Income Taxes (Details 3) (USD $) In Thousands, unless otherwise specified	Dec. 31, 2011	Dec. 31, 2010
Deferred tax assets:
Net operating loss carryforwards	$ 342,128	$ 318,257
Research and other credits	51,125	49,657
Capitalized research expenses	9,514	5,797
Deferred revenue	48,732	31,411
Property and equipment	8,081	7,654
Reserve and accruals	8,083	5,732
Stock-based compensation	32,268	28,157
Other	3,895	4,275
Deferred tax assets before valuation allowance	503,826	450,940
Valuation allowance for deferred tax assets	(503,689)	(450,781)
Total deferred tax assets	137	159
Deferred tax liabilities:
Property and equipment	(75)	0
Total deferred tax liabilities	(75)	0
Net deferred tax assets	$ 62	$ 159