Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Operating activities:
Net loss	$ (106,754)	$ (117,275)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,414	4,686
Gain on sale of available for sale securities	(33)	(8)
Net amortization of premiums on marketable securities	941	1,169
Amortization of debt discount	1,766	1,405
Amortization of loan fees	134	189
Warrant expense related to vesting of ADM Warrant	72	478
Debt conversion expense	0	1,766
Restructuring charges	372	0
Stock-based compensation expense	12,312	18,693
Loss from equity method investments	17,896	15,677
Revaluation of warrant liability	0	(688)
Revaluation of derivative liabilities	(27)	(6,478)
Changes in operating assets and liabilities:
Accounts receivable	(5,168)	(3,631)
Unbilled revenues	2,731	(4,581)
Inventories	2,516	(5,572)
Prepaid expenses and other current assets	(1,208)	(918)
Other assets	(45)	3,582
Accounts payable	(2,300)	4,674
Accrued liabilities	(1,586)	6,712
Deferred revenue	77	(63)
Other current and long-term liabilities	4,870	736
Net cash used in operating activities	(69,020)	(79,447)
Investing activities:
Purchases of property, plant and equipment	(1,162)	(5,638)
Proceeds from the sale of equipment	119	0
Purchases of marketable securities	(23,349)	(169,789)
Maturities of marketable securities	86,952	84,605
Proceeds from sales of marketable securities	31,277	6,551
Capital contributions in unconsolidated joint venture	(19,494)	(30,550)
Capitalized interest related to unconsolidated joint venture	0	(620)
Restricted certificates of deposit	181	(732)
Net cash provided by (used in) investing activities	74,524	(116,173)
Financing activities:
Repayments under loan agreements	(6)	(10,417)
Proceeds from the issuance of Senior Convertible Notes, net of discount	0	143,894
Proceeds from the issuance of common stock	183	7,427
Proceeds from issuance of common stock, pursuant to ESPP	537	1,441
Proceeds from issuance of common stock in a public offering, net of underwriting discounts and commission	0	59,259
Early exercise of stock options subject to repurchase	0	(4)
Payment for loan costs and fees	0	(465)
Cash settlement of vested restricted stock units	(32)	(68)
Net cash provided by financing activities	682	201,067
Effect of exchange rate changes on cash and cash equivalents	(633)	(119)
Net increase in cash and cash equivalents	5,553	5,328
Cash and cash equivalents - beginning of period	42,689	54,977
Cash and cash equivalents - end of period	48,242	60,305
Supplemental disclosures of cash flow information:
Interest paid in cash, net of capitalized interest	7,438	3,838
Income taxes paid in cash	$ 0	$ 0