Commitments and Contingencies (Details) (USD $)	3 Months Ended	12 Months Ended			0 Months Ended	1 Months Ended				12 Months Ended	0 Months Ended
	Sep. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2011	Jul. 27, 2007 830 Winter Street, Waltham, MA item sqft	Apr. 30, 2012 830 Winter Street, Waltham, MA sqft	Dec. 31, 2009 830 Winter Street, Waltham, MA sqft	Jul. 31, 2007 830 Winter Street, Waltham, MA	Jul. 27, 2007 830 Winter Street, Waltham, MA Maximum	Jun. 30, 2013 Norwood, MA	Apr. 30, 2013 100 River Ridge Drive, Norwood, MA sqft
Operating leases
Area of space leased (in square feet)					89,000	7,310					7,507
Initial lease term period					12 years	3 years					5 years 2 months
Number of additional terms for which lease agreement can be extended					2
Additional term period for which lease agreement can be extended					5 years					5 years	5 years
Area of property covered under sublease agreement (in square feet)							14,100
Additional period for which sublease agreement can be extended							2 years
Construction allowance received									$ 13,300,000
Leasehold improvements recorded under construction allowance					12,000,000
Receipts from the landlord towards leasehold improvements								10,800,000
Facilities rent expense, net of sublease income		4,800,000	4,800,000	4,600,000
Minimum rental commitments under the non-cancelable operating lease agreements
2013		6,636,000
2014		6,780,000
2015		6,549,000
2016		6,624,000
2017		6,831,000
Thereafter		10,029,000
Total minimum lease payments		43,449,000
Total minimum rental payments from subleases		(1,088,000)
Total minimum lease payments, net		42,361,000
Collaborations
Potential future success-based milestone and third-party payments cancelled under license agreement with Janssen Biotech	41,000,000
Maximum amount payable in the future under the Company's current collaborative agreements		2,000,000
Amount reimbursable by a third party		$ 1,400,000