Failure to approve the money could delay ship production and drive up costs by as much as $500 million, company argues.
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GAO says formal plan for testing, sample collection needed; schedule for contract to develop vaccine is too stringent.
A Senate committee recently recommended completely overhauling the agency and giving it a new name.
Since 2003, the department has allocated more than $2.1 billion to states for communications equipment and training.
Estimated cost of project to electronically store forms is $190 million over eight years.
Parties also discuss selection of jurors for trial of ex-GSA chief of staff David Safavian.