Income Taxes (Details) (USD $)	1 Months Ended	12 Months Ended
	Aug. 31, 2010	Dec. 31, 2011 Percent	Dec. 31, 2010	Dec. 31, 2009
Income Taxes [Abstract]
Income tax benefit		$ (1,132,000)	$ 0	$ (4,122,000)
Income tax expense (benefit) resulting from provision in Worker, Homeownership, and Business Assistance Act of 2009				(2,700,000)
Income tax expense (benefit) resulting from provision in American Recovery and Reinvestment Act of 2009		(700,000)		(700,000)
Income tax expense (benefit) in connection with the net tax effect of unrealized gain on 'available for sale' marketable securities		(400,000)		(700,000)
Deferred tax assets:
Net operating loss carry-forward		282,480,000	243,893,000
Fixed assets		14,847,000	13,600,000
Deferred revenue		120,490,000	70,443,000
Deferred compensation		47,092,000	39,120,000
Research and experimental and other tax credit carry-forwards		67,734,000	45,588,000
Capitalized research and development costs		31,371,000	38,865,000
Other		15,956,000	10,863,000
Deferred tax assets, gross		579,970,000	462,372,000
Deferred tax liabilities:
Convertible senior notes		(1,428,000)
Net deferred tax assets		578,542,000
Valuation allowance		(578,542,000)	(462,372,000)
Deferred tax assets (liabilities), net		0	0
Advance payment received due to amended licensing agreement	165,000,000
Effective income tax reconciliation [Abstract]
U.S federal statutory income tax rate (in hundredths)		35.00%
Unrecognized tax benefits [Roll forward]
Balance, as of January 1		12,819,000
Gross increases related to current year tax positions		2,192,000	3,550,000
Gross increases related to prior year tax positions			9,269,000
Gross decreases due to settlements and lapse of statute of limitations		(9,415,000)
Balance, as of December 31		5,596,000	12,819,000
Research and Experimental and Other [Member]
Tax Credit Carryforward [Line Items]
Tax credit carry-forwards, expiration dates		2012 to 2031
U.S. Federal and New York State [Member]
Operating Loss Carryforwards [Line Items]
Unused net operating loss carry-forwards		800,200,000
Net operating loss carry-forwards, expiration dates		2018 to 2031
Net operating loss carry-forwards related to exercises of Nonqualified Stock Options and disqualifying dispositions of Incentive Stock Options		96,200,000
Net Operating Loss Carryforward and Tax Credit Carryforwards [Member]
Valuation Allowance [Line Items]
Increase in valuation allowance		$ 116,200,000	$ 63,000,000