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Condensed Consolidated Statements of Cash Flows - USD ($)
$ in Thousands
 6 Months Ended
Jun. 30, 2015
Jun. 30, 2014
CASH FLOWS FROM OPERATING ACTIVITIES:    
Net loss $ (59,569) $ (125,422)
Adjustments to reconcile net loss to net cash provided by (used) in operating activities:    
Depreciation and accretion 6,624 12,614
Stock-based compensation expense 3,778 51,583
Loss on disposal of property and equipment 12  
Write off of derivative liability   (363)
Other, net (6)  
Changes in assets and liabilities:    
Inventory (10,146)  
Receivables from Collaboration 45,688  
Prepaid expenses and other current assets 6,130 1,789
Deferred product costs from collaboration (10,831)  
Other assets (866) (296)
Accounts payable (2,236) 1,567
Accrued expenses and other current liabilities (7,800) (3,315)
Deferred product sales from collaboration 12,968  
Other liabilities 1,465 1,435
Net cash used in operating activities (14,789) (60,408)
CASH FLOWS FROM INVESTING ACTIVITIES:    
Purchase of property and equipment (8,737) (9,667)
Net cash used in investing activities (8,737) (9,667)
CASH FLOWS FROM FINANCING ACTIVITIES:    
Issuance of common stock and warrants, net of issuance costs 12,820 20,622
Proceeds from issuance of Tranche B of the facility financing obligation   20,000
Milestone payment (4,220)  
Other 40  
Proceeds from issuance of common stock pursuant to ATM issuance 2,050  
Payment of employment taxes related to vested restricted stock units (818) (123)
Net cash provided by financing activities 9,872 40,499
NET INCREASE (DECREASE) IN CASH AND CASH EQUIVALENTS (13,654) (29,576)
CASH AND CASH EQUIVALENTS, BEGINNING OF PERIOD 120,841 70,790
CASH AND CASH EQUIVALENTS, END OF PERIOD 107,187 41,214
SUPPLEMENTAL CASH FLOWS DISCLOSURES:    
Interest paid in cash, net of amounts capitalized 6,644 5,296
Issuance of common stock pursuant to conversion of facility financing obligation   93,500
Non-cash construction in progress and property and equipment $ 623 2,965
Reclassification of share-based awards to liability   (19,926)
Tranche B Commitment Asset   $ 1,753