Collaborative and Other Agreements	12 Months Ended
Dec. 31, 2015
Collaborative and Other Agreements [Abstract]
Collaborative and Other Agreements	9. Collaborative and Other Agreements In September 2015, the Company entered into a non-exclusive patent license agreement with Takara Bio Inc. (the Takara Agreement). Under this agreement Takara licensed certain patents related to AAV1 Vector gene delivery systems, for which the Company is an exclusive licensor with the University of Pennsylvania. The Company received a $40,000 non-refundable, up-front licensing payment which was recognized in revenue in 2015 and is entitled to receive royalties from Takara of 12.0% of net license product sales and 6.0% of service revenues associated with the licensed products. The agreement calls for minimum annual royalties of $15,000 beginning in 2015 which are payable in arrears in February on each anniversary thereafter. The minimum royalty amount was recognized in revenue in 2015. In addition, the Takara Agreement provides milestone fees to the Company of $30,000 of the first $1,000,000 of licensed product revenues by Takara and an additional $40,000 when cumulative net sales of the licensed product by Takara exceed $2,000,000. The Company is party to other sub-licensing agreements for its former gene delivery systems. The Company receives annual maintenance fees and royalties based on the activities of the licensees. The amounts are reported in revenues in accordance with our revenue recognition policy. In June 2013, the Company entered into a Collaborative Research and Development Agreement with the United States Army Medical Research and Materiel Command and the Walter Reed Army Institute of Research. The Collaborative Research and Development Agreement is focused on developing and commercializing bacteriophage therapeutics to treat S. aureus infections. During the year ended December 31, 2015, the Company recorded no payments under the Collaborative Research and Development Agreement. During the year ended December 31, 2014, the Company paid Walter Reed Army Institute of Research $207,000 for services provided under the Collaborative Research and Development Agreement. This amount is included in research and development expense in 2014. In April 2013, the Company entered into a collaboration agreement with the University of Leicester to develop a phage therapy that targets and kills all toxin types of C. difficile. In August 2013, the Company entered into a collaboration agreement with both the University of Leicester and the University of Glasgow to carry out certain animal model development work. Under these agreements, which are referred to collectively as the Leicester Development Agreements, the Company provides payments to the University of Leicester to carry out in vitro and to the University of Glasgow to carry out animal model development work on the University of Leicester’s development of a bacteriophage therapeutic to resolve C. difficile infections. The Company licensed related patents, materials and know-how from the University of Leicester. Under the Leicester Development Agreements, the University of Leicester will provide the bacteriophage and act as overall project coordinator for the development work. All rights, title and interest to any intellectual property developed under the Leicester Development Agreements belong to the Company. Under the Leicester License Agreement, the Company has exclusive rights to certain background intellectual property of the University of Leicester, for which it will pay the University of Leicester royalties based on product sales and make certain milestone payments based on product development. In November 2015, the Company renewed this collaboration, effective as of November 12, 2015. This agreement expires November 12, 2018. During the year ended December 31, 2015, the Company recorded $265,000 in expenses to the University of Leicester under the Leicester Development Agreements, with cash payments totaling $290,000. During the year ended December 31, 2014, the Company recorded $232,000 in expenses to the University of Leicester under the Leicester Development Agreements, with cash payments totaling $182,000. During the year ended year ended December 31, 2015, the Company paid and expensed amounts to the University of Glasgow under the Leicester Development Agreements of $61,000. During the year ended December 31, 2014, the Company paid and expensed amounts to the University of Glasgow under the Leicester Development Agreements of $184,000. In March 2013, the Company entered into an Exclusive Channel Collaboration Agreement with Intrexon Corporation. This agreement allows the Company to utilize Intrexon’s synthetic biology platform for the identification, development and production of bacteriophage-containing human therapeutics. The Company paid a one-time technology access fee in 2013 to Intrexon of $3,000,000 in common stock. Pursuant to the agreement, the Company is required to pay Intrexon, in cash or stock to be valued based on the market price of our common stock, milestone fees of $2,500,000 for the initiation and commencement of the first Phase 2 trial and $5,000,000 upon the first regulatory approval of any product in any major market country. With regard to each product sold by the Company, the Company is required to pay, in cash, tiered royalties on a quarterly basis based on net sales of AmpliPhi Products, calculated on a product-by-product basis. No milestones have been met and no milestone payments have been paid or accrued for through December 31, 2015. The Exclusive Channel Collaboration is effective until terminated by either Intrexon or the Company. Intrexon may terminate the Exclusive Channel Collaboration if the Company fails to use diligent efforts to develop and commercialize AmpliPhi Product candidates or if the Company elects not to pursue the development of an AmpliPhi Program identified by Intrexon that is a “Superior Therapy” as defined in the Exclusive Channel Collaboration. The Company has the right to terminate the Exclusive Channel Collaboration upon 90 days’ written notice to Intrexon at any time. Both the Company and Intrexon have the right to terminate the Exclusive Channel Collaboration upon written notice to the other party if the other party commits a material breach of the agreement and fails to cure such breach within 60 days following written notice. During the year ended December 31, 2015, the Company recorded $178,000, in expenses under the Exclusive Channel Collaboration Agreement, with cash payments totaling $125,000. During the year ended December 31, 2014, the Company recorded $862,000, in expenses under the Exclusive Channel Collaboration Agreement, with cash payments totaling $941,000.

9. Collaborative and Other Agreements

In September 2015, the Company entered into a non-exclusive patent license agreement with Takara Bio Inc. (the Takara Agreement). Under this agreement Takara licensed certain patents related to AAV1 Vector gene delivery systems, for which the Company is an exclusive licensor with the University of Pennsylvania. The Company received a $40,000 non-refundable, up-front licensing payment which was recognized in revenue in 2015 and is entitled to receive royalties from Takara of 12.0% of net license product sales and 6.0% of service revenues associated with the licensed products. The agreement calls for minimum annual royalties of $15,000 beginning in 2015 which are payable in arrears in February on each anniversary thereafter. The minimum royalty amount was recognized in revenue in 2015. In addition, the Takara Agreement provides milestone fees to the Company of $30,000 of the first $1,000,000 of licensed product revenues by Takara and an additional $40,000 when cumulative net sales of the licensed product by Takara exceed $2,000,000.

The Company is party to other sub-licensing agreements for its former gene delivery systems. The Company receives annual maintenance fees and royalties based on the activities of the licensees. The amounts are reported in revenues in accordance with our revenue recognition policy.

In June 2013, the Company entered into a Collaborative Research and Development Agreement with the United States Army Medical Research and Materiel Command and the Walter Reed Army Institute of Research. The Collaborative Research and Development Agreement is focused on developing and commercializing bacteriophage therapeutics to treat S. aureus infections. During the year ended December 31, 2015, the Company recorded no payments under the Collaborative Research and Development Agreement. During the year ended December 31, 2014, the Company paid Walter Reed Army Institute of Research $207,000 for services provided under the Collaborative Research and Development Agreement. This amount is included in research and development expense in 2014.

In April 2013, the Company entered into a collaboration agreement with the University of Leicester to develop a phage therapy that targets and kills all toxin types of C. difficile. In August 2013, the Company entered into a collaboration agreement with both the University of Leicester and the University of Glasgow to carry out certain animal model development work. Under these agreements, which are referred to collectively as the Leicester Development Agreements, the Company provides payments to the University of Leicester to carry out in vitro and to the University of Glasgow to carry out animal model development work on the University of Leicester’s development of a bacteriophage therapeutic to resolve C. difficile infections. The Company licensed related patents, materials and know-how from the University of Leicester. Under the Leicester Development Agreements, the University of Leicester will provide the bacteriophage and act as overall project coordinator for the development work. All rights, title and interest to any intellectual property developed under the Leicester Development Agreements belong to the Company. Under the Leicester License Agreement, the Company has exclusive rights to certain background intellectual property of the University of Leicester, for which it will pay the University of Leicester royalties based on product sales and make certain milestone payments based on product development. In November 2015, the Company renewed this collaboration, effective as of November 12, 2015. This agreement expires November 12, 2018. During the year ended December 31, 2015, the Company recorded $265,000 in expenses to the University of Leicester under the Leicester Development Agreements, with cash payments totaling $290,000. During the year ended December 31, 2014, the Company recorded $232,000 in expenses to the University of Leicester under the Leicester Development Agreements, with cash payments totaling $182,000. During the year ended year ended December 31, 2015, the Company paid and expensed amounts to the University of Glasgow under the Leicester Development Agreements of $61,000. During the year ended December 31, 2014, the Company paid and expensed amounts to the University of Glasgow under the Leicester Development Agreements of $184,000.

In March 2013, the Company entered into an Exclusive Channel Collaboration Agreement with Intrexon Corporation. This agreement allows the Company to utilize Intrexon’s synthetic biology platform for the identification, development and production of bacteriophage-containing human therapeutics. The Company paid a one-time technology access fee in 2013 to Intrexon of $3,000,000 in common stock. Pursuant to the agreement, the Company is required to pay Intrexon, in cash or stock to be valued based on the market price of our common stock, milestone fees of $2,500,000 for the initiation and commencement of the first Phase 2 trial and $5,000,000 upon the first regulatory approval of any product in any major market country. With regard to each product sold by the Company, the Company is required to pay, in cash, tiered royalties on a quarterly basis based on net sales of AmpliPhi Products, calculated on a product-by-product basis. No milestones have been met and no milestone payments have been paid or accrued for through December 31, 2015. The Exclusive Channel Collaboration is effective until terminated by either Intrexon or the Company. Intrexon may terminate the Exclusive Channel Collaboration if the Company fails to use diligent efforts to develop and commercialize AmpliPhi Product candidates or if the Company elects not to pursue the development of an AmpliPhi Program identified by Intrexon that is a “Superior Therapy” as defined in the Exclusive Channel Collaboration. The Company has the right to terminate the Exclusive Channel Collaboration upon 90 days’ written notice to Intrexon at any time. Both the Company and Intrexon have the right to terminate the Exclusive Channel Collaboration upon written notice to the other party if the other party commits a material breach of the agreement and fails to cure such breach within 60 days following written notice. During the year ended December 31, 2015, the Company recorded $178,000, in expenses under the Exclusive Channel Collaboration Agreement, with cash payments totaling $125,000. During the year ended December 31, 2014, the Company recorded $862,000, in expenses under the Exclusive Channel Collaboration Agreement, with cash payments totaling $941,000.