Seattle supercomputing company Cray (NASDAQ: CRAY) is cutting about 50 jobs as it reconfigures its employee mix, according to a regulatory filing. The company didn’t specify what types of jobs were being cut, or say where they were located, other than to indicate the losses aren’t concentrated in any particular place or category.

Cray’s headquarters are in Seattle and its two other major domestic facilities are in St. Paul, MN, and Chippewa Falls, WI. Cray said the layoffs would be “substantially offset” by future additions in key areas including software development and custom engineering. Cray said those hiring plans mean its overall headcount will stay roughly flat this year. It looks like the news was first reported locally by The Seattle Times’ Brier Dudley.

Spokesman Nick Davis says Cray had about 885 employees total at the end of 2010. The company’s job-posting site shows four jobs currently open in Seattle: director of compensation and benefits, financial analyst, senior product marketing manager and a software developer.

“We need to hire a significant number of employees in critical areas of the company to deliver on our growth plan, and we couldn’t do the hiring we need on top of our current cost structure,” Davis says. “This is a very difficult decision for us. We are working very hard to provide the support for those people who are directly impacted.”

Cray, a historic giant of the computing business, was on our radar screen quite a few times in 2010 as it continued to rack up large contracts worldwide. That included about $60 million from the University of Stuttgart, a $25 million partnership with Nvidia for DARPA projects, and $47 million from the Department of Energy.

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When most people hear the word “earmark,” they probably think of a bridge to nowhere, gilded Pentagon plumbing fixtures, or a dubious construction project in some fat-cat congressman’s hometown.

But federal earmarks can also fuel innovative research and development in life sciences, high tech, and clean energy—at least, they could until President Obama vowed to veto any of the direct grants in last month’s State of the Union speech.

I thought it would be interesting to see just what kind of spending the president would be cutting off for Washington state’s innovation community, so I put together this list.

It shows 25 projects that were seeking $2 million or more in earmarked spending, and the details are pretty interesting. Among the requests that stood out:

• Seattle’s PATH, a nonprofit global health R&D center, was hoping to get money for an array of projects, including $5 million for work on malaria vaccines and $2 million to develop large “electrochlorinator” devices, which use simple battery power to produce chlorine for purifying drinking water—a major global health concern.

• At Washington State University, researchers were seeking $3 million to support their work on capturing and storing high-energy positrons, $2.5 million for turning algae into biofuels, and up to $5 million to examine the ways that environmental toxin exposure can affect how genes are expressed in children.

• The University of Washington and Vancouver, WA-based Renewable Energy Composite Solutions were each hoping for $4 million or more to advance work on tidal energy technology for the Navy.

A little background for those unfamiliar with Capitol Hill lingo: Earmarks are specific, noncompetitive grants that members of Congress put in the federal budget to make sure dollars flow straight to the projects they want to finance back home.

Earmarks often become a political hot potato, but in reality experts say they only make up about 1 percent or less of the federal budget.

Howard Grimes is a vice president for research at WSU. He says the loss of earmarks isn’t leading to dramatic cuts or shutdown of the projects we listed. But it certainly crimps researchers’ … Next Page »

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SAIC, the San Diego-based government contractor also known as Science Applications International Corp., said today it received a five-year contract that could be worth as much as $300 million to modernize the web-based system for federal student aid. The contract awarded by the Department of Education calls for overhauling the online system used to process FAFSA, the Free Application for Federal Student Aid. College-bound students and parents typically fill out the FAFSA form, which is used extensively by U.S. colleges and universities to evaluate their students’ financial need and as the fundamental qualifying form for all federal and government-guaranteed student loan programs.

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