Codexis (CDXS) 10-Q 8 Aug 14 2014 Q2 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	6 Months Ended
	Jun. 30, 2014	Jul. 31, 2014
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'CODEXIS INC	'
Entity Central Index Key	'0001200375	'
Document Type	'10-Q	'
Document Period End Date	30-Jun-14	'
Amendment Flag	'false	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q2	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	39,132,713

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$20,090	$22,130
Marketable securities, current	0	3,005
Accounts receivable, net of allowances of $548 at June 30, 2014 and $460 at December 31, 2013	2,944	5,413
Inventories	1,963	1,487
Prepaid expenses and other current assets	1,618	1,567
Assets held for sale	292	2,179
Total current assets	26,907	35,781
Restricted cash	711	711
Marketable securities, non-current	1,453	795
Property and equipment, net	4,853	8,446
Intangible assets, net	7,873	9,560
Goodwill	3,241	3,241
Other non-current assets	205	306
Total assets	45,243	58,840
Current liabilities:	'	'
Accounts payable	3,329	3,961
Accrued compensation	1,978	3,625
Other accrued liabilities	2,833	1,612
Deferred revenues	2,654	2,001
Total current liabilities	10,794	11,199
Deferred revenues, net of current portion	907	1,114
Other long-term liabilities	4,214	5,044
Total liabilities	15,915	17,357
Commitments and contingencies (note 10)	'	'
Stockholders’ equity:	'	'
Preferred stock, $0.0001 par value; 5,000 shares authorized, none issued and outstanding	0	0
Common stock, $0.0001 par value; 100,000 shares authorized at June 30, 2014 and December 31, 2013; 38,860 and 38,351 shares issued and outstanding at June 30, 2014 and December 31, 2013, respectively	4	4
Additional paid-in capital	300,663	298,370
Accumulated other comprehensive income (loss)	374	-32
Accumulated deficit	-271,713	-256,859
Total stockholders’ equity	29,328	41,483
Total liabilities and stockholders’ equity	$45,243	$58,840

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parenthetical) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, except Share data, unless otherwise specified
Statement of Financial Position [Abstract]	'	'
Accounts receivable, allowances	$548	$460
Preferred Stock, Par or Stated Value Per Share	$0.00	$0.00
Preferred Stock, Shares Authorized	5,000,000	5,000,000
Preferred Stock, Shares Issued	0	0
Preferred Stock, Shares Outstanding	0	0
Preferred Stock, Shares Outstanding	$0.00	$0.00
Common Stock, Shares Authorized	100,000,000	100,000,000
Common Stock, Shares, Issued	38,860,000	38,351,000
Common Stock, Shares, Outstanding	38,860,000	38,351,000

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Revenues:	'	'	'	'
Biocatalyst products	$2,776	$4,948	$5,761	$14,085
Biocatalyst research and development	1,666	1,609	3,812	2,909
Revenue sharing arrangement	2,128	417	4,071	1,461
Total revenues	6,570	6,974	13,644	18,455
Costs and operating expenses:	'	'	'	'
Cost of biocatalyst product revenues	2,123	3,631	4,647	9,296
Research and development	7,733	8,624	12,567	15,946
Selling, general and administrative	5,625	7,169	11,737	15,293
Total costs and operating expenses	15,481	19,424	28,951	40,535
Loss from operations	-8,911	-12,450	-15,307	-22,080
Interest income	3	16	12	43
Other expenses	-8	-183	-126	-268
Loss before income taxes	-8,916	-12,617	-15,421	-22,305
Benefit from income taxes	-437	-12	-567	-77
Net loss	($8,479)	($12,605)	($14,854)	($22,228)
Net loss per share, basic and diluted (dollars per share)	($0.22)	($0.33)	($0.39)	($0.59)
Weighted average common shares used in computing net loss per share, basic and diluted (shares)	37,980	38,060	37,862	37,951

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Statement of Comprehensive Income [Abstract]	'	'	'	'
Net loss	($8,479)	($12,605)	($14,854)	($22,228)
Other comprehensive income:	'	'	'	'
Unrealized gain on marketable securities, net of tax of $2 and $249 for the three months and six months ended June 30, 2014, respectively, and $32 and $155 for the three months and six months ended June 30, 2013, respectively.	4	50	406	242
Other comprehensive income	4	50	406	242
Total comprehensive loss	($8,475)	($12,555)	($14,448)	($21,986)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Comprehensive Loss (Parenthetical) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Statement of Comprehensive Income [Abstract]	'	'	'	'
Unrealized gain on marketable securities, tax	$2	$32	$249	$155

Condensed_Consolidated_Stateme3

Condensed Consolidated Statements of Cash Flows (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Operating activities:	'	'
Net loss	($14,854)	($22,228)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'
Amortization of intangible assets	1,687	1,687
Depreciation and amortization of property and equipment	2,078	3,541
Impairment of property and equipment	1,841	0
Change in fair value of assets held for sale	755	0
Loss on disposal of property and equipment	-78	141
Gain on sale of Hungarian subsidiary	-760	0
Stock-based compensation	2,575	2,735
Amortization of premium (accretion of discount) on marketable securities	2	-48
Changes in operating assets and liabilities:	'	'
Accounts receivable	2,513	5,954
Inventories	-476	-30
Prepaid expenses and other current assets	-703	3,116
Other assets	-238	-38
Accounts payable	-631	-2,108
Accrued compensation	-1,498	-160
Other accrued liabilities	1,002	-3,209
Deferred revenues	446	87
Net cash used in operating activities	-6,339	-10,560
Investing activities:	'	'
Purchase of property and equipment	-111	-641
Proceeds from maturities of marketable securities	3,000	10,909
Proceeds from sale of Hungarian subsidiary, net of selling costs	1,500	0
Proceeds from the sale of assets held for sale	4	0
Proceeds from sale of property and equipment	187	0
Decrease in restricted cash	0	400
Net cash provided by investing activities	4,580	10,668
Financing activities:	'	'
Proceeds from exercises of stock options	62	281
Taxes paid related to net share settlement of equity awards	-343	0
Net cash provided by (used in) financing activities	-281	281
Net increase (decrease) in cash and cash equivalents	-2,040	389
Cash and cash equivalents at the beginning of the period	22,130	32,003
Cash and cash equivalents at the end of the period	$20,090	$32,392

Description_of_Business

Description of Business	6 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Description of Business	'
	Description of Business
	Codexis, Inc. (the “Company”) was incorporated in the State of Delaware in January 2002. The Company develops biocatalysts for the pharmaceutical and fine chemicals markets. Its proven technologies enable scale-up and implementation of biocatalytic solutions to meet customer needs for rapid, cost-effective and sustainable process development, from research to manufacturing.
	Biocatalysts are enzymes or microbes that initiate and/or accelerate chemical reactions. Manufacturers have historically used naturally occurring biocatalysts to produce many goods used in everyday life. However, inherent limitations in naturally occurring biocatalysts have restricted their commercial use. The Company’s proprietary technology platform is able to overcome many of these limitations, allowing us to evolve and optimize biocatalysts to perform specific and desired chemical reactions at commercial scale.
	The Company has commercialized its technology and products in the pharmaceuticals market, which is the Company’s primary business focus. The Company’s pharmaceutical customers, which include several of the largest global pharmaceutical companies, use the Company’s technology, products and services in their manufacturing process development, including in the production of some of the world's bestselling and fastest growing drugs.
	The Company has recently begun to use its technology to develop biocatalysts for use in the fine chemicals market. The fine chemicals market is similar to the Company’s pharmaceutical business and consists of several large market segments, including food, animal feed, polymers, flavors and fragrances and agricultural chemicals.
	The Company creates its biocatalyst products by applying its CodeEvolver® directed evolution technology platform, which introduces genetic mutations into microorganisms, giving rise to changes in the enzymes that they produce. Once the Company identifies potentially beneficial mutations, it tests combinations of these mutations until it has created variant enzymes that exhibit marketable performance characteristics superior to competitive products. This process allows the Company to make continuous, efficient improvements to the performance of its enzymes.
	In these Notes to Consolidated Financial Statements, the “Company” refers to Codexis, Inc. and its subsidiaries on a consolidated basis.

Basis_of_Presentation_and_Summ

Basis of Presentation and Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Basis of Presentation and Summary of Significant Accounting Policies	'
	Basis of Presentation and Summary of Significant Accounting Policies
	Basis of Presentation and Principles of Consolidation
	The accompanying condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”) and the applicable rules and regulations of the Securities and Exchange Commission (“SEC”) for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2013. The condensed consolidated balance sheet at December 31, 2013 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures including notes required by GAAP for complete financial statements.
	The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly its financial position as of June 30, 2014 and results of its operations, comprehensive loss and cash flows for the three and six months ended June 30, 2014 and 2013. The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Certain prior period amounts have been reclassified to conform to current period presentation.
	The unaudited interim condensed consolidated financial statements include the amounts of Codexis, Inc. and its wholly-owned subsidiaries in the United States, Brazil, Hungary (through the sale date of March 13, 2014), India, Mauritius, The Netherlands and Singapore. All significant intercompany balances and transactions have been eliminated in consolidation.
	Use of Estimates
	The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. The Company's management regularly assesses these estimates which primarily affect revenue recognition, the valuation of marketable securities and accounts receivable, held for sale assets, intangible assets, goodwill arising out of business acquisitions, inventories, accrued liabilities, stock awards and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements.
	Segment Reporting
	Operating segments are defined as components of an enterprise about which separate financial information is available that is evaluated regularly by the chief operating decision maker, or decision making group, in deciding how to allocate resources and in assessing performance. The Company's chief operating decision maker is its Chief Executive Officer. The Chief Executive Officer and the Company's board of directors review financial information presented on a consolidated basis, accompanied by information about revenues by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity and there are no segment managers who are held accountable for operations, operating results beyond revenue goals or plans for levels or components below the consolidated unit level. Accordingly, the Company has a single reporting segment.
	Foreign Currency Translation
	The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.
	Where the United States dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in interest expense and other, net in the accompanying condensed consolidated statements of operations. Gains and losses realized from transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity’s functional currency, are included in interest expense and other, net in the accompanying consolidated statements of operations.
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to concentration of credit risk consist principally of: cash equivalents, marketable securities, accounts receivable, and restricted cash.
	The Company invests cash that is not required for immediate operating needs principally in money market funds and corporate securities through banks and other financial institutions in the United States, as well as in other foreign countries.
	Accounts receivable are concentrated in the pharmaceutical industry. Accordingly, the Company may be exposed to credit risk generally associated with pharmaceutical companies or specific to the collaboration arrangements with Merck and Arch. The Company does not require collateral from its customers, but does perform periodic credit evaluations of its customers’ financial condition and requires immediate payment in certain circumstances.
	Credit risk with respect to accounts receivable exists to the extent of amounts presented in the condensed consolidated financial statements. The Company estimates an allowance for doubtful accounts through specific identification of potentially uncollectible accounts receivable based on an analysis of its accounts receivable aging. Uncollectible accounts receivable are written off against the allowance for doubtful accounts when all efforts to collect them have been exhausted. Recoveries are recognized when they are received. Actual collection losses may differ from its estimates and could be material to its consolidated financial position, results of operations, and cash flows.
	Customers whose accounts receivable balance accounted for 10% or more of net accounts receivable were Merck of 27% and Novartis of 25% at June 30, 2013 and Novartis of 51% at December 31, 2013.
	Customer Concentration
	Customers whose revenue accounted for 10% or more of total revenues were as follows:
		Three Months Ended June 30,				Six months ended June 30,
		2014		2013		2014		2013
	Exela (related party)	32	%	*		30	%	*
	Merck	28	%	65	%	25	%	50	%
	Novartis	12	%	—	%	20	%	*
	Arch	—	%	—	%	—	%	12	%
	* less than 10%
	Fair Value of Financial Instruments
	The carrying amounts of certain of the Company's financial instruments, including cash and cash equivalents, restricted cash, accounts receivable and accounts payable, approximate fair value due to their short maturities.
	Fair value is considered to be the price at which an asset could be exchanged or a liability transferred (an exit price) in an orderly transaction between knowledgeable, willing parties in the principal or most advantageous market for the asset or liability. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments and the instruments’ complexity.
	Cash and Cash Equivalents
	The Company considers all highly liquid investments with maturity dates of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents consist of cash on deposit with banks and money market funds. The majority of cash and cash equivalents are maintained with major financial institutions in North America. Deposits with these financial institutions may exceed the amount of insurance provided on such deposits. Cash and cash equivalents was $20.1 million at June 30, 2014, and was comprised of cash of $4.5 million and money market funds of $15.6 million.
	Marketable Securities
	Marketable securities included in current assets are comprised of corporate bonds. The Company's investment in common shares of CO2 Solutions Inc. (“CO2 Solutions”) is included in non-current marketable securities.
	The Company performs separate evaluations of impaired debt and equity securities to determine if the unrealized losses as of the balance sheet date are other-than-temporary impairment.
	For the Company's investments in equity securities, its evaluation considers a number of factors including, but not limited to, the length of time and extent to which the fair value has been less than cost, the financial condition and near term prospects of the issuer, and its management’s ability and intent to hold the securities until fair value recovers. The assessment of the ability and intent to hold these securities to recovery focuses on its current and forecasted liquidity requirements and capital requirements. As of June 30, 2014, there were no unrealized losses related to the Company's equity securities.
	For the Company's investments in debt securities, management determines whether it intends to sell or if it is more-likely-than-not that the Company will be required to sell impaired securities. This determination considers current and forecasted liquidity requirements and capital requirements. For all impaired debt securities for which there was no intent or expected requirement to sell, the evaluation considers all available evidence to assess whether it is likely the amortized cost value will be recovered. The Company conducts a regular assessment of its debt securities with unrealized losses to determine whether the securities have other-than-temporary impairment considering, among other factors, the nature of the securities, credit rating or financial condition of the issuer, the extent and duration of the unrealized loss, expected cash flows of underlying collateral and market conditions. As of June 30, 2014, there were no unrealized losses related to the Company's debt securities.
	The Company's investments in debt and equity securities are classified as available-for-sale and are carried at fair value. Unrealized gains and losses are reported on the condensed consolidated statement of comprehensive loss unless considered other-than-temporary. Amortization of purchase premiums and accretion of purchase discounts, realized gains and losses of debt securities and declines in value deemed to be other than temporary, if any, are included in interest income or other expenses. The cost of securities sold is based on the specific-identification method. There were no significant realized gains or losses from sales of marketable securities for the three and six months ended June 30, 2014 and 2013.
	Impairment of Long-Lived Assets and Intangible Assets
	Long-lived and intangible assets with finite lives are reviewed for impairment whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of these assets is measured by comparison of their carrying amounts to future undiscounted cash flows the assets are expected to generate.
	The Company's intangible assets with finite lives consist of customer relationships, developed core technology, trade names, and the intellectual property (“IP”) rights associated with the acquisition of Maxygen Inc.'s ("Maxygen") directed evolution technology in 2010. Intangible assets were recorded at their fair values at the date the Company acquired the assets and, for those assets having finite useful lives, are amortized using the straight-line method over their estimated useful lives. The Company's long-lived assets include property, plant and equipment, and other non-current assets.
	The Company determined that it has a single entity wide asset group (“Asset Group”). The directed evolution technology patent portfolio acquired from Maxygen (“Core IP”) is the most significant component of the Asset Group since it is the base technology for all aspects of the Company's research and development activities, and represents the basis for all of the Company's identifiable cash flow generating capacity. Consequently, the Company does not believe that identification of independent cash flows associated with its long-lived assets is currently possible at any lower level than the Asset Group.
	The Core IP is the only finite-lived intangible asset on the Company's condensed consolidated balance sheet as of June 30, 2014 and is considered the primary asset within the Asset Group. There has been no significant change in the utilization or estimated life of the Core IP since the Company acquired the technology patent portfolio from Maxygen.
	The carrying value of the Company's long-lived assets in the Asset Group may not be recoverable based upon the existence of one or more indicators of impairment which could include: a significant decrease in the market price of the Company's common stock; current period cash flow losses or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the assets; slower growth rates in the Company's industry; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the assets; loss of significant customers or partners; or the current expectation that the assets will more likely than not be sold or disposed of significantly before the end of their estimated useful life.
	The Company evaluates recoverability of its long-lived assets and intangible assets based on the sum of the undiscounted cash flows expected to result from the use, and the eventual disposal of, the Asset Group. The Company makes estimates and judgments about the future undiscounted cash flows over the remaining useful life of the Asset Group. The Company's anticipated future cash flows include its estimates of existing or in process product revenues, production and operating costs, future capital expenditures, working capital needs, and assumptions regarding the ultimate sale of the Asset Group at the end of the life of the primary asset. The useful life of the Asset Group was based on the estimated useful life of the Core IP, the primary asset at the time of acquisition. There has been no change in the estimated useful life of the Asset Group. Although the Company's cash flow forecasts are based on assumptions that are consistent with its plans, there is significant judgment involved in determining the cash flows attributable to the Asset Group over its estimated remaining useful life.
	In the fourth quarter of 2013, the Company determined that its continued annual operating losses and a decline in market price of the Company’s common stock, reduced anticipated future cash flows related to potential CodeXyme® cellulase enzyme and CodeXol® detergent alcohols transactions and reduced future revenue growth to reflect the Company’s most recent outlook were indicators of impairment. As a result, the Company undertook an impairment analysis in the fourth quarter of 2013.
	The results of the Company's fourth quarter 2013 impairment analysis indicated that the undiscounted cash flows for the Asset Group were greater than the carrying value of the Asset Group by approximately 37%. Based on the results obtained, the Company determined there was no impairment of the Company's intangible assets as of December 31, 2013.
	During the six months ended June 30, 2014, the Company made no changes to the underlying forecasts nor did the Company identify any additional indicators of potential impairment of intangible assets or other new information that would have a material impact on the forecast or the impairment analysis prepared as of December 31, 2013.
	Valuation of Goodwill
	The Company reviews goodwill impairment annually in the fourth quarter of each of its fiscal years and whenever events or changes in circumstances indicate the carrying value of goodwill may not be recoverable.
	The Company determined that it has only one operating segment and reporting unit under the criteria in ASC 280, Segment Reporting. Accordingly, the Company's review of goodwill impairment indicators is performed at the Company level.
	The goodwill impairment test consists of a two-step process. The first step of the goodwill impairment test, used to identify potential impairment, compares the fair value of the reporting unit to its carrying value. If the fair value of the reporting unit exceeds its carrying amount, goodwill of the reporting unit is considered not impaired, and the second step of the impairment test is not required.
	The Company uses its market capitalization as an indicator of fair value. The Company believes that since its reporting unit is publicly traded, the ability of a controlling stockholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of the Company's reporting unit as a whole to exceed its market capitalization. However, the Company believes that the fair value measurement need not be based solely on the quoted market price of an individual share of the Company's common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.
	If the Company were to use an income approach it would establish a fair value by estimating the present value of its projected future cash flows expected to be generated from its business. The discount rate applied to the projected future cash flows to arrive at the present value would be intended to reflect all risks of ownership and the associated risks of realizing the stream of projected future cash flows. The Company's discounted cash flow methodology would consider projections of financial performance for a period of several years combined with an estimated residual value. The most significant assumptions it would use in a discounted cash flow methodology are the discount rate, the residual value and expected future revenues, gross margins and operating costs, along with considering any implied control premium.
	Should the Company's market capitalization be less than the total stockholder's equity as of the Company's annual test date or as of any interim impairment testing date, the Company would also consider market comparables, recent trends in the Company's stock price over a reasonable period and, if appropriate, use an income approach to determine whether the fair value of its reporting unit is greater than the carrying amount.
	The second step, if required, compares the implied fair value of the reporting unit goodwill with the carrying amount of that goodwill. If the carrying amount of the reporting unit's goodwill exceeds its implied fair value, an impairment charge is recognized in an amount equal to that excess. Implied fair value is the excess of the fair value of the reporting unit over the fair value of all identified assets and liabilities. The Company bases its fair value estimates on assumptions it believes to be reasonable. Actual future results may differ from those estimates.
	Goodwill was tested for impairment in the fourth quarter of 2013. The Company concluded that the fair value of the reporting unit exceeded the carrying value and no impairment existed. No impairment charges were recorded for the year ended December 31, 2013. For the six months ended June 30, 2014, the Company did not identify any indicators of impairment that would indicate that the carrying value of goodwill may not be recoverable.
	Restricted Cash
	Restricted cash consisted of amounts invested in money market accounts primarily for purposes of securing a standby letter of credit as collateral for the Company's Redwood City, California facility lease agreement.
	Revenue Recognition
	Revenues are recognized when the four basic revenue recognition criteria are met: (1) persuasive evidence of an arrangement exists; (2) products have been delivered, transfer of technology has been completed or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured.
	The Company's primary sources of revenues consist of biocatalyst product revenues, biocatalyst research and development agreements and revenue sharing arrangements. Biocatalyst research and development agreements typically provide the Company with multiple revenue streams, including up-front fees for licensing, exclusivity and technology access, fees for full time employee ("FTE") services and the potential to earn milestone payments upon achievement of contractual criteria and royalty fees based on future product sales or cost savings achieved by the Company's customers.
	For each source of biocatalyst research and development revenues, biocatalyst product revenues and revenue sharing revenues, the Company applies the following revenue recognition criteria:
Biocatalyst product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria, if any, have been met, provided all other revenue recognition criteria have also been met. Product revenues consist of sales of biocatalyst intermediates, active pharmaceutical ingredients and Codex Biocatalyst Panels and Kits. Cost of product revenues includes both internal and third party fixed and variable costs including amortization of purchased technology, materials and supplies, labor, facilities and other overhead costs associated with the Company's biocatalyst product revenues.
Revenue sharing arrangement revenues are recognized based upon sales of licensed products by the Company's revenue share partner Exela (see Note 9 "Related Party Transactions"). Revenue share amounts received are net of product and selling costs. The Company bases its estimates of earned revenue on notification from its revenue share partner of the Company’s share of net profit based on the contractual percentage from the sale of licensed product. The Company bases its estimates on notification of the sale of revenue sharing products and related costs by its revenue share partner.
Up-front fees received in connection with biocatalyst research and development agreements, including license fees, technology access fees, and exclusivity fees, are deferred upon receipt, are not considered a separate unit of accounting and are recognized as revenues over the relevant performance periods related to the combined units of accounting appropriate for each customer arrangement.
Revenues related to FTE services recognized as research services are performed over the related performance periods for each contract. The Company performs biocatalyst research and development activities as specified in each respective customer agreement. The payments received are not refundable and are based on a contractual reimbursement rate per FTE working on the project. When up-front payments are combined with FTE services in a single unit of accounting, the Company recognizes the up-front payments using the proportionate performance method of revenue recognition based upon the actual amount of research and development labor hours incurred relative to the amount of the total expected labor hours to be incurred by the Company, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, the Company is required to make estimates of the total hours required to perform the Company's obligations. Research and development expenses related to FTE services under the collaborative research and development agreements approximate the research funding over the term of the respective agreements.
A payment that is contingent upon the achievement of a substantive milestone is recognized in its entirety in the period in which the milestone is achieved. A milestone is an event (i) that can only be achieved based in whole or in part on either the Company's performance or on the occurrence of a specific outcome resulting from its performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved, and (iii) results in additional payments being due to the Company. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either the Company's performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from its performance, (ii) relates solely to past performance, and (iii) is reasonable relative to all deliverable and payment terms in the arrangement.
Other payments received for which such payments are contingent solely upon the passage of time or the result of a collaborative partner’s performance are recognized as revenue when earned in accordance with the contract terms and when such payments can be reasonably estimated and collectability is reasonably assured.
The Company recognizes revenues from royalties based on licensees’ sales of products using the Company's technologies. Royalties are recognized as earned in accordance with the contract terms when royalties from licensees can be reasonably estimated and collectability is reasonably assured. The Company bases its estimates on notification the sale of licensed products from licensees.
Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in the Company's cost of biocatalyst products revenues. Such charges were not significant in any of the periods presented.
Income Taxes
The Company uses the liability method of accounting for income taxes, whereby deferred tax assets or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized.
The Company makes certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenues and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to the Company's tax provision in a subsequent period.
In assessing the realizability of deferred tax assets, the Company considers whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. The Company has recorded a deferred tax asset in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur.
The Company makes estimates and judgments about its future taxable income that are based on assumptions that are consistent with its plans and estimates. Should the actual amounts differ from its estimates, the amount of its valuation allowance could be materially impacted. Any adjustment to the deferred tax asset valuation allowance would be recorded in the income statement for the periods in which the adjustment is determined to be required. With the sale of the Hungarian subsidiary for the quarter ended March 31, 2014, the related net operating losses and other tax attributes are no longer available to the Company. The related deferred tax assets had a full valuation allowance and, as a result, their removal did not have a material impact to the financial statements.
The Company accounts for uncertainty in income taxes as required by the provisions of ASC Topic 740, Income Taxes, which clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the position will be sustained on audit, including resolution of related appeals or litigation processes, if any. The second step is to estimate and measure the tax benefit as the largest amount that is more than 50% likely of being realized upon ultimate settlement. It is inherently difficult and subjective to estimate such amounts, as this requires us to determine the probability of various possible outcomes. The Company considers many factors when evaluating and estimating the Company's tax positions and tax benefits, which may require periodic adjustments and may not accurately anticipate actual outcomes.
The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company should experience an ownership change, as defined, utilization of the Company's federal and state net operating loss carryforwards could be limited.
Benefit from Income taxes totaled $437,000 for the three months and $567,000 for the six months ended June 30, 2014, and $12,000 for the three months and $77,000 for the six months ended June 30, 2013. The total tax benefit for the three-month and six-month period ended June 30, 2014 primarily consisted of income tax benefit attributable to foreign operations (release of previous tax provision related to a liquidated entity) offset by the tax effect on the unrecognized gain from our investment in CO2 Solutions, as well as the recognition of previously unrecognized tax benefits. The company maintains a full valuation allowance against net deferred tax assets as the company believes that it is more likely than not that the majority of deferred tax assets will not be realized.
Stock-Based Compensation
The Company uses the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under its equity incentive plans. The Black-Scholes-Merton option valuation model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. The Company uses the "simplified" method as described in Staff Accounting Bulletin No. 107, "Share-Based Payment," for the expected option term because the usage of its historical option exercise data is limited due to the Company's initial public offering in 2010. The Company uses its historical volatility to estimate expected stock price volatility. The risk-free rate assumption was based on United States Treasury instruments whose terms were consistent with the terms of the Company's stock options. The expected dividend assumption was based on the Company's history and expectation of dividend payouts.
Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.
Stock-based compensation expense was calculated based on awards ultimately expected to vest and was reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. The estimated annual forfeiture rates for stock options, RSUs and RSAs are based on the Company's historical forfeiture experience.
The estimated fair value of stock options, RSUs and RSAs is expensed on a straight-line basis over the expected term of the grant and the estimated fair value of performance-contingent RSUs is expensed using an accelerated method over the term of the award once management has determined that it is probable that performance milestones will be achieved. Compensation expense for RSUs that contain performance conditions is based on the grant date fair value of the award. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. Management assesses the probability of the performance milestones being met on a continuous basis.
The Company accounts for stock awards issued to non-employees based on their estimated fair value determined using the Black-Scholes-Merton option-pricing model. Compensation expense for the stock awards granted to non-employees is recognized based on the fair value of awards as they vest, during the period the related services are rendered.
The Company has not recognized, and does not expect to recognize in the near future, any income tax benefit related to employee stock-based compensation expense as a result of the full valuation allowance on our deferred tax assets including deferred tax assets related to its net operating loss carryforwards.
Net Loss per Share
Basic net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture. Diluted net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture, plus all additional common shares that would have been outstanding, assuming dilutive potential common shares had been issued for other dilutive securities.
For the three months and six months ended June 30, 2014 and for the three months and six months ended June 30, 2013, diluted and basic net loss per share were identical since potential common shares were excluded from the calculation, as their effect was anti-dilutive.
Anti-Dilutive Securities
The following common equivalent shares were not included in the computation of diluted net loss per share because their effect was anti-dilutive:
	Three Months Ended June 30,				Six Months Ended June 30,
	2014		2013		2014		2013
Options to purchase common stock	3,888		4,996		3,888		4,996
Restricted stock units/awards	2,504		1,827		2,504		1,827
Performance stock units	722		—		722		—
Warrants to purchase common stock	75		75		75		75
Total shares excluded as anti-dilutive	7,189		6,898		7,189		6,898
Recently Issued and Adopted Accounting Guidance
From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standards setting bodies that are adopted by us as of the specified effective date. Unless otherwise discussed, the Company's management believes that the impact of recently issued standards that are not yet effective will not have a material impact on its consolidated financial statements upon adoption.
In May 2014, the Financial Accounting Standards Board issued Accounting Standards Update (“ASU”) 2014-09, Revenue from Contracts with Customers. This standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance, including industry-specific guidance. The main principle of ASU 2014-09 is to recognize revenues when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received for those goods or services. ASU 2014-09 provides companies with two implementation methods: (i) apply the standard retrospectively to each prior reporting period presented (full retrospective application); or (ii) apply the standard retrospectively with the cumulative effect of initially applying the standard as an adjustment to the opening balance of retained earnings of the annual reporting period that includes the date of initial application (modified retrospective application). This guidance is effective for annual reporting periods beginning after December 15, 2016, including interim periods within that reporting period, and early application is not permitted. The Company is currently in the process of evaluating the impact of the pending adoption of ASU 2014-09 on its consolidated financial statements.

Collaborative_Arrangements

Collaborative Arrangements	6 Months Ended
	Jun. 30, 2014
Research and Development [Abstract]	'
Collaborative Arrangements	'
	Collaborative Arrangements
	Merck Research and Development Collaboration
	On February 1, 2012, the Company entered into a 5 year Sitagliptin Catalyst Supply Agreement ("Sitagliptin Catalyst Supply Agreement") whereby Merck Sharp and Dohme Corp. ("Merck") may obtain commercial scale substance for their use in the manufacture of one of its products, Januvia®. Merck may extend the term of the Sitagliptin Catalyst Supply Agreement for an additional five years at its sole discretion.
	The Sitagliptin Catalyst Supply Agreement calls for Merck to pay an annual license fee for the rights to the Sitagliptin technology each year for the term of the Sitagliptin Catalyst Supply Agreement. The license fee is being recognized as collaborative research and development revenue ratably over the five year term of the Sitagliptin Catalyst Supply Agreement. As of June 30, 2014, the Company has a deferred revenue balance of $2.5 million from Merck related to the license fee. The Company recognized license fees of $0.5 million for three months ended June 30, 2014 and 2013, and $1.0 million for the six months ended June 30, 2014, and $0.5 million for the three months ended June 30, 2013 and $0.8 million for the six months ended June 30, 2013, as Biocatalyst Research and Development revenue. In addition, pursuant to the Sitagliptin Catalyst Supply Agreement, Merck may purchase supply from the Company for a fee based on contractually stated prices.
	Arch Manufacturing Collaboration
	From 2006 through November 2012, Arch of Mumbai, India manufactured substantially all of the Company's commercialized intermediates and active pharmaceutical ingredients ("APIs") for sale to generic and innovator pharmaceutical manufacturers. Prior to November 2012, Arch produced atorva-family API's and intermediates for the Company and it sold these directly to end customers primarily in India. In November 2012, the Company entered into a new commercial arrangement with Arch (the "New Arch Enzyme Supply Agreement") whereby the Company agreed to supply Arch with enzymes for use in the manufacture of atorva family products and Arch agreed to market these products directly to end customers. The Company recognized product revenue for the sale of enzyme inventory to Arch pursuant to the New Arch Enzyme Supply Agreement of $0.2 million for the three months ended June 30, 2014 and $0.2 million for the six months ended June 30, 2014, and nil for the three months ended three months ended June 30, 2013 and $2.1 million for the six months ended June 30, 2013, as Biocatalyst Product revenue. During 2013, the Company recorded an allowance for bad debt of approximately $387,000 due to a write-off of an accounts receivable from Arch.

Cash_Equivalents_and_Marketabl

Cash Equivalents and Marketable Securities	6 Months Ended
	Jun. 30, 2014
Cash Equivalents and Marketable Securities [Abstract]	'
Cash Equivalents and Marketable Securities	'
	Cash Equivalents and Marketable Securities
	At June 30, 2014, cash equivalents and marketable securities consisted of the following (in thousands):
		30-Jun-14
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds (1)	$	15,598	$	—	$	—	$	15,598	n/a
	Common shares of CO2 Solutions	563		890		—		1,453		n/a
	Total	$	16,161	$	890	$	—	$	17,051
	(1) Money market funds are classified in cash and cash equivalents on the Company’s condensed consolidated balance sheets.
	At December 31, 2013, cash equivalents and marketable securities consisted of the following (in thousands):
		31-Dec-13
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds (1)	$	16,089	$	—	$	—	$	16,089	n/a
	Corporate bonds	1,002		3		—		1,005		140
	U.S. Treasury obligations	2,000		—		—		2,000		59
	Common shares of CO2 Solutions	563		232		—		795		n/a
	Total	$	19,654	$	235	$	—	$	19,889
	(1) Money market funds are classified in cash and cash equivalents on the Company’s condensed consolidated balance sheets.

Fair_Value_Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2014
Fair Value, Assets, Liabilities and Stockholders' Equity Measured on Recurring Basis [Abstract]	'
Fair Value Measurements	'
	Fair Value Measurements
	Assets and liabilities recorded at fair value in the condensed consolidated financial statements are categorized based upon the level of judgment associated with the inputs used to measure their fair value. Hierarchical levels which are directly related to the amount of subjectivity associated with the inputs to the valuation of these assets or liabilities are as follows:
	Level 1 - Inputs that are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date.
	Level 2 - Inputs (other than quoted prices included in Level 1) that are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument's anticipated life.
	Level 3 - Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities and which reflect management's best estimate of what market participants would use in pricing the asset or liability at the measurement date.
	For Level 2 financial instruments, the Company's investment adviser provides monthly account statements documenting the value of corporate bonds and U.S. Treasury obligations based on prices received from an independent third-party valuation service provider. This third party evaluates the types of securities in the Company's investment portfolio and calculates a fair value using a multi-dimensional pricing model that includes a variety of inputs, including quoted prices for similar assets and liabilities in active markets, quoted prices for identical or similar assets or liabilities in markets that are not active, interest rates and yield curves observable at commonly quoted intervals, volatilities, prepayment speeds, loss severities, credit risks and default rates that are observable at commonly quoted intervals. As the Company is ultimately responsible for the determination of the fair value of these instruments, it performs quarterly analyses using prices obtained from another independent provider of financial instrument valuations, to validate that the prices the Company has used are reasonable estimates of fair value.
	Fair Value of Financial Instruments
	The following table presents the financial instruments that were measured at fair value on a recurring basis at June 30, 2014 by level within the fair value hierarchy (in thousands):
		30-Jun-14
		Level 1		Level 2		Level 3		Total
	Money market funds	$	15,598	$	—	$	—	$	15,598
	Common shares of CO2 Solutions	—		1,453		—		1,453
	Total	$	15,598	$	1,453	$	—	$	17,051
	The following table presents the financial instruments that were measured at fair value on a recurring basis at December 31, 2013 by level within the fair value hierarchy (in thousands):
		31-Dec-13
		Level 1		Level 2		Level 3		Total
	Money market funds	$	16,089	$	—	$	—	$	16,089
	Corporate bonds	—		1,005		—		1,005
	U.S. Treasury obligations	—		2,000		—		2,000
	Common shares of CO2 Solutions	—		795		—		795
	Total	$	16,089	$	3,800	$	—	$	19,889
	Fair Value of Assets Held for Sale
	As of June 30, 2014, the Company had assets held for sale related to lab equipment located in the United States. The fair value of these assets was determined based on Level 3 inputs, primarily sales data for similar assets. For further discussion, see Note 7 "Assets Held for Sale".
	The fair value of assets held for sale at June 30, 2014, measured on a nonrecurring basis, is as follows (in thousands):
		30-Jun-14
		Level 1		Level 2		Level 3		Total
	Assets held for sale	$	—	$	—	$	292	$	292
	The fair value of assets held for sale at December 31, 2013 , measured on a nonrecurring basis, is as follows (in thousands):
		31-Dec-13
		Level 1		Level 2		Level 3		Total
	Assets held for sale	$	—	$	—	$	2,179	$	2,179

Balance_Sheets_Details

Balance Sheets Details	6 Months Ended
	Jun. 30, 2014
Balance Sheets Details [Abstract]	'
Balance Sheets Details	'
	Balance Sheets Details
	Inventories, net
	Inventory, net consisted of the following (in thousands):
		June 30,				December 31,
		2014				2013
	Raw materials	$	452			$	763
	Work in process	229				31
	Finished goods	1,282				693
	Inventory, net	$	1,963			$	1,487
	Property and Equipment, net
	Property and equipment, net consisted of the following (in thousands):
		June 30,					December 31,
		2014					2013
	Laboratory equipment	$	23,774				$	23,949
	Leasehold improvements	9,493					9,493
	Computer equipment	3,249					3,196
	Office furniture and equipment	1,227					1,228
		37,743					37,866
	Less: accumulated depreciation and amortization	(31,064		)			(29,461		)
		6,679					8,405
	Construction in progress	15					41
	Property and equipment	6,694					8,446
	Less: Impairment of laboratory equipment	(1,841		)	-1		—
	Property and equipment, net	$	4,853				$	8,446
	(1)    Plans to utilize certain CodeXol® assets changed in the second quarter of 2014 such that assets with a a carrying value of $1.8 million were no longer recoverable. Accordingly, the Company recorded an impairment charge of $1.8 million, reducing the carrying value to zero (their estimated fair value, net of costs). The impairment charge was recorded within Research and Development Expense for the three and six months ended June 30, 2014.
	Intangible Assets
	Intangible assets consisted of the following (in thousands):
		30-Jun-14										31-Dec-13
		Gross				Accumulated				Net		Gross		Accumulated			Net		Weighted-
		Carrying				Amortization				Carrying		Carrying		Amortization			Carrying		Average
		Amount								Amount		Amount					Amount		Amortization
																			Period
																			(years)
	Customer relationships	$	3,098			$	(3,098	)		$	—	$	3,098	$	(3,098	)	$	—	5
	Developed and core technology	1,534				(1,534		)		—		1,534		(1,534		)	—		5
	Maxygen intellectual property	20,244				(12,371		)		7,873		20,244		(10,684		)	9,560		6
	Total	$	24,876			$	(17,003	)		$	7,873	$	24,876	$	(15,316	)	$	9,560
	The estimated future amortization expense to be charged to research and development through the year ending December 31, 2016 is as follows (in thousands):
	Year ending December 31:	Total
	2014 (remaining 6 months)	$	1,687
	2015	3,374
	2016	2,812
		$	7,873
	Goodwill
	There were no changes in the carrying value of goodwill of $3,241,000 for the three and six months ended June 30, 2014 and 2013.

Assets_Held_for_Sale

Assets Held for Sale	6 Months Ended
	Jun. 30, 2014
Assets Held for Sale [Abstract]	'
Assets Held for Sale	'
	Assets Held for Sale
	In the fourth quarter of 2013, the Company announced that it would begin winding down its CodeXyme® cellulase enzyme program. As a result of the termination of this research program and corresponding reductions in headcount, the Company concluded that certain excess research and development equipment, including assets at the Company's Hungarian subsidiary, were no longer held for use, and these assets were determined to meet the criteria to be classified as held for sale at December 31, 2013. In conjunction with classifying certain assets as held for sale, in 2013, the Company performed a detailed review of its excess research and development equipment with the assistance of a third party and determined that the estimated net sales price, less selling costs, was below the carrying value. A charge of $1,571,000 was recorded in the fourth quarter of 2013 to research and development expenses to reduce the value of held for sale assets to their estimated fair market value net of selling expenses. The Company reclassified the adjusted carrying value to Assets Held for Sale as of December 31, 2013.
	In March 2014, the Company sold its Hungarian subsidiary including all of the equipment at this facility classified as assets held for sale. The sale of the assets was recorded at their adjusted carrying value of $779,000.
	During the second quarter of 2014, the Company made changes to its plan to sell the U.S. excess research and development equipment and certain equipment was retained by the Company and reclassified approximately $333,000 of equipment as Held for Use. Some of the unutilized equipment reclassified as Held for Use was exchanged for more suitable research equipment. In addition to the exchange of equipment, the Company recognized a loss of approximately $188,000. As a result of the above changes to its plan to use the excess research and development equipment, the Company determined that further impairment charges should be recorded in the second quarter of 2014. Total impairment charges related to excess research and development equipment totaled $568,000 for the three months ended June 30, 2014. The Company revised the estimated fair value for the sale of the remaining equipment as Held for Sale to be approximately $292,000.
	Total assets reclassified as Assets Held for Sale at June 30, 2014, were (in thousands):
	Assets Held for Sale	Adjusted Carrying Value
	Research & development equipment classified as held for sale at December 31, 2013	$	2,179
	Hungarian assets sold for the three months ended March 31, 2014	(779		)
	U.S. assets sold for the three months ended March 31, 2014	(6		)
	Research & development equipment classified as held for sale at March 31, 2014	$	1,394
	Research & development equipment reclassified as held for use	(333		)
	U.S. assets sold for the three months ended June 30, 2014	(13		)
	Loss on exchange of assets	(188		)
	Change in estimated fair value of research equipment during three months ended June 30, 2014	(568		)
	Research & development equipment classified as held for sale at June 30, 2014	$	292
	Assets held for sale located in the United States were sold for proceeds of $4,000 for the six months ended June 30, 2014, resulting in a loss on the sale of approximately $2,000.

Sale_of_Hungarian_Subsidiary

Sale of Hungarian Subsidiary	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Sale of Hungarian Subsidiary	'
	Sale of Hungarian Subsidiary
	On March 13, 2014, the Company entered into an agreement with Intrexon Corporation to sell 100% of its equity interests in its Hungarian subsidiary, Codexis Laboratories Hungary Kft. On March 15, 2014, the sale transaction closed and the Company received cash proceeds of $1,500,000 from the sale and recorded a net gain of $760,000 which was included in research and development expenses in connection with the sale. As part of the purchase, the buyer obtained all the Hungarian assets held for sale and assumed all employment and facility lease related contract obligations. There were no transaction related costs incurred other than legal fees, which were recorded in selling, general and administrative expenses.

Related_Party_Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2014
Related Party Transaction, Due from (to) Related Party [Abstract]	'
Related Party Transactions	'
	Related Party Transactions
	Exela PharmaSci, Inc.
	The Company signed a commercialization agreement with Exela PharmaSci, Inc. (“Exela”) in 2007, whereby Exela agreed to pay to the Company a contractual percentage share of Exela’s net profit from the sales of licensed products.
	CMEA Ventures, which owns approximately 7.6% of the Company's common stock, owns over 10% of Exela’s outstanding capital stock. Thomas R. Baruch, one of the Company's directors, also serves on the board of directors of Exela and, as a limited partner in the CMEA Ventures funds that hold such shares of Exela, has an indirect pecuniary interest in the shares of Exela held by CMEA Ventures.
	The Company recognized revenue from the revenue sharing arrangement of $2.1 million for the three months and $4.1 million for the six months ended June 30, 2014, and $0.4 million for the three months and $1.5 million for the six months ended June 30, 2013. The Company had no receivables from Exela at June 30, 2014.
	Alexander A. Karsner
	Alexander A. Karsner is a director of Codexis and provided consulting services to the Company for the six months ended June 30, 2014 and 2013. Consulting services paid to Mr. Karsner was $30,000 for each of the three months ended June 30, 2014 and 2013, and $60,000 for each of the six months ended June 30, 2014 and 2013. The Company owed Mr. Karsner $30,000 at June 30, 2014, which is reflected in accounts payable in its condensed consolidated balance sheet.

Commitments_and_Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Commitments and Contingencies	'
	Commitments and Contingencies
	Operating Leases
	The Company's headquarters are located in Redwood City, California where it leases approximately 107,000 square feet of office and laboratory space in four buildings within the same business park from Metropolitan Life Insurance Company ("MetLife"). The Company entered into the initial lease with MetLife for a portion of this space in 2004 and the lease has been amended numerous times since then to add and subtract space and amend the terms of the lease, with the latest amendment being in 2012. The various terms for the spaces under the lease have expiration dates that range from January 2017 through January 2020.
	As of December 31, 2012, the Company incurred $3,600,000 of capital improvement costs related to the facilities leased from MetLife and received $3,100,000 of reimbursements from the landlord out of the tenant improvement and HVAC allowances for the completed construction. The reimbursements are being amortized on a straight line basis over the term of the lease as a reduction in rent expense. As of June 30, 2014, the lease incentive obligation remaining was classified with other long-term liabilities on the condensed consolidated balance sheet for $1,948,000.
	As part of a restructuring plan that the Company undertook in the third quarter of 2012, the Company began the process of vacating the 101 Saginaw Drive, Redwood City, California space and marketed the space for sublease. In March 2014, the Company entered into a three-year sublease agreement with a subtenant, which terminates in April 2017, with the option to extend for two consecutive one-year terms thereafter. Sublease income is being recorded as a reduction of the Company's rent expense and was $0.1 million for the three and six months ended June 30, 2014.
	The Company's lease obligations for the facility in Hungary were transferred to the buyer of the Company's Hungarian subsidiary in March 2014.
	Rent expense is recognized on a straight-line basis over the term of the lease. In accordance with the terms of the amended lease agreement, the Company exercised the Company's right to deliver letters of credit in lieu of a security deposit. The letters of credit in the amount of $707,000 as of June 30, 2014 were collateralized by deposit balances held by the Company's bank. These deposits are recorded as restricted cash on the condensed consolidated balance sheets.
	As of June 30, 2014, the Company had estimated asset retirement obligations of approximately $109,000 from operating leases, requiring the Company to restore the facilities that the Company is renting to their original form. The Company is expensing the asset retirement obligation over the terms of the respective leases. The Company reviews the estimated obligation each period and makes adjustments for any changes in estimates.
	Future minimum payments under noncancellable operating leases are as follows at June 30, 2014 (in thousands):
		Lease payments
	6 months ending December 31,
	2014	$	1,338
	Years ending December 31,
	2015	2,743
	2016	2,827
	2017	2,677
	2018	2,736
	2019 and beyond	3,054
	Total	$	15,375
	Litigation
	The Company has been subject to various legal proceedings related to matters that have arisen during the ordinary course of business. Although there can be no assurance as to the ultimate disposition of these matters, the Company has determined, based upon the information available, that the expected outcome of these matters, individually or in the aggregate, will not have a material adverse effect on the condensed consolidated financial position, results of operations or cash flows.
	Other Contingencies
	On July 30, 2013, Dyadic International, Inc. ("Dyadic") delivered notice to the Company alleging that it is in breach under the Dyadic license agreement and stating that Dyadic intended to terminate the Dyadic license agreement in 60 days if the alleged breach was not cured to Dyadic's satisfaction. This notice was subsequently withdrawn by Dyadic in February 2014 in light of the Company's decision to wind down its CodeXyme® cellulase enzyme program. Although the Company does not believe that the use of the licensed technology in its CodeXyme® cellulase enzyme program constituted a breach of the Dyadic license agreement, the Company can make no assurances that Dyadic will not make such allegations again in the future, or regarding the Company's ability to resolve any possible future disputes with Dyadic on commercially reasonable terms or the Company's ability to dispute with success, through legal action or otherwise, any possible future allegations by Dyadic that such use may have breached the Dyadic license agreement.
	In November 2009, one of the Company's foreign subsidiaries sold intellectual property to Codexis, Inc. Under the local laws, the sale of intellectual property to a nonresident legal entity is deemed an export and is not subject to VAT. However, there is uncertainty regarding whether the items sold represented intellectual property or research and development services, which would subject the sale to VAT. The Company believes that the uncertainty results in an exposure to pay VAT that is more than remote but less than likely to occur and, accordingly, has not recorded an accrual for this exposure. If the sale is deemed a sale of research and development services, the Company could be obligated to pay an estimated amount of $600,000.
	Indemnifications
	The Company is required to recognize a liability for the fair value of any obligations the Company assumes upon the issuance of a guarantee. The Company has certain agreements with licensors, licensees and collaborators that contain indemnification provisions. In such provisions, the Company typically agrees to indemnify the licensor, licensee and collaborator against certain types of third party claims. The maximum amount of the indemnifications is not limited. The Company accrues for known indemnification issues when a loss is probable and can be reasonably estimated. There were no accruals for expenses related to indemnification issues for any periods presented.

StockBased_Compensation

Stock-Based Compensation	6 Months Ended
	Jun. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-Based Compensation	'
	Stock-Based Compensation
	Stock Plans
	In 2002, the Company adopted the 2002 Stock Plan (the “2002 Plan”), pursuant to which its board of directors issued incentive stock options, non-statutory stock options and stock purchase rights to its employees, officers, directors and consultants. In March 2010, the Company's board of directors and stockholders approved the 2010 Equity Incentive Award Plan (the “2010 Plan”), which became effective upon the completion of its initial public offering ("IPO") in April 2010. The 2010 Plan is similar to the 2002 Plan but allows for issuance of additional awards, such as a restricted stock unit (“RSU”), performance stock unit (“PSU”), deferred stock award and stock appreciation rights. A total of 1,100,000 shares of common stock were initially reserved for future issuance under the 2010 Plan and any shares of common stock reserved for future grant or issuance under the Company's 2002 Plan that remained unissued at the time of completion of the IPO became available for future grant or issuance under the 2010 Plan. In addition, the shares reserved for issuance pursuant to the exercise of any outstanding awards under the 2002 Plan that expire unexercised will also become available for future issuance under the 2010 Plan. The 2010 Plan also provides for automatic annual increases in the number of shares reserved for future issuance. As of June 30, 2014, total shares remaining available for issuance were approximately 5.4 million.
	Performance Stock Units
	PSUs awarded may be conditional upon the attainment of one or more performance objectives over a specified period. Total compensation expense for PSUs is determined by the product of the number of shares eligible to be awarded and expected to vest, and the market price of the Company's common stock, commencing at the inception of the requisite service period. The fair value of such an award is equal to the closing price of our common stock on the grant date. At the end of the performance period, if the goals are attained, the awards are granted. The Company recognizes compensation expense of these awards on a straight-line basis over the vesting period.
	The Company awarded 775,000 PSUs for the six months ended June 30, 2014 and 523,048 PSUs for the six months ended June 30, 2013 under the 2010 Plan based upon achieving certain cash flow performance goals for each respective year. These PSUs vest such that one-half of the PSUs subject to the award vest one year following the grant, and the remainder of the PSUs vest two years following the grant, subject to the recipient’s continued service to the Company on each vesting date and the Company achieving the performance goals. If the performance goal is achieved at the threshold level the number of shares issuable in respect of the PSUs would be equal to half the number of PSUs granted. If the performance goal is achieved at the target level, the number of shares issuable in respect of the PSUs would be equal to the number of PSUs granted. If the performance goal is achieved at the superior level, the number of shares issuable in respect of the PSUs would be equal to two times the number PSUs granted. The number of shares issuable upon achievement of the performance goal at the levels between the threshold and target levels or target level and superior levels is determined using linear interpolation. Achievement below the threshold level results in no shares being issuable in respect of the PSUs.
	During 2013, the Company revised its estimate of forecasted performance criteria and concluded that the performance target would not likely be achieved for the PSUs that were granted in 2013. The 358,308 outstanding PSUs that were granted in 2013 were canceled in February 2014 when the Company determined that it had not attained the threshold performance target for the 2013 awards.
	Stock-Based Compensation Expense
	The following table presents total stock-based compensation expense by functional areas included in the condensed consolidated statements of operations for the three and six months ended June 30, 2014 and 2013 (in thousands):
		Three Months Ended June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Research and development	$	268		$	502		$	507		$	1,706
	Selling, general and administrative	1,078			760			2,068			1,029
	Total	$	1,346		$	1,262		$	2,575		$	2,735
	Total stock-based compensation expense capitalized to inventory was not material for the periods presented.
	The following table presents total stock-based compensation expense by security types included in the condensed consolidated statements of operations for the three and six months ended June 30, 2014 and 2013 (in thousands):
		Three Months Ended June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Stock options	$	320		$	531		$	596		$	1,141
	RSUs and RSAs	792			604			1,661			1,296
	PSUs	234			127			318			298
	Total	$	1,346		$	1,262		$	2,575		$	2,735
	As of June 30, 2014, unrecognized stock-based compensation expense, net of expected forfeitures, was: $2.0 million related to unvested employee stock options; $3.8 million related to unvested RSUs and RSAs; and $0.9 million related to unvested PSUs.
	Valuation Assumptions
	The range of weighted-average assumptions used to estimate the fair value of employee stock options granted was as follows:
		Three months ended June 30,						Six months ended June 30,
		2014			2013			2014			2013
	Expected term (in years)	—			6			6			6
	Volatility	—			0.652			0.6394			0.652
	Risk-free interest rate	—		%	1.13		%	0.19		%	1.07%-1.13%
	Dividend yield	—		%	—		%	—		%	—		%
	Weighted-average estimated fair value of stock options granted	$	—		$	1.26		$	1.15		$	1.36
	No employee stock options are shown for the three months ended June 30, 2014, as no stock options were granted during this period.

Stockholders_Equity

Stockholders' Equity	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Stockholders' Equity	'
	Stockholders' Equity
	Exercise of options
	For the six months ended June 30, 2014, 61,331 shares were exercised at a weighted-average exercise price of $1.01 per share, for total cash proceeds of less than $0.1 million.
	Accumulated Other Comprehensive Income
	The components of accumulated other comprehensive income, net of tax, and other comprehensive income are summarized as follows (in thousands):
		Net Unrealized Gains on Marketable Securities				Accumulated Other Comprehensive Income
	Balance at December 31, 2013	$	(32	)		$	(32	)
	Other comprehensive income	405				405
	Amounts reclassified to interest income	1				1
	Balance at June 30, 2014	$	374			$	374
	Warrants
	The Company's outstanding warrants are exercisable for common stock at any time during their respective terms. As of June 30, 2014, the following warrants remain outstanding:
	30-Jun-14
	Issue Date	Shares Subject		Exercise Price				Expiration
		to warrants		per Share
	July 17, 2007	2,834		$	12.45			February 9, 2016
	September 28, 2007	72,727		$	8.25			September 28, 2017

Segment_Reporting

Segment Reporting	6 Months Ended
	Jun. 30, 2014
Segment Reporting [Abstract]	'
Segment Reporting	'
	Segment Reporting
	The following table represents revenues that are identified in the corresponding geographic regions based on the customer's ship-to locations (in thousands):
		Three Months Ended June 30,				Six Months Ended June 30,
		2014		2013		2014		2013
	Revenues
	United States	$	4,197	$	2,181	$	7,771	$	4,301
	Asia
	India	324		289		411		2,508
	Singaore	—		3,073		—		6,721
	Others	339		254		680		543
	Europe
	Ireland	784		—		2,744		1,219
	Others	910		1,177		2,022		3,163
	Other	16		—		16		—
	Total Revenues	$	6,570	$	6,974	$	13,644	$	18,455
	The following table represents identifiable long-lived assets in the corresponding regions (in thousands):
		June 30,		December 31,
		2014		2013
	Long-lived assets
	United States	$	12,726	$	16,189
	Europe (1)	—		2,123
	Total long-lived assets	$	12,726	$	18,312
	-1	Primarily Hungary

Restructuring

Restructuring	6 Months Ended
	Jun. 30, 2014
Restructuring Costs [Abstract]	'
Restructuring	'
	Restructuring
	Q4 2013 Restructuring Plan
	During the fourth quarter of 2013, the Company's board of directors approved and committed to a restructuring plan (the “Q4 2013 Restructuring Plan”) to reduce its cost structure resulting from the Company's decision to begin winding down its CodeXyme® cellulase enzymes program, which included a total of 15 employee terminations in the United States. For the year ended December 31, 2013, costs of $809,000 of employee severance and other termination benefits have been recognized, consisting of $573,000 in research and development expenses and $236,000 in selling, general and administrative expenses. For the three months ended March 31, 2014, the Company made severance payments of $238,000 and there was no remaining liability at March 31, 2014. Associated with the Q4 2013 Restructuring Plan, the Company announced it was selling certain research and development assets that have become excess to future requirements (see Note 7 "Assets Held for Sale"). The Company does not anticipate recording any further costs under this restructuring plan.
	The following table summarizes the activity in the restructuring accrual for the three months ended March 31, 2014 and the three months ended June 30, 2014 (in thousands):
		Q4 2013 Restructuring Plan
	Balance at December 31, 2013	$	277
	Cash payments for the first quarter of 2014	(238		)
	Adjustments to previously accrued charges	(39		)
	Balance at March 31, 2014	$	—
	Cash payments for the second quarter of 2014	$	—
	Adjustment to previously accrued charges	$	—
	Balance at June 30, 2014	$	—

Subsequent_Event

Subsequent Event	6 Months Ended
	Jun. 30, 2014
Subsequent Events [Abstract]	'
Subsequent Event	'
	Subsequent Event
	In July 2014, the Company and entered into a platform technology license agreement (the "License Agreement") with GlaxoSmithKline (GSK).
	Under the terms of the License Agreement, the Company granted GSK a license to use the Company's proprietary CodeEvolver® protein engineering platform technology.
	The Company is eligible to receive up to $25.0 million, $6.0 million of which was paid upfront after executing the License Agreement and an additional $19.0 million to be received over the next two years subject to satisfactory completion of technology transfer milestones. The Company also has the potential to receive numerous additional milestone payments that range from $5.75 million to $38.5 million per project based on GSK's successful application of the licensed technology. In addition, the Company will be eligible to receive royalties based on net sales, if any, of a limited set of products developed by GSK using the Company's CodeEvolver protein engineering platform technology.

Basis_of_Presentation_and_Summ1

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Basis of Presentation and Principles of Consolidation	'
	Basis of Presentation and Principles of Consolidation
	The accompanying condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”) and the applicable rules and regulations of the Securities and Exchange Commission (“SEC”) for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company's Annual Report on Form 10-K for the year ended December 31, 2013. The condensed consolidated balance sheet at December 31, 2013 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures including notes required by GAAP for complete financial statements.
	The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly its financial position as of June 30, 2014 and results of its operations, comprehensive loss and cash flows for the three and six months ended June 30, 2014 and 2013. The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Certain prior period amounts have been reclassified to conform to current period presentation.
	The unaudited interim condensed consolidated financial statements include the amounts of Codexis, Inc. and its wholly-owned subsidiaries in the United States, Brazil, Hungary (through the sale date of March 13, 2014), India, Mauritius, The Netherlands and Singapore. All significant intercompany balances and transactions have been eliminated in consolidation.
Use of Estimates	'
	Use of Estimates
	The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenues and expenses during the reporting period. The Company's management regularly assesses these estimates which primarily affect revenue recognition, the valuation of marketable securities and accounts receivable, held for sale assets, intangible assets, goodwill arising out of business acquisitions, inventories, accrued liabilities, stock awards and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements.
Foreign Currency Translation	'
	Foreign Currency Translation
	The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.
	Where the United States dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in interest expense and other, net in the accompanying condensed consolidated statements of operations. Gains and losses realized from transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity’s functional currency, are included in interest expense and other, net in the accompanying consolidated statements of operations.
Concentrations of Credit Risk	'
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to concentration of credit risk consist principally of: cash equivalents, marketable securities, accounts receivable, and restricted cash.
	The Company invests cash that is not required for immediate operating needs principally in money market funds and corporate securities through banks and other financial institutions in the United States, as well as in other foreign countries.
	Accounts receivable are concentrated in the pharmaceutical industry. Accordingly, the Company may be exposed to credit risk generally associated with pharmaceutical companies or specific to the collaboration arrangements with Merck and Arch. The Company does not require collateral from its customers, but does perform periodic credit evaluations of its customers’ financial condition and requires immediate payment in certain circumstances.
	Credit risk with respect to accounts receivable exists to the extent of amounts presented in the condensed consolidated financial statements. The Company estimates an allowance for doubtful accounts through specific identification of potentially uncollectible accounts receivable based on an analysis of its accounts receivable aging. Uncollectible accounts receivable are written off against the allowance for doubtful accounts when all efforts to collect them have been exhausted. Recoveries are recognized when they are received. Actual collection losses may differ from its estimates and could be material to its consolidated financial position, results of operations, and cash flows.
Fair Value of Financial Instruments	'
	Fair Value of Financial Instruments
	The carrying amounts of certain of the Company's financial instruments, including cash and cash equivalents, restricted cash, accounts receivable and accounts payable, approximate fair value due to their short maturities.
	Fair value is considered to be the price at which an asset could be exchanged or a liability transferred (an exit price) in an orderly transaction between knowledgeable, willing parties in the principal or most advantageous market for the asset or liability. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments and the instruments’ complexity.
Cash, Cash Equivalents and Marketable Securities	'
	Cash and Cash Equivalents
	The Company considers all highly liquid investments with maturity dates of three months or less at the date of purchase to be cash equivalents. Cash and cash equivalents consist of cash on deposit with banks and money market funds. The majority of cash and cash equivalents are maintained with major financial institutions in North America. Deposits with these financial institutions may exceed the amount of insurance provided on such deposits. Cash and cash equivalents was $20.1 million at June 30, 2014, and was comprised of cash of $4.5 million and money market funds of $15.6 million.
	Marketable Securities
	Marketable securities included in current assets are comprised of corporate bonds. The Company's investment in common shares of CO2 Solutions Inc. (“CO2 Solutions”) is included in non-current marketable securities.
	The Company performs separate evaluations of impaired debt and equity securities to determine if the unrealized losses as of the balance sheet date are other-than-temporary impairment.
	For the Company's investments in equity securities, its evaluation considers a number of factors including, but not limited to, the length of time and extent to which the fair value has been less than cost, the financial condition and near term prospects of the issuer, and its management’s ability and intent to hold the securities until fair value recovers. The assessment of the ability and intent to hold these securities to recovery focuses on its current and forecasted liquidity requirements and capital requirements. As of June 30, 2014, there were no unrealized losses related to the Company's equity securities.
	For the Company's investments in debt securities, management determines whether it intends to sell or if it is more-likely-than-not that the Company will be required to sell impaired securities. This determination considers current and forecasted liquidity requirements and capital requirements. For all impaired debt securities for which there was no intent or expected requirement to sell, the evaluation considers all available evidence to assess whether it is likely the amortized cost value will be recovered. The Company conducts a regular assessment of its debt securities with unrealized losses to determine whether the securities have other-than-temporary impairment considering, among other factors, the nature of the securities, credit rating or financial condition of the issuer, the extent and duration of the unrealized loss, expected cash flows of underlying collateral and market conditions. As of June 30, 2014, there were no unrealized losses related to the Company's debt securities.
	The Company's investments in debt and equity securities are classified as available-for-sale and are carried at fair value. Unrealized gains and losses are reported on the condensed consolidated statement of comprehensive loss unless considered other-than-temporary. Amortization of purchase premiums and accretion of purchase discounts, realized gains and losses of debt securities and declines in value deemed to be other than temporary, if any, are included in interest income or other expenses. The cost of securities sold is based on the specific-identification method.
Impairment of Long-Lived Assets and Intangible Assets	'
	Impairment of Long-Lived Assets and Intangible Assets
	Long-lived and intangible assets with finite lives are reviewed for impairment whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of these assets is measured by comparison of their carrying amounts to future undiscounted cash flows the assets are expected to generate.
	The Company's intangible assets with finite lives consist of customer relationships, developed core technology, trade names, and the intellectual property (“IP”) rights associated with the acquisition of Maxygen Inc.'s ("Maxygen") directed evolution technology in 2010. Intangible assets were recorded at their fair values at the date the Company acquired the assets and, for those assets having finite useful lives, are amortized using the straight-line method over their estimated useful lives. The Company's long-lived assets include property, plant and equipment, and other non-current assets.
	The Company determined that it has a single entity wide asset group (“Asset Group”). The directed evolution technology patent portfolio acquired from Maxygen (“Core IP”) is the most significant component of the Asset Group since it is the base technology for all aspects of the Company's research and development activities, and represents the basis for all of the Company's identifiable cash flow generating capacity. Consequently, the Company does not believe that identification of independent cash flows associated with its long-lived assets is currently possible at any lower level than the Asset Group.
	The Core IP is the only finite-lived intangible asset on the Company's condensed consolidated balance sheet as of June 30, 2014 and is considered the primary asset within the Asset Group. There has been no significant change in the utilization or estimated life of the Core IP since the Company acquired the technology patent portfolio from Maxygen.
	The carrying value of the Company's long-lived assets in the Asset Group may not be recoverable based upon the existence of one or more indicators of impairment which could include: a significant decrease in the market price of the Company's common stock; current period cash flow losses or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the assets; slower growth rates in the Company's industry; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the assets; loss of significant customers or partners; or the current expectation that the assets will more likely than not be sold or disposed of significantly before the end of their estimated useful life.
	The Company evaluates recoverability of its long-lived assets and intangible assets based on the sum of the undiscounted cash flows expected to result from the use, and the eventual disposal of, the Asset Group. The Company makes estimates and judgments about the future undiscounted cash flows over the remaining useful life of the Asset Group. The Company's anticipated future cash flows include its estimates of existing or in process product revenues, production and operating costs, future capital expenditures, working capital needs, and assumptions regarding the ultimate sale of the Asset Group at the end of the life of the primary asset. The useful life of the Asset Group was based on the estimated useful life of the Core IP, the primary asset at the time of acquisition. There has been no change in the estimated useful life of the Asset Group. Although the Company's cash flow forecasts are based on assumptions that are consistent with its plans, there is significant judgment involved in determining the cash flows attributable to the Asset Group over its estimated remaining useful life.
Valuation of Goodwill	'
	Valuation of Goodwill
	The Company reviews goodwill impairment annually in the fourth quarter of each of its fiscal years and whenever events or changes in circumstances indicate the carrying value of goodwill may not be recoverable.
	The Company determined that it has only one operating segment and reporting unit under the criteria in ASC 280, Segment Reporting. Accordingly, the Company's review of goodwill impairment indicators is performed at the Company level.
	The goodwill impairment test consists of a two-step process. The first step of the goodwill impairment test, used to identify potential impairment, compares the fair value of the reporting unit to its carrying value. If the fair value of the reporting unit exceeds its carrying amount, goodwill of the reporting unit is considered not impaired, and the second step of the impairment test is not required.
	The Company uses its market capitalization as an indicator of fair value. The Company believes that since its reporting unit is publicly traded, the ability of a controlling stockholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of the Company's reporting unit as a whole to exceed its market capitalization. However, the Company believes that the fair value measurement need not be based solely on the quoted market price of an individual share of the Company's common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.
	If the Company were to use an income approach it would establish a fair value by estimating the present value of its projected future cash flows expected to be generated from its business. The discount rate applied to the projected future cash flows to arrive at the present value would be intended to reflect all risks of ownership and the associated risks of realizing the stream of projected future cash flows. The Company's discounted cash flow methodology would consider projections of financial performance for a period of several years combined with an estimated residual value. The most significant assumptions it would use in a discounted cash flow methodology are the discount rate, the residual value and expected future revenues, gross margins and operating costs, along with considering any implied control premium.
	Should the Company's market capitalization be less than the total stockholder's equity as of the Company's annual test date or as of any interim impairment testing date, the Company would also consider market comparables, recent trends in the Company's stock price over a reasonable period and, if appropriate, use an income approach to determine whether the fair value of its reporting unit is greater than the carrying amount.
	The second step, if required, compares the implied fair value of the reporting unit goodwill with the carrying amount of that goodwill. If the carrying amount of the reporting unit's goodwill exceeds its implied fair value, an impairment charge is recognized in an amount equal to that excess. Implied fair value is the excess of the fair value of the reporting unit over the fair value of all identified assets and liabilities. The Company bases its fair value estimates on assumptions it believes to be reasonable. Actual future results may differ from those estimates.
Restricted Cash	'
	Restricted Cash
	Restricted cash consisted of amounts invested in money market accounts primarily for purposes of securing a standby letter of credit as collateral for the Company's Redwood City, California facility lease agreement.
Revenue Recognition	'
	Revenue Recognition
	Revenues are recognized when the four basic revenue recognition criteria are met: (1) persuasive evidence of an arrangement exists; (2) products have been delivered, transfer of technology has been completed or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured.
	The Company's primary sources of revenues consist of biocatalyst product revenues, biocatalyst research and development agreements and revenue sharing arrangements. Biocatalyst research and development agreements typically provide the Company with multiple revenue streams, including up-front fees for licensing, exclusivity and technology access, fees for full time employee ("FTE") services and the potential to earn milestone payments upon achievement of contractual criteria and royalty fees based on future product sales or cost savings achieved by the Company's customers.
	For each source of biocatalyst research and development revenues, biocatalyst product revenues and revenue sharing revenues, the Company applies the following revenue recognition criteria:
	Biocatalyst product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria, if any, have been met, provided all other revenue recognition criteria have also been met. Product revenues consist of sales of biocatalyst intermediates, active pharmaceutical ingredients and Codex Biocatalyst Panels and Kits. Cost of product revenues includes both internal and third party fixed and variable costs including amortization of purchased technology, materials and supplies, labor, facilities and other overhead costs associated with the Company's biocatalyst product revenues.
	Revenue sharing arrangement revenues are recognized based upon sales of licensed products by the Company's revenue share partner Exela (see Note 9 "Related Party Transactions"). Revenue share amounts received are net of product and selling costs. The Company bases its estimates of earned revenue on notification from its revenue share partner of the Company’s share of net profit based on the contractual percentage from the sale of licensed product. The Company bases its estimates on notification of the sale of revenue sharing products and related costs by its revenue share partner.
	Up-front fees received in connection with biocatalyst research and development agreements, including license fees, technology access fees, and exclusivity fees, are deferred upon receipt, are not considered a separate unit of accounting and are recognized as revenues over the relevant performance periods related to the combined units of accounting appropriate for each customer arrangement.
	Revenues related to FTE services recognized as research services are performed over the related performance periods for each contract. The Company performs biocatalyst research and development activities as specified in each respective customer agreement. The payments received are not refundable and are based on a contractual reimbursement rate per FTE working on the project. When up-front payments are combined with FTE services in a single unit of accounting, the Company recognizes the up-front payments using the proportionate performance method of revenue recognition based upon the actual amount of research and development labor hours incurred relative to the amount of the total expected labor hours to be incurred by the Company, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, the Company is required to make estimates of the total hours required to perform the Company's obligations. Research and development expenses related to FTE services under the collaborative research and development agreements approximate the research funding over the term of the respective agreements.
	A payment that is contingent upon the achievement of a substantive milestone is recognized in its entirety in the period in which the milestone is achieved. A milestone is an event (i) that can only be achieved based in whole or in part on either the Company's performance or on the occurrence of a specific outcome resulting from its performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved, and (iii) results in additional payments being due to the Company. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either the Company's performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from its performance, (ii) relates solely to past performance, and (iii) is reasonable relative to all deliverable and payment terms in the arrangement.
	Other payments received for which such payments are contingent solely upon the passage of time or the result of a collaborative partner’s performance are recognized as revenue when earned in accordance with the contract terms and when such payments can be reasonably estimated and collectability is reasonably assured.
	The Company recognizes revenues from royalties based on licensees’ sales of products using the Company's technologies. Royalties are recognized as earned in accordance with the contract terms when royalties from licensees can be reasonably estimated and collectability is reasonably assured. The Company bases its estimates on notification the sale of licensed products from licensees.
	Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in the Company's cost of biocatalyst products revenues. Such charges were not significant in any of the periods presented.
Income Taxes	'
	Income Taxes
	The Company uses the liability method of accounting for income taxes, whereby deferred tax assets or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized.
	The Company makes certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenues and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to the Company's tax provision in a subsequent period.
	In assessing the realizability of deferred tax assets, the Company considers whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. The Company has recorded a deferred tax asset in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur.
	The Company makes estimates and judgments about its future taxable income that are based on assumptions that are consistent with its plans and estimates. Should the actual amounts differ from its estimates, the amount of its valuation allowance could be materially impacted. Any adjustment to the deferred tax asset valuation allowance would be recorded in the income statement for the periods in which the adjustment is determined to be required. With the sale of the Hungarian subsidiary for the quarter ended March 31, 2014, the related net operating losses and other tax attributes are no longer available to the Company. The related deferred tax assets had a full valuation allowance and, as a result, their removal did not have a material impact to the financial statements.
	The Company accounts for uncertainty in income taxes as required by the provisions of ASC Topic 740, Income Taxes, which clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the position will be sustained on audit, including resolution of related appeals or litigation processes, if any. The second step is to estimate and measure the tax benefit as the largest amount that is more than 50% likely of being realized upon ultimate settlement. It is inherently difficult and subjective to estimate such amounts, as this requires us to determine the probability of various possible outcomes. The Company considers many factors when evaluating and estimating the Company's tax positions and tax benefits, which may require periodic adjustments and may not accurately anticipate actual outcomes.
	The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company should experience an ownership change, as defined, utilization of the Company's federal and state net operating loss carryforwards could be limited.
Stock-Based Compensation	'
	Stock-Based Compensation
	The Company uses the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under its equity incentive plans. The Black-Scholes-Merton option valuation model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. The Company uses the "simplified" method as described in Staff Accounting Bulletin No. 107, "Share-Based Payment," for the expected option term because the usage of its historical option exercise data is limited due to the Company's initial public offering in 2010. The Company uses its historical volatility to estimate expected stock price volatility. The risk-free rate assumption was based on United States Treasury instruments whose terms were consistent with the terms of the Company's stock options. The expected dividend assumption was based on the Company's history and expectation of dividend payouts.
	Restricted Stock Units (RSUs) and Restricted Stock Awards (RSAs) are measured based on the fair market values of the underlying stock on the dates of grant.
	Stock-based compensation expense was calculated based on awards ultimately expected to vest and was reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differed from those estimates. The estimated annual forfeiture rates for stock options, RSUs and RSAs are based on the Company's historical forfeiture experience.
	The estimated fair value of stock options, RSUs and RSAs is expensed on a straight-line basis over the expected term of the grant and the estimated fair value of performance-contingent RSUs is expensed using an accelerated method over the term of the award once management has determined that it is probable that performance milestones will be achieved. Compensation expense for RSUs that contain performance conditions is based on the grant date fair value of the award. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. Management assesses the probability of the performance milestones being met on a continuous basis.
	The Company accounts for stock awards issued to non-employees based on their estimated fair value determined using the Black-Scholes-Merton option-pricing model. Compensation expense for the stock awards granted to non-employees is recognized based on the fair value of awards as they vest, during the period the related services are rendered.
Net Loss per Share	'
	Net Loss per Share
	Basic net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture. Diluted net loss per share is computed by dividing net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture, plus all additional common shares that would have been outstanding, assuming dilutive potential common shares had been issued for other dilutive securities.
Recently Issued and Adopted Accounting Guidance	'
	Recently Issued and Adopted Accounting Guidance
	From time to time, new accounting pronouncements are issued by the Financial Accounting Standards Board (“FASB”) or other standards setting bodies that are adopted by us as of the specified effective date. Unless otherwise discussed, the Company's management believes that the impact of recently issued standards that are not yet effective will not have a material impact on its consolidated financial statements upon adoption.
	In May 2014, the Financial Accounting Standards Board issued Accounting Standards Update (“ASU”) 2014-09, Revenue from Contracts with Customers. This standard outlines a single comprehensive model for entities to use in accounting for revenue arising from contracts with customers and supersedes most current revenue recognition guidance, including industry-specific guidance. The main principle of ASU 2014-09 is to recognize revenues when promised goods or services are transferred to customers in an amount that reflects the consideration that is expected to be received for those goods or services. ASU 2014-09 provides companies with two implementation methods: (i) apply the standard retrospectively to each prior reporting period presented (full retrospective application); or (ii) apply the standard retrospectively with the cumulative effect of initially applying the standard as an adjustment to the opening balance of retained earnings of the annual reporting period that includes the date of initial application (modified retrospective application). This guidance is effective for annual reporting periods beginning after December 15, 2016, including interim periods within that reporting period, and early application is not permitted. The Company is currently in the process of evaluating the impact of the pending adoption of ASU 2014-09 on its consolidated financial statements.

Basis_of_Presentation_and_Summ2

Basis of Presentation and Summary of Significant Accounting Policies (Tables)	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Schedules of Concentration of Risk, by Risk Factor	'
	Customers whose revenue accounted for 10% or more of total revenues were as follows:
		Three Months Ended June 30,				Six months ended June 30,
		2014		2013		2014		2013
	Exela (related party)	32	%	*		30	%	*
	Merck	28	%	65	%	25	%	50	%
	Novartis	12	%	—	%	20	%	*
	Arch	—	%	—	%	—	%	12	%
	* less than 10%
Securities not included in the net loss per common share calculations	'
	The following common equivalent shares were not included in the computation of diluted net loss per share because their effect was anti-dilutive:
		Three Months Ended June 30,				Six Months Ended June 30,
		2014		2013		2014		2013
	Options to purchase common stock	3,888		4,996		3,888		4,996
	Restricted stock units/awards	2,504		1,827		2,504		1,827
	Performance stock units	722		—		722		—
	Warrants to purchase common stock	75		75		75		75
	Total shares excluded as anti-dilutive	7,189		6,898		7,189		6,898

Cash_Equivalents_and_Marketabl1

Cash Equivalents and Marketable Securities (Tables)	6 Months Ended
	Jun. 30, 2014
Cash Equivalents and Marketable Securities [Abstract]	'
Schedule of cash equivalents and marketable securities	'
	At June 30, 2014, cash equivalents and marketable securities consisted of the following (in thousands):
		30-Jun-14
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds (1)	$	15,598	$	—	$	—	$	15,598	n/a
	Common shares of CO2 Solutions	563		890		—		1,453		n/a
	Total	$	16,161	$	890	$	—	$	17,051
	(1) Money market funds are classified in cash and cash equivalents on the Company’s condensed consolidated balance sheets.
	At December 31, 2013, cash equivalents and marketable securities consisted of the following (in thousands):
		31-Dec-13
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds (1)	$	16,089	$	—	$	—	$	16,089	n/a
	Corporate bonds	1,002		3		—		1,005		140
	U.S. Treasury obligations	2,000		—		—		2,000		59
	Common shares of CO2 Solutions	563		232		—		795		n/a
	Total	$	19,654	$	235	$	—	$	19,889
	(1) Money market funds are classified in cash and cash equivalents on the Company’s condensed consolidated balance sheets.

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2014
Fair Value, Assets, Liabilities and Stockholders' Equity Measured on Recurring Basis [Abstract]	'
Summary of financial instruments measured at fair value on a recurring basis	'
	The following table presents the financial instruments that were measured at fair value on a recurring basis at June 30, 2014 by level within the fair value hierarchy (in thousands):
		30-Jun-14
		Level 1				Level 2		Level 3		Total
	Money market funds	$	15,598			$	—	$	—	$	15,598
	Common shares of CO2 Solutions	—				1,453		—		1,453
	Total	$	15,598			$	1,453	$	—	$	17,051
	The following table presents the financial instruments that were measured at fair value on a recurring basis at December 31, 2013 by level within the fair value hierarchy (in thousands):
		31-Dec-13
		Level 1				Level 2		Level 3		Total
	Money market funds	$	16,089			$	—	$	—	$	16,089
	Corporate bonds	—				1,005		—		1,005
	U.S. Treasury obligations	—				2,000		—		2,000
	Common shares of CO2 Solutions	—				795		—		795
	Total	$	16,089			$	3,800	$	—	$	19,889
Disclosure of Long Lived Assets Held-for-sale	'
	The fair value of assets held for sale at June 30, 2014, measured on a nonrecurring basis, is as follows (in thousands):
		30-Jun-14
		Level 1				Level 2		Level 3		Total
	Assets held for sale	$	—			$	—	$	292	$	292
	The fair value of assets held for sale at December 31, 2013 , measured on a nonrecurring basis, is as follows (in thousands):
		31-Dec-13
		Level 1				Level 2		Level 3		Total
	Assets held for sale	$	—			$	—	$	2,179	$	2,179
	Total assets reclassified as Assets Held for Sale at June 30, 2014, were (in thousands):
	Assets Held for Sale		Adjusted Carrying Value
	Research & development equipment classified as held for sale at December 31, 2013		$	2,179
	Hungarian assets sold for the three months ended March 31, 2014		(779		)
	U.S. assets sold for the three months ended March 31, 2014		(6		)
	Research & development equipment classified as held for sale at March 31, 2014		$	1,394
	Research & development equipment reclassified as held for use		(333		)
	U.S. assets sold for the three months ended June 30, 2014		(13		)
	Loss on exchange of assets		(188		)
	Change in estimated fair value of research equipment during three months ended June 30, 2014		(568		)
	Research & development equipment classified as held for sale at June 30, 2014		$	292

Balance_Sheets_Details_Tables

Balance Sheets Details (Tables)	6 Months Ended
	Jun. 30, 2014
Balance Sheets Details [Abstract]	'
Schedule of inventory components	'
	Inventory, net consisted of the following (in thousands):
		June 30,				December 31,
		2014				2013
	Raw materials	$	452			$	763
	Work in process	229				31
	Finished goods	1,282				693
	Inventory, net	$	1,963			$	1,487
Schedule of property and equipment, net	'
	Property and equipment, net consisted of the following (in thousands):
		June 30,					December 31,
		2014					2013
	Laboratory equipment	$	23,774				$	23,949
	Leasehold improvements	9,493					9,493
	Computer equipment	3,249					3,196
	Office furniture and equipment	1,227					1,228
		37,743					37,866
	Less: accumulated depreciation and amortization	(31,064		)			(29,461		)
		6,679					8,405
	Construction in progress	15					41
	Property and equipment	6,694					8,446
	Less: Impairment of laboratory equipment	(1,841		)	-1		—
	Property and equipment, net	$	4,853				$	8,446
	(1)    Plans to utilize certain CodeXol® assets changed in the second quarter of 2014 such that assets with a a carrying value of $1.8 million were no longer recoverable. Accordingly, the Company recorded an impairment charge of $1.8 million, reducing the carrying value to zero (their estimated fair value, net of costs). The impairment charge was recorded within Research and Development Expense for the three and six months ended June 30, 2014.
Schedule of Finite-Lived Intangible Assets	'
	Intangible assets consisted of the following (in thousands):
		30-Jun-14										31-Dec-13
		Gross				Accumulated				Net		Gross		Accumulated			Net		Weighted-
		Carrying				Amortization				Carrying		Carrying		Amortization			Carrying		Average
		Amount								Amount		Amount					Amount		Amortization
																			Period
																			(years)
	Customer relationships	$	3,098			$	(3,098	)		$	—	$	3,098	$	(3,098	)	$	—	5
	Developed and core technology	1,534				(1,534		)		—		1,534		(1,534		)	—		5
	Maxygen intellectual property	20,244				(12,371		)		7,873		20,244		(10,684		)	9,560		6
	Total	$	24,876			$	(17,003	)		$	7,873	$	24,876	$	(15,316	)	$	9,560
Schedule of Finite-Lived Intangible Assets, Future Amortization Expense	'
	The estimated future amortization expense to be charged to research and development through the year ending December 31, 2016 is as follows (in thousands):
	Year ending December 31:	Total
	2014 (remaining 6 months)	$	1,687
	2015	3,374
	2016	2,812
		$	7,873

Assets_Held_for_Sale_Tables

Assets Held for Sale (Tables)	6 Months Ended
	Jun. 30, 2014
Assets Held for Sale [Abstract]	'
Disclosure of Long Lived Assets Held-for-sale	'
	The fair value of assets held for sale at June 30, 2014, measured on a nonrecurring basis, is as follows (in thousands):
		30-Jun-14
		Level 1				Level 2		Level 3		Total
	Assets held for sale	$	—			$	—	$	292	$	292
	The fair value of assets held for sale at December 31, 2013 , measured on a nonrecurring basis, is as follows (in thousands):
		31-Dec-13
		Level 1				Level 2		Level 3		Total
	Assets held for sale	$	—			$	—	$	2,179	$	2,179
	Total assets reclassified as Assets Held for Sale at June 30, 2014, were (in thousands):
	Assets Held for Sale		Adjusted Carrying Value
	Research & development equipment classified as held for sale at December 31, 2013		$	2,179
	Hungarian assets sold for the three months ended March 31, 2014		(779		)
	U.S. assets sold for the three months ended March 31, 2014		(6		)
	Research & development equipment classified as held for sale at March 31, 2014		$	1,394
	Research & development equipment reclassified as held for use		(333		)
	U.S. assets sold for the three months ended June 30, 2014		(13		)
	Loss on exchange of assets		(188		)
	Change in estimated fair value of research equipment during three months ended June 30, 2014		(568		)
	Research & development equipment classified as held for sale at June 30, 2014		$	292

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Schedule of future minimum payments under non-cancellable operating leases	'
	Future minimum payments under noncancellable operating leases are as follows at June 30, 2014 (in thousands):
		Lease payments
	6 months ending December 31,
	2014	$	1,338
	Years ending December 31,
	2015	2,743
	2016	2,827
	2017	2,677
	2018	2,736
	2019 and beyond	3,054
	Total	$	15,375

StockBased_Compensation_Tables

Stock-Based Compensation (Tables)	6 Months Ended
	Jun. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Schedule of stock-based compensation expense	'
	The following table presents total stock-based compensation expense by functional areas included in the condensed consolidated statements of operations for the three and six months ended June 30, 2014 and 2013 (in thousands):
		Three Months Ended June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Research and development	$	268		$	502		$	507		$	1,706
	Selling, general and administrative	1,078			760			2,068			1,029
	Total	$	1,346		$	1,262		$	2,575		$	2,735
Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity	'
	The following table presents total stock-based compensation expense by security types included in the condensed consolidated statements of operations for the three and six months ended June 30, 2014 and 2013 (in thousands):
		Three Months Ended June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Stock options	$	320		$	531		$	596		$	1,141
	RSUs and RSAs	792			604			1,661			1,296
	PSUs	234			127			318			298
	Total	$	1,346		$	1,262		$	2,575		$	2,735
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions	'
	The range of weighted-average assumptions used to estimate the fair value of employee stock options granted was as follows:
		Three months ended June 30,						Six months ended June 30,
		2014			2013			2014			2013
	Expected term (in years)	—			6			6			6
	Volatility	—			0.652			0.6394			0.652
	Risk-free interest rate	—		%	1.13		%	0.19		%	1.07%-1.13%
	Dividend yield	—		%	—		%	—		%	—		%
	Weighted-average estimated fair value of stock options granted	$	—		$	1.26		$	1.15		$	1.36

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Schedule of Accumulated Other Comprehensive Income (Loss)	'
	The components of accumulated other comprehensive income, net of tax, and other comprehensive income are summarized as follows (in thousands):
		Net Unrealized Gains on Marketable Securities				Accumulated Other Comprehensive Income
	Balance at December 31, 2013	$	(32	)		$	(32	)
	Other comprehensive income	405				405
	Amounts reclassified to interest income	1				1
	Balance at June 30, 2014	$	374			$	374
Schedule of common stock warrants issued and outstanding	'
	As of June 30, 2014, the following warrants remain outstanding:
	30-Jun-14
	Issue Date	Shares Subject		Exercise Price				Expiration
		to warrants		per Share
	July 17, 2007	2,834		$	12.45			February 9, 2016
	September 28, 2007	72,727		$	8.25			September 28, 2017

Segment_Reporting_Tables

Segment Reporting (Tables)	6 Months Ended
	Jun. 30, 2014
Segment Reporting [Abstract]	'
Schedule of revenues by geographical area	'
	The following table represents revenues that are identified in the corresponding geographic regions based on the customer's ship-to locations (in thousands):
		Three Months Ended June 30,				Six Months Ended June 30,
		2014		2013		2014		2013
	Revenues
	United States	$	4,197	$	2,181	$	7,771	$	4,301
	Asia
	India	324		289		411		2,508
	Singaore	—		3,073		—		6,721
	Others	339		254		680		543
	Europe
	Ireland	784		—		2,744		1,219
	Others	910		1,177		2,022		3,163
	Other	16		—		16		—
	Total Revenues	$	6,570	$	6,974	$	13,644	$	18,455
Schedule of long-lived assets by geographical area	'
	The following table represents identifiable long-lived assets in the corresponding regions (in thousands):
		June 30,		December 31,
		2014		2013
	Long-lived assets
	United States	$	12,726	$	16,189
	Europe (1)	—		2,123
	Total long-lived assets	$	12,726	$	18,312
	-1	Primarily Hungary

Restructuring_Tables

Restructuring (Tables)	6 Months Ended
	Jun. 30, 2014
Restructuring Costs [Abstract]	'
Summary of changes in restructuring accrual	'
	The following table summarizes the activity in the restructuring accrual for the three months ended March 31, 2014 and the three months ended June 30, 2014 (in thousands):
		Q4 2013 Restructuring Plan
	Balance at December 31, 2013	$	277
	Cash payments for the first quarter of 2014	(238		)
	Adjustments to previously accrued charges	(39		)
	Balance at March 31, 2014	$	—
	Cash payments for the second quarter of 2014	$	—
	Adjustment to previously accrued charges	$	—
	Balance at June 30, 2014	$	—

Basis_of_Presentation_and_Summ3

Basis of Presentation and Summary of Significant Accounting Policies (Textual) (Details) (USD $)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013	Dec. 31, 2012
			operating_segment
			reporting_unit
Accounting Policies [Line Items]	'	'	'	'	'	'
Number of Operating Segments	'	'	1	'	'	'
Maturity Date of Highly Liquid Investments	'	'	'3 months	'	'	'
Cash and Cash Equivalents, at Carrying Value	$20,090,000	$32,392,000	$20,090,000	$32,392,000	$22,130,000	$32,003,000
Cash	4,500,000	'	4,500,000	'	'	'
Money market funds	15,600,000	'	15,600,000	'	'	'
Number of Reportable Segments	'	'	1	'	'	'
Goodwill Impairment	'	'	'	'	0	'
Benefit from income taxes	437,000	12,000	567,000	77,000	'	'
Equity Securities [Member]	'	'	'	'	'	'
Accounting Policies [Line Items]	'	'	'	'	'	'
Gross unrealized losses	'	'	0	'	'	'
Debt Securities [Member]	'	'	'	'	'	'
Accounting Policies [Line Items]	'	'	'	'	'	'
Gross unrealized losses	'	'	0	'	'	'
Intellectual Property [Member]	'	'	'	'	'	'
Accounting Policies [Line Items]	'	'	'	'	'	'
Percentage of Undiscounted Cash Flows Greater Than Carry Value of Asset Group	'	'	'	'	37.00%	'
Available-for-sale Securities [Member]	'	'	'	'	'	'
Accounting Policies [Line Items]	'	'	'	'	'	'
Significant realized gains or losses from sales of marketable securities	$0	$0	$0	$0	'	'

Basis_of_Presentation_and_Summ4

Basis of Presentation and Summary of Significant Accounting Policies (Top Revenue Customers) (Details) (Customer Concentration Risk [Member])

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2013

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Exela (related party) [Member]

Exela (related party) [Member]

Merck [Member]

Merck [Member]

Merck [Member]

Merck [Member]

Merck [Member]

Novartis [Member]

Novartis [Member]

Novartis [Member]

Novartis [Member]

Novartis [Member]

Arch [Member]

Arch [Member]

Arch [Member]

Arch [Member]

Sales [Member]

Sales [Member]

Accounts Receivable [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Accounts Receivable [Member]

Accounts Receivable [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Sales [Member]

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Concentration Risk, Percentage

32.00%

30.00%

27.00%

28.00%

65.00%

25.00%

50.00%

25.00%

51.00%

12.00%

0.00%

20.00%

0.00%

0.00%

0.00%

12.00%

Basis_of_Presentation_and_Summ5

Basis of Presentation and Summary of Significant Accounting Policies (Anti-Dilutive Securities) (Details)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total shares excluded as anti-dilutive	7,189	6,898	7,189	6,898
Stock options [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total shares excluded as anti-dilutive	3,888	4,996	3,888	4,996
Restricted stock units [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total shares excluded as anti-dilutive	2,504	1,827	2,504	1,827
Performance stock units [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total shares excluded as anti-dilutive	722	0	722	0
Warrant [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total shares excluded as anti-dilutive	75	75	75	75

Collaborative_Arrangements_Det

Collaborative Arrangements (Details) (USD $)	3 Months Ended	0 Months Ended	3 Months Ended	6 Months Ended		3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2013	Feb. 01, 2012	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
		Merck [Member]	Merck [Member]	Merck [Member]	Merck [Member]	Arch [Member]	Arch [Member]	Arch [Member]	Arch [Member]	Arch [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]	'	'	'	'	'	'	'	'	'	'
Term of collaborative research and development agreement (years)	'	'5 years	'	'	'	'	'	'	'	'
Deferred Revenue	'	'	$2,500,000	$2,500,000	'	'	'	'	'	'
License and Services Revenue	500,000	'	500,000	1,000,000	800,000	'	'	'	'	'
Sales Revenue, Goods, Net	'	'	'	'	'	200,000	0	200,000	2,100,000	'
Allowance for Doubtful Accounts Receivable, Charge-offs	'	'	'	'	'	'	'	'	'	$387,000

Cash_Equivalents_and_Marketabl2

Cash Equivalents and Marketable Securities (Components of Cash Equivalents and Marketable Securities) (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified			Money market funds [Member]	Money market funds [Member]	Corporate bonds (unamortized cost) [Member]	U.S. Treasury obligations (unamortized cost) [Member]	Common shares of CO2 Solution [Member]	Common shares of CO2 Solution [Member]
Cash Equivalents and Marketable Securities [Line Items]	'	'	'	'	'	'	'	'
Adjusted Cost	$16,161	$19,654	$15,598	$16,089	$1,002	$2,000	$563	$563
Gross Unrealized Gains	890	235	0	0	3	0	890	232
Gross Unrealized Losses	0	0	0	0	0	0	0	0
Estimated Fair Value	$17,051	$19,889	$15,598	$16,089	$1,005	$2,000	$1,453	$795
Average Contractual Maturities (in days)	'	'	'	'	'140 days	'59 days	'	'

Fair_Value_Measurements_Schedu

Fair Value Measurements (Schedule of Financial Instruments Measured at Fair Value on Recurring Basis) (Details) (USD $)	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	$17,051	'	$19,889
Assets held for sale	292	1,394	2,179
Assets Held-for-sale [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Assets held for sale	292	'	2,179
Level 1 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	15,598	'	16,089
Level 1 [Member] | Assets Held-for-sale [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Assets held for sale	0	'	0
Level 2 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	1,453	'	3,800
Level 2 [Member] | Assets Held-for-sale [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Assets held for sale	0	'	0
Level 3 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	0	'	0
Level 3 [Member] | Assets Held-for-sale [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Assets held for sale	292	'	2,179
Money market funds [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	15,598	'	16,089
Money market funds [Member] | Level 1 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	15,598	'	16,089
Money market funds [Member] | Level 2 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	0	'	0
Money market funds [Member] | Level 3 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	0	'	0
Corporate bonds [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	1,005
Corporate bonds [Member] | Level 1 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	0
Corporate bonds [Member] | Level 2 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	1,005
Corporate bonds [Member] | Level 3 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	0
U.S. Treasury obligations [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	2,000
U.S. Treasury obligations [Member] | Level 1 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	0
U.S. Treasury obligations [Member] | Level 2 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	2,000
U.S. Treasury obligations [Member] | Level 3 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	'	'	0
Common shares of CO2 Solution [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	1,453	'	795
Common shares of CO2 Solution [Member] | Level 1 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	0	'	0
Common shares of CO2 Solution [Member] | Level 2 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	1,453	'	795
Common shares of CO2 Solution [Member] | Level 3 [Member]	'	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'	'
Total financial assets measured at fair value on a recurring basis	$0	'	$0

Balance_Sheets_Details_Invento

Balance Sheets Details (Inventory) (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Schedule of Inventory Components	'	'
Raw materials	$452	$763
Work in process	229	31
Finished goods	1,282	693
Inventory, net	$1,963	$1,487

Balance_Sheets_Details_Propert

Balance Sheets Details (Property and Equipment) (Details) (USD $)	3 Months Ended	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	$37,743	$37,743	'	$37,866
Less: accumulated depreciation and amortization	-31,064	-31,064	'	-29,461
Property and equipment, net, excluding construction in progress	6,679	6,679	'	8,405
Property and equipment	6,694	6,694	'	8,446
Less: Impairment of laboratory equipment	-1,841	-1,841	0	'
Property and equipment, net	4,853	4,853	'	8,446
Laboratory equipment [Member]	'	'	'	'
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	23,774	23,774	'	23,949
Leasehold Improvements [Member]	'	'	'	'
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	9,493	9,493	'	9,493
Computer equipment [Member]	'	'	'	'
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	3,249	3,249	'	3,196
Office equipment and furniture [Member]	'	'	'	'
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	1,227	1,227	'	1,228
Construction in Progress [Member]	'	'	'	'
Property, Plant and Equipment [Line Items]	'	'	'	'
Property and equipment, gross	$15	$15	'	$41

Balance_Sheets_Details_Intangi

Balance Sheets Details (Intangible Assets) (Details) (USD $)	3 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	$24,876	$24,876
Accumulated Amortization	-17,003	-15,316
Net Carrying Amount	7,873	9,560
2014 (remaining 6 months)	1,687	'
2015	3,374	'
2016	2,812	'
Customer Relationships [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	3,098	3,098
Accumulated Amortization	-3,098	-3,098
Net Carrying Amount	0	0
Weighted- Average Amortization Period	'5 years	'
Technology-Based Intangible Assets [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	1,534	1,534
Accumulated Amortization	-1,534	-1,534
Net Carrying Amount	0	0
Weighted- Average Amortization Period	'5 years	'
Intellectual Property [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	20,244	20,244
Accumulated Amortization	-12,371	-10,684
Net Carrying Amount	$7,873	$9,560
Weighted- Average Amortization Period	'6 years	'

Balance_Sheets_Details_Goodwil

Balance Sheets Details (Goodwill) (Details) (USD $)	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Balance Sheets Details [Abstract]	'	'	'
Changes in the carrying value of goodwill	$0	$0	'
Goodwill	$3,241,000	$3,241,000	$3,241,000

Assets_Held_for_Sale_Textual_D

Assets Held for Sale (Textual) (Details) (USD $)	1 Months Ended	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Mar. 31, 2014	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014	Jun. 30, 2013
Assets Held for Sale [Abstract]	'	'	'	'	'
Asset impairment charges	'	'	$1,571	'	'
Research & development equipment reclassified as held for use	'	333	'	'	'
Loss on exchange of assets	'	188	'	'	'
Change in estimated fair value of research equipment	'	568	'	'	'
Assets held for sale	1,394	292	2,179	292	'
Long Lived Assets Held-for-sale [Line Items]	'	'	'	'	'
Proceeds from sale of property and equipment	779	'	'	187	0
Gain (Loss) on Disposition of Property Plant Equipment	'	'	'	78	-141
UNITED STATES [Member]	'	'	'	'	'
Long Lived Assets Held-for-sale [Line Items]	'	'	'	'	'
Proceeds from sale of property and equipment	'	'	'	4	'
Gain (Loss) on Disposition of Property Plant Equipment	'	'	'	$2	'

Assets_Held_for_Sale_Details

Assets Held for Sale (Details) (USD $)	3 Months Ended		3 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014	Mar. 31, 2014	Mar. 31, 2014
			UNITED STATES [Member]	UNITED STATES [Member]	HUNGARY
Long Lived Assets Held-for-sale [Line Items]	'	'	'	'	'
Assets Held-for-sale, Beginning Balance	$1,394	$2,179	'	'	'
Assets sold	'	'	-13	-6	-779
Research & development equipment reclassified as held for use	-333	'	'	'	'
Loss on exchange of assets	-188	'	'	'	'
Change in estimated fair value of research equipment during three months ended June 30, 2014	-568	'	'	'	'
Assets Held-for-sale, Ending Balance	$292	$2,179	'	'	'

Sale_of_Hungarian_Subsidiary_D

Sale of Hungarian Subsidiary (Details) (USD $)	6 Months Ended		0 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Mar. 15, 2014	Mar. 13, 2014
			Hungarian Subsidiary [Member]	Hungarian Subsidiary [Member]
Income Statement, Balance Sheet and Additional Disclosures by Disposal Groups, Including Discontinued Operations [Line Items]	'	'	'	'
Equity Method Investment, Ownership Percentage	'	'	'	100.00%
Proceeds from sale of Hungarian subsidiary, net of selling costs	$1,500	$0	$1,500	'
Gain (Loss) on Sale of Stock in Subsidiary	$760	$0	$760	'

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Related Party Transaction [Line Items]	'	'	'	'
Revenue sharing arrangement	$2,128,000	$417,000	$4,071,000	$1,461,000
Exela PharmaSci, Inc [Member]	'	'	'	'
Related Party Transaction [Line Items]	'	'	'	'
Accounts Receivable, Related Parties	0	'	0	'
Director [Member]	'	'	'	'
Related Party Transaction [Line Items]	'	'	'	'
Related Party Transaction, Expenses from Transactions with Related Party	30,000	30,000,000	60,000	60,000,000
Accounts Payable, Related Parties	$30,000	'	$30,000	'
Parent Company [Member] | CMEA Ventures [Member] | Affiliated Entity [Member]	'	'	'	'
Related Party Transaction [Line Items]	'	'	'	'
Investment, Ownership Percentage	7.60%	'	7.60%	'
Exela PharmaSci, Inc [Member] | CMEA Ventures [Member] | Affiliated Entity [Member]	'	'	'	'
Related Party Transaction [Line Items]	'	'	'	'
Investment, Ownership Percentage	10.00%	'	10.00%	'

Commitments_and_Contingencies_1

Commitments and Contingencies (Textual) (Details) (USD $)	1 Months Ended	3 Months Ended	6 Months Ended	12 Months Ended			6 Months Ended
	Mar. 31, 2014	Jun. 30, 2014	Jun. 30, 2014	Dec. 31, 2012	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014
	extension			Fifth Amendment [Member]	Sixth Amendment [Member]	Headquarters, Redwood City [Member]	Penobscot Space, Building 2 Space, and Saginaw Space [Member]	Chesapeake Space [Member]
						Fifth Amendment [Member]	Fifth Amendment [Member]
						sqft
Commitments and Contingencies [Line Items]	'	'	'	'	'	'	'	'
Lease area space occupancy (square feet)	'	'	'	'	'	107,000	'	'
Expiration date of lease	'	'	'	'	'	'	31-Jan-20	31-Jan-17
Payments for Capital Improvements	'	'	'	$3,600,000	'	'	'	'
Tenant Reimbursements	'	'	'	3,100,000	'	'	'	'
Incentive from Lessor	'	1,948,000	1,948,000	'	'	'	'	'
Term of sublease	'3 years	'	'	'	'	'	'	'
Number of sublease renewal options	2	'	'	'	'	'	'	'
Term of sublease renewal	'1 year	'	'	'	'	'	'	'
Sublease income	'	100,000	100,000	'	'	'	'	'
Letters of credit	'	'	'	'	707,000	'	'	'
Asset retirement obligations	'	109,000	109,000	'	'	'	'	'
Estimated obligation payable	'	$600,000	$600,000	'	'	'	'	'

Commitments_and_Contingencies_2

Commitments and Contingencies (Future Minimum Lease Payments) (Details) (USD $)	Jun. 30, 2014
In Thousands, unless otherwise specified
Future minimum payments under non-cancellable operating leases	'
Lease payments, 6 months ending December 31, 2014	$1,338
Lease payments, Year ending December 31, 2015	2,743
Lease payments, Year ending December 31, 2016	2,827
Lease payments, Year ending December 31, 2017	2,677
Lease payments, Year ending December 31, 2018	2,736
Lease payments, Year ending December 31, 2019 and beyond	3,054
Lease payments, Total	$15,375

StockBased_Compensation_Textua

Stock-Based Compensation (Textual) (Details) (USD $)	Jun. 30, 2014	Mar. 31, 2010	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
In Millions, except Share data, unless otherwise specified	2010 Plan [Member]	2010 Plan [Member]	Stock options [Member]	Restricted stock units [Member]	Performance stock units [Member]	Performance stock units [Member]	Performance stock units [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'	'	'	'
Shares reserved for future issuance (shares)	'	1,100,000	'	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Number of Shares Available for Grant	5,400,000	'	'	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Non-Option Equity Instruments, Granted	'	'	'	'	775,000	523,048	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number	'	'	'	'	'	'	358,308
Employee Service Share-based Compensation, Nonvested Awards, Compensation Not yet Recognized, Stock Options	'	'	$2	'	'	'	'
Employee Service Share-based Compensation, Nonvested Awards, Compensation Not yet Recognized, Share-based Awards Other than Options	'	'	'	$3.80	$0.90	'	'

StockBased_Compensation_StockB

Stock-Based Compensation (Stock-Based Compensation Expense) (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	$1,346	$1,262	$2,575	$2,735
Stock options [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	320	531	596	1,141
Restricted stock units [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	792	604	1,661	1,296
Performance stock units [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	234	127	318	298
Research and development [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	268	502	507	1,706
Selling, general and administrative [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	$1,078	$760	$2,068	$1,029

StockBased_Compensation_Valuat

Stock-Based Compensation (Valuation Assumptions) (Details) (Stock options [Member], Stock options [Member], USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Expected term (in years)	'0 years	'6 years	'6 years	'6 years
Volatility	0.00%	65.20%	63.94%	65.20%
Risk-free interest rate	0.00%	1.13%	0.19%	'
Dividend yield	0.00%	0.00%	0.00%	0.00%
Weighted-average estimated fair value of stock options granted	$0	$1.26	$1.15	$1.36
Minimum [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Risk-free interest rate	'	'	'	1.07%
Maximum [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'	'
Risk-free interest rate	'	'	'	1.13%

Stockholders_Equity_Textual_De

Stockholders' Equity (Textual) (Details) (USD $)	6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013
Equity [Abstract]	'	'
Stock options exercised	61,331	'
Weighted average exercise price of stock options exercised	$1.01	'
Proceeds from exercises of stock options	$62	$281

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014
Available-for-sale Securities Adjustment, Net of Tax [Roll Forward]	'
Beginning Balance	($32)
Other comprehensive income	405
Amounts reclassified to interest income	1
Ending Balance	374
Accumulated Other Comprehensive Income	'
Beginning Balance	-32
Other comprehensive income	405
Amounts reclassified to interest income	1
Ending Balance	$374

Stockholders_Equity_Warrants_D

Stockholders' Equity (Warrants) (Details) (USD $)	Jun. 30, 2014
Warrants Issued on July 17, 2007 and Expiring on February 9, 2016 [Member]	'
Class of Warrant or Right [Line Items]	'
Shares Subject to warrants	2,834
Exercise Price per Share	$12.45
Warrants Issued on September 28, 2007 and Expiring on September 28, 2017 [Member]	'
Class of Warrant or Right [Line Items]	'
Shares Subject to warrants	72,727
Exercise Price per Share	$8.25

Revenues_by_Geographic_Area_De

(Revenues by Geographic Area) (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	$6,570	$6,974	$13,644	$18,455
UNITED STATES [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	4,197	2,181	7,771	4,301
India [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	324	289	411	2,508
Singapore [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	0	3,073	0	6,721
Other Asian Countries [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	339	254	680	543
IRELAND [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	784	0	2,744	1,219
Other European Countries [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	910	1,177	2,022	3,163
Other Countries [Member]	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'
Total Revenues	$16	$0	$16	$0

LongLived_Assets_by_Geographic

(Long-Lived Assets by Geographic Area) (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Schedule of long-lived assets by geographical area	'	'
Total long-lived assets	$12,726	$18,312
UNITED STATES [Member]	'	'
Schedule of long-lived assets by geographical area	'	'
Total long-lived assets	12,726	16,189
Europe [Member]	'	'
Schedule of long-lived assets by geographical area	'	'
Total long-lived assets	$0	$2,123

Restructuring_Textual_Details

Restructuring (Textual) (Details) (USD $)	3 Months Ended	12 Months Ended			3 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Jun. 30, 2014	Mar. 31, 2014
	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	Quarter Four Two Thousand Thirteen Restructuring Plan [Member]
	employee		Research and Development Expense [Member]	Selling, General and Administrative Expenses [Member]
Restructuring Cost and Reserve [Line Items]	'	'	'	'	'	'
Employee terminations (employee)	15	'	'	'	'	'
Restructuring Charges	'	$809	$573	$236	'	'
Restructuring Reserve, Settled with Cash	'	'	'	'	$0	($238)

Restructuring_Changes_in_Restr

Restructuring (Changes in Restructuring Accrual) (Details) (Quarter Four Two Thousand Thirteen Restructuring Plan [Member], USD $)	3 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Mar. 31, 2014
Quarter Four Two Thousand Thirteen Restructuring Plan [Member]	'	'
Summary of changes in restructuring accrual	'	'
Beginning balance	$0	$277
Cash payments	0	-238
Adjustments to previously accrued charges	0	-39
Ending balance	$0	$0

Subsequent_Event_Details

Subsequent Event (Details) (Subsequent Event [Member], USD $)	1 Months Ended
	Jul. 31, 2014
Subsequent Event [Member]	'
Subsequent Event [Line Items]	'
Milestone agreement value	$25,000,000
Proceeds from license fees received	6,000,000
Milestones receivable	19,000,000
Term of milestone agreement	'2 years
Minimum milestone receivable	5,750,000
Maximum milestone receivable	$38,500,000