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Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($)
$ in Thousands
 6 Months Ended
Jun. 30, 2015
Jun. 30, 2014
Cash flows from operating activities:    
Net loss $ (18,837) $ (78,838)
Adjustments to reconcile net loss to net cash provided by (used in) operating activities:    
Non-cash royalty revenue related to sale of future royalties (8,702) (10,610)
Non-cash interest expense on liability related to sale of future royalties 10,202 10,521
Stock-based compensation 9,737 8,525
Depreciation and amortization 5,833 6,519
Other non-cash transactions (621) 865
Changes in operating assets and liabilities:    
Accounts receivable, net (73) (818)
Inventory 2,828 (659)
Other assets 190 738
Accounts payable (10) (1,818)
Accrued compensation 5,075 (2,868)
Accrued clinical trial expenses 1,238 (3,697)
Other accrued expenses 1,859 (314)
Deferred revenue (4,434) 7,636
Other liabilities 11,772 (6,557)
Net cash provided by (used in) operating activities 16,057 (71,375)
Cash flows from investing activities:    
Maturities of investments 111,001 118,777
Purchases of investments (124,468) (166,496)
Sale of investments 5,215 0
Purchases of property, plant and equipment (4,584) (5,192)
Net cash used in investing activities (12,836) (52,911)
Cash flows from financing activities:    
Payment of capital lease obligations (2,484) (1,650)
Repayment of proceeds from sale of future royalties 0 (7,000)
Issuance of common stock, net of issuance costs 0 116,601
Proceeds from shares issued under equity compensation plans 7,798 7,961
Net cash provided by financing activities 5,314 115,912
Effect of exchange rates on cash and cash equivalents (25) 6
Net increase (decrease) in cash and cash equivalents 8,510 (8,368)
Cash and cash equivalents at beginning of period 12,365 39,067
Cash and cash equivalents at end of period 20,875 30,699
Supplemental disclosure of cash flow information:    
Cash paid for interest $ 8,320 $ 8,622