who will contribute to NCGR’s DNA sequencing work.
Chief Science Officer Bill Beavis said that prior to the layoffs, NCGR employed 26 full-time staff and four part-timers. Of that number, Beavis said six software engineers were let go. Currently, seven software engineers remain.
Scott Wolff, director of software engineering, was among those released. In addition, second-in-command Beavis is on his way back to his alma mater, Iowa State University, where he will become a professor of plant genomics beginning in mid-August. Beavis told BioInform that the university will allow him to return and work at NCGR during the summers as a private investigator.
“I’d been thinking about [leaving NCGR] even before [the layoffs] happened,” Beavis told BioInform this week, stressing that he was not one of the employees laid off.
Beavis said, though, that NCGR’s shift toward sequencing was the result of “feedback” the center received on “many, many grants and proposals,” which indicated that bioinformatics was “not what the marketplace is going to support.”
A former NCGR employee told GenomeWeb Daily News that staffers were told that the center was “having trouble winning [government] grants, and our PIs thought it would be best if we [abandoned] the cyberinfrastructure/bioinformatics/software-engineering type of business model, and that we should put all our efforts into the sequencing model.”
In particular, the center recently learned that it had not won a grant under the National Science Foundation’s $50 million Plant Science Cyberinfrastructure Collaborative program, the researcher said, noting that since “all of our eggs were in that one basket … we’re not going to be able to support everyone.”
Software Still ‘Essential’
Even as funding has dried up for bioinformatics, NCGR has seen some early success in its role as a sequencing center. In January, the state of New Mexico awarded NCGR $600,000 to create the New Mexico Genome Sequencing Center in collaboration with the New Mexico Institute of Mining and Technology [BioInform 01-21-07].
Stephen Kingsmore, NCGR president, told BioInform at the time that the creation of the sequencing center was not a sign that NCGR was deemphasizing its bioinformatics activities in favor of sequencing. On the contrary, he said, the new role was expected to accelerate the development of new informatics tools for analyzing and managing data from next-generation sequencing platforms.
According to Beavis, that strategy is still intact. “We are still building software; it’s essential for the new sequencing technologies. … This is more of a change of emphasis,” he told BioInform this week.
Beavis said that he expects NCGR to continue to support the various software platforms it has developed over the last 13 years. “I don’t know of any we are ending,” he said. “As far as I know, they are still viable and active.”
He noted that most of NCGR’s software is open source, with the exception of any tools developed under contract for commercial entities. “For example, Pfizer contracts with us to build some software for them, [and] we still do that,” Beavis said. “It’s not that we’re no longer building software; we still build software … it’s not a black and white situation.”
Previously, he said, NCGR’s efforts were more focused on the end product. Now, however, the center is moving more toward the prototype-building side of the equation. “Releasing beta versions 1, 2, that kind of stuff,” Beavis said.

“I don’t know of any we are ending. As far as I know, the software platforms] are still viable and active.”

“As an example, we were working on being [Capability Maturity Model Integration]-compliant, a software engineering certificate that requires a lot of configuration management activities — and [there are] a lot of processes involved … the engineering process, which we won’t be doing anymore,” he said. “That doesn’t mean we won’t keep best practices; [but] we won’t make it one of our goals to make it [to] Level 3 compliance. We are already at Level 2.”
Beavis said that the Legume Information System, GEYSIR (Genomic Explorer y Survey of Immune Response), and “several other things” are “still in operation and are supported by federal grants from NIH, DOE, NSF, and so on.”
Those packages, therefore, are “under rules that basically say we need to open-source those,” he said. “We’ve been living on an open-source model for two to three years, and I think it will continue that way.”
Rocky Past, Uncertain Future
NCGR has had its ups and downs since it was founded by the Department of Energy more than a decade ago.
When the funding for the Human Genome Project shifted to the National Institutes of Health in the late 1990s, the project’s informatics activities were managed by the National Center for Biotechnology Information, depriving NCGR of its core mission.
In addition, in 1997, PE Corp. (now Applied Biosystems) acquired NCGR spin-off Molecular Informatics for an undisclosed sum, which created a double-edged sword for NCGR. Terms of the sale gave the NCGR an endowment to fund the center’s activities for several years, but also carried a non-compete clause that prevented it from engaging in human health-related research until 2003 and limited its scope to agricultural studies.
In 2004, NCGR hired as CEO Stephen Kingsmore with the goal of ramping up its grant-writing activities and fully exploiting its newfound status as a human health research institute. But it appears that the timing just wasn’t right for the center, which has been forced to make some difficult decisions in the face of dwindling funds.
A source close to the situation told BioInform that while NCGR has made an effort to find jobs for the displaced — in particular, by bringing in an outplacement service to assist in their rehiring — this individual was not aware that everyone had yet found positions.
Beavis was under the impression, at press time, that NCGR was making serious efforts to reassign the individuals.
“As far as I know, we’ve found everybody jobs,” he said.

Both the Department of Energy’s Joint Genome Institute and 454 Life Sciences, both NCGR collaborators, declined to comment.

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