Commitments and Contingencies (Details) (USD $)	3 Months Ended	12 Months Ended			1 Months Ended					12 Months Ended	1 Months Ended
	Sep. 30, 2012	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2012	Apr. 30, 2014 830 Winter Street, Waltham, MA item	Apr. 30, 2012 830 Winter Street, Waltham, MA sqft	Dec. 31, 2009 830 Winter Street, Waltham, MA sqft	Dec. 31, 2013 830 Winter Street, Waltham, MA sqft	Jul. 27, 2007 830 Winter Street, Waltham, MA sqft	Jun. 30, 2014 Norwood, MA	Jul. 31, 2013 100 River Ridge Drive, Norwood, MA	Apr. 30, 2013 100 River Ridge Drive, Norwood, MA sqft
Operating leases
Area of space leased (in square feet)									89,000			7,507
Initial lease term period						3 years					5 years 2 months
Additional area of space leased (in square feet)								19,000
Construction allowance receivable					$ 1,100,000			$ 746,000
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)						7,310	14,100
Additional period for which sublease agreement can be extended							2 years
Facilities rent expense, net of sublease income		5,400,000	4,800,000	4,800,000
Minimum rental commitments under the non-cancelable operating lease agreements
2015		7,150,000
2016		6,924,000
2017		6,941,000
2018		7,046,000
2019		6,235,000
Thereafter		43,887,000
Total minimum lease payments		78,183,000
Total minimum rental income from subleases		(408,000)
Total minimum lease payments, net		77,775,000
Obligations under capital leases		0
Collaborations
Potential future success-based milestone and third-party payments cancelled under license agreement with Janssen Biotech	41,000,000
Potential milestone payments receivable		162,000,000
Amount reimbursable by a third party		$ 1,400,000