Income Taxes (Details 3) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Deferred Tax Assets:
Net operating loss carryovers	$ 260,462,000	$ 244,539,000
R&D credits	65,600,000	46,928,000
Capitalized R&D	2,736,000	22,223,000
Deferred revenue	28,555,000	7,285,000
Accrued restructuring	3,304,000	3,605,000
Other	7,107,000	18,931,000
Total deferred tax assets	367,764,000	343,511,000
Deferred Tax Liabilities:
Convertible debt	(20,895,000)	(23,322,000)
Intangible and capital assets	(4,614,000)	(6,784,000)
Net deferred tax asset	342,255,000	313,405,000
Valuation allowance	(342,255,000)	(313,405,000)
Expected increase in shareholders' equity when deferred tax assets on non-qualified stock options and incentive stock options are ultimately realized	27,800,000
Federal
Operating loss carryforwards
Net operating loss carryforwards	685,800,000
California
Operating loss carryforwards
Net operating loss carryforwards	$ 894,900,000