Condensed Consolidated Statements of Cash Flows (USD $) In Thousands, unless otherwise specified	9 Months Ended
	Sep. 30, 2014	Sep. 30, 2013
Operating activities:
Net loss	$ (117,275)	$ (83,053)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	4,686	3,592
Gain on sale of available for sale securities	(8)	0
Net amortization of premiums on marketable securities	1,169	1,332
Amortization of debt discount	1,405	941
Amortization of loan fees	189	307
Warrant expense related to vesting of ADM Warrant	478	0
Debt conversion expense	1,766	0
Stock-based compensation expense	18,693	14,452
Loss from equity method investments	15,677	5,541
Revaluation of warrant liability	(688)	425
Revaluation of derivative liabilities	(6,478)	4,386
Changes in operating assets and liabilities:
Accounts receivable	(3,631)	(6,925)
Unbilled revenue	(4,581)	595
Inventories	(5,572)	(1,591)
Prepaid expenses and other current assets	(918)	469
Other assets	3,582	0
Accounts payable	4,674	(850)
Accrued liabilities	6,712	1,795
Deferred revenue	(63)	2,154
Other current and long-term liabilities	736	(487)
Net cash used in operating activities	(79,447)	(56,917)
Investing activities:
Purchases of property, plant and equipment	(5,638)	(6,528)
Purchases of marketable securities	(169,789)	(115,110)
Maturities of marketable securities	84,605	94,801
Proceeds from sales of marketable securities	6,551	9,419
Capital contributions in unconsolidated joint venture	(30,550)	(7,431)
Capitalized interest related to unconsolidated joint venture	(620)	(831)
Restricted cash	(732)	0
Net cash used in investing activities	(116,173)	(25,680)
Financing activities:
Repayments under loan agreements	(10,417)	(14,902)
Proceeds from the issuance of senior subordinated convertible notes, net of debt discount	143,894	119,750
Proceeds from the issuance of common stock	7,427	3,260
Proceeds from issuance of common stock, pursuant to ESPP	1,441	1,039
Proceeds from issuance of common stock in a public offering, net of underwriting discounts and commission	59,259	0
Early exercise of stock options subject to repurchase	(4)	(26)
Proceeds from borrowings under loan agreements	0	10,369
Payment for loan costs and fees	(465)	(541)
Cash settlement of vested restricted stock units	(68)	0
Net cash provided by financing activities	201,067	118,949
Effect of exchange rate changes on cash and cash equivalents	(119)	10
Net increase of cash and cash equivalents	5,328	36,362
Cash and cash equivalents - beginning of period	54,977	30,818
Cash and cash equivalents - end of period	60,305	67,180
Supplemental disclosures of cash flow information:
Interest paid in cash, net of capitalized interest	3,838	3,480
Income taxes paid in cash	0	0
Supplemental disclosure of noncash investing and financing activities:
Capital assets in accounts payable and accrued liabilities	432	1,115
Change in unrealized (loss) gain on marketable securities	(206)	(235)
Foreign currency translation adjustment related to unconsolidated joint venture	(2,629)	0
Payment Of Capital Contribution	6,500	0
Common stock issued in lieu of cash bonus	0	121
Common stock issued in connection with use and operation of the Clinton Facility	0	2,655
Conversion of Senior Convertible Notes to common stock	2,461	40,616
Early conversion payment on Senior Convertible Notes settled in common stock	217	3,602
Conversion of Senior Convertible Notes pursuant to inducement settled in common stock	$ 18,125	$ 0