CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (Unaudited) (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013
Operating activities:
Net loss	$ (70,037)	$ (36,368)
Adjustments to reconcile net loss to net cash (used in) provided by operating activities:
Depreciation	4,791	4,995
Amortization of patents	841	891
Amortization of licenses	1,412	1,531
Amortization of premium on investments, net	5,649	3,742
Amortization of debt issuance costs	412	308
Amortization of 2 3/4 percent convertible senior notes discount	5,103	4,715
Amortization of long-term financing liability for leased facility	4,962	4,919
Stock-based compensation expense	22,894	8,318
Gain on investments, net	(675)	(2,073)
Non-cash losses related to patents, licensing and property, plant and equipment	753	429
Changes in operating assets and liabilities:
Contracts receivable	(15,211)	(12,123)
Inventories	948	(1,264)
Other current and long-term assets	(1,239)	(1,535)
Accounts payable	1,414	(2,293)
Accrued compensation	(5,004)	(1,225)
Deferred rent	126	173
Accrued liabilities	7,046	443
Deferred contract revenue	(28,584)	104,402
Net cash (used in) provided by operating activities	(64,399)	77,985
Investing activities:
Purchases of short-term investments	(250,580)	(303,862)
Proceeds from the sale of short-term investments	222,896	135,130
Purchases of property, plant and equipment	(3,969)	(1,113)
Acquisition of licenses and other assets, net	(2,443)	(2,721)
Proceeds from the sale of strategic investments	2,036	2,110
Net cash used in investing activities	(32,060)	(170,456)
Financing activities:
Proceeds from equity awards	17,709	56,898
Net proceeds from public common stock offering	0	173,292
Proceeds from equipment financing arrangement	0	2,513
Principal payments on debt and capital lease obligations	(8,003)	(8,306)
Net cash provided by financing activities	9,706	224,397
Net (decrease) increase in cash and cash equivalents	(86,753)	131,926
Cash and cash equivalents at beginning of period	159,973	124,482
Cash and cash equivalents at end of period	73,220	256,408
Supplemental disclosures of cash flow information:
Interest paid	2,977	3,079
Income taxes paid	0	2
Supplemental disclosures of non-cash investing and financing activities:
Amounts accrued for capital and patent expenditures	$ 3,204	$ 835