Precigen (PGEN) 10-Q/A 21 Oct 13 2013 Q2 Quarterly report (amended) Financial data

Document_and_Entity_Informatio

Document and Entity Information	6 Months Ended
	Jun. 30, 2013	Sep. 16, 2013
Document And Entity Information [Abstract]
Document Type	10-Q
Amendment Flag	FALSE
Document Period End Date	30-Jun-13
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q2
Entity Registrant Name	INTREXON CORP
Entity Central Index Key	1356090
Current Fiscal Year End Date	-19
Entity Filer Category	Non-accelerated Filer
Entity Common Stock, Shares Outstanding		96,987,331

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets
Cash and cash equivalents	$34,461	$10,403
Short-term investments	95,454	260
Receivables
Trade	258	141
Related parties	820	531
Other	227	35
Prepaid expenses and other	3,098	2,163
Total current assets	134,318	13,533
Property, plant and equipment, net	18,410	18,687
Intangible assets, net	42,972	29,506
Goodwill	13,846
Investment in affiliate		5,726
Other assets	8,692	1,078
Total assets	283,451	151,646
Current liabilities
Accounts payable	1,486	632
Accrued compensation and benefits	3,324	3,766
Other accrued liabilities	4,166	2,208
Deferred revenue	8,270	9,963
Capital lease obligations, current	32	49
Current portion of long term debt	223
Related party payables	10	99
Total current liabilities	17,511	16,717
Capital lease obligations, net of current portion	25	42
Long term debt, net of current portion	2,074
Deferred revenue	56,409	48,673
Other long term liabilities	1,098	1,108
Total liabilities	77,117	66,540
Commitments and contingencies (Note 12)
Total deficit
Common stock, no par value, 185,000,000 shares and 160,000,000 shares authorized as of June 30, 2013 and December 31, 2012, respectively; 5,671,636 and 5,661,525 shares issued and outstanding as of June 30, 2013 and December 31, 2012, respectively
Additional paid-in capital
Accumulated deficit	-376,163	-321,553
Accumulated other comprehensive income	14
Total Intrexon shareholders' deficit	-376,149	-321,553
Noncontrolling interest	14,625
Total deficit	-361,524	-321,553
Total liabilities, redeemable convertible preferred stock and total deficit	283,451	151,646
Collaborative Partner Securities [Member]
Receivables
Equity securities	65,213	83,116
Series A Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	1,400	1,358
Series B Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	684	669
Series B-1 Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	1,390	1,360
Series C Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	7,348	7,134
Series C-1 Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	35,226	34,201
Series C-2 Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	45,849	44,512
Series C-3 Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	30,657	29,770
Series D Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	78,527	76,252
Series E Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	217,786	211,403
Series F Redeemable Convertible Preferred Stock [Member]
Current liabilities
Redeemable convertible preferred stock	$148,991

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, except Share data, unless otherwise specified
Common stock, par value
Common stock, authorized	185,000,000	160,000,000
Common stock, issued	5,671,636	5,661,525
Common stock, outstanding	5,671,636	5,661,525
Series A Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$1.21	$1.21
Liquidation preference	$1,448	$1,406
Redeemable convertible preferred stock, authorized	705,400	705,400
Redeemable convertible preferred stock, issued	705,400	705,400
Redeemable convertible preferred stock, outstanding	705,400	705,400
Series B Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$0.72	$0.72
Liquidation preference	724	709
Redeemable convertible preferred stock, authorized	694,000	694,000
Redeemable convertible preferred stock, issued	694,000	694,000
Redeemable convertible preferred stock, outstanding	694,000	694,000
Series B-1 Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$0.83	$0.83
Liquidation preference	1,410	1,380
Redeemable convertible preferred stock, authorized	1,212,360	1,212,360
Redeemable convertible preferred stock, issued	1,212,360	1,212,360
Redeemable convertible preferred stock, outstanding	1,212,360	1,212,360
Series C Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$1.10	$1.10
Liquidation preference	7,376	7,162
Redeemable convertible preferred stock, authorized	4,546,360	4,546,360
Redeemable convertible preferred stock, issued	4,546,360	4,546,360
Redeemable convertible preferred stock, outstanding	4,546,360	4,546,360
Series C-1 Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$1.57	$1.57
Liquidation preference	35,247	34,222
Redeemable convertible preferred stock, authorized	15,934,528	15,934,528
Redeemable convertible preferred stock, issued	15,934,528	15,934,528
Redeemable convertible preferred stock, outstanding	15,934,528	15,934,528
Series C-2 Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$1.88	$1.88
Liquidation preference	45,951	44,614
Redeemable convertible preferred stock, authorized	18,617,020	18,617,020
Redeemable convertible preferred stock, issued	18,617,020	18,617,020
Redeemable convertible preferred stock, outstanding	18,617,020	18,617,020
Series C-3 Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$1.88	$1.88
Liquidation preference	30,706	29,819
Redeemable convertible preferred stock, authorized	13,297,872	13,297,872
Redeemable convertible preferred stock, issued	13,297,872	13,297,872
Redeemable convertible preferred stock, outstanding	13,297,872	13,297,872
Series D Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$3.38	$3.38
Liquidation preference	78,622	76,347
Redeemable convertible preferred stock, authorized	19,803,685	19,803,685
Redeemable convertible preferred stock, issued	19,803,685	19,803,685
Redeemable convertible preferred stock, outstanding	19,803,685	19,803,685
Series E Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$5.25	$5.25
Liquidation preference	220,469	214,086
Redeemable convertible preferred stock, authorized	38,095,239	38,095,239
Redeemable convertible preferred stock, issued	38,095,239	38,095,239
Redeemable convertible preferred stock, outstanding	38,095,239	38,095,239
Series F Redeemable Convertible Preferred Stock [Member]
Redeemable convertible preferred stock, par value
Redeemable convertible preferred stock, stated value	$7.88
Liquidation preference	$152,139
Redeemable convertible preferred stock, authorized	19,047,619
Redeemable convertible preferred stock, issued	19,047,619
Redeemable convertible preferred stock, outstanding	19,047,619

Consolidated_Statements_of_Ope

Consolidated Statements of Operations (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Revenues
Collaboration revenues	$6,674	$2,705	$10,538	$4,259
Other revenues	107	21	219	85
Total revenues	6,781	2,726	10,757	4,344
Operating Expenses
Research and development	13,602	17,641	25,104	36,620
General and administrative	7,433	6,333	13,913	14,093
Total operating expenses	21,035	23,974	39,017	50,713
Operating loss	-14,254	-21,248	-28,260	-46,369
Other Income (Expense)
Unrealized appreciation (depreciation) in fair value of equity securities	7,734	4,756	-21,635	15,971
Gain on previously held equity investment			7,415
Interest expense	-11	-18	-25	-25
Investment income	66	1	71	2
Other expense	-54	-26	-57	-26
Total other income (expense)	7,735	4,713	-14,231	15,922
Equity in net loss of affiliate			-390
Net loss	-6,519	-16,535	-42,881	-30,447
Net loss attributable to the noncontrolling interest	507		558
Net loss attributable to Intrexon	-6,012	-16,535	-42,323	-30,447
Accretion of dividends on redeemable convertible preferred shares	-7,942	-5,362	-14,347	-10,822
Net loss attributable to common shareholders	($13,954)	($21,897)	($56,670)	($41,269)
Net loss attributable to common shareholders per share, basic and diluted	($2.46)	($3.99)	($10)	($7.54)
Weighted average shares outstanding, basic and diluted	5,667,557	5,484,572	5,664,665	5,470,415

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Statement Of Income And Comprehensive Income [Abstract]
Net loss	($6,519)	($16,535)	($42,881)	($30,447)
Other comprehensive income (loss):
Unrealized loss on short-term investments	-15		-15
Foreign currency translation adjustments	71		54
Comprehensive loss	-6,463	-16,535	-42,842	-30,447
Comprehensive loss attributable to the noncontrolling interest	474		533
Comprehensive loss attributable to Intrexon	($5,989)	($16,535)	($42,309)	($30,447)

Consolidated_Statements_of_Sha

Consolidated Statements of Shareholders' and Total Deficit (USD $)	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income [Member]	Accumulated Deficit [Member]	Total Intrexon Shareholders' Deficit [Member]	Noncontrolling Interest [Member]
In Thousands, except Share data	USD ($)		USD ($)	USD ($)	USD ($)	USD ($)	USD ($)
Beginning balance at Dec. 31, 2012	($321,553)				($321,553)	($321,553)
Beginning balance, shares at Dec. 31, 2012	5,661,525	5,661,525
Stock-based compensation expense	1,196		1,195			1,195	1
Exercises of stock options	9		5			5	4
Exercises of stock options, shares		1,357
Contribution of services by shareholder	775		775			775
Shares issued to nonemployee members of the Board of Directors	85		85			85
Shares issued to nonemployee members of the Board of Directors, shares		8,754
Accretion of dividends on redeemable convertible preferred shares	-14,347		-2,060		-12,287	-14,347
Adjustments for noncontrolling interest	15,153						15,153
Net loss	-42,881				-42,323	-42,323	-558
Other comprehensive income	39			14		14	25
Ending balance at Jun. 30, 2013	($361,524)			$14	($376,163)	($376,149)	$14,625
Ending balance, shares at Jun. 30, 2013	5,671,636	5,671,636

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012
Cash flows from operating activities
Net loss	($42,881)	($30,447)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	3,694	3,912
Loss on disposal of property and equipment	6	26
Unrealized (appreciation) depreciation on equity securities	21,635	-15,971
Amortization of discount/premium of short term investments	51
Equity in net loss of affiliate	390
Gain on previously held equity investment	-7,415
Stock-based compensation expense	1,196	520
Contribution of services by shareholder	775	775
Shares issued to nonemployee members of the Board of Directors	85	76
Receivables:
Trade	-112	-178
Related parties	-489	-260
Other	-184	933
Prepaid expenses and other	747	-605
Other assets	-7,547	311
Accounts payable	722	-582
Accrued compensation and benefits	-537	1,273
Other accrued liabilities	39	-754
Deferred revenue	2,311	7,246
Related party payables	-89	-249
Other long term liabilities	-10	58
Net cash used in operating activities	-27,613	-33,916
Cash flows from investing activities
Purchases of short term investments	-95,246	-1
Purchases of equity securities		-10,000
Acquisition of business, net of cash received	512
Purchases of property and equipment	-776	-6,965
Proceeds from sale of property and equipment		5
Issuance of related party note receivable	-300
Proceeds from related party notes receivable	500	34
Net cash used in investing activities	-95,310	-16,927
Cash flows from financing activities
Payments of capital lease obligations	-34	-38
Proceeds from long term debt	171
Payments of long term debt	-18
Proceeds from stock option exercises	9	184
Payment of stock issuance costs	-3,148	-11
Net cash provided by financing activities	146,980	50,546
Effect of exchange rate changes on cash and cash equivalents	1
Net increase (decrease) in cash and cash equivalents	24,058	-297
Cash and cash equivalents
Beginning of period	10,403	19,628
End of period	34,461	19,331
Supplemental disclosure of cash flow information
Cash paid during the period for interest	48	6
Significant noncash financing and investing activities
Accretion of dividends on redeemable convertible preferred shares	14,347	10,822
Stock received as consideration for collaboration agreements	3,732	6,588
IPO fees included in accrued expenses	1,526
Series E Redeemable Convertible Preferred Stock [Member]
Cash flows from financing activities
Proceeds from issuance of redeemable convertible preferred shares		50,560
Significant noncash financing and investing activities
Accretion of dividends on redeemable convertible preferred shares	6,383
Series F Redeemable Convertible Preferred Stock [Member]
Cash flows from financing activities
Proceeds from issuance of redeemable convertible preferred shares	150,000
Significant noncash financing and investing activities
Accretion of dividends on redeemable convertible preferred shares	2,139
Subscriptions Payable [Member] | Series E Redeemable Convertible Preferred Stock [Member]
Significant noncash financing and investing activities
Conversion of subscriptions payable into Series E redeemable convertible preferred shares		$7,440

Organization_and_Basis_of_Pres

Organization and Basis of Presentation	6 Months Ended
	Jun. 30, 2013
Accounting Policies [Abstract]
Organization and Basis of Presentation	1. Organization and Basis of Presentation
	Intrexon Corporation (the “Company” or “Intrexon”) was formed in 1998. The Company is a Virginia corporation. During 2011, the Company formed or acquired three subsidiaries in connection with certain acquisitions. On March 15, 2013, the Company began consolidating AquaBounty Technologies, Inc. (“AquaBounty”) (Note 6). Intrexon uses synthetic biology for the fabrication of distinct products for collaboration with partners. The Company has operations in California, Florida, Maryland, North Carolina, South Carolina and Virginia. There are currently no treatments or products in production.
	These consolidated financial statements are presented in U.S. dollars and are prepared under accounting principles generally accepted in the United States of America (“U.S. GAAP”). All share and per share data of the Company’s common stock, including shares of common stock underlying stock options and warrants, have been retroactively adjusted in the accompanying consolidated financial statements to reflect a reverse stock split (Note 15).

Summary_of_Significant_Account

Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2013

Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.

Unaudited Financial Information

The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with U.S. GAAP. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company’s financial position as of June 30, 2013 and results of operations and cash flows for the interim periods ended June 30, 2013 and 2012. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2013, or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto for the year ended December 31, 2012, included in the Prospectus that forms a part of the Company’s Registration Statement on Form S-1 (File No. 333-189853), which was filed with the Securities and Exchange Commission pursuant to Rule 424 on August 8, 2013.

Revenue Recognition

The Company generates revenue through contractual agreements with collaborative partners (known as exclusive channel collaborations, “ECC” or “ECCs”) whereby the partners obtain exclusive access to the Company’s proprietary technology for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Generally, the terms of these collaborative agreements provide that the Company receive some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific application provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration.

The Company’s collaboration agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. Effective January 1, 2011, the Company adopted the provisions of Accounting Standards Update (“ASU”) No. 2009-13, Revenue Recognition (Topic 605): Multiple Deliverable Revenue Arrangements (“ASU 2009-13”). In accordance with the provisions of ASU 2009-13, the Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborative partner on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement.

Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”) of selling price or third-party evidence of selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of selling price exists, the Company uses its best estimate of the selling price (“BESP”) for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations.

The terms of the Company’s agreements may provide for milestone payments upon achievement of certain defined events. The Company applies ASU No. 2010-17, Revenue Recognition – Milestone Method (“ASU 2010-17” or “Milestone Method”). Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:

-1

The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity’s performance to achieve the milestone;

-2

The consideration relates solely to past performance; and

-3

The consideration is reasonable relative to all of the deliverables and payment terms with the arrangement.

In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments.

Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration agreements and the Company considers these services to be inseparable from the license to the core technology; thus, reimbursements of services performed are recognized as revenue. Further, because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonable assured. Payments received from manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned.

The Company also generates revenue from other licenses of certain technologies and rental and other income from sublease agreements. License revenue is recognized on a straight-line basis over the term of the license agreement. Deferred revenue is recorded on the consolidated balance sheet when cash is received prior to the period in which the revenue is earned. Sublease and laboratory services revenues are recognized in the period in which they are earned.

Research and Development

The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses.

The Company has research and development arrangements with third parties that include upfront and milestone payments. At June 30, 2013 and December 31, 2012, the Company had research and development commitments with third parties totaling $3,393 and $3,164, respectively, of which $1,235 and $1,431, respectively, had not yet been incurred. The commitments are generally cancellable by the Company at any time upon written notice.

Cash and Cash Equivalents

All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions. Recoverability of investments is dependent upon the performance of the issuer. At June 30, 2013 and December 31, 2012, the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $28,857 and $9,384, respectively.

Short-term Investments

Short-term investments at December 31, 2012 include certificates of deposit with original maturities between three months and one year. In June 2013, the Company’s board of directors approved an investment policy to invest cash in excess of immediate requirements in securities to preserve principal and maintain sufficient liquidity. Accordingly, in June 2013, the Company purchased U.S. government debt securities, commercial paper and certificates of deposit. The Company’s written investment policy requires short-term investments to be explicitly rated by two of the three following rating services: Standard & Poor’s, Moody’s and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.

Equity Securities

The Company holds equity securities received and/or purchased from certain collaborative partners. Other than the investment in AquaBounty which was accounted for using the equity method and discussed below, the Company elected the fair value option to account for its equity securities held in these partners, including Ziopharm Oncology, Inc. (“Ziopharm”) which is an equity method investment. These equity securities are recorded at fair value at each reporting date. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. These equity securities are classified as noncurrent in the consolidated balance sheet as the Company does not currently intend to sell these equity securities within one year. The Company has not sold any of these equity securities to date.

The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator’s security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.

Fair Value of Financial Instruments

Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows:

Level 1:

Quoted prices in active markets for identical assets and liabilities;

Level 2:

Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and

Level 3:

Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.

As discussed in “Equity Securities” above, the Company elected the fair value option for the equity securities held in certain collaborative partners.

Concentrations of Risk

Due to the Company’s mix of fixed and variable rate securities holdings, the Company’s short-term investment portfolio is susceptible to changes in short-term interest rates. As of June 30, 2013, the Company’s short-term investments had gross unrealized losses of $15. From time to time, the Company may liquidate some or all of its short-term investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which short-term investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses.

Equity Method Investments

Through March 15, 2013, the Company accounted for its investment in AquaBounty, a biotechnology company focused on improving productivity in commercial aquaculture, using the equity method of accounting as the Company had the ability to exercise significant influence over, but not control, the operating activities of AquaBounty. Under the equity method of accounting, the Company included its pro-rata share of AquaBounty’s operating results, adjusted for accretion of basis difference, on a separate line in the consolidated statement of operations called “Equity in net loss of affiliate.” On the consolidated balance sheet as of December 31, 2012, the Company presented its investment in AquaBounty as a separate non-current asset called “Investment in affiliate.” The excess cost over the Company’s pro-rata share of AquaBounty’s net assets was identifiable intangible assets and equity-method goodwill. This equity-method goodwill was not amortized; however, the investment in AquaBounty was analyzed for impairment on a periodic basis or if an event occurred or circumstances changed that indicate the carrying amount may be impaired. On March 15, 2013, the Company acquired additional ownership interests in AquaBounty resulting in the Company gaining control over and thus consolidating AquaBounty. See Note 6 for additional discussion of this transaction.

The Company determined that it has significant influence over one of its collaborators, Ziopharm, a publicly traded small molecule late-stage oncology drug development company, as of June 30, 2013 and December 31, 2012, based on its ownership interest, representation on Ziopharm’s board of directors, as well as other qualitative factors. The Company accounts for this investment using the fair value option. The fair value of the Company’s equity securities of Ziopharm is $28,555 and $56,298 as of June 30, 2013 and December 31, 2012, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership percentage of Ziopharm is 16.2% and 16.3% at June 30, 2013 and December 31, 2012, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Ziopharm is $3,789 and $5,443 for the three months ended June 30, 2013 and 2012, respectively, and $(27,743) and $13,721 for the six months ended June 30, 2013 and 2012, respectively. Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2013 and 2012 are as follows:

Three months ended

Six months ended

June 30,

June 30,

2013

2012

2013

2012

Revenues

$

200

$

200

$

400

$

400

Operating expenses

18,496

23,166

42,279

41,999

Loss from operations

(18,296

)

(22,966

)

(41,879

)

(41,599

)

Other

(396

)

(647

)

10,388

(6,484

)

Net loss

$

(18,692

)

$

(23,613

)

$

(31,491

)

$

(48,083

)

Variable Interest Entities

The Company identifies entities that either (1) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (2) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities (“VIE or VIEs”). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are a VIE. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (1) the power to direct activities that most significantly impact the VIE’s economic performance and (2) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If the Company has both these criterion, the Company is identified as the primary beneficiary of the VIE. As of December 31, 2012, the Company’s investment in affiliate, AquaBounty, is identified as a VIE. The Company is not the primary beneficiary for this entity as the Company does not have the power to direct the activities that most significantly impact the economic performance of the VIE. As of December 31, 2012, the total carrying value of the Company’s investment in the VIE was $5,726, which is the investment in AquaBounty. On March 15, 2013, the Company began consolidating AquaBounty in the Company’s results of operations and financial position as a result of the Company’s ownership in AquaBounty exceeding 50% (Note 6). The Company’s maximum exposure to loss related to this VIE as of December 31, 2012 was limited to the carrying value of the investment in affiliate. As of June 30, 2013, two of the Company’s collaborators, AmpliPhi Biosciences Corporation (“AmpliPhi”) and Genopaver, LLC (“Genopaver”), were identified as VIEs. The Company is not the primary beneficiary for either of these entities as the Company does not have the power to direct the activities that most significantly impact the economic performance of the VIEs. As of June 30, 2013, the total carrying value of the Company’s investment in the VIEs was $3,973, which is equal to the value of the equity securities holdings in those VIEs.

Property, Plant and Equipment

Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are charged to the property accounts while repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated on the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows:

Years

Building

13

Furniture and fixtures

7

Lab equipment

2–7

Computer hardware

5–7

Software

3–5

Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to four years.

Goodwill

Goodwill is an asset that represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Note 6). Goodwill is reviewed for impairment at least annually. The Company has the option to perform a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required.

If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit’s goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed.

The Company intends to perform its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.

Intangible Assets

Intangible assets subject to amortization consist of patents and related technologies acquired in mergers and acquisitions and a favorable lease asset acquired upon the assumption of a lease agreement. These intangible assets subject to amortization were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired as a result of a step acquisition (Note 6) and is recorded at fair value at the date of the step acquisition.

The Company applies the provisions of ASC Topic 350, Intangibles, Goodwill and Other, which requires the amortization of long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from seven to fourteen years for the patents and related technologies, and through the end of the original lease term, February 1, 2013, for the favorable lease asset.

Impairment of Long-Lived Assets

Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable.

Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon regulatory approval.

Income Taxes

Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized.

The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in general and administrative expenses.

Net Loss per Share

Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, preferred stock, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented.

Segment Information

The Company has determined that it operates in one segment. The Company uses synthetic biology for the creation of distinct products for collaboration with partners. All of the Company’s revenues are derived in the United States of America. Substantially all of the Company’s assets are located in the United States of America.

Recently Issued Accounting Pronouncements

In February 2013, the FASB issued ASU No. 2013-02, Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income (“ASU 2013-02”). ASU 2013-02 requires that companies present either in a single note or parenthetically on the face of the financial statements, the effect of significant amounts reclassified from each component of accumulated other comprehensive income based on its source and the income statement line items affected by the reclassification. If a component is not required to be reclassified to net income in its entirety, companies would instead cross reference to the related footnote for additional information. ASU 2013-02 is effective for interim and annual reporting periods beginning after December 15, 2012. The Company has implemented the provisions of ASU 2013-02 as of January 1, 2013. The adoption of this amendment did not have a material impact on the Company’s consolidated financial statements.

In December 2011, the FASB issued ASU No. 2011-11, Balance Sheet (Topic 210): Disclosures about Offsetting Assets and Liabilities (“ASU 2011-11”). ASU 2011-11 requires an entity to disclose information about offsetting and related arrangements to enable users of financial statements to understand the effect of those arrangements on its financial position, and to allow investors to better compare financial statements prepared under U.S. GAAP with financial statements prepared under IFRS. The new standards are effective for annual periods beginning January 1, 2013 and interim periods within those annual periods. Retrospective application is required. The Company has implemented the provisions of ASU 2011-11 as of January 1, 2013. The adoption of this amendment did not have a material impact on the Company’s consolidated financial statements.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.

Collaboration_Revenue

Collaboration Revenue	6 Months Ended
	Jun. 30, 2013
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Collaboration Revenue	3. Collaboration Revenue
	Deferred revenue primarily consists of consideration received for upfront and milestone payments in connection with the Company’s collaborators and prepayments for research and development services performed for collaborators. Deferred revenue consists of the following:
		June 30,		December 31,
		2013		2012
	Upfront and milestone payments	$	61,814	$	51,359
	Prepaid research and development services		2,819		7,229
	Other		46		48
	Total	$	64,679	$	58,636
	Current portion of deferred revenue		8,270		9,963
	Long-term portion of deferred revenue		56,409		48,673
	Total	$	64,679	$	58,636
	Ziopharm Oncology, Inc. ECC
	Effective January 6, 2011, the Company entered into a worldwide ECC with Ziopharm. Under the ECC, Ziopharm received a license to the Company’s technology platform within the field of oncology as defined more specifically in the agreement. Upon execution of the ECC, the Company received 3,636,926 shares of Ziopharm’s common stock valued at $17,457 as upfront consideration. The Company is entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 7.495% of Ziopharm’s outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by Ziopharm using the Company’s technology (“Ziopharm Milestone”). The Company receives reimbursement payments for research and development services provided and manufacturing services for Company materials provided to Ziopharm during the ECC. Subject to certain expense allocations, Ziopharm will pay the Company 50% of the quarterly net profits derived from the sale of products developed from the ECC. Ziopharm is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of product candidates. The term of the ECC commenced on January 6, 2011 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Ziopharm upon 90 days written notice to the Company provided that no voluntary termination by Ziopharm can be made during the first two years of the ECC. See Note 13 for additional transactions with Ziopharm.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, two clinical-stage product candidates, services to transition the two clinical-stage product candidates, participation on the joint steering committee (“JSC”), the research and development services, and any manufacturing services to be provided. The Company grouped the deliverables into three units of accounting based on the nature of the deliverables and the separation criteria: (i) the two clinical-stage product candidates and related services to transition these product candidates to Ziopharm (“Ziopharm Unit of Accounting 1”), which had standalone value to Ziopharm at inception of the ECC; (ii) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Ziopharm Unit of Accounting 2”), as these deliverables could not be separated; and (iii) manufacturing services to be provided for any Company materials in an approved product from the ECC (“Ziopharm Unit of Accounting 3”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Ziopharm Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on the two clinical programs that were transferred to Ziopharm to approximate the cost to recreate the deliverables included in this unit of accounting. In establishing BESP for Ziopharm Unit of Accounting 2, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Ziopharm to approximate the cost to recreate the deliverables included in this unit of accounting. The upfront consideration was allocated to Ziopharm Unit of Accounting 1 and Ziopharm Unit of Accounting 2 based on the relative selling price method. Ziopharm Unit of Accounting 3 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and require manufacturing by the Company. As a result of the relative selling price method, $1,115 of the upfront consideration was allocated to Ziopharm Unit of Accounting 1, all of which was recognized as collaboration revenue for the year ended December 31, 2011 since the Company had completed its obligations to deliver this unit of accounting. The remaining $16,342 of upfront consideration was allocated to Ziopharm Unit of Accounting 2 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $314 and $315 of this allocated amount as collaboration revenue in the three months ended June 30, 2013 and 2012, respectively, and $628 and $629 in the six months ended June 30, 2013 and 2012, respectively. The remaining balance of $13,200 of upfront consideration allocated to Ziopharm Unit of Accounting 2 is recorded as deferred revenue at June 30, 2013.
	The Company recognizes the reimbursement payments received for research and development services provided pursuant to the agreement in the period when the services are performed and collection is reasonably assured. On March 21, 2012, the Company received $10,000 from Ziopharm as a prepayment of research and development services to be provided in conjunction with the ECC. The Company recorded this amount as deferred revenue and recognizes collaboration revenue as services are performed. The Company recognized $2,291 and $2,014 of collaboration revenue for research and development services performed in the three months ended June 30, 2013 and 2012, respectively, of which $2,291 and $1,265 was applied against the $10,000 prepayment received, respectively. The Company recognized $3,721 and $2,958 of collaboration revenue for research and development services performed in the six months ended June 30, 2013 and 2012, respectively, of which $3,721 and $2,007 was applied against the $10,000 prepayment received, respectively. The balance of $1,141 is included in deferred revenue on the June 30, 2013 consolidated balance sheet. Any remaining balance of this prepayment is refundable to Ziopharm in the event the ECC is terminated.
	At inception of the agreement, the Company determined that the Ziopharm Milestone is not substantive and cannot be recognized when earned in accordance with ASU 2010-17 as the Milestone Method substantive criteria discussed in Note 2 were not met. On October 24, 2012, the Ziopharm Milestone was achieved and the Company received 3,636,926 shares of Ziopharm’s common stock valued at $18,330 as milestone consideration, which is the sole milestone under this ECC. Since the Ziopharm Milestone was not substantive, the Company allocated the milestone consideration to Ziopharm Unit of Accounting 1 and Ziopharm Unit of Accounting 2 using the same relative selling price allocation as the upfront consideration. As a result, $1,171 of the milestone consideration was allocated to Ziopharm Unit of Accounting 1 and immediately recognized as collaboration revenue for the year ended December 31, 2012 and the remaining $17,159 was allocated to Ziopharm Unit of Accounting 2. The Company recognized $2,420 of the milestone consideration allocated to Ziopharm Unit of Accounting 2 as collaboration revenue at the date the Ziopharm Milestone was achieved, which represented the amount that would have been recognized from inception of the ECC through the milestone achievement date had the payment been received upfront. The remaining $14,739 was recorded as deferred revenue and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $330 and $660 of this deferred milestone consideration for the three and six months ended June 30, 2013, respectively, and the remaining $13,859 is included as deferred revenue on the June 30, 2013 consolidated balance sheet.
	Royalties related to product sales will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	Synthetic Biologics, Inc. ECCs
	Effective November 18, 2011, the Company entered into a worldwide ECC with Synthetic Biologics, Inc. (“Synthetic Biologics”), a publicly traded company focused on the development of innovative disease-modifying medicines for serious illnesses. Under the ECC, at the transaction effective date, Synthetic Biologics received a license to the Company’s technology platform within a designated field (“Field One”). Upon execution of the ECC, the Company received 3,123,558 shares of Synthetic Biologics’ common stock valued at $1,687 as upfront consideration. The Company is entitled to additional shares of common stock representing the lesser of (i) the original shares received or (ii) the number of shares representing 9.995% of Synthetic Biologics’ outstanding shares at the date of the dosing of the first patient in a Phase II clinical trial of a product candidate created, produced or developed by Synthetic Biologics using the Company’s technology (“Synthetic Biologics Field One Milestone”). The Company will receive reimbursement payments for research and development services provided pursuant to the agreement and manufacturing services for Company materials provided to Synthetic Biologics during the ECC. Subject to certain expense allocations, Synthetic Biologics will pay the Company 50% of the quarterly net profits derived from the sale of products developed from the ECC. Synthetic Biologics is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced on November 18, 2011 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Synthetic Biologics upon 90 days written notice to the Company provided that no voluntary termination by Synthetic Biologics can be made during the first 18 months of the ECC.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and any manufacturing services to be provided. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Synthetic Biologics Field One Unit of Accounting 1”), as these deliverables could not be separated, and (ii) manufacturing services to be provided for any Company materials in an approved product from the ECC (“Synthetic Biologics Field One Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Synthetic Biologics Field One Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Synthetic Biologics to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration was allocated to Synthetic Biologics Field One Unit of Accounting 1. Synthetic Biologics Field One Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and require manufacturing by the Company. The $1,687 of upfront consideration was allocated to Synthetic Biologics Field One Unit of Accounting 1 and was recognized over the expected life of the Company’s technology platform using a straight-line approach. On April 16, 2013, the Company terminated its ECC with Synthetic Biologics in Field One. As a result of this termination, all licenses granted by the Company under the ECC for use in Field One reverted back to the Company and the Company recognized the balance of deferred revenue associated with the upfront consideration as collaboration revenue in April 2013. The Company recognized $1,503 and $32 of collaboration revenue for the three months ended June 30, 2013 and 2012, respectively, and $1,535 and $64 for the six months ended June 30, 2013, respectively.
	On August 6, 2012, the Company entered into its second worldwide ECC with Synthetic Biologics. Under this ECC, at the transaction effective date, Synthetic Biologics received a license to the Company’s technology platform within a second designated field (“Field Two”). Upon Synthetic Biologics’ shareholders’ approval on October 5, 2012, the Company received a technology access fee of 3,552,210 shares of Synthetic Biologics common stock valued at $7,815 as upfront consideration. Upon the filing by Synthetic Biologics of an investigational new drug application with the U.S. Food and Drug Administration, or FDA, the Company will receive cash or common stock at the option of Synthetic Biologics valued at $2,000. Upon the first to occur of either the first commercial sale of a product developed under the ECC or the granting of regulatory approval of a product developed under the ECC, the Company will receive cash or common stock at the option of Synthetic Biologics valued at $3,000. The ECC initially targets three infectious diseases and Synthetic Biologics may elect to target up to five more infectious diseases by paying the Company a field expansion fee of $2,000 in either cash or common stock for each additional infectious disease selected. The regulatory milestones and field expansion fee(s) are referred to as the “Synthetic Biologics Field Two Milestones.” The Company receives reimbursement payments for research and development services provided pursuant to the agreement and manufacturing services for preclinical Company materials provided to Synthetic Biologics during the ECC. The Company has the option to propose, and Synthetic Biologics can select, the Company to be the bulk manufacturer of products developed from the ECC. On a quarterly basis, Synthetic Biologics will pay the Company royalties with percentages ranging from upper-single digits to lower double digits of net sales of products developed from the ECC. Synthetic Biologics is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on August 6, 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Synthetic Biologics upon 90 days written notice to the Company provided that no voluntary termination by Synthetic Biologics can be made during the first 18 months of the ECC.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and the potential manufacturing services of a product(s) to be provided if the Company is elected as the manufacturer. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Synthetic Biologics Field Two Unit of Accounting 1”), as these deliverables could not be separated, and (ii) the potential manufacturing services to be provided for a product(s) from the ECC (“Synthetic Biologics Field Two Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Synthetic Biologics Field Two Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Synthetic Biologics to approximate the cost to recreate the deliverables included in this unit of accounting. All up-front consideration was allocated to Synthetic Biologics Field Two Unit of Accounting 1. Synthetic Biologics Field Two Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether any approved products would be developed and whether the Company is elected by Synthetic Biologics to be the manufacturer of any approved products. The $7,815 of upfront consideration was allocated to Synthetic Biologics Field Two Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $163 and $326 of collaboration revenue for the three and six months ended June 30, 2013, respectively. The remaining $7,326 is recorded as deferred revenue at June 30, 2013.
	At inception of the agreement, the Company determined that the Synthetic Biologics Field Two Milestones are not substantive and cannot be recognized when earned in accordance with ASU 2010-17 as the Milestone Method substantive criteria discussed in Note 2 were not met. Royalties related to product net sales will be recognized when earned as the Company has determined that these sales based milestones are not considered a milestone payment under ASU 2010-17.
	The Company recognizes the reimbursement payments received for research services in the period when the services are performed and collection is reasonably assured. The Company recognized $314 and $62 of collaboration revenue for research and development services performed in the three months ended June 30, 2013 and 2012, respectively, for both ECCs with Synthetic Biologics and $689 and $123 in the six months ended June 30, 2013 and 2012, respectively. On December 17, 2012, the Company received $2,500 from Synthetic Biologics as a prepayment of research and development services to be provided in conjunction with either of the two ECCs. The Company recorded this amount as deferred revenue and recognizes collaboration revenue as services are performed. All collaboration revenue recognized in the three and six months ended June 30, 2013 was applied against the $2,500 prepayment received. The balance of $1,678 is included in deferred revenue on the June 30, 2013 consolidated balance sheet. Any remaining balance of this prepayment is refundable to Synthetic Biologics in the event both ECCs are terminated.
	Elanco ECC
	Effective November 28, 2011, the Company entered into a worldwide ECC with Elanco, the animal health division of Eli Lilly and Company (“Elanco”). The Company received cash upfront and is entitled to additional amounts up to an aggregate of $2,250 per product candidate based on the occurrence of separate performance, regulatory and sales-based milestones. The Company receives reimbursement payments for research services provided to Elanco during the ECC up to a certain maximum per calendar year. Elanco will pay the Company royalties with percentages ranging from mid-to-upper single digits to lower double digits based on net sales of products developed from the ECC. The term of the ECC commenced on November 28, 2011 and continues until terminated pursuant to the agreement. The ECC may be terminated by either party in the event of certain material breaches and may be voluntarily terminated in its entirety or on target-by-target basis upon 90 days written notice to the Company or 180 days written notice if the Company is performing research services on a product target.
	The Company identified the deliverables at the inception of the ECC which are the license to the Company’s technology platform, participation on the ECC’s JSC, the research services and potential manufacturing services. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research services to be provided (“Elanco Unit of Accounting 1”), as these deliverables could not be separated, and (ii) if approved by Elanco, manufacturing services to be provided for any Company materials in an approved product from the ECC (“Elanco Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Elanco Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Elanco to approximate the cost to recreate the deliverables included in this unit of accounting. All the upfront consideration was allocated to Elanco Unit of Accounting 1. Elanco Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and whether the Company would be approved by Elanco to provide such manufacturing. The upfront consideration was allocated to Elanco Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach.
	The Company recognizes the reimbursement payments received for research services provided pursuant to the agreement in the period when the services are performed and collection is reasonably assured. The Company recognized $111 and $234 of collaboration revenue for research and development services performed in the three months ended June 30, 2013 and 2012, respectively, and recognized $199 and $434 in the six months ended June 30, 2013 and 2012, respectively, of which $111 is included as trade receivables on the June 30, 2013 consolidated balance sheet.
	At inception of the agreement, the Company determined that the performance milestone is substantive and can be recognized when earned in accordance with ASU 2010-17 as the milestone met all the criteria required by ASU 2010-17 to be considered substantive. The regulatory milestone is not substantive as the milestone did not meet all of the criteria required by ASU 2010-17 to be considered substantive. The sales-based milestone and royalties will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	Oragenics, Inc. ECC
	Effective June 5, 2012, the Company entered into a worldwide ECC with Oragenics, Inc. (“Oragenics”), a publicly traded company focused on becoming the world leader in novel antibiotics against infectious disease and probiotics for oral health for humans and pets. Under the ECC, at the transaction effective date, Oragenics received a license to the Company’s technology platform within the field of lantibiotics for the treatment of infectious diseases in humans and companion animals as defined more specifically in the agreement. Upon execution of the ECC, the Company received a technology access fee of 4,392,425 shares of Oragenics’ common stock valued at $6,588 as upfront consideration. The Company is entitled to receive additional shares of common stock, or at Oragenics’ option, receive a cash payment based upon the fair market value of the shares, upon the separate achievement of certain regulatory milestones of the first product candidate developed from the ECC (“Oragenics Milestones”). The Oragenics Milestones include: (i) 1% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the filing of the first Investigative New Drug Application with the U.S. Food and Drug Administration (“U.S. FDA”) for a product candidate created, produced or developed using the Company’s technology (“Oragenics Product”); (ii) 1.5% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase II clinical trial of an Oragenics Product; (iii) 2% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the dosing of the first patient in the first Phase III clinical trial of an Oragenics Product; (iv) 2.5% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the first New Drug Application or Biologics License Application with the U.S. FDA for an Oragenics Product, or alternatively the first equivalent regulatory filing with a foreign agency; and (v) 3% of Oragenics’ outstanding shares as defined in the ECC agreement at the date of the granting of the first regulatory approval of an Oragenics Product. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Oragenics during the ECC. Oragenics will pay the Company 25% of the quarterly profits derived from the sale of products developed from the ECC.
	Oragenics is responsible for funding the further development of lantibiotics toward the goal of commercialization, conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization or manufacturing of the product candidates. The term of the ECC commenced on June 5, 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Oragenics upon 90 days written notice to the Company provided that no voluntary termination by Oragenics can be made during the first 18 months of the ECC. See Note 13 for additional arrangements with Oragenics.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and any manufacturing services to be provided. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Oragenics Unit of Accounting 1”), as these deliverables could not be separated, and (ii) any manufacturing services to be provided for any Company materials in an approved product from the ECC (“Oragenics Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Oragenics Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Oragenics to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration was allocated to Oragenics Unit of Accounting 1. Oragenics Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and require manufacturing by the Company and whether the Company would elect to be the manufacturer. The $6,588 of upfront consideration was allocated to Oragenics Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $137 and $274 of collaboration revenue for the three and six months ended June 30, 2013, respectively. The remaining balance of $5,995 is recorded as deferred revenue at June 30, 2013.
	The Company recognizes the reimbursement payments received for research services in the period when the services are performed and collection is reasonably assured. The Company recognized $334 and $713 of collaboration revenue for research and development services performed in the three and six months ended June 30, 2013, respectively, of which $212 is included as related party receivables on the June 30, 2013 consolidated balance sheet.
	At inception of the agreement, the Company determined that the Oragenics Milestones are not substantive and cannot be recognized when earned in accordance with ASU 2010-17 as the Milestone Method substantive criteria discussed in Note 2 were not met. Royalties related to product sales will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	Fibrocell Science, Inc. ECC
	Effective October 5, 2012, the Company entered into an ECC with Fibrocell Science, Inc. (“Fibrocell”), a publicly traded, autologous cellular therapeutic company focused on the development of innovative products for aesthetic, medical and scientific applications. Under the ECC, at the transaction effective date, Fibrocell received a license to the Company’s technology platform to develop and commercialize genetically modified and non-genetically modified autologous fibroblasts and autologous dermal cells in the United States of America. Upon execution of the ECC, the Company received a technology access fee of 1,317,520 shares of Fibrocell’s common stock valued at $7,576 as upfront consideration. The number of shares received reflects a 1-for-25 reverse stock split of Fibrocell’s common stock effective April 30, 2013. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to Fibrocell during the ECC. On a quarterly basis, Fibrocell will pay the Company royalties of 7% of net sales up to $25,000 and 14% of net sales above $25,000 on each product developed from the ECC. If Fibrocell uses the Company’s technology platform to improve the production of a current or new Fibrocell products not developed from the ECC, Fibrocell will pay the Company a quarterly royalty equal to 33% of the cost of goods sold savings generated by the improvement. Fibrocell is responsible for conducting preclinical and clinical development of product candidates, as well as for other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on October 5, 2012 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Fibrocell upon 90 days written notice to the Company.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and any manufacturing services to be provided. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Fibrocell Unit of Accounting 1”), as these deliverables could not be separated, and (ii) any manufacturing services to be provided for any Company materials in an approved product from the ECC (“Fibrocell Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Fibrocell Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Fibrocell to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration was allocated to Fibrocell Unit of Accounting 1. Fibrocell Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and require manufacturing by the Company and whether the Company would elect to be the manufacturer. The $7,576 of upfront consideration was allocated to Fibrocell Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $158 and $316 of collaboration revenue for the three and six months ended June 30, 2013, respectively. The remaining balance of $7,102 is recorded as deferred revenue at June 30, 2013.
	Effective June 28, 2013, the Company entered into an amendment to the ECC with Fibrocell. The amendment expands the field of use defined in the ECC agreement. Under the terms of the amendment to the ECC, the Company received 1,243,781 shares of Fibrocell’s common stock valued at $7,612 as a supplemental technology access fee, which is recorded as deferred revenue at June 30, 2013. These shares were received in July 2013. The Company allocated this additional consideration to Fibrocell Unit of Accounting 1and will recognize it over the remaining expected life of the Company’s technology platform using a straight-line approach.
	The Company recognizes the reimbursement payments received for research services in the period when the services are performed and collection is reasonably assured. The Company recognized $615 and $1,045 of collaboration revenue for research and development services performed in the three and six months ended June 30, 2013, respectively, of which $361 is included as related party receivables on the June 30, 2013 consolidated balance sheet.
	AmpliPhi ECC
	Effective March 29, 2013, the Company entered into a worldwide ECC with AmpliPhi, a developer of bacteriophage-based antibacterial therapies to treat drug resistant infections. Under the ECC, at the transaction effective date, AmpliPhi received a license to the Company’s technology platform to develop and commercialize new bacteriophage-based therapies to target specific antibiotic resistant infections as defined more specifically in the agreement. Upon execution of the ECC, the Company received a technology access fee of 24,000,000 shares of AmpliPhi’s common stock valued at $2,400 as upfront consideration. The Company is entitled to additional consideration up to an aggregate amount of $7,500 per product payable either in cash or common stock at the option of AmpliPhi, upon the achievement of certain regulatory milestones (“AmpliPhi Milestones”). The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC and manufacturing services for Company materials provided to AmpliPhi during the ECC. On a quarterly basis, AmpliPhi will pay the Company royalties with percentages ranging from upper-single digits to lower-double digits of net sales of products developed under the ECC. AmpliPhi is responsible for conducting preclinical and clinical development of product candidates, as well as other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on March 29, 2013 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined the agreement and may be terminated voluntarily by AmpliPhi upon 90 days written notice to the Company.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and any manufacturing services to be provided. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“AmpliPhi Unit of Accounting 1”), as these deliverables could not be separated, and (ii) any manufacturing services to be provided for any Company materials in an approved product from the ECC (“AmpliPhi Unit of Accounting 2”), which have standalone value and are contingent due to uncertainties on whether an approved product would be developed and require manufacturing by the Company. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for AmpliPhi Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to AmpliPhi to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration was allocated to AmpliPhi Unit of Accounting 1. AmpliPhi Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainties surrounding whether an approved product would be developed and require manufacturing by the Company and whether the Company would elect to be the manufacturer. The $2,400 of upfront consideration was allocated to AmpliPhi Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $55 of collaboration revenue for the three and six months ended June 30, 2013. The remaining balance of $2,345 is recorded as deferred revenue at June 30, 2013.
	The Company recognizes the reimbursement payments received for research services as collaboration revenue in the period when the services are performed and collection is reasonably assured. The Company recognized $34 of collaboration revenue for research and development services performed in the three and six months ended June 30, 2013, all of which is included as related party receivables on the June 30, 2013 consolidated balance sheet. At inception of the agreement, the Company determined that the AmpliPhi Milestones are not substantive and cannot be recognized when earned in accordance with ASU 2010-17 as the Milestone Method substantive criteria discussed in Note 2 were not met. Royalties related to product sales will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	Genopaver ECC
	Effective March 29, 2013, the Company entered into a worldwide ECC with Genopaver, a limited liability company formed by affiliates of Third Security, LLC (Note 13). Genopaver was formed for the purpose of entering into the ECC and developing and commercializing products in the field of the fermentative production of alkaloids through genetically modified cell-lines and substrate feeds for use as active pharmaceutical ingredients or as commercially sold intermediates in the manufacture of active pharmaceutical ingredients. Upon execution of the ECC, the Company received a technology access fee of $3,000 as upfront consideration. The Company receives reimbursement payments for research and development services provided pursuant to the agreement during the ECC. Genopaver will pay the Company a royalty as a percentage in the lower-double digits on the quarterly gross profits of product sales from products developed under the ECC. Genopaver is responsible for the development and commercialization of the product candidates. The term of the ECC commenced on March 29, 2013 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined in the agreement and may be terminated voluntarily by Genopaver upon 90 days written notice to the Company.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, and the research and development services to be provided. The Company grouped the deliverables into one unit of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Genopaver Unit of Accounting”), as the deliverables could not be separated. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Genopaver Unit of Accounting, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Genopaver to approximate the cost to recreate the deliverables included in the unit of accounting. The $3,000 of upfront consideration was allocated to the Genopaver Unit of Accounting and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $68 of collaboration revenue for the three and six months ended June 30, 2013. The remaining balance of $2,932 is recorded as deferred revenue at June 30, 2013.
	The Company recognizes the reimbursement payments received for research services as collaboration revenue in the period when the services are performed and collection is reasonably assured. The Company recognized $213 of collaboration revenue for research and development services performed in the three and six months ended June 30, 2013, all of which is included as related party receivables on the June 30, 2013 consolidated balance sheet. Royalties related to product sales will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	Soligenix ECC
	Effective April 27, 2013, the Company entered into a worldwide ECC with Soligenix, Inc. (“Soligenix”), a clinical stage biopharmaceutical company focused on developing products to treat inflammatory diseases and biodefense countermeasures. Under the ECC, at the transaction effective date, Soligenix received a license to the Company’s technology platform to develop and commercialize human monoclonal antibody therapies for the treatment of melioidosis. Upon execution of the ECC, the Company received a technology access fee of 1,034,483 shares of Soligenix’s common stock valued at $1,331 as upfront consideration. The Company is entitled to additional consideration up to an aggregate amount of $7,000 per product payable either in cash or common stock at the option of Soligenix, upon the achievement of certain regulatory milestones (“Soligenix Milestones”). The Company receives reimbursement payments for research and development services and manufacturing services for Company materials provided to Soligenix during the term of the ECC. On a quarterly basis, Soligenix will pay the Company royalties with percentages ranging from upper-single digits to lower-double digits of net sales of products developed under the ECC. Soligenix is responsible for conducting preclinical and clinical development of product candidates, as well as other aspects of commercialization and manufacturing of the product candidates. The term of the ECC commenced on April 27, 2013 and continues until terminated pursuant to the ECC agreement. The ECC may be terminated by either party in the event of certain material breaches defined the agreement and may be terminated voluntarily by Soligenix upon 90 days written notice to the Company.
	The Company identified the deliverables at the inception of the ECC which include the license to the Company’s technology platform, participation on the JSC, the research and development services and any manufacturing services to be provided. The Company grouped the deliverables into two units of accounting based on the nature of the deliverables and the separation criteria: (i) the license to the Company’s technology platform, the Company’s participation on the JSC and research and development services to be provided (“Soligenix Unit of Accounting 1”), as these deliverables could not be separated, and (ii) any manufacturing services to be provided for any Company materials in an approved product from the ECC (“Soligenix Unit of Accounting 2”), which have standalone value and are contingent due to the uncertainty of whether an approved product would be developed and require manufacturing by the Company and whether the Company would elect to be the manufacturer. As VSOE and third party evidence of selling price was not available or practical, the BESP for each unit of accounting was determined using a historical cost approach due to the early stage of development of the Company’s technology. In establishing BESP for Soligenix Unit of Accounting 1, the Company used the accumulated costs incurred as of the ECC by the Company on its technology platform licensed to Soligenix to approximate the cost to recreate the deliverables included in this unit of accounting. All upfront consideration was allocated to Soligenix Unit of Accounting 1. Soligenix Unit of Accounting 2 was determined to be a contingent deliverable at the inception of the ECC due to the uncertainty of whether an approved product would be developed and require manufacturing by the Company and whether the Company would elect to be the manufacturer. The $1,331 of upfront consideration was allocated to Soligenix Unit of Accounting 1 and will be recognized over the expected life of the Company’s technology platform using a straight-line approach. The Company recognized $20 of collaboration revenue for the three and six months ended June 30, 2013. The remaining balance of $1,311 is recorded as deferred revenue at June 30, 2013.
	The Company recognizes the reimbursement payments received for research services as collaboration revenue in the period when the services are performed and collection is reasonably assured. At inception of the agreement, the Company determined that the Soligenix Milestones are not substantive and cannot be recognized when earned in accordance with ASU 2010-17 as the Milestone Method substantive criteria discussed in Note 2 were not met. Royalties related to product sales will be recognized when earned as the payments relate directly to products that have been fully developed and for which the Company has satisfied all of its obligations.
	AquaBounty ECC
	On February 14, 2013, the Company entered into an ECC with AquaBounty. The Company will be reimbursed for research and development services as provided for in the ECC agreement. In the event of product sales from a product developed from the ECC, the Company will receive 16.66% of quarterly gross profits for each product. All revenues and expenses related to this ECC will be eliminated in consolidation (Note 6).

Shortterm_Investments

Short-term Investments	6 Months Ended
	Jun. 30, 2013
Investments Debt And Equity Securities [Abstract]
Short-term Investments	4. Short-term Investments
	The Company’s short-term investments have remaining maturities of less than twelve months and are classified as available-for-sale. The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of short-term investments as of June 30, 2013:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	87,453	$	—	$	(11	)	$	87,442
	Commercial paper		5,999		—		—			5,999
	Certificates of deposit		2,017		—		(4	)		2,013
	Total	$	95,469	$	—	$	(15	)	$	95,454
	For more information on our method for determining the fair value of our assets, see Note 2 – “Fair Value of Financial Instruments”.
	Changes in market interest rates and bond yields cause certain of our short-term investments to fall below their cost basis, resulting in unrealized losses on short-term investments. As of June 30, 2013, we had unrealized losses of $15 related to short-term investments that had a fair value of $77,186. The unrealized losses of the Company’s short-term investments were primarily a result of unfavorable changes in interest rates subsequent to the initial purchase of these investments and have been in a loss position for less than 12 months.
	As of June 30, 2013, we did not consider any of our short-term investments to be other-than-temporarily impaired. When evaluating our short-term investments for other-than-temporary impairment, we review factors such as the length of time and extent to which fair value has been below its cost basis, the financial condition of the issuer, our ability and intent to hold the security and whether it is more likely than not that we will be required to sell the investment before recovery of its cost basis.

Fair_Value_Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2013
Fair Value Disclosures [Abstract]
Fair Value Measurements	5. Fair Value Measurements
	The carrying amount of cash and cash equivalents, receivables, prepaid expenses and other current assets, accounts payable, accrued compensation and benefits, other accrued liabilities, and related party payables approximate fair value due to the short maturity of these instruments.
	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at June 30, 2013:
		Quoted		Significant		Significant		June 30,
		prices		other		unobservable		2013
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 4)	$	—	$	87,442	$	—	$	87,442
	Commercial paper (Note 4)		—		5,999		—		5,999
	Certificates of deposit (Note 4)		—		2,013		—		2,013
	Equity securities (Note 3)		48,100		17,113		—		65,213
		$	48,100	$	112,567	$	—	$	160,667
	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2012:
		Quoted		Significant		Significant		December 31,
		prices		other		unobservable		2012
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	Certificates of deposit (Note 4)	$	—	$	260	$	—	$	260
	Equity securities (Note 3)		72,988		10,128		—		83,116
		$	72,988	$	10,388	$	—	$	83,376
	There were no financial liabilities measured on a recurring basis at June 30, 2013 and December 31, 2012.
	The method used to estimate the fair value of the Level 1 assets in the tables above is based on observable market data as these equity securities are publicly-traded. The method used to estimate the fair value of the Level 2 short-term investments in the tables above is based on professional pricing sources for identical or comparable instruments, rather than direct observations of quote prices in active markets. The method used to estimate the fair value of the Level 2 equity securities in the tables above is based on the quoted market price of the publicly-traded security, adjusted for a discount for lack of marketability.
	There were no transfers between levels of the fair value hierarchy in the three and six months ended June 30, 2013.

Investment_in_AquaBounty

Investment in AquaBounty	6 Months Ended
	Jun. 30, 2013
Business Combinations [Abstract]
Investment in AquaBounty	6. Investment in AquaBounty
	On November 16, 2012, the Company acquired 48,631,444 shares of AquaBounty common stock, representing 47.56% of the then outstanding shares of AquaBounty, for $6,000 through a definitive purchase agreement with an existing AquaBounty shareholder and its affiliate. The carrying amount of the investment in AquaBounty was $5,726 at December 31, 2012. Based on closing quoted market prices (Level 1), the fair value of the investment in AquaBounty was approximately $14,300 at December 31, 2012.
	On November 29, 2012, the Company entered into a promissory note purchase agreement (“promissory note”) with AquaBounty. The promissory note allows for the Company to loan up to $500 to AquaBounty. Draws on the promissory note by AquaBounty accrued annual interest of 3% and were set to mature no later than May 28, 2013. As of December 31, 2012, AquaBounty had drawn $200 on the promissory note. This outstanding balance plus accrued interest is included in related party receivables on the December 31, 2012 consolidated balance sheet. In January and February 2013, AquaBounty borrowed additional installments of $200 and $100, respectively, on the promissory note. On March 15, 2013, AquaBounty repaid the $500 promissory note plus accrued interest in its entirety.
	On March 15, 2013, the Company acquired 18,714,814 shares of AquaBounty for $4,907 in a private subscription offering, thereby increasing the Company’s ownership in AquaBounty to 53.82%, resulting in the Company gaining control over AquaBounty, and began consolidating. Commencing on that date, the Company includes AquaBounty in its consolidated results of operations and financial position pursuant to the step acquisition guidance in ASC 805, Business Combinations. The Company recognized a gain of $7,415 to account for the difference between the carrying value and the fair value of the previously held 47.56% equity interest. The fair value of the consideration transferred included:
	Consideration paid	$	4,907
	Fair value of noncontrolling interest		15,153
	Fair value of the Company’s investment in affiliate held before the business combination		12,751
	Fair value of the consideration transferred	$	32,811
	The Company used the private subscription price to measure fair value of the Company’s previously held investment and noncontrolling interest. The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:
	Cash	$	5,419
	Short-term investments		14
	Trade receivables		4
	Other receivables		9
	Prepaid expenses and other		200
	Property, plant and equipment		1,241
	Intangible assets		14,900
	Other assets		22
	Total assets acquired		21,809
	Accounts payable		156
	Accrued compensation and benefits		94
	Other accrued liabilities		395
	Long-term debt		2,199
	Total liabilities assumed		2,844
	Net assets acquired		18,965
	Goodwill		13,846
	Total consideration	$	32,811
	The fair value of assets acquired and liabilities assumed at the acquisition date are considered preliminary and is subject to revision when the valuation of intangible assets is finalized upon receipt of the final valuation report from a third party valuation expert. The preliminary fair value of acquired intangible assets was determined using the multi-period excess earnings method, a variation of the income approach. The multi-period excess earnings method estimates the value of an intangible asset equal to the present value of the incremental after-tax cash flows attributable to the intangible asset. The acquired intangible assets consist of in-process research and development until regulatory approval is obtained, at which point the intangible assets will be accounted for as definite lived intangible assets and amortized over the expected useful life of fifteen years. The goodwill consists of future revenue opportunities and the potential for expansion of AquaBounty products. The goodwill is not expected to be deductible for tax purposes. The fair value of assets acquired and liabilities assumed at the acquisition date are also subject to revision upon the Company’s continued evaluation of the fair value of long term debt.
	The results of operations of AquaBounty are included in the consolidated statement of operations beginning on the acquisition date. The following unaudited condensed pro forma financial information for the three months ended June 30 2012 and the six months ended June 30, 2013 and 2012 is presented as if the acquisition had been consummated on January 1, 2012:
		Three Months Ended			Six Months Ended
		June 30,			June 30,
		2012			2013			2012
					Pro forma
	Revenues	$	2,726		$	10,757		$	4,344
	Net loss		(17,619	)		(50,418	)		(25,375	)
	Net loss attributable to noncontrolling interest		501			940			1,082
	Net loss attributable to Intrexon		(17,118	)		(49,478	)		(24,293	)
	Accretion of dividends on redeemable convertible preferred stock, not declared		(5,362	)		(14,347	)		(10,822	)
	Net loss attributable to Intrexon common shareholders	$	(22,480	)	$	(63,825	)	$	(35,115	)
	Net loss attributable to Intrexon common shareholders per share, basic and diluted	$	(4.10	)	$	(11.27	)	$	(6.42	)
	The pro forma net loss for the six months ended June 30, 2013 excludes the $7.4 million non-recurring gain on remeasurement of the Company’s previously held investment in AquaBounty. The pro forma net loss for the six months ended June 30, 2012 includes this non-recurring gain on remeasurement.

Property_Plant_and_Equipment_n

Property, Plant and Equipment, net	6 Months Ended
	Jun. 30, 2013
Property Plant And Equipment [Abstract]
Property, Plant and Equipment, net	7. Property, Plant and Equipment, net
	Property, plant and equipment consist of the following:
		June 30,			December 31,
		2013			2012
	Land	$	55		$	—
	Building		945			—
	Furniture and fixtures		859			857
	Lab equipment		22,847			22,195
	Leasehold improvements		5,159			4,972
	Computer hardware		3,173			3,136
	Construction in progress		—			14
	Software		958			888
			33,996			32,062
	Less: Accumulated depreciation and amortization		(15,586	)		(13,375	)
	Property, plant and equipment, net	$	18,410		$	18,687
	Depreciation expense was $1,114 and $1,264 for the three months ended June 30, 2013 and 2012, respectively, and $2,260 and $2,398 for the six months ended June 30, 2013 and 2012, respectively.

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets, net	6 Months Ended
	Jun. 30, 2013
Goodwill And Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets, net	8. Goodwill and Intangible Assets, net
	The changes in the carrying amount of goodwill for the six months ended June 30, 2013 are as follows:
	Balance as of December 31, 2012	$	—
	Acquisitions		13,846
	Balance as of June 30, 2013	$	13,846
	No goodwill or accumulated impairment losses existed as of December 31, 2012. There are no accumulated impairment losses as of June 30, 2013.
	Intangible assets consist of the following at June 30, 2013:
		Gross Carrying		Accumulated			Net
		Amount		Amortization
	Patents and related technologies	$	34,342	$	(6,270	)	$	28,072
	In-process research and development		14,900		—			14,900
	Total	$	49,242	$	(6,270	)	$	42,972
	Intangible assets consist of the following at December 31, 2012:
		Gross Carrying		Accumulated			Net
		Amount		Amortization
	Patents and related technologies	$	34,342	$	(4,851	)	$	29,491
	Favorable rent asset		646		(631	)		15
	Total	$	34,988	$	(5,482	)	$	29,506
	Amortization expense was $709 and $757 for the three months ended June 30, 2013 and 2012, respectively, and $1,434 and $1,514 for the six months ended June 30, 2013 and 2012, respectively. At June 30, 2013, the weighted average useful life for patents and related technology was 12.4 years.

Income_Taxes

Income Taxes	6 Months Ended
	Jun. 30, 2013
Income Tax Disclosure [Abstract]
Income Taxes	9. Income Taxes
	There is no income tax benefit recognized for the three months ended June 30, 2013 and 2012 and for the six months ended June 30, 2013 and 2012 due to the Company’s history of net losses combined with an inability to confirm recovery of the tax benefits of the Company’s losses and other net deferred tax assets. In assessing the realizability of deferred tax assets, management considers whether it is more likely than not that some portion or all of the deferred tax assets will not be realized. The ultimate realization of deferred tax assets is dependent upon the generation of future taxable income during the periods in which those temporary differences become deductible. Management considers the scheduled reversal of deferred tax liabilities, projected future taxable income and tax planning strategies in making this assessment. Due to the Company’s history of net losses incurred from inception, no income tax benefit has been recorded and the corresponding deferred tax assets have been fully reserved as the Company cannot sufficiently be assured that these deferred tax assets will be realized.
	At June 30, 2013, the Company has loss carryforwards for federal income tax purposes of approximately $225,100 available to offset future taxable income and federal and state research and development tax credits of approximately $6,600, prior to consideration of annual limitations that may be imposed under Section 382. These carryforwards will begin to expire in 2022.

Redeemable_Convertible_Preferr

Redeemable Convertible Preferred Stock and Shareholders' Deficit	6 Months Ended
	Jun. 30, 2013
Text Block [Abstract]
Redeemable Convertible Preferred Stock and Shareholders' Deficit	10. Redeemable Convertible Preferred Stock and Shareholders’ Deficit
	The tables below represent a rollforward of the Redeemable Convertible Preferred Stock:
		Series A					Series B				Series B-1
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		705,400	$	1,358			694,000	$	669		1,212,360	$	1,360
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		42			—		15		—		30
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		705,400	$	1,400			694,000	$	684		1,212,360	$	1,390
		Series C					Series C-1				Series C-2
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		4,546,360	$	7,134			15,934,528	$	34,201		18,617,020	$	44,512
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		214			—		1,025		—		1,337
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		4,546,360	$	7,348			15,934,528	$	35,226		18,617,020	$	45,849
		Series C-3					Series D				Series E
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		13,297,872	$	29,770			19,803,685	$	76,252		38,095,239	$	211,403
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		887			—		2,275		—		6,383
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		13,297,872	$	30,657			19,803,685	$	78,527		38,095,239	$	217,786
		Series F
		redeemable
		convertible
		preferred stock
		Shares		Amount
	Balances at December 31, 2012		—	$	—
	Issuance of shares		19,047,619		150,000
	Accretion of dividends		—		2,139
	Stock issuance costs		—		(3,148	)
	Balances at June 30, 2013		19,047,619	$	148,991
	The Series F Redeemable Convertible Preferred Stock (“Series F”), Series E Redeemable Convertible Preferred Stock (“Series E”), Series D Redeemable Convertible Preferred Stock (“Series D”), Series C-3 Redeemable Convertible Preferred Stock (“Series C-3”), Series C-2 Redeemable Convertible Preferred Stock (“Series C-2”), Series C-1 Redeemable Convertible Preferred Stock (“Series C-1”), Series C Redeemable Convertible Preferred Stock (“Series C”), Series B-1 Redeemable Convertible Preferred Stock (“Series B-1”), Series B Redeemable Convertible Preferred Stock (“Series B”) and Series A Redeemable Convertible Preferred Stock (“Series A”) collectively shall be referred as the “Series Preferred”.
	Rights, Preferences and Terms of Capital
	The following is a summary of the current rights, preferences and terms of the Company’s outstanding equity instruments:
	Liquidation Preference
	In the event of any liquidation, dissolution, or winding up of the Company, distributions will first be made to the holders of Series F, second to the holders of the Series E, third to the holders of the Series D, fourth to the holders of the Series C-3, fifth to the holders of the Series C-2, sixth to the holders of the Series C-1, seventh to the holders of the Series C, eighth to the holders of Series B and B-1 together as a class, and ninth to the holders of the Series A, and thereafter to the holders of Series F, Series E, Series D, Series C-3, Series C-2, Series C-1, Series C, Series B, Series B-1, Series A and the common who shall receive all remaining funds available for distribution in proportion to the common held by each holder and the common that each of the holders of preferred shares have the right to acquire upon conversion of their preferred stock to common stock.
	Optional Redemption
	After May 25, 2016, but prior to the occurrence of a qualified IPO, the holders of greater than three-fourths of then issued and outstanding shares of the Series F, Series E, Series D, Series C-3, Series C-2, Series C-1 and Series C, voting as a separate class, may elect by written notice to require the Company to redeem all of the then issued and outstanding shares of Series F, Series E, Series D, Series C-3, Series C-2, Series C-1 and Series C at an amount equal to the stated price adjusted for any stock dividends, combination or splits plus all accrued but unpaid dividends. Upon receipt of such written notice, the Company must notify the holders of the Series B-1, Series B and Series A of the redemption notice, upon which the holders of each of those classes may require the Company to redeem all of the then issued and outstanding shares of such class.
	As a result of this optional redemption provision, the Company accretes changes in the redemption value from the date of issuance of all Series Preferred shares with a resultant change to additional paid-in capital or accumulated deficit in the absence of additional paid-in capital. The following table represents the aggregate redemption price per share for each class of Series Preferred:
		June 30,		December 31,
		2013		2012
	Series F	$	7.99	$	—
	Series E		5.79		5.62
	Series D		3.97		3.86
	Series C-3		2.31		2.24
	Series C-2		2.47		2.4
	Series C-1		2.21		2.15
	Series C		1.62		1.58
	Series B-1		1.16		1.14
	Series B		1.04		1.02
	Series A		2.05		1.99
	The redemption will occur in the following order of preference: Series F, Series E, Series D, Series C-3, Series C-2, Series C-1, Series C, Series B-1 and Series B together as a class, and Series A.
	Series A Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series A shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series A shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series A shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series A stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue. No dividends have been declared to date.
Conversion
The holders of Series A at any time may elect to convert all or any of their Series A into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The Company will automatically convert all of the outstanding Series A into common stock upon the closing of a qualified IPO, or upon the written election of the holders of a majority of the outstanding Series A. Series A convert to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series A, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series B and B-1 Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series B and B-1 shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series B and B-1 shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series B and B-1 shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series B and B-1 stated value. Once declared, dividends will be accrued annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series B and B-1 at any time may elect to convert all or any of their Series B and B-1 into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series B and B-1 shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series B and B-1. Series B and B-1 convert to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series B and B-1, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series C Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series C shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series C shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series C shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series C stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series C at any time may elect to convert all or any of their Series C into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series C shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series C. Series C convert to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series C, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series C-1 Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series C-1 shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series C-1 shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series C-1 shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series C-1 stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series C-1 at any time may elect to convert all or any of their Series C-1 into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series C-1 shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series C-1. Series C-1 converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series C-1, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series C-2 Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series C-2 shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series C-2 shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series C-2 shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series C-2 stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series C-2 at any time may elect to convert all or any of their Series C-2 into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series C-2 shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series C-2. Series C-2 converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series C-2, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series C-3 Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series C-3 shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series C-3 shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series C-3 shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series C-3 stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series C-3 at any time may elect to convert all or any of their Series C-3 into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series C-3 shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series C-3. Series C-3 converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series C-3, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series D Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series D shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series D shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series D shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series D stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series D at any time may elect to convert all or any of their Series D into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series D shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series D. Series D converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series D, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series E Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series E shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series E shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series E shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series E stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series E at any time may elect to convert all or any of their Series E into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series E shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series E. Series E converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series E, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
Series F Redeemable Convertible Preferred Stock
Liquidity
In the event of any liquidation, dissolution, or winding up of the Company, all distributions will be made to Series F shareholders in the order described within Liquidation Preference above.
Voting
The holders of Series F shall be entitled to the number of votes on each matter submitted to a vote of the shareholders equal to the number of shares of common stock into which said shares could be converted. Any matter which requires approval of the Series Preferred shall require the approval of a majority of the outstanding Series Preferred.
Dividends
The holders of Series F shall be entitled to receive, when and if declared by the Board of Directors out of the retained earnings of the Company, dividends, payable in cash or shares of common stock, at the rate of six percent (6%) per annum on the Series F stated value. Once declared, dividends will be accrued and compounded annually from the initial date of issue and paid quarterly. No dividends have been declared to date.
Conversion
The holders of Series F at any time may elect to convert all or any of their Series F into common stock, fully paid and nonassessable and free from all taxes, liens or charges. The shares of Series F shall be automatically converted into fully paid and nonassessable common stock upon the closing of a qualified IPO or at the election of the holders of a majority of the outstanding Series F. Series F converts to common stock on a one to one basis and is subject to adjustment for stock splits and stock dividends. Upon automatic conversion of Series F, cumulative dividends are converted to common stock at a price per share equal to the fair market value of a common share at the time of conversion.
The following table presents the aggregate and per-share amounts of arrearages in cumulative preferred dividends in ascending order of preference at December 31, 2012:
	Arrearage		Arrearage
	total		per share
Series E Redeemable Convertible Preferred Shares	$	14,086	$	0.37
Series D Redeemable Convertible Preferred Shares		9,411		0.48
Series C-3 Redeemable Convertible Preferred Shares		4,819		0.36
Series C-2 Redeemable Convertible Preferred Shares		9,614		0.52
Series C-1 Redeemable Convertible Preferred Shares		9,222		0.58
Series C Redeemable Convertible Preferred Shares		2,162		0.48
Series B-1 Redeemable Convertible Preferred Shares		380		0.31
Series B Redeemable Convertible Preferred Shares		209		0.3
Series A Redeemable Convertible Preferred Shares		556		0.78
Of the arrearage amounts above, $50,459 has been accreted to the redemption price for each Series Preferred on the Company’s December 31, 2012 consolidated balance sheet.
The following table presents the aggregate and per-share amounts of arrearages in cumulative preferred dividends in ascending order of preference at June 30, 2013:
	Arrearage		Arrearage
	total		per share
Series F Redeemable Convertible Preferred Shares	$	2,139	$	0.11
Series E Redeemable Convertible Preferred Shares		20,469		0.54
Series D Redeemable Convertible Preferred Shares		11,686		0.59
Series C-3 Redeemable Convertible Preferred Shares		5,706		0.43
Series C-2 Redeemable Convertible Preferred Shares		10,951		0.59
Series C-1 Redeemable Convertible Preferred Shares		10,247		0.64
Series C Redeemable Convertible Preferred Shares		2,376		0.52
Series B-1 Redeemable Convertible Preferred Shares		410		0.34
Series B Redeemable Convertible Preferred Shares		224		0.32
Series A Redeemable Convertible Preferred Shares		598		0.85
Of the arrearage amounts above, $64,806 has been accreted to the redemption price for each Series Preferred on the Company’s June 30, 2013 unaudited consolidated balance sheet.
All shares of common stock are subordinate to the preferred shares with respect to dividend rights and rights upon the event of liquidation, winding up and/or dissolution of the Company.
See additional discussion about the conversion of the Series Preferred to common stock upon the closing of the Company’s initial public offering (“IPO”) at Note 15.

Stock_Option_Plans

Stock Option Plans	6 Months Ended
	Jun. 30, 2013
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Stock Option Plans	11. Stock Option Plans
	Intrexon Stock Option Plan
	The Company records the fair value of stock options issued to employees and non-employees as of the grant date as stock-based compensation expense. Stock-based compensation expense for employees and non-employees is recognized over the requisite service period, which is typically the vesting period. Stock-based compensation cost that has been included in research and development expenses and general and administrative expenses amounted to $147 and $641, respectively, for the three months ended June 30, 2013, and $154 and $213, respectively, for the three months ended June 30, 2012. Stock-based compensation cost that has been included in research and development expenses and general and administrative expenses amounted to $300 and $895, respectively, for the six months ended June 30, 2013, and $16 and $504, respectively, for the six months ended June 30, 2012.
	On April 18, 2008, the Company adopted the 2008 Equity Incentive Plan (the “2008 Plan”) for employees and nonemployees pursuant to which the Company’s board of directors may grant share based awards to officers, key employees and nonemployees. During 2011, the 2008 Plan was amended to increase the number of authorized awards under the 2008 plan from 2,857,142 to 5,714,285. Awards issued pursuant to the Company’s 2004 Stock Option Plan, the 2004 Stock Option Plan for Nonemployees and the 2006 Stock Option Plan were consolidated into the 2008 Plan and are subject to, and administered under the terms of the 2008 Plan.
	See discussion of the 2013 Omnibus Incentive Plan at Note 15.
	Stock option activity during the years indicated is as follows:
			Number			Weighted			Weighted
			of			average			average
			shares			exercise			remaining
						price			contractual
									term
	Balances at December 31, 2012			2,313,526			5.9			7.87
	Granted			703,714			9.67
	Exercised			(1,357	)		(3.43	)
	Forfeited			(129,893	)		(6.84	)
	Expired			(29,085	)		(4.65	)
	Balances at June 30, 2013			2,856,905			6.79			8.07
	Exercisable at June 30, 2013			931,762			4.46			6.35
	Vested and Expected to Vest at June 30, 2013(1)			2,560,259			5.94			7.44
	-1	The number of stock options expected to vest takes into account an estimate of expected forfeitures.
	Total unrecognized compensation costs related to nonvested awards at June 30, 2013 and December 31, 2012 were $4,364 and $4,910, respectively, and are expected to be recognized over a weighted-average period of approximately three years.
	The Company currently uses authorized and unissued shares to satisfy share award exercises.
	AquaBounty Stock Option Plan
	The AquaBounty 2006 Equity Incentive Plan (the “AquaBounty Plan”) provides for the issuance of incentive stock options to employees of AquaBounty and non-qualified stock options and awards of restricted and direct stock purchases to its directors, officers, employees and consultants of AquaBounty. Unless otherwise indicated, options issued to employees, directors and non-employees are vested over one to three years and are exercisable for a term of ten years from the date of issuance. As of June 30, 2013, there were 6,552,000 options outstanding under the AquaBounty Plan at a weighted average exercise price of $0.25 per share of which 5,552,000 were exercisable. Stock based compensation cost for the three months ended and six months ended June 30, 2013 amounted to $21 and $1, respectively, and is included in general and administrative expenses.

Commitments_and_Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2013
Commitments And Contingencies Disclosure [Abstract]
Commitments and Contingencies	12. Commitments and Contingencies
	Operating Leases
	The Company leases its facilities and certain equipment under noncancelable operating leases. The equipment leases are renewable at the option of the Company. At June 30, 2013, future minimum lease payments under noncancelable operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:
	2013	$	1,416
	2014		2,918
	2015		2,492
	2016		1,863
	2017		927
	2018		72
		$	9,688
	Rent expense, including other facility expenses, was $1,742 and $1,229 in the three months ended June 30, 2013 and 2012, respectively, and $3,012 and $2,484 in the six months ended June 30, 2013 and 2012, respectively.
	During 2012, the Company subleased space in two of its facilities to two different entities, one of which is an affiliate of certain holders of preferred stock. One of these agreements was terminated during 2012. The second agreement remained in effect as of June 30, 2013. Rental income under sublease agreements was $92 and $10 for the three months ended June 30, 2013 and 2012, respectively, and $183 and $64 for the six months ended June 30, 2013 and 2012, respectively. Future rental income for the sublease agreement in effect at June 30, 2013 is $182 for 2013, $365 for 2014, and $152 for 2015.
	Research and Development
	The Company has commitments with third parties in connection with research and development collaborations. See Note 2 for further discussion.
	Long Term Debt
	In January 2009, the Atlantic Canada Opportunities Agency (“ACOA”), a Canadian government agency, awarded AquaBounty a grant to provide funding of a research and development project. The total amount available under the award is C$2,872, or USD$2,728 as of June 30, 2013, which AquaBounty can claim over a five year period. All amounts claimed by AquaBounty must be repaid in the form of a 10% royalty on any products commercialized out of this research and development project until fully paid. The timing of repayment is uncertain. As of June 30, 2013, the total amount claimed by AquaBounty is $2,074 and is included in long term debt on the June 30, 2013 consolidated balance sheet.
	In October 2003, AquaBounty obtained a term loan with the ACOA in the amount of C$250, or USD$238 as of June 30, 2013. AquaBounty repays this loan through monthly principal payments and the loan matures in December 2013. The outstanding balance as of June 30, 2013 is $13 and is included in the current portion of long term debt on the June 30, 2013 consolidated balance sheet.
	In August 2003, AquaBounty obtained a term loan with Enterprise PEI, a Canadian provincial government agency, in the amount of C$300, or USD$285 as of June 30, 2013. AquaBounty repays this loan through monthly principal and interest payments and the loan matures in December 2013. The outstanding balance as of June 30, 2013 is $20 and is included in the current portion of long term debt on the June 30, 2013 consolidated balance sheet.
	In November 1999, Technology Partnership Canada (“TPC”), a Canadian government agency, agreed to provide AquaBounty funding up to C$2,965, or USD$2,817 as of June 30, 2013, to support AquaBounty’s research and development. This funding was completed in 2003. The funding provided by TPC is repayable to TPC in the form of a 5.2% royalty on revenues generated from AquaBounty’s technology. Per the funding agreement with TPC, AquaBounty has no repayment obligations after June 30, 2014 even if the total amount has not been repaid as of such date. As of June 30, 2013, the estimated balance to be paid by June 30, 2014 is $190 and is included in the current portion of long term debt on the June 30, 2013 consolidated balance sheet.
	Contingencies
	The Company may become subject to claims and assessments from time to time in the ordinary course of business. Such matters are subject to many uncertainties and outcomes are not predictable with assurance. The Company accrues liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated. As of June 30, 2013 and December 31, 2012, the Company does not believe that any such matters, individually or in the aggregate, will have a material adverse effect on the Company’s business, financial condition, results of operations, or cash flows.

Related_Party_Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2013
Related Party Transactions [Abstract]
Related Party Transactions	13. Related Party Transactions
	Third Security, LLC (“Third Security”) and Affiliates
	Certain affiliates of Third Security are shareholders of the Series B, B-1, C, C-1, C-2, C-3, D, E, and F Redeemable Convertible Preferred Stock.
	On June 6, 2011, the Company entered into a worldwide exclusive licensing agreement with Halozyme Therapeutics, Inc. (“Halozyme”) for the use of Halozyme’s proprietary enzyme in one of the Company’s targeted therapeutics. The Company and Halozyme are related parties through common ownership by affiliates of Third Security. The Company’s CEO also serves on Halozyme’s board of directors. Under the terms of the agreement, the Company paid a license fee of $9,000 upon execution of the agreement. The Company is required to pay an annual exclusivity fee of $1,000 commencing June 6, 2012 and on each anniversary of the effective date of the agreement thereafter until a certain development event occurs. If the Company successfully develops a product candidate using the license in the exclusive field of use and achieves an established sales target, the Company could pay up to $54 million in milestone payments. The Company is obligated to pay tiered royalties on net sales of the approved product. The Company may terminate this agreement in whole or on a product-by-product basis at any time upon 90 days written notice to Halozyme.
	The Manager of Third Security who is also a member of the Company’s Board of Directors, (“Board Member”) assumed the role of CEO of the Company in April 2009 and served on a part-time basis in that capacity through 2011. In 2012, the CEO began serving in this role on a full-time basis. Although the CEO has not received compensation for his services as CEO, the Company recorded $387 in compensation expense for each of the three months ended June 30, 2013 and 2012, respectively, and $775 for each of the six months ended June 30, 2013 and 2012, respectively, based on the estimated salary and benefits appropriate for the role.
	Transactions with Other Shareholders
	At June 30, 2013 and December 31, 2012, the Company leased two office facilities from an affiliate of certain holders of preferred stock. The Company has a receivable due from this affiliate in the form of security deposits which are included in other long term assets of $66 at June 30, 2013 and December 31, 2012. During the three months ended June 30, 2013 and 2012, the Company incurred rent and other facility expenses of $221 and $223, respectively. During the six months ended June 30, 2013 and 2012, the Company incurred rent and other facility expenses of $447 and $442, respectively.
	In the six months ended June 30, 2013, the Company paid transaction fees in conjunction with the closing of the first and second rounds of Series F to a shareholder.
	Transactions with ECC Parties
	On January 6, 2011, in conjunction with the ECC with Ziopharm (Note 3), the Company purchased 2,426,235 shares of common stock at $4.80 per share at closing in a private placement. The Company agreed to purchase up to an additional $50,000 of common stock in conjunction with securities offerings that may be conducted by Ziopharm in the future, subject to certain conditions and limitations. On February 7, 2011, the Company purchased 1,910,000 shares of Ziopharm common stock at $5.75 per share in the first such securities offering. On January 20, 2012, the Company purchased 1,923,075 shares of Ziopharm common stock at $5.20 per share in another securities offering. At June 30, 2013, the Company had approximately $29,000 remaining on its purchase commitment. In conjunction with the ECC and the initial share purchase, the CEO of the Company joined the board of directors of Ziopharm.
	In conjunction with the ECC with Synthetic Biologics (Note 3), the Company is entitled to, at its election, purchase up to 19.99% of securities offerings that may be conducted by Synthetic Biologics in the future, subject to certain conditions and limitations. The Company has been granted the right to make purchases of Synthetic Biologics’ common stock in the open market up to an additional 10% of Synthetic Biologics’ common stock. The Company has made no purchases of Synthetic Biologics’ common stock.
	In conjunction with the ECC with Oragenics (Note 3), the Company is entitled to, at its election, purchase up to 30% of securities offerings that may be conducted by Oragenics in the future, subject to certain conditions and limitations. The Company has made no purchases of Oragenics’ common stock.
	In conjunction with the ECC with Soligenix (Note 3), the Company is entitled to, at its election, participate in securities offerings conducted by Soligenix in the future, subject to certain conditions and limitations. The Company has made no purchases of Soligenix’s common stock.

Net_Loss_per_Share

Net Loss per Share	6 Months Ended
	Jun. 30, 2013
Earnings Per Share [Abstract]
Net Loss per Share	14. Net Loss per Share
	The following table presents the historical computation of basic and diluted net loss per share and the unaudited pro forma basic and diluted net loss per share:
		Three months ended						Six months ended
		June 30,						June 30,
		2013			2012			2013			2012
	Historical net loss per share:
	Numerator:
	Net loss attributable to Intrexon	$	(6,012	)	$	(16,535	)	$	(42,323	)	$	(30,447	)
	Add: Accretion of dividends on redeemable convertible preferred stock, not declared		(7,942	)		(5,362	)		(14,347	)		(10,822	)
	Net loss attributable to common shareholders	$	(13,954	)	$	(21,897	)	$	(56,670	)	$	(41,269	)
	Denominator:
	Weighted average shares outstanding, basic and diluted		5,667,557			5,484,572			5,664,665			5,470,415
	Net loss attributable to common shareholders per share, basic and diluted	$	(2.46	)	$	(3.99	)	$	(10.00	)	$	(7.54	)
	The following potentially dilutive securities have been excluded from the computations of diluted weighted average shares outstanding as of June 30, 2013 and 2012, as they would have been anti-dilutive:
		June 30,
		2013			2012
	Common shares issuable upon conversion of all Series Preferred		75,402,332			61,796,890
	Options		2,856,905			2,876,388
	Warrants		511,098			511,098
	Total		78,770,335			65,184,376
	In addition to the potentially dilutive securities in the table above, Series Preferred cumulative dividends convertible into common shares at a price per share equal to the fair market value of a common share at the time of conversion have been excluded from the computation of diluted weighted-average shares outstanding as of June 30, 2013 and 2012.

Subsequent_Events

Subsequent Events	6 Months Ended
	Jun. 30, 2013
Subsequent Events [Abstract]
Subsequent Events	15. Subsequent Events
	Effective July 26, 2013, the Company’s board of directors and shareholders approved a reverse stock split of 1-for-1.75 of the Company’s shares of common stock. Shareholders entitled to fractional shares as a result of the reverse stock split will receive a cash payment in lieu of receiving fractional shares. Shares of common stock underlying outstanding stock options and warrants were proportionately reduced and the respective exercise prices were proportionately increased in accordance with the terms of the agreements governing such securities.
	On July 17, 2013, the Company entered into a sublease for administrative offices. The lease term begins on September 1, 2013 and terminates on December 31, 2017. Total annual rent payments are $94, $370, $464, $478 and $492 for the years ended December 31, 2013, 2014, 2015, 2016 and 2017, respectively.
	On August 13, 2013, the Company completed its initial public offering (“IPO”), whereby the Company sold 11,499,998 shares of common stock, inclusive of 1,499,999 shares of common stock sold by the Company pursuant to the full exercise of an overallotment option granted to the underwriters in connection with the IPO, at a price of $16.00 per share. The shares began trading on the NYSE on August 8, 2013. The aggregate net proceeds from the IPO were $168.3 million, net of underwriting discounts and commissions and estimated offering expenses payable by the Company.
	Upon the closing of the IPO, all Series Preferred shares, including accrued but unpaid dividends thereon, converted into 79,705,130 shares of common stock. Additionally, in connection with the closing of the IPO, the Company amended and restated its articles of incorporation to increase the number of authorized shares of common stock to 200,000,000 and decrease the number of authorized shares of preferred stock to 25,000,000.
	In July 2013, the Company’s shareholders and board of directors approved the adoption of the 2013 Omnibus Incentive Plan (the “2013 Plan”). The 2013 Plan became effective upon the closing of the IPO and replaces the 2008 Plan. There are 7,000,000 shares of common stock reserved for issuance under the 2013 Plan. Upon the effectiveness of the 2013 Plan, no new awards may be granted under the 2008 Plan.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2013

Accounting Policies [Abstract]

Principles of Consolidation

Principles of Consolidation

The accompanying consolidated financial statements reflect the operations of the Company and its subsidiaries. All intercompany accounts and transactions have been eliminated.

Unaudited Financial Information

Unaudited Financial Information

The accompanying interim consolidated financial statements are unaudited and have been prepared in accordance with U.S. GAAP. Certain information and footnote disclosures normally included in the Company’s annual financial statements have been condensed or omitted. These interim consolidated financial statements, in the opinion of management, reflect all normal recurring adjustments necessary for fair statement of the Company’s financial position as of June 30, 2013 and results of operations and cash flows for the interim periods ended June 30, 2013 and 2012. These interim financial results are not necessarily indicative of the results to be expected for the year ending December 31, 2013, or for any other future annual or interim period. The accompanying interim unaudited consolidated financial statements should be read in conjunction with the audited consolidated financial statements and related notes thereto for the year ended December 31, 2012, included in the Prospectus that forms a part of the Company’s Registration Statement on Form S-1 (File No. 333-189853), which was filed with the Securities and Exchange Commission pursuant to Rule 424 on August 8, 2013.

Revenue Recognition

Revenue Recognition

The Company generates revenue through contractual agreements with collaborative partners (known as exclusive channel collaborations, “ECC” or “ECCs”) whereby the partners obtain exclusive access to the Company’s proprietary technology for use in the research, development and commercialization of products and/or treatments in a contractually specified field of use. Generally, the terms of these collaborative agreements provide that the Company receive some or all of the following: (i) upfront payments upon consummation of the agreement, (ii) reimbursements for costs incurred by the Company for research and development and/or manufacturing efforts related to specific application provided for in the agreement, (iii) milestone payments upon the achievement of specified development, regulatory and commercial activities, and (iv) royalties on sales of products arising from the collaboration.

The Company’s collaboration agreements typically contain multiple elements, or deliverables, including technology licenses, research and development services, and in certain cases manufacturing services. Effective January 1, 2011, the Company adopted the provisions of Accounting Standards Update (“ASU”) No. 2009-13, Revenue Recognition (Topic 605): Multiple Deliverable Revenue Arrangements (“ASU 2009-13”). In accordance with the provisions of ASU 2009-13, the Company identifies the deliverables within the agreements and evaluates which deliverables represent separate units of accounting. Analyzing the agreements to identify deliverables requires the use of judgment. A deliverable is considered a separate unit of accounting when the deliverable has value to the collaborative partner on a standalone basis based on the consideration of the relevant facts and circumstances for each agreement.

Consideration received is allocated at the inception of the agreement to all identified units of accounting based on their relative selling price. When available, the relative selling price for each deliverable is determined using vendor specific objective evidence (“VSOE”) of selling price or third-party evidence of selling price, if VSOE does not exist. If neither VSOE nor third-party evidence of selling price exists, the Company uses its best estimate of the selling price (“BESP”) for the deliverable. The amount of allocable consideration is limited to amounts that are fixed or determinable. The consideration received is allocated among the separate units of accounting, and the applicable revenue recognition criteria are applied to each of the separate units. The Company recognizes the revenue allocated to each unit of accounting as the Company delivers the related goods or services. If the Company determines that certain deliverables should be treated as a single unit of accounting, then the revenue is recognized using either a proportional performance or straight-line method, depending on whether the Company can reasonably estimate the level of effort required to complete its performance obligations under an arrangement and whether such performance obligations are provided on a best-efforts basis. As the Company cannot reasonably estimate its performance obligations related to its collaborators, the Company recognizes revenue on a straight-line basis over the period it expects to complete its performance obligations.

The terms of the Company’s agreements may provide for milestone payments upon achievement of certain defined events. The Company applies ASU No. 2010-17, Revenue Recognition – Milestone Method (“ASU 2010-17” or “Milestone Method”). Under the Milestone Method, the Company recognizes consideration that is contingent upon the achievement of a milestone in its entirety as revenue in the period in which the milestone is achieved only if the milestone is substantive in its entirety. A milestone is considered substantive when it meets all of the following criteria:

-1

The consideration is commensurate with either the entity’s performance to achieve the milestone or the enhancement of the value of the delivered item or items as a result of a specific outcome resulting from the entity’s performance to achieve the milestone;

-2

The consideration relates solely to past performance; and

-3

The consideration is reasonable relative to all of the deliverables and payment terms with the arrangement.

In the event that a milestone is not considered substantive, the Company recognizes the milestone consideration as revenue using the same method applied to upfront payments.

Research and development services are a deliverable satisfied by the Company in accordance with the terms of the collaboration agreements and the Company considers these services to be inseparable from the license to the core technology; thus, reimbursements of services performed are recognized as revenue. Further, because reimbursement (i) is contingent upon performance of the services by the Company, (ii) does not include a profit component, and (iii) does not relate to any future deliverable, the revenue is recognized during the period in which the related services are performed and collection of such amounts is reasonable assured. Payments received from manufacturing services will be recognized when the earnings process related to the manufactured materials has been completed. Royalties to be received under the agreements will be recognized as earned.

The Company also generates revenue from other licenses of certain technologies and rental and other income from sublease agreements. License revenue is recognized on a straight-line basis over the term of the license agreement. Deferred revenue is recorded on the consolidated balance sheet when cash is received prior to the period in which the revenue is earned. Sublease and laboratory services revenues are recognized in the period in which they are earned.

Research and Development

Research and Development

The Company considers that regulatory and other uncertainties inherent in the research and development of new products preclude it from capitalizing such costs. Research and development expenses include salaries and related costs of research and development personnel, and the costs of consultants, facilities, materials and supplies associated with research and development projects as well as various laboratory studies. Indirect research and development costs include depreciation, amortization and other indirect overhead expenses.

The Company has research and development arrangements with third parties that include upfront and milestone payments. At June 30, 2013 and December 31, 2012, the Company had research and development commitments with third parties totaling $3,393 and $3,164, respectively, of which $1,235 and $1,431, respectively, had not yet been incurred. The commitments are generally cancellable by the Company at any time upon written notice.

Cash and Cash Equivalents

Cash and Cash Equivalents

All highly liquid investments with an original maturity of three months or less at the date of purchase are considered to be cash equivalents. Cash balances at a limited number of banks may periodically exceed insurable amounts. The Company believes that it mitigates its risk by investing in or through major financial institutions. Recoverability of investments is dependent upon the performance of the issuer. At June 30, 2013 and December 31, 2012, the Company had cash equivalent investments in highly liquid money market accounts at major financial institutions of $28,857 and $9,384, respectively.

Short-term Investments

Short-term Investments

Short-term investments at December 31, 2012 include certificates of deposit with original maturities between three months and one year. In June 2013, the Company’s board of directors approved an investment policy to invest cash in excess of immediate requirements in securities to preserve principal and maintain sufficient liquidity. Accordingly, in June 2013, the Company purchased U.S. government debt securities, commercial paper and certificates of deposit. The Company’s written investment policy requires short-term investments to be explicitly rated by two of the three following rating services: Standard & Poor’s, Moody’s and/or Fitch and to have a minimum rating of A1, P1 and/or F-1, respectively, from those agencies. In addition, the investment policy limits the amount of credit exposure to any one issuer.

Equity Securities

Equity Securities

The Company holds equity securities received and/or purchased from certain collaborative partners. Other than the investment in AquaBounty which was accounted for using the equity method and discussed below, the Company elected the fair value option to account for its equity securities held in these partners, including Ziopharm Oncology, Inc. (“Ziopharm”) which is an equity method investment. These equity securities are recorded at fair value at each reporting date. Unrealized gains and losses resulting from fair value adjustments are reported in the consolidated statement of operations. These equity securities are classified as noncurrent in the consolidated balance sheet as the Company does not currently intend to sell these equity securities within one year. The Company has not sold any of these equity securities to date.

The Company records the fair value of securities received on the date the collaboration is consummated or the milestone is achieved using the closing, quoted price of the collaborator’s security on that date, assuming the transfer of consideration is considered perfunctory. If the transfer of the consideration is not considered perfunctory, the Company considers the specific facts and circumstances to determine the appropriate date on which to evaluate fair value. The Company also evaluates whether any discounts for trading restrictions or other basis for lack of marketability should be applied to the fair value of the securities at inception of the collaboration. In the event the Company concludes that a discount should be applied, the fair value of the securities is adjusted at inception of the collaboration and re-evaluated at each reporting period thereafter.

Fair Value of Financial Instruments

Fair Value of Financial Instruments

Fair value is the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. As such, fair value is a market-based measurement that should be determined based on assumptions that market participants would use in pricing an asset and liability. As a basis for considering such assumptions, the Company uses a three-tier fair value hierarchy that prioritizes the inputs used in its fair value measurements. The hierarchy gives the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1 measurements) and the lowest priority to unobservable inputs (Level 3 measurements). The three levels of the fair value hierarchy are as follows:

Level 1:

Quoted prices in active markets for identical assets and liabilities;

Level 2:

Other than quoted prices included in Level 1 inputs that are observable for the asset or liability, either directly or indirectly; and

Level 3:

Unobservable inputs for the asset or liability used to measure fair value to the extent that observable inputs are not available.

As discussed in “Equity Securities” above, the Company elected the fair value option for the equity securities held in certain collaborative partners.

Concentrations of Risk

Concentrations of Risk

Due to the Company’s mix of fixed and variable rate securities holdings, the Company’s short-term investment portfolio is susceptible to changes in short-term interest rates. As of June 30, 2013, the Company’s short-term investments had gross unrealized losses of $15. From time to time, the Company may liquidate some or all of its short-term investments to fund operational needs or other activities, such as capital expenditures or business acquisitions. Depending on which short-term investments the Company liquidates to fund these activities, the Company could recognize a portion, or all, of the gross unrealized losses.

Equity Method Investments

Equity Method Investments

Through March 15, 2013, the Company accounted for its investment in AquaBounty, a biotechnology company focused on improving productivity in commercial aquaculture, using the equity method of accounting as the Company had the ability to exercise significant influence over, but not control, the operating activities of AquaBounty. Under the equity method of accounting, the Company included its pro-rata share of AquaBounty’s operating results, adjusted for accretion of basis difference, on a separate line in the consolidated statement of operations called “Equity in net loss of affiliate.” On the consolidated balance sheet as of December 31, 2012, the Company presented its investment in AquaBounty as a separate non-current asset called “Investment in affiliate.” The excess cost over the Company’s pro-rata share of AquaBounty’s net assets was identifiable intangible assets and equity-method goodwill. This equity-method goodwill was not amortized; however, the investment in AquaBounty was analyzed for impairment on a periodic basis or if an event occurred or circumstances changed that indicate the carrying amount may be impaired. On March 15, 2013, the Company acquired additional ownership interests in AquaBounty resulting in the Company gaining control over and thus consolidating AquaBounty. See Note 6 for additional discussion of this transaction.

The Company determined that it has significant influence over one of its collaborators, Ziopharm, a publicly traded small molecule late-stage oncology drug development company, as of June 30, 2013 and December 31, 2012, based on its ownership interest, representation on Ziopharm’s board of directors, as well as other qualitative factors. The Company accounts for this investment using the fair value option. The fair value of the Company’s equity securities of Ziopharm is $28,555 and $56,298 as of June 30, 2013 and December 31, 2012, respectively, and is included as equity securities in the respective consolidated balance sheets. The Company’s ownership percentage of Ziopharm is 16.2% and 16.3% at June 30, 2013 and December 31, 2012, respectively. Unrealized appreciation (depreciation) in the fair value of the Company’s equity securities held in Ziopharm is $3,789 and $5,443 for the three months ended June 30, 2013 and 2012, respectively, and $(27,743) and $13,721 for the six months ended June 30, 2013 and 2012, respectively. Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2013 and 2012 are as follows:

Three months ended

Six months ended

June 30,

June 30,

2013

2012

2013

2012

Revenues

$

200

$

200

$

400

$

400

Operating expenses

18,496

23,166

42,279

41,999

Loss from operations

(18,296

)

(22,966

)

(41,879

)

(41,599

)

Other

(396

)

(647

)

10,388

(6,484

)

Net loss

$

(18,692

)

$

(23,613

)

$

(31,491

)

$

(48,083

)

Variable Interest Entities

Variable Interest Entities

The Company identifies entities that either (1) do not have sufficient equity investment at risk to permit the entity to finance its activities without additional subordinated financial support or (2) in which the equity investors lack an essential characteristic of a controlling financial interest as variable interest entities (“VIE or VIEs”). The Company performs an initial and on-going evaluation of the entities with which the Company has variable interests to determine if any of these entities are a VIE. If an entity is identified as a VIE, the Company performs an assessment to determine whether the Company has both (1) the power to direct activities that most significantly impact the VIE’s economic performance and (2) have the obligation to absorb losses from or the right to receive benefits of the VIE that could potentially be significant to the VIE. If the Company has both these criterion, the Company is identified as the primary beneficiary of the VIE. As of December 31, 2012, the Company’s investment in affiliate, AquaBounty, is identified as a VIE. The Company is not the primary beneficiary for this entity as the Company does not have the power to direct the activities that most significantly impact the economic performance of the VIE. As of December 31, 2012, the total carrying value of the Company’s investment in the VIE was $5,726, which is the investment in AquaBounty. On March 15, 2013, the Company began consolidating AquaBounty in the Company’s results of operations and financial position as a result of the Company’s ownership in AquaBounty exceeding 50% (Note 6). The Company’s maximum exposure to loss related to this VIE as of December 31, 2012 was limited to the carrying value of the investment in affiliate. As of June 30, 2013, two of the Company’s collaborators, AmpliPhi Biosciences Corporation (“AmpliPhi”) and Genopaver, LLC (“Genopaver”), were identified as VIEs. The Company is not the primary beneficiary for either of these entities as the Company does not have the power to direct the activities that most significantly impact the economic performance of the VIEs. As of June 30, 2013, the total carrying value of the Company’s investment in the VIEs was $3,973, which is equal to the value of the equity securities holdings in those VIEs

Property, Plant and Equipment

Property, Plant and Equipment

Property, plant and equipment are stated at cost, less accumulated depreciation and amortization. Major additions or betterments are charged to the property accounts while repairs and maintenance are generally expensed as incurred. Depreciation and amortization is calculated on the straight-line method over the estimated useful lives of the assets. The estimated useful lives of these assets are as follows:

Years

Building

13

Furniture and fixtures

7

Lab equipment

2–7

Computer hardware

5–7

Software

3–5

Leasehold improvements are amortized over the shorter of the useful life of the asset or the applicable lease term, generally one to four years.

Goodwill

Goodwill

Goodwill is an asset that represents the future economic benefits arising from other assets acquired in a business combination that are not individually identified and separately recognized (Note 6). Goodwill is reviewed for impairment at least annually. The Company has the option to perform a qualitative assessment to determine whether it is more-likely-than-not that the fair value of a reporting unit is less than its carrying amount prior to performing the two-step goodwill impairment test. If this is the case, the two-step goodwill impairment test is required. If it is more-likely-than-not that the fair value of a reporting unit is greater than the carrying amount, the two-step goodwill impairment test is not required.

If the two-step goodwill impairment test is required, first, the fair value of the reporting unit is compared with its carrying amount (including goodwill). If the fair value of the reporting unit is less than its carrying amount, an indication of goodwill impairment exists for the reporting unit and the entity must perform step two of the impairment test. Under step two, an impairment loss is recognized for any excess of the carrying amount of the reporting unit’s goodwill over the implied fair value of that goodwill. The implied fair value of goodwill is determined by allocating the fair value of the reporting unit in a manner similar to a purchase price allocation and the residual fair value after this allocation is the implied fair value of the reporting unit goodwill. Fair value of the reporting unit is determined using a discounted cash flow analysis. If the fair value of the reporting unit exceeds its carrying amount, step two does not need to be performed.

The Company intends to perform its annual impairment review of goodwill in the fourth quarter, or sooner if a triggering event occurs prior to the annual impairment review.

Intangible Assets

Intangible Assets

Intangible assets subject to amortization consist of patents and related technologies acquired in mergers and acquisitions and a favorable lease asset acquired upon the assumption of a lease agreement. These intangible assets subject to amortization were recorded at fair value at the date of acquisition and are stated net of accumulated amortization. Indefinite-lived intangible assets consist of in-process research and development acquired as a result of a step acquisition (Note 6) and is recorded at fair value at the date of the step acquisition.

The Company applies the provisions of ASC Topic 350, Intangibles, Goodwill and Other, which requires the amortization of long-lived intangible assets to reflect the pattern in which the economic benefits of the intangible asset are expected to be realized. The intangible assets are amortized over their remaining estimated useful lives, ranging from seven to fourteen years for the patents and related technologies, and through the end of the original lease term, February 1, 2013, for the favorable lease asset.

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

Long-lived assets to be held and used, including property, plant and equipment and intangible assets subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of the assets may not be recoverable. Conditions that would necessitate an impairment assessment include a significant decline in the observable market value of an asset, a significant change in the extent or manner in which an asset is used, or a significant adverse change that would indicate that the carrying amount of an asset or group of assets is not recoverable.

Indefinite-lived intangible assets, including in-process research and development, are tested for impairment annually, or more frequently if events or circumstances between annual tests indicate that the asset may be impaired. Impairment losses on indefinite-lived intangible assets are recognized based solely on a comparison of their fair value to carrying value, without consideration of any recoverability test. The Company monitors the progression of its in-process research and development, as the likelihood of success is contingent upon regulatory approval.

Income Taxes

Income Taxes

Income taxes are accounted for under the asset and liability method. Deferred tax assets and liabilities are recognized for the future tax consequences attributable to both differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases as well as operating loss and tax credit carryforwards. Deferred tax assets and liabilities are measured using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. The effect on deferred tax assets and liabilities of a change in tax rates is recognized in income in the period that includes the enactment date of the change. Valuation allowances are established when necessary to reduce deferred tax assets to the amount expected to be realized.

The Company identifies any uncertain income tax positions and recognizes the effect of income tax positions only if those positions are more likely than not of being sustained. Recognized income tax positions are measured at the largest amount that is greater than 50% likely of being realized. Changes in recognition or measurement are reflected in the period in which the change in judgment occurs. The Company records interest, if any, related to unrecognized tax benefits as a component of interest expense. Penalties, if any, are recorded in general and administrative expenses.

Net Loss per Share

Net Loss per Share

Basic net loss per share is calculated by dividing net loss attributable to common shareholders by the weighted average shares outstanding during the period, without consideration of common stock equivalents. Diluted net loss per share is calculated by adjusting weighted average shares outstanding for the dilutive effect of common stock equivalents outstanding for the period, determined using the treasury-stock method. For purposes of the diluted net loss per share calculation, preferred stock, stock options and warrants are considered to be common stock equivalents but are excluded from the calculation of diluted net loss per share because their effect would be anti-dilutive and, therefore, basic and diluted net loss per share were the same for all periods presented.

Segment Information

Segment Information

The Company has determined that it operates in one segment. The Company uses synthetic biology for the creation of distinct products for collaboration with partners. All of the Company’s revenues are derived in the United States of America. Substantially all of the Company’s assets are located in the United States of America

Recently Issued Accounting Pronouncements

Recently Issued Accounting Pronouncements

In February 2013, the FASB issued ASU No. 2013-02, Reporting of Amounts Reclassified Out of Accumulated Other Comprehensive Income (“ASU 2013-02”). ASU 2013-02 requires that companies present either in a single note or parenthetically on the face of the financial statements, the effect of significant amounts reclassified from each component of accumulated other comprehensive income based on its source and the income statement line items affected by the reclassification. If a component is not required to be reclassified to net income in its entirety, companies would instead cross reference to the related footnote for additional information. ASU 2013-02 is effective for interim and annual reporting periods beginning after December 15, 2012. The Company has implemented the provisions of ASU 2013-02 as of January 1, 2013. The adoption of this amendment did not have a material impact on the Company’s consolidated financial statements.

In December 2011, the FASB issued ASU No. 2011-11, Balance Sheet (Topic 210): Disclosures about Offsetting Assets and Liabilities (“ASU 2011-11”). ASU 2011-11 requires an entity to disclose information about offsetting and related arrangements to enable users of financial statements to understand the effect of those arrangements on its financial position, and to allow investors to better compare financial statements prepared under U.S. GAAP with financial statements prepared under IFRS. The new standards are effective for annual periods beginning January 1, 2013 and interim periods within those annual periods. Retrospective application is required. The Company has implemented the provisions of ASU 2011-11 as of January 1, 2013. The adoption of this amendment did not have a material impact on the Company’s consolidated financial statements.

Use of Estimates

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States of America requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, the disclosure of contingent assets and liabilities at the date of the financial statements, and the reported amounts of revenues and expenses during the reporting periods. Actual results could differ from those estimates.

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2013
Accounting Policies [Abstract]
Summarized Unaudited Financial Information	Summarized unaudited financial information for Ziopharm for the three and six months ended June 30, 2013 and 2012 are as follows:
		Three months ended						Six months ended
		June 30,						June 30,
		2013			2012			2013			2012
	Revenues	$	200		$	200		$	400		$	400
	Operating expenses		18,496			23,166			42,279			41,999
	Loss from operations		(18,296	)		(22,966	)		(41,879	)		(41,599	)
	Other		(396	)		(647	)		10,388			(6,484	)
	Net loss	$	(18,692	)	$	(23,613	)	$	(31,491	)	$	(48,083	)
Estimated Useful Lives of Property, Plant and Equipment	The estimated useful lives of these assets are as follows:
		Years
	Building		13
	Furniture and fixtures		7
	Lab equipment		2–7
	Computer hardware		5–7
	Software		3–5

Collaboration_Revenue_Tables

Collaboration Revenue (Tables)	6 Months Ended
	Jun. 30, 2013
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Summary of Deferred Revenue	Deferred revenue consists of the following:
		June 30,		December 31,
		2013		2012
	Upfront and milestone payments	$	61,814	$	51,359
	Prepaid research and development services		2,819		7,229
	Other		46		48
	Total	$	64,679	$	58,636
	Current portion of deferred revenue		8,270		9,963
	Long-term portion of deferred revenue		56,409		48,673
	Total	$	64,679	$	58,636

Shortterm_Investments_Tables

Short-term Investments (Tables)	6 Months Ended
	Jun. 30, 2013
Investments Debt And Equity Securities [Abstract]
Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Short-term Investments	The following table summarizes the amortized cost, gross unrealized gains and losses and fair value of short-term investments as of June 30, 2013:
		Amortized		Gross		Gross			Aggregate
		Cost		Unrealized		Unrealized			Fair Value
				Gains		Losses
	U.S. government debt securities	$	87,453	$	—	$	(11	)	$	87,442
	Commercial paper		5,999		—		—			5,999
	Certificates of deposit		2,017		—		(4	)		2,013
	Total	$	95,469	$	—	$	(15	)	$	95,454

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2013
Fair Value Disclosures [Abstract]
Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at June 30, 2013:
		Quoted		Significant		Significant		June 30,
		prices		other		unobservable		2013
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	U.S. government debt securities (Note 4)	$	—	$	87,442	$	—	$	87,442
	Commercial paper (Note 4)		—		5,999		—		5,999
	Certificates of deposit (Note 4)		—		2,013		—		2,013
	Equity securities (Note 3)		48,100		17,113		—		65,213
		$	48,100	$	112,567	$	—	$	160,667
	The following table presents the placement in the fair value hierarchy of financial assets that are measured at fair value on a recurring basis, including the items for which the fair value option has been elected, at December 31, 2012:
		Quoted		Significant		Significant		December 31,
		prices		other		unobservable		2012
		in active		observable		inputs
		markets		inputs		(level 3)
		(level 1)		(level 2)
	Assets
	Certificates of deposit (Note 4)	$	—	$	260	$	—	$	260
	Equity securities (Note 3)		72,988		10,128		—		83,116
		$	72,988	$	10,388	$	—	$	83,376

Investment_in_AquaBounty_Table

Investment in AquaBounty (Tables)	6 Months Ended
	Jun. 30, 2013
Summary of Fair Value of the Consideration Transferred	The fair value of the consideration transferred included:
	Consideration paid	$	4,907
	Fair value of noncontrolling interest		15,153
	Fair value of the Company’s investment in affiliate held before the business combination		12,751
	Fair value of the consideration transferred	$	32,811
AquaBounty [Member]
Summary of Preliminary Estimated Fair Value of Assets Acquired and Liabilities Assumed at the Acquisition Date	The preliminary estimated fair value of assets acquired and liabilities assumed at the acquisition date is shown below:
	Cash	$	5,419
	Short-term investments		14
	Trade receivables		4
	Other receivables		9
	Prepaid expenses and other		200
	Property, plant and equipment		1,241
	Intangible assets		14,900
	Other assets		22
	Total assets acquired		21,809
	Accounts payable		156
	Accrued compensation and benefits		94
	Other accrued liabilities		395
	Long-term debt		2,199
	Total liabilities assumed		2,844
	Net assets acquired		18,965
	Goodwill		13,846
	Total consideration	$	32,811
Summary of Unaudited Condensed Proforma Financial Information	The following unaudited condensed pro forma financial information for the three months ended June 30 2012 and the six months ended June 30, 2013 and 2012 is presented as if the acquisition had been consummated on January 1, 2012:
		Three Months Ended			Six Months Ended
		June 30,			June 30,
		2012			2013			2012
					Pro forma
	Revenues	$	2,726		$	10,757		$	4,344
	Net loss		(17,619	)		(50,418	)		(25,375	)
	Net loss attributable to noncontrolling interest		501			940			1,082
	Net loss attributable to Intrexon		(17,118	)		(49,478	)		(24,293	)
	Accretion of dividends on redeemable convertible preferred stock, not declared		(5,362	)		(14,347	)		(10,822	)
	Net loss attributable to Intrexon common shareholders	$	(22,480	)	$	(63,825	)	$	(35,115	)
	Net loss attributable to Intrexon common shareholders per share, basic and diluted	$	(4.10	)	$	(11.27	)	$	(6.42	)

Property_Plant_and_Equipment_n1

Property, Plant and Equipment, net (Tables)	6 Months Ended
	Jun. 30, 2013
Property Plant And Equipment [Abstract]
Schedule of Property Plant and Equipment	Property, plant and equipment consist of the following:
		June 30,			December 31,
		2013			2012
	Land	$	55		$	—
	Building		945			—
	Furniture and fixtures		859			857
	Lab equipment		22,847			22,195
	Leasehold improvements		5,159			4,972
	Computer hardware		3,173			3,136
	Construction in progress		—			14
	Software		958			888
			33,996			32,062
	Less: Accumulated depreciation and amortization		(15,586	)		(13,375	)
	Property, plant and equipment, net	$	18,410		$	18,687

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets, net (Tables)	6 Months Ended
	Jun. 30, 2013
Goodwill And Intangible Assets Disclosure [Abstract]
Schedule of Changes in Carrying Amount of Goodwill	The changes in the carrying amount of goodwill for the six months ended June 30, 2013 are as follows:
	Balance as of December 31, 2012	$	—
	Acquisitions		13,846
	Balance as of June 30, 2013	$	13,846
Schedule of Intangible Assets	Intangible assets consist of the following at June 30, 2013:
		Gross Carrying		Accumulated			Net
		Amount		Amortization
	Patents and related technologies	$	34,342	$	(6,270	)	$	28,072
	In-process research and development		14,900		—			14,900
	Total	$	49,242	$	(6,270	)	$	42,972
	Intangible assets consist of the following at December 31, 2012:
		Gross Carrying		Accumulated			Net
		Amount		Amortization
	Patents and related technologies	$	34,342	$	(4,851	)	$	29,491
	Favorable rent asset		646		(631	)		15
	Total	$	34,988	$	(5,482	)	$	29,506

Redeemable_Convertible_Preferr1

Redeemable Convertible Preferred Stock and Shareholders' Deficit (Tables)	6 Months Ended
	Jun. 30, 2013
Text Block [Abstract]
Summary of Redeemable Convertible Preferred Stock	The tables below represent a rollforward of the Redeemable Convertible Preferred Stock:
		Series A					Series B				Series B-1
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		705,400	$	1,358			694,000	$	669		1,212,360	$	1,360
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		42			—		15		—		30
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		705,400	$	1,400			694,000	$	684		1,212,360	$	1,390
		Series C					Series C-1				Series C-2
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		4,546,360	$	7,134			15,934,528	$	34,201		18,617,020	$	44,512
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		214			—		1,025		—		1,337
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		4,546,360	$	7,348			15,934,528	$	35,226		18,617,020	$	45,849
		Series C-3					Series D				Series E
		redeemable					redeemable				redeemable
		convertible					convertible				convertible
		preferred stock					preferred stock				preferred stock
		Shares		Amount			Shares		Amount		Shares		Amount
	Balances at December 31, 2012		13,297,872	$	29,770			19,803,685	$	76,252		38,095,239	$	211,403
	Issuance of shares		—		—			—		—		—		—
	Accretion of dividends		—		887			—		2,275		—		6,383
	Stock issuance costs		—		—			—		—		—		—
	Balances at June 30, 2013		13,297,872	$	30,657			19,803,685	$	78,527		38,095,239	$	217,786
		Series F
		redeemable
		convertible
		preferred stock
		Shares		Amount
	Balances at December 31, 2012		—	$	—
	Issuance of shares		19,047,619		150,000
	Accretion of dividends		—		2,139
	Stock issuance costs		—		(3,148	)
	Balances at June 30, 2013		19,047,619	$	148,991
Summary of Aggregate Redemption Price Per Share	The following table represents the aggregate redemption price per share for each class of Series Preferred:
		June 30,		December 31,
		2013		2012
	Series F	$	7.99	$	—
	Series E		5.79		5.62
	Series D		3.97		3.86
	Series C-3		2.31		2.24
	Series C-2		2.47		2.4
	Series C-1		2.21		2.15
	Series C		1.62		1.58
	Series B-1		1.16		1.14
	Series B		1.04		1.02
	Series A		2.05		1.99
Summary of Aggregate and Per Share Amount	The following table presents the aggregate and per-share amounts of arrearages in cumulative preferred dividends in ascending order of preference at December 31, 2012:
		Arrearage		Arrearage
		total		per share
	Series E Redeemable Convertible Preferred Shares	$	14,086	$	0.37
	Series D Redeemable Convertible Preferred Shares		9,411		0.48
	Series C-3 Redeemable Convertible Preferred Shares		4,819		0.36
	Series C-2 Redeemable Convertible Preferred Shares		9,614		0.52
	Series C-1 Redeemable Convertible Preferred Shares		9,222		0.58
	Series C Redeemable Convertible Preferred Shares		2,162		0.48
	Series B-1 Redeemable Convertible Preferred Shares		380		0.31
	Series B Redeemable Convertible Preferred Shares		209		0.3
	Series A Redeemable Convertible Preferred Shares		556		0.78
	Of the arrearage amounts above, $50,459 has been accreted to the redemption price for each Series Preferred on the Company’s December 31, 2012 consolidated balance sheet.
	The following table presents the aggregate and per-share amounts of arrearages in cumulative preferred dividends in ascending order of preference at June 30, 2013:
		Arrearage		Arrearage
		total		per share
	Series F Redeemable Convertible Preferred Shares	$	2,139	$	0.11
	Series E Redeemable Convertible Preferred Shares		20,469		0.54
	Series D Redeemable Convertible Preferred Shares		11,686		0.59
	Series C-3 Redeemable Convertible Preferred Shares		5,706		0.43
	Series C-2 Redeemable Convertible Preferred Shares		10,951		0.59
	Series C-1 Redeemable Convertible Preferred Shares		10,247		0.64
	Series C Redeemable Convertible Preferred Shares		2,376		0.52
	Series B-1 Redeemable Convertible Preferred Shares		410		0.34
	Series B Redeemable Convertible Preferred Shares		224		0.32
	Series A Redeemable Convertible Preferred Shares		598		0.85

Stock_Option_Plans_Tables

Stock Option Plans (Tables)	6 Months Ended
	Jun. 30, 2013
Disclosure Of Compensation Related Costs Sharebased Payments [Abstract]
Schedule of Stock Option Activity	Stock option activity during the years indicated is as follows:
			Number			Weighted			Weighted
			of			average			average
			shares			exercise			remaining
						price			contractual
									term
	Balances at December 31, 2012			2,313,526			5.9			7.87
	Granted			703,714			9.67
	Exercised			(1,357	)		(3.43	)
	Forfeited			(129,893	)		(6.84	)
	Expired			(29,085	)		(4.65	)
	Balances at June 30, 2013			2,856,905			6.79			8.07
	Exercisable at June 30, 2013			931,762			4.46			6.35
	Vested and Expected to Vest at June 30, 2013(1)			2,560,259			5.94			7.44
	-1	The number of stock options expected to vest takes into account an estimate of expected forfeitures.

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2013
Commitments And Contingencies Disclosure [Abstract]
Future Minimum Lease Payments Under Noncancelable Operating Leases	At June 30, 2013, future minimum lease payments under noncancelable operating leases having initial or remaining noncancelable lease terms in excess of one year are as follows:
	2013	$	1,416
	2014		2,918
	2015		2,492
	2016		1,863
	2017		927
	2018		72
		$	9,688

Net_Loss_per_Share_Tables

Net Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2013
Earnings Per Share [Abstract]
Historical Computation of Basic and Diluted Net Loss per Share	The following table presents the historical computation of basic and diluted net loss per share and the unaudited pro forma basic and diluted net loss per share:
		Three months ended						Six months ended
		June 30,						June 30,
		2013			2012			2013			2012
	Historical net loss per share:
	Numerator:
	Net loss attributable to Intrexon	$	(6,012	)	$	(16,535	)	$	(42,323	)	$	(30,447	)
	Add: Accretion of dividends on redeemable convertible preferred stock, not declared		(7,942	)		(5,362	)		(14,347	)		(10,822	)
	Net loss attributable to common shareholders	$	(13,954	)	$	(21,897	)	$	(56,670	)	$	(41,269	)
	Denominator:
	Weighted average shares outstanding, basic and diluted		5,667,557			5,484,572			5,664,665			5,470,415
	Net loss attributable to common shareholders per share, basic and diluted	$	(2.46	)	$	(3.99	)	$	(10.00	)	$	(7.54	)
Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share	The following potentially dilutive securities have been excluded from the computations of diluted weighted average shares outstanding as of June 30, 2013 and 2012, as they would have been anti-dilutive:
		June 30,
		2013			2012
	Common shares issuable upon conversion of all Series Preferred		75,402,332			61,796,890
	Options		2,856,905			2,876,388
	Warrants		511,098			511,098
	Total		78,770,335			65,184,376

Organization_and_Basis_of_Pres1

Organization and Basis of Presentation - Additional Information (Detail)	12 Months Ended
	Dec. 31, 2011
	Subsidiary
Organization Consolidation And Presentation Of Financial Statements [Abstract]
Number of subsidiaries acquired	3

Summary_of_Significant_Account3

Summary of Significant Accounting Policies - Additional Information (Detail) (USD $)

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

12 Months Ended

6 Months Ended

12 Months Ended

6 Months Ended

In Thousands, unless otherwise specified

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Dec. 31, 2012

Jun. 30, 2013

Dec. 31, 2012

Jun. 30, 2013

Dec. 31, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Dec. 31, 2012

Dec. 31, 2012

Jun. 30, 2013

Jun. 30, 2013

Dec. 31, 2012

Jun. 30, 2013

Jun. 30, 2013

Collaborator

Segment

Equity Securities [Member]

Equity Securities [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Minimum [Member]

Minimum [Member]

Minimum [Member]

Maximum [Member]

Maximum [Member]

Maximum [Member]

Collaborator

Equity Securities [Member]

Equity Securities [Member]

Equity Securities [Member]

Equity Securities [Member]

Equity Securities [Member]

Patents and Related Technologies [Member]

Leasehold Improvements [Member]

Patents and Related Technologies [Member]

Leasehold Improvements [Member]

Organization And Significant Accounting Policies [Line Items]

Research and development commitments with third parties

$3,393

$3,393

$3,164

Research and development commitments with third parties not incurred

1,235

1,235

1,431

Maturity period of liquid investment

3 months

Cash equivalent investments in highly liquid money market accounts

28,857

28,857

9,384

Maturity of certificate of deposits

3 Months

1 Year

Short-term investments gross unrealized losses

15

Fair value of the Company's equity securities

160,667

160,667

83,376

65,213

83,116

28,555

28,555

56,298

Company's ownership percentage of Ziopharm

16.20%

16.30%

Unrealized appreciation (depreciation) in the fair value of the Company's equity securities

7,734

4,756

-21,635

15,971

3,789

5,443

-27,743

13,721

Carrying value of investment in VIEs

$3,973

$3,973

$5,726

Number of collaborators identified as VIEs

2

2

Life of the asset

1 year

4 years

Period of estimated useful lives

7 years

14 years

Percentage of recognized income tax positions

50.00%

Number of segment

1

Summary_of_Significant_Account4

Summary of Significant Accounting Policies - Summarized Unaudited Financial Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Schedule of Equity Method Investments [Line Items]
Revenues	$6,781	$2,726	$10,757	$4,344
Operating expenses	21,035	23,974	39,017	50,713
Loss from operations	-14,254	-21,248	-28,260	-46,369
Net loss	-6,519	-16,535	-42,881	-30,447
Ziopharm [Member]
Schedule of Equity Method Investments [Line Items]
Revenues	200	200	400	400
Operating expenses	18,496	23,166	42,279	41,999
Loss from operations	-18,296	-22,966	-41,879	-41,599
Other	-396	-647	10,388	-6,484
Net loss	($18,692)	($23,613)	($31,491)	($48,083)

Summary_of_Significant_Account5

Summary of Significant Accounting Policies - Estimated Useful Lives of Property, Plant and Equipment (Detail)	6 Months Ended
	Jun. 30, 2013
Building [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	13 years
Furniture and Fixtures [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years
Minimum [Member] | Lab Equipment [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	2 years
Minimum [Member] | Computer Hardware [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	5 years
Minimum [Member] | Software [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	3 years
Maximum [Member] | Lab Equipment [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years
Maximum [Member] | Computer Hardware [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	7 years
Maximum [Member] | Software [Member]
Property, Plant and Equipment [Line Items]
Property plant and equipment, useful life	5 years

Collaboration_Revenue_Summary_

Collaboration Revenue - Summary of Deferred Revenue (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Deferred Revenue Arrangement [Line Items]
Current portion of deferred revenue	$8,270	$9,963
Long-term portion of deferred revenue	56,409	48,673
Deferred revenue	64,679	58,636
Upfront and Milestone Payments [Member]
Deferred Revenue Arrangement [Line Items]
Deferred revenue	61,814	51,359
Prepaid Research and Development Services [Member]
Deferred Revenue Arrangement [Line Items]
Deferred revenue	2,819	7,229
Other [Member]
Deferred Revenue Arrangement [Line Items]
Deferred revenue	$46	$48

Collaboration_Revenue_Addition

Collaboration Revenue - Additional Information (Detail) (USD $)

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

1 Months Ended

0 Months Ended

1 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

1 Months Ended

1 Months Ended

3 Months Ended

6 Months Ended

1 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

1 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

0 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

In Thousands, except Share data, unless otherwise specified

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Dec. 31, 2012

Jun. 30, 2013

Dec. 31, 2012

Jan. 06, 2011

Jan. 06, 2011

Oct. 24, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Mar. 21, 2012

Nov. 18, 2011

Nov. 18, 2011

Aug. 06, 2012

Oct. 05, 2012

Nov. 28, 2011

Nov. 28, 2011

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 05, 2012

Jun. 05, 2012

Jun. 30, 2013

Jun. 30, 2013

Oct. 05, 2012

Oct. 05, 2012

Jun. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Mar. 31, 2013

Mar. 31, 2013

Jun. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Mar. 31, 2013

Jun. 30, 2013

Jun. 30, 2013

Feb. 14, 2013

Jan. 06, 2011

Oct. 24, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jan. 06, 2011

Oct. 24, 2012

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Dec. 17, 2012

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 28, 2013

Mar. 31, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Apr. 27, 2013

Apr. 27, 2013

Apr. 27, 2013

Jun. 30, 2013

Jun. 30, 2013

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Ziopharm Oncology ECC [Member]

Synthetic Biologics Field One ECC [Member]

Synthetic Biologics Field One ECC [Member]

Synthetic Biologics Field Two ECC [Member]

Synthetic Biologics Field Two ECC [Member]

Elanco ECC [Member]

Elanco ECC [Member]

Elanco ECC [Member]

Elanco ECC [Member]

Elanco ECC [Member]

Elanco ECC [Member]

Oragenics ECC [Member]

Oragenics ECC [Member]

Oragenics ECC [Member]

Oragenics ECC [Member]

Fibrocell Science ECC [Member]

Fibrocell Science ECC [Member]

Fibrocell Science ECC [Member]

Fibrocell Science ECC [Member]

AmpliPhi ECC [Member]

AmpliPhi ECC [Member]

AmpliPhi ECC [Member]

AmpliPhi ECC [Member]

AmpliPhi ECC [Member]

Genopaver ECC [Member]

Genopaver ECC [Member]

Genopaver ECC [Member]

Genopaver ECC [Member]

AquaBounty ECC [Member]

Ziopharm Oncology ECC Unit of Accounting One [Member]

Ziopharm Oncology ECC Unit of Accounting One [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Ziopharm Oncology ECC Unit of Accounting Two [Member]

Synthetic Biologics Field One ECC Unit of Accounting One [Member]

Synthetic Biologics Field One ECC Unit of Accounting One [Member]

Synthetic Biologics Field One ECC Unit of Accounting One [Member]

Synthetic Biologics Field One ECC Unit of Accounting One [Member]

Synthetic Biologics Field Two ECC Unit of Accounting One [Member]

Synthetic Biologics Field Two ECC Unit of Accounting One [Member]

Synthetic Biologics [Member]

Synthetic Biologics [Member]

Synthetic Biologics [Member]

Synthetic Biologics [Member]

Synthetic Biologics [Member]

Oragenics ECC Unit of Accounting One [Member]

Oragenics ECC Unit of Accounting One [Member]

Fibrocell Science ECC Unit of Accounting One [Member]

Fibrocell Science ECC Unit of Accounting One [Member]

Fibrocell Science ECC Unit of Accounting One [Member]

AmpliPhi ECC Unit of Accounting One [Member]

AmpliPhi ECC Unit of Accounting One [Member]

AmpliPhi ECC Unit of Accounting One [Member]

Genopaver ECC Unit of Accounting One [Member]

Genopaver ECC Unit of Accounting One [Member]

Soligenix ECC [Member]

Soligenix ECC [Member]

Soligenix ECC [Member]

Soligenix ECC Unit of Accounting One [Member]

Soligenix ECC Unit of Accounting One [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Maximum [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Maximum [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Research and Development Services [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Maximum [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront and Milestone Payments [Member]

Upfront [Member]

Milestone One [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Milestone One [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Milestone One [Member]

Milestone One [Member]

Milestone One [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Supplemental Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Upfront [Member]

Collaboration Agreements [Line Items]

Collaborative arrangement consideration received, shares

3,636,926

3,636,926

3,123,558

3,552,210

4,392,425

1,317,520

24,000,000

1,243,781

1,034,483

Collaborative arrangement consideration received, value

$17,457

$18,330

$1,687

$7,815

$6,588

$7,576

$2,400

$3,000

$1,171

$17,159

$2,400

$1,331

Percent of shares outstanding at the date of achievement of future milestone

7.50%

10.00%

1.00%

Royalty rate as a percentage of net profit

50.00%

50.00%

25.00%

Required notice period for voluntary termination of collaborative agreement

90 days

90 days

90 days

90 days

90 days

90 days

90 days

90 days

90 days

Period when agreement cannot be voluntarily terminated

2 years

18 months

18 months

18 months

Collaboration revenue

6,674

2,705

10,538

4,259

2,291

2,014

3,721

2,958

111

234

199

434

334

713

615

1,045

34

34

213

213

1,115

314

315

628

629

2,420

330

660

1,503

32

1,535

64

163

326

314

62

689

123

137

274

158

316

55

55

68

68

20

20

Deferred revenue

64,679

64,679

58,636

61,814

51,359

1,141

1,141

10,000

13,200

13,200

16,342

14,739

13,859

13,859

7,326

7,326

1,678

1,678

2,500

5,995

5,995

7,102

7,102

7,612

2,345

2,345

2,932

2,932

1,311

1,311

Collaboration revenue for research and development services applied against the prepayment

2,291

1,265

3,721

2,007

Consideration to be received upon achievement of future milestone 1

2,000

Consideration to be received upon achievement of future milestone 2

3,000

Field expansion fee

2,000

Aggregate consideration to be received upon achievement of future milestones per product

2,250

7,500

7,000

Required notice period for voluntary termination of collaboration agreement if services in progress

180 days

Trade receivables

258

258

141

111

111

Percentage of shares outstanding at the date of achievement of future milestone 2

1.50%

Percentage of shares outstanding at the date of achievement of future milestone 3

2.00%

Percentage of shares outstanding at the date of achievement of future milestone 4

2.50%

Percentage of shares outstanding at the date of achievement of future milestone 5

3.00%

Related party receivables

820

820

531

212

212

361

361

Number of reverse stock split

1-for-25 reverse stock split

Royalty rate as a percentage of net sales, tier 1

7.00%

Royalty rate as a percentage of net sales, tier 2

14.00%

Royalty rate of savings from improvement

33.00%

Level of net sales at which royalty rate changes to tier 2

$25,000

Royalty rate as a percentage of gross profit

16.66%

Shortterm_Investments_Summary_

Short-term Investments - Summary of Amortized Cost, Gross Unrealized Gains and Losses and Fair Value of Short-term Investments (Detail) (USD $)	Jun. 30, 2013
In Thousands, unless otherwise specified
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	$95,469
Gross Unrealized Gains
Gross Unrealized Losses	-15
Aggregate Fair Value	95,454
U.S. Government Debt Securities [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	87,453
Gross Unrealized Gains
Gross Unrealized Losses	-11
Aggregate Fair Value	87,442
Commercial Paper [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	5,999
Gross Unrealized Gains
Gross Unrealized Losses
Aggregate Fair Value	5,999
Certificates of Deposit [Member]
Schedule of Available-for-sale Securities [Line Items]
Amortized Cost	2,017
Gross Unrealized Gains
Gross Unrealized Losses	-4
Aggregate Fair Value	$2,013

Shortterm_Investments_Addition

Short-term Investments - Additional Information (Detail) (USD $)	Jun. 30, 2013
In Thousands, unless otherwise specified
Amortized Cost And Fair Value Debt Securities [Abstract]
Unrealized losses	$15
Fair value of short-term investments with unrealized losses	$77,186

Fair_Value_Measurements_Summar

Fair Value Measurements - Summary of Placement in the Fair Value Hierarchy of Financial Assets that are Measured at Fair Value on a Recurring Basis (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Assets
Fair value of assets	$160,667	$83,376
US Government Debt Securities [Member]
Assets
Fair value of assets	87,442
Commercial Paper [Member]
Assets
Fair value of assets	5,999
Certificates of Deposit [Member]
Assets
Fair value of assets	2,013	260
Equity Securities [Member]
Assets
Fair value of assets	65,213	83,116
Quoted Prices in Active Markets (Level 1) [Member]
Assets
Fair value of assets	48,100	72,988
Quoted Prices in Active Markets (Level 1) [Member] | US Government Debt Securities [Member]
Assets
Fair value of assets
Quoted Prices in Active Markets (Level 1) [Member] | Commercial Paper [Member]
Assets
Fair value of assets
Quoted Prices in Active Markets (Level 1) [Member] | Certificates of Deposit [Member]
Assets
Fair value of assets
Quoted Prices in Active Markets (Level 1) [Member] | Equity Securities [Member]
Assets
Fair value of assets	48,100	72,988
Significant Other Observable Inputs (Level 2) [Member]
Assets
Fair value of assets	112,567	10,388
Significant Other Observable Inputs (Level 2) [Member] | US Government Debt Securities [Member]
Assets
Fair value of assets	87,442
Significant Other Observable Inputs (Level 2) [Member] | Commercial Paper [Member]
Assets
Fair value of assets	5,999
Significant Other Observable Inputs (Level 2) [Member] | Certificates of Deposit [Member]
Assets
Fair value of assets	2,013	260
Significant Other Observable Inputs (Level 2) [Member] | Equity Securities [Member]
Assets
Fair value of assets	17,113	10,128
Significant Unobservable Inputs (Level 3) [Member]
Assets
Fair value of assets
Significant Unobservable Inputs (Level 3) [Member] | US Government Debt Securities [Member]
Assets
Fair value of assets
Significant Unobservable Inputs (Level 3) [Member] | Commercial Paper [Member]
Assets
Fair value of assets
Significant Unobservable Inputs (Level 3) [Member] | Certificates of Deposit [Member]
Assets
Fair value of assets
Significant Unobservable Inputs (Level 3) [Member] | Equity Securities [Member]
Assets
Fair value of assets

Fair_Value_Measurements_Additi

Fair Value Measurements - Additional Information (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Fair Value Disclosures [Abstract]
Financial liabilities measured on a recurring basis	$0	$0

Investment_in_AquaBounty_Addit

Investment in AquaBounty - Additional Information (Detail) (USD $)	0 Months Ended			1 Months Ended		6 Months Ended		12 Months Ended
In Thousands, except Share data, unless otherwise specified	Mar. 15, 2013	Nov. 29, 2012	Nov. 16, 2012	Feb. 28, 2013	Jan. 31, 2013	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012
Business Combination Transactions [Line Items]
Carrying amount of the investment								$5,726
Amount drawn on promissory note						300
Promissory note repaid						500	34
Gain recognized						7,415
AquaBounty [Member]
Business Combination Transactions [Line Items]
Number of shares acquired			48,631,444
Percentage of outstanding shares			47.56%
Definitive purchase agreement amount			6,000
Carrying amount of the investment								5,726
Fair value of the investment								14,300
Amount of loan allowed in promissory note		500
Annual interest rate		3.00%
Amount drawn on promissory note				100	200			200
Promissory note repaid	500
Maturity date of promissory note		28-May-13
Number of shares acquired	18,714,814
Amount from private subscription offering	4,907
Aggregate percentage of ownership	53.82%
Gain recognized	$7,415					$7,400	$7,400
Percentage of equity interest previously held	47.56%
AquaBounty [Member] | In- Process Research and Development [Member]
Business Combination Transactions [Line Items]
Expected useful life of intangible asset						15 years

Investment_in_AquaBounty_Summa

Investment in AquaBounty - Summary of Fair Value of the Consideration Transferred (Detail) (USD $)	6 Months Ended	0 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Mar. 15, 2013
		AquaBounty [Member]
Business Combination Transactions [Line Items]
Consideration paid		$4,907
Fair value of noncontrolling interest	15,153	15,153
Fair value of the Company's investment in affiliate held before the business combination		12,751
Fair value of the consideration transferred		$32,811

Investment_in_AquaBounty_Summa1

Investment in AquaBounty - Summary of Preliminary Estimated Fair Value of Assets Acquired and Liabilities Assumed at the Acquisition Date (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012	Mar. 15, 2013
In Thousands, unless otherwise specified			AquaBounty [Member]
			Scenario, Plan [Member]
Business Acquisition [Line Items]
Cash			$5,419
Short-term investments			14
Trade receivables			4
Other receivables			9
Prepaid expenses and other			200
Property, plant and equipment			1,241
Intangible assets			14,900
Other assets			22
Total assets acquired			21,809
Accounts payable			156
Accrued compensation and benefits			94
Other accrued liabilities			395
Long-term debt			2,199
Total liabilities assumed			2,844
Net assets acquired			18,965
Goodwill	13,846		13,846
Total consideration			$32,811

Investment_in_AquaBounty_Summa2

Investment in AquaBounty - Summary of Unaudited Condensed Proforma Financial Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Business Acquisition Pro Forma Information [Line Items]
Net loss	($6,519)	($16,535)	($42,881)	($30,447)
Net loss attributable to noncontrolling interest	507		558
Accretion of dividends on redeemable convertible preferred stock, not declared			-14,347	-10,822
Net loss attributable to common shareholders	-13,954	-21,897	-56,670	-41,269
Net loss attributable to Intrexon common shareholders per share, basic and diluted	($2.46)	($3.99)	($10)	($7.54)
AquaBounty [Member] | Pro Forma [Member]
Business Acquisition Pro Forma Information [Line Items]
Revenues		2,726	10,757	4,344
Net loss		-17,619	-50,418	-25,375
Net loss attributable to noncontrolling interest		501	940	1,082
Net loss attributable to Intrexon		-17,118	-49,478	-24,293
Accretion of dividends on redeemable convertible preferred stock, not declared		-5,362	-14,347	-10,822
Net loss attributable to common shareholders		($22,480)	($63,825)	($35,115)
Net loss attributable to Intrexon common shareholders per share, basic and diluted		($4.10)	($11.27)	($6.42)

Recovered_Sheet1

Property, Plant and Equipment, Net - Schedule of Property Plant and Equipment (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Property Plant And Equipment [Abstract]
Land	$55
Building	945
Furniture and fixtures	859	857
Lab equipment	22,847	22,195
Leasehold improvements	5,159	4,972
Computer hardware	3,173	3,136
Construction in progress		14
Software	958	888
Property, plant and equipment, gross	33,996	32,062
Less: Accumulated depreciation and amortization	-15,586	-13,375
Property, plant and equipment, net	$18,410	$18,687

Recovered_Sheet2

Property, Plant and Equipment, Net - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Property Plant And Equipment [Abstract]
Depreciation expense	$1,114	$1,264	$2,260	$2,398

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets, Net - Schedule of Changes in Carrying Amount of Goodwill (Detail) (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013
Goodwill And Intangible Assets Disclosure [Abstract]
Beginning Balance
Acquisitions	13,846
Ending Balance	$13,846

Goodwill_and_Intangible_Assets3

Goodwill and Intangible Assets, Net - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012
Goodwill And Intangible Assets [Line Items]
Goodwill	$13,846		$13,846
Accumulated impairment losses	0		0		0
Amortization expense	$709	$757	$1,434	$1,514
Weighted Average [Member] | Patents and Related Technologies [Member]
Goodwill And Intangible Assets [Line Items]
Weighted average useful life			12 years 4 months 24 days

Goodwill_and_Intangible_Assets4

Goodwill and Intangible Assets, Net - Schedule of Intangible Assets (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Intangible Assets [Line Items]
Gross Carrying Amount	$49,242	$34,988
Accumulated Amortization	-6,270	-5,482
Net	42,972	29,506
Patents and Related Technologies [Member]
Intangible Assets [Line Items]
Gross Carrying Amount	34,342	34,342
Accumulated Amortization	-6,270	-4,851
Net	28,072	29,491
In- Process Research and Development [Member]
Intangible Assets [Line Items]
Gross Carrying Amount	14,900
Accumulated Amortization
Net	14,900
Favorable Rent Asset [Member]
Intangible Assets [Line Items]
Gross Carrying Amount		646
Accumulated Amortization		-631
Net		$15

Income_Taxes_Additional_Inform

Income Taxes - Additional Information (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Income Tax Disclosure [Abstract]
Income tax benefit recognized	$0	$0	$0	$0
Federal income tax loss carryforwards	225,100		225,100
Federal and state research and development tax credits	$6,600		$6,600
Expiration date of Federal income tax loss carryforwards			2022

Redeemable_Convertible_Preferr2

Redeemable Convertible Preferred Stock and Shareholders' Deficit - Summary of Redeemable Convertible Preferred Stock (Detail) (USD $)	6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012
Temporary Equity [Line Items]
Accretion of dividends	$14,347	$10,822
Series A Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	1,358
Issuance of shares
Accretion of dividends	42
Stock issuance costs
Ending Balance	1,400
Beginning Balance, Shares	705,400
Issuance of shares, Shares
Ending Balance, Shares	705,400
Series B Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	669
Issuance of shares
Accretion of dividends	15
Stock issuance costs
Ending Balance	684
Beginning Balance, Shares	694,000
Issuance of shares, Shares
Ending Balance, Shares	694,000
Series B-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	1,360
Issuance of shares
Accretion of dividends	30
Stock issuance costs
Ending Balance	1,390
Beginning Balance, Shares	1,212,360
Issuance of shares, Shares
Ending Balance, Shares	1,212,360
Series C Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	7,134
Issuance of shares
Accretion of dividends	214
Stock issuance costs
Ending Balance	7,348
Beginning Balance, Shares	4,546,360
Issuance of shares, Shares
Ending Balance, Shares	4,546,360
Series C-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	34,201
Issuance of shares
Accretion of dividends	1,025
Stock issuance costs
Ending Balance	35,226
Beginning Balance, Shares	15,934,528
Issuance of shares, Shares
Ending Balance, Shares	15,934,528
Series C-2 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	44,512
Issuance of shares
Accretion of dividends	1,337
Stock issuance costs
Ending Balance	45,849
Beginning Balance, Shares	18,617,020
Issuance of shares, Shares
Ending Balance, Shares	18,617,020
Series C-3 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	29,770
Issuance of shares
Accretion of dividends	887
Stock issuance costs
Ending Balance	30,657
Beginning Balance, Shares	13,297,872
Issuance of shares, Shares
Ending Balance, Shares	13,297,872
Series D Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	76,252
Issuance of shares
Accretion of dividends	2,275
Stock issuance costs
Ending Balance	78,527
Beginning Balance, Shares	19,803,685
Issuance of shares, Shares
Ending Balance, Shares	19,803,685
Series E Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance	211,403
Issuance of shares
Accretion of dividends	6,383
Stock issuance costs
Ending Balance	217,786
Beginning Balance, Shares	38,095,239
Issuance of shares, Shares
Ending Balance, Shares	38,095,239
Series F Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Beginning Balance
Issuance of shares	150,000
Accretion of dividends	2,139
Stock issuance costs	-3,148
Ending Balance	$148,991
Beginning Balance, Shares
Issuance of shares, Shares	19,047,619
Ending Balance, Shares	19,047,619

Redeemable_Convertible_Preferr3

Redeemable Convertible Preferred Stock and Shareholders' Deficit - Summary of Aggregate Redemption of Shares (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012
Series F Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$7.99
Series E Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$5.79	$5.62
Series D Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$3.97	$3.86
Series C-3 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$2.31	$2.24
Series C-2 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$2.47	$2.40
Series C-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$2.21	$2.15
Series C Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$1.62	$1.58
Series B-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$1.16	$1.14
Series B Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$1.04	$1.02
Series A Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Aggregate redemption price per share	$2.05	$1.99

Redeemable_Convertible_Preferr4

Redeemable Convertible Preferred Stock and Shareholders' Deficit - Additional Information (Detail) (USD $)	6 Months Ended	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2013	Dec. 31, 2012
Temporary Equity [Line Items]
Redemption price of arrearage amount	$64,806	$50,459
Series A Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	598	556
Series B Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	224	209
Series B-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	410	380
Series C Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	2,376	2,162
Series C-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	10,247	9,222
Series C-2 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	10,951	9,614
Series C-3 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	5,706	4,819
Series D Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	11,686	9,411
Series E Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	20,469	14,086
Series F Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Dividend rate per annum	6.00%
Dividend declared	$0
Redemption price of arrearage amount	$2,139

Redeemable_Convertible_Preferr5

Redeemable Convertible Preferred Stock and Shareholders' Deficit - Summary of Aggregate and Per Share Amount (Detail) (USD $)	6 Months Ended	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2013	Dec. 31, 2012
Temporary Equity [Line Items]
Arrearage total	$64,806	$50,459
Series F Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	2,139
Arrearage per share	$0.11
Series E Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	20,469	14,086
Arrearage per share	$0.54	$0.37
Series D Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	11,686	9,411
Arrearage per share	$0.59	$0.48
Series C-3 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	5,706	4,819
Arrearage per share	$0.43	$0.36
Series C-2 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	10,951	9,614
Arrearage per share	$0.59	$0.52
Series C-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	10,247	9,222
Arrearage per share	$0.64	$0.58
Series C Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	2,376	2,162
Arrearage per share	$0.52	$0.48
Series B-1 Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	410	380
Arrearage per share	$0.34	$0.31
Series B Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	224	209
Arrearage per share	$0.32	$0.30
Series A Redeemable Convertible Preferred Stock [Member]
Temporary Equity [Line Items]
Arrearage total	$598	$556
Arrearage per share	$0.85	$0.78

Stock_Option_Plans_Additional_

Stock Option Plans - Additional Information (Detail) (USD $)

6 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

In Thousands, except Share data, unless otherwise specified

Jun. 30, 2013

Dec. 31, 2012

Jun. 30, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2010

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

Intrexon Stock Option Plan [Member]

AquaBounty Stock Option Plan [Member]

AquaBounty Stock Option Plan [Member]

AquaBounty Stock Option Plan [Member]

AquaBounty Stock Option Plan [Member]

AquaBounty Stock Option Plan [Member]

Research and Development Expense [Member]

Research and Development Expense [Member]

Research and Development Expense [Member]

Research and Development Expense [Member]

General and Administrative Expense [Member]

General and Administrative Expense [Member]

General and Administrative Expense [Member]

General and Administrative Expense [Member]

Minimum [Member]

Maximum [Member]

General and Administrative Expense [Member]

General and Administrative Expense [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Stock based compensation cost

$147

$154

$300

$16

$641

$213

$895

$504

$21

$1

Number of authorized awards

5,714,285

2,857,142

Unrecognized compensation costs related to nonvested awards

$4,364

$4,910

Recognized over weighted-average period

3 years

3 years

Option issued

1 year

3 years

Term of issuance of option

10 years

Options outstanding

2,856,905

2,313,526

6,552,000

Weighted average price of option

$6.79

$5.90

$0.25

Options exercisable

931,762

5,552,000

Stock_Option_Plans_Schedule_of

Stock Option Plans - Schedule of Stock Option Activity (Detail) (Intrexon Stock Option Plan [Member], USD $)	6 Months Ended	12 Months Ended
	Jun. 30, 2013	Dec. 31, 2012
Intrexon Stock Option Plan [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Balances at December 31, 2012	2,313,526
Granted, Number of shares	703,714
Exercised, Number of shares	-1,357
Forfeited, Number of shares	-129,893
Expired, Number of shares	-29,085
Balances at June 30, 2013	2,856,905	2,313,526
Exercisable at June 30, 2013	931,762
Vested and Expected to Vest at June 30, 2013	2,560,259
Balances at December 31, 2012	$5.90
Granted, Weighted average exercise price	$9.67
Exercised, Weighted average exercise price	($3.43)
Forfeited, Weighted average exercise price	($6.84)
Expired, Weighted average exercise price	($4.65)
Balances at June 30, 2013	$6.79	$5.90
Exercisable at June 30, 2013	$4.46
Vested and Expected to Vest at June 30, 2013	$5.94
Balances at period end	8 years 26 days	7 years 10 months 13 days
Exercisable at period end	6 years 4 months 6 days
Vested and Expected to Vest at period end	7 years 5 months 9 days

Commitments_and_Contingencies_1

Commitments and Contingencies - Future Minimum Lease Payments Under Noncancelable Operating Leases (Detail) (USD $)	Jun. 30, 2013
In Thousands, unless otherwise specified
Commitments And Contingencies Disclosure [Abstract]
2013	$1,416
2014	2,918
2015	2,492
2016	1,863
2017	927
2018	72
Future minimum operating lease payments, Total	$9,688

Commitments_and_Contingencies_2

Commitments and Contingencies - Additional Information (Detail)	3 Months Ended		6 Months Ended		12 Months Ended	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012	Dec. 31, 2012	Jun. 30, 2013	Jun. 30, 2013	Jun. 30, 2013	Jun. 30, 2013	Jun. 30, 2013	Jun. 30, 2013
	USD ($)	USD ($)	USD ($)	USD ($)	Lease	AquaBounty [Member]	AquaBounty [Member]	AquaBounty [Member]	AquaBounty [Member]	AquaBounty [Member]	AquaBounty [Member]
	Lease			Lease		USD ($)	CAD	Term Loan [Member]	Term Loan [Member]	Term Loan [Member]	Term Loan [Member]
								ACOA [Member]	ACOA [Member]	Enterprise PEI [Member]	Enterprise PEI [Member]
								USD ($)	CAD	USD ($)	CAD
Commitment And Contingencies [Line Items]
Rent expenses	$1,742	$1,229	$3,012	$2,484
Subleasing spaces					2
Number of entities under sublease agreement	1			1	2
Rental income under sublease agreement	92	10	183	64
Future rental income for the sublease agreement in 2013	182		182
Future rental income for the sublease agreement in 2014	365		365
Future rental income for the sublease agreement in 2015	152		152
Amount available under the grant for Research and Development						2,728	2,872
Claims period						5 years	5 years
Royalty on products						10.00%	10.00%
Total amount claimed						2,074
Original principal of term loans								238	250	285	300
Maturity period of term loan								2013-12	2013-12	2013-12	2013-12
Outstanding balance								13		20
AquaBounty funding						2,817	2,965
Percentage of royalty on revenues						5.20%	5.20%
Estimated balance to be paid						$190

Related_Party_Transactions_Add

Related Party Transactions - Additional Information (Detail) (USD $)

3 Months Ended

6 Months Ended

1 Months Ended

6 Months Ended

1 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

6 Months Ended

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jan. 20, 2012

Feb. 07, 2011

Jan. 06, 2011

Jun. 30, 2013

Jun. 30, 2013

Jun. 30, 2013

Jun. 06, 2012

Jun. 06, 2011

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2013

Jun. 30, 2012

Dec. 31, 2012

Jun. 30, 2013

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Ziopharm [Member]

Synthetic Biologics [Member]

Oragenics [Member]

Affiliates Of Third Security [Member]

Affiliates Of Third Security [Member]

Chief Executive Officer [Member]

Chief Executive Officer [Member]

Chief Executive Officer [Member]

Chief Executive Officer [Member]

Affiliates Of Preferred Shareholders [Member]

Affiliates Of Preferred Shareholders [Member]

Affiliates Of Preferred Shareholders [Member]

Affiliates Of Preferred Shareholders [Member]

Affiliates Of Preferred Shareholders [Member]

Soligenix Inc [Member]

Office

Office

Office

Related Party Transaction [Line Items]

Payment of license fee

$9,000,000

Annual exclusivity fee

1,000,000

Milestone payments

54,000,000

Termination period

90 days

Compensation expense

387,000

387,000

775,000

775,000

Company leased facility

2

2

2

Other long term assets

66,000

66,000

66,000

Rent and other facility expenses

1,742,000

1,229,000

3,012,000

2,484,000

221,000

223,000

447,000

442,000

Shares of common stock purchased from collaborative partners

1,923,075

1,910,000

2,426,235

0

0

0

Price per share of common shares

$5.20

$5.75

$4.80

Purchase of additional common stock

50,000,000

Purchase commitment

$29,000,000

Maximum percentage of shares of future securities offerings of collaborative partners to which the entity is entitled to purchase

19.99%

30.00%

Additional shares of collaborative partner to which the entity is entitled to purchase on the open market

10.00%

Net_Loss_Per_Share_Historical_

Net Loss Per Share - Historical Computation of Basic and Diluted Net Loss Per Share (Detail) (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2013	Jun. 30, 2012	Jun. 30, 2013	Jun. 30, 2012
Numerator:
Net loss attributable to Intrexon	($6,012)	($16,535)	($42,323)	($30,447)
Add: Accretion of dividends on redeemable convertible preferred stock, not declared	-7,942	-5,362	-14,347	-10,822
Net loss attributable to common shareholders	($13,954)	($21,897)	($56,670)	($41,269)
Denominator:
Weighted average shares outstanding, basic and diluted	5,667,557	5,484,572	5,664,665	5,470,415
Net loss attributable to common shareholders per share, basic and diluted	($2.46)	($3.99)	($10)	($7.54)

Net_Loss_Per_Share_Potentially

Net Loss Per Share - Potentially Dilutive Securities Excluded from Calculation of Net Loss per Share (Detail)	6 Months Ended
	Jun. 30, 2013	Jun. 30, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	78,770,335	65,184,376
Common Shares Issuable Upon Conversion of all Series Preferred [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	75,402,332	61,796,890
Options [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	2,856,905	2,876,388
Warrant [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive securities excluded from computation of earnings per share, amount	511,098	511,098

Subsequent_Events_Additional_I

Subsequent Events - Additional Information (Detail) (USD $)	Jun. 30, 2013	Dec. 31, 2012	Aug. 13, 2013	Jul. 26, 2013	Jul. 17, 2013	Aug. 13, 2013
			Subsequent Event [Member]	Subsequent Event [Member]	Subsequent Event [Member]	Subsequent Event [Member]
						IPO [Member]
Subsequent Event [Line Items]
Shareholders approved a reverse stock split description				1-for-1.75
Lease term terminates					31-12-2017
Total annual rent payments, 2013	$1,416,000				$94,000
Total annual rent payments, 2014	2,918,000				370,000
Total annual rent payments, 2015	2,492,000				464,000
Total annual rent payments, 2016	1,863,000				478,000
Total annual rent payments, 2017	927,000				492,000
Shares of common stock						11,499,998
Shares of common stock issued to underwriters						1,499,999
IPO price per share						$16
Aggregate net proceeds			$168,300,000
Shares of common stock			79,705,130
Number of authorized shares of common stock	185,000,000	160,000,000	200,000,000
Number of authorized shares of preferred stock			25,000,000
Shares of common stock reserved for issuance			7,000,000