Codexis (CDXS) 10-Q 12 Nov 13 2013 Q3 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	9 Months Ended
	Sep. 30, 2013	Oct. 25, 2013
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'CODEXIS INC	'
Entity Central Index Key	'0001200375	'
Document Type	'10-Q	'
Document Period End Date	30-Sep-13	'
Amendment Flag	'false	'
Document Fiscal Year Focus	'2013	'
Document Fiscal Period Focus	'Q3	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Accelerated Filer	'
Entity Common Stock, Shares Outstanding	'	38,105,532

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$26,911	$32,003	[1]
Marketable securities	3,009	13,524	[1]
Accounts receivable, net of allowances of $478 and $150 at September 30, 2013 and December 31, 2012, respectively	2,688	7,545	[1]
Inventories	2,101	1,302	[1]
Prepaid expenses and other current assets	1,935	5,395	[1]
Total current assets	36,644	59,769	[1]
Restricted cash	911	1,511	[1]
Non-current marketable securities	1,067	3,623	[1]
Property and equipment, net	13,809	16,650	[1]
Intangible assets, net	10,403	12,934	[1]
Goodwill	3,241	3,241	[1]
Other non-current assets	361	2,237	[1]
Total assets	66,436	99,965	[1]
Current liabilities:	'	'
Accounts payable	1,490	3,654	[1]
Accrued compensation	3,340	3,495	[1]
Other accrued liabilities	2,140	6,948	[1]
Deferred revenues	2,248	2,186	[1]
Total current liabilities	9,218	16,283	[1]
Deferred revenues, net of current portion	1,161	1,299	[1]
Other long-term liabilities	5,183	3,943	[1]
Commitments and contingencies (note 8)	'	'	[1]
Stockholders’ equity:	'	'
Common stock	4	4	[1]
Additional paid-in capital	297,776	294,128	[1]
Accumulated other comprehensive income (loss)	139	-136	[1]
Accumulated deficit	-247,045	-215,556	[1]
Total stockholders’ equity	50,874	78,440	[1]
Total liabilities and stockholders’ equity	$66,436	$99,965	[1]
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Condensed_Consolidated_Balance1

Condensed Consolidated Balance Sheets (Parenthetical) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Statement of Financial Position [Abstract]	'	'
Accounts receivable, allowances	$478	$150

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Revenues:	'	'	'	'
Product	$1,076	$7,140	$15,161	$29,090
Collaborative research and development	2,867	18,569	7,236	49,049
Government awards	0	632	0	2,247
Total revenues	3,943	26,341	22,397	80,386
Costs and operating expenses:	'	'	'	'
Cost of product revenues	494	6,397	9,790	24,868
Research and development	6,831	14,191	22,776	46,190
Selling, general and administrative	5,832	7,909	21,126	24,093
Total costs and operating expenses	13,157	28,497	53,692	95,151
Loss from operations	-9,214	-2,156	-31,295	-14,765
Interest income	9	61	53	210
Other expenses	-22	-45	-288	-320
Loss before (benefit) provision for income taxes	-9,227	-2,140	-31,530	-14,875
(Benefit) provision for income taxes	35	169	-41	443
Net loss	($9,262)	($2,309)	($31,489)	($15,318)
Net loss per share, basic and diluted (dollars per share)	($0.24)	($0.06)	($0.83)	($0.42)
Weighted average common shares used in computing net loss per share, basic and diluted (shares)	38,102	37,116	38,002	36,494

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Statement of Other Comprehensive Income [Abstract]	'	'	'	'
Net loss	($9,262)	($2,309)	($31,489)	($15,318)
Other comprehensive income (loss):	'	'	'	'
Foreign currency translation adjustments	0	0	0	165
Unrealized gain (loss) on marketable securities, net of tax of $17 and $172 for the three and nine months ended September 30, 2013, and $58 and $58 for the three and nine months ended September 30, 2012	32	724	275	88
Other comprehensive income	32	724	275	253
Total comprehensive loss	($9,230)	($1,585)	($31,214)	($15,065)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Comprehensive Loss (Parenthetical) (USD $)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Statement of Other Comprehensive Income [Abstract]	'	'	'	'
Unrealized gain (loss) on marketable securities, tax	$17	$58	$172	$58

Condensed_Consolidated_Stateme3

Condensed Consolidated Statements of Cash Flows (USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013		Sep. 30, 2012
Operating activities:	'		'
Net loss	($31,489)		($15,318)
Adjustments to reconcile net loss to net cash used in operating activities:	'		'
Amortization of intangible assets	2,531		2,665
Depreciation and amortization of property and equipment	5,307		6,822
Loss on disposal of property and equipment	62		93
Allowance for bad debt	328		0
Stock-based compensation	3,361		4,543
Accretion of asset retirement obligation	0		22
Impairment of marketable securities	'		753
(Accretion of discount) amortization of premium on marketable securities	-63		508
Changes in operating assets and liabilities:	'		'
Accounts receivable	833		2,390
Inventories	-614		1,727
Prepaid expenses and other current assets	4		-2,824
Other assets	-37		-1,321
Accounts payable	-2,164		-4,077
Accrued compensation	-155		-2,077
Other accrued liabilities	1,080		581
Deferred revenues	1,923		-1,642
Net cash used in operating activities	-19,093		-7,155
Investing activities:	'		'
Decrease in restricted cash	600		0
Purchase of property and equipment	-447		-2,632
Purchase of marketable securities	0		-20,638
Proceeds from sale of marketable securities	0		8,376
Proceeds from maturities of marketable securities	13,410		20,800
Proceeds from disposal of property and equipment	150		0
Net cash provided by investing activities	13,713		5,906
Financing activities:	'		'
Proceeds from exercises of stock options	288		894
Net cash provided by financing activities	288		894
Effect of exchange rate changes on cash and cash equivalents	0		166
Net decrease in cash and cash equivalents	-5,092		-189
Cash and cash equivalents at the beginning of the period	32,003	[1]	25,762
Cash and cash equivalents at the end of the period	26,911		25,573
Long term deposit in other assets transferred to property and equipment	$1,912		$0
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Description_of_Business

Description of Business	9 Months Ended
	Sep. 30, 2013
Description of Business [Abstract]	'
Description of Business	'
	Description of Business
	Codexis, Inc. (the "Company") was incorporated in the state of Delaware in January 2002. The Company engineers enzymes for the pharmaceutical and complex chemistry industries. 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.
	The Company has commercialized its technology and products in the pharmaceuticals market, which is its primary business focus. There are currently over 50 pharmaceutical firms using its 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 assists customers in discovering or enhancing enzymes variants 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 Condensed 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	9 Months Ended
	Sep. 30, 2013
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, 2012. The condensed consolidated balance sheet at December 31, 2012 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 September 30, 2013 and results of its operations, comprehensive loss and cash flows for the three and nine months ended September 30, 2013 and 2012. 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, 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, intangible assets, goodwill arising out of business acquisitions, inventories, accrued liabilities, common stock, and stock options 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.
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash and cash equivalents, marketable securities, accounts receivable and restricted cash. Cash and cash equivalents, marketable securities and restricted cash are invested through banks and other financial institutions in the United States, as well as in other foreign countries. Such deposits may be in excess of insured limits.
	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.
	The Company's top five customers accounted for 59% and 81% of the Company's total revenues for the three and nine months ended September 30, 2013. Accounts receivable balances for the top five customers were 89% and 84% of total balances as of September 30, 2013 and December 31, 2012, respectively. Major customers that represent more than 10% of total Company revenue include Customer A at 34% and 47% and Customer B at 21% and 10% for the three and nine months ended September 30, 2013, respectively.
	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
	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. Marketable securities included in current assets are comprised of corporate bonds, commercial paper, and United States Treasury obligations. Marketable securities included in non-current assets are comprised of corporate bonds and United States Treasury obligations that have a maturity date greater than one year. 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. Based on these evaluation criteria, the Company concluded during the third quarter of 2012 the unrealized losses related to its equity investment in the common shares of CO2 Solutions were other-than-temporary and as a result, the Company recorded $0.8 million as a selling, general and administrative expense in its condensed consolidated statement of operations (see Note 6). As of September 30, 2013, 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 September 30, 2013, 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 during the three and nine months ended September 30, 2013 and 2012.
	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 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, and represents the basis for all of its identifiable cash flow generating capacity. The Core IP consist of 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.
	The Core IP is the only finite-lived intangible asset on the balance sheet as of September 30, 2013 and is considered the primary asset within the Asset Group. The Core IP is being amortized ratably over the six years from the acquisition date. There has been no significant change in the utilization of the Core IP since the Company acquired the technology patent portfolio from Maxygen. 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 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 anticipated future cash flows include the Company's 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.
	As of September 30, 2013, the Company determined that its projected annual operating losses, the potential impact of the Dyadic notice from Dyadic International, Inc. (see Note 8), and the decreasing market price of the Company’s common stock were indicators of impairment. Consequently, the Company tested its long-lived assets and intangible assets for impairment as of September 30, 2013. This approach is consistent with the Company’s impairment analysis performed as of December 31, 2012, as described in the Company's Annual Report on Form 10-K for the year ended December 31, 2012.
	The Company performed the recoverability test and calculated estimated cashflows through the remaining period of the estimated useful life of the Core IP. The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 18% (“Estimated Weighted-Average Cost of Capital”), long term growth rate of 2%, and a capitalization factor of 6.25. The 18% discount rate reflects the nature and the risk of the underlying forecast, and includes such financial components as the risk free rate, systemic stock price risk based on an evaluation with peer companies (“beta”), equity risk premium, size premium, and company specific risk. The long term growth rate of 2% reflects projected inflation and general economic conditions. While the methodology for determining recoverability was consistent with that used in the Company's impairment analysis performed as of December 31, 2012, certain assumptions changed in the third quarter based on activity within the quarter, including reduced anticipated future cashflows related to potential CodeXyme® and CodeXol® transactions and reduced future revenue growth to reflect the Company’s most recent outlook. Following this analysis, the Company determined that its estimated future undiscounted cash flows for the Asset Group are greater than the carrying value of the Asset Group Core IP asset fair value as of September 30, 2013.
	The Company supplementally performed an analysis to determine the fair value of the Core IP. In determining the fair value, the Company prepared cash flow forecasts over the remaining economic life of the Core IP primarily related to final patent expiration from the Maxygen patent portfolio. The Company utilized the multi-period Excess Earnings model and obtained key financial inputs from review of market participants, Company specific factors and generally accepted valuation methods. The Company utilized a discount rate of 19% which reflects the nature and the risk of the underlying forecast and includes other financial components.
	Based on these estimates, judgments and factors, the Company has determined that the fair value of the Core IP exceeded its carrying value by 38% as of September 30, 2013. No impairment loss was recorded as of September 30, 2013.
	Valuation of Goodwill
	The Company reviews goodwill impairment annually 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, and accordingly, all of the goodwill is associated with the Company. 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 shareholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of our 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 our common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.
	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 as of October 1, 2012, the date of the Company's annual impairment review. The Company concluded that the fair value of the reporting unit exceeded the carrying value and no impairment existed. No impairment charges were recorded through September 30, 2013.
	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 and for the purpose of securing a working capital line of credit.
	Revenue Recognition
	The Company has generally recognized revenue from multiple element arrangements under collaborative research agreements, including license payments, research and development services, milestones, and royalties. Revenue arrangements with multiple deliverables are divided into separate units of accounting if certain criteria are met.
	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 product revenues, collaborative research and development agreements and government awards. Collaborative 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 equivalent (“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 by the Company's customers.
	Up-front fees received in connection with collaborative 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.
	Income Taxes
	The Company uses the liability method of accounting for income taxes. Deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the consolidated financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets are recognized for deductible temporary differences, along with net operating loss (“NOL”) carry forwards, if it is more likely than not that the tax benefits will be realized. To the extent a deferred tax asset cannot be recognized under the preceding criteria, a valuation allowance is established. Deferred tax assets and liabilities are measured using enacted tax rates in effect for the year in which those temporary differences are expected to be recovered or settled. The Company recognizes the financial statement effects of an uncertain tax position when it is more likely than not, based on the technical merits, that the position will be sustained upon examination.
	Net Loss per Share
	Basic net loss per share of common stock is computed by dividing the net loss by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potential common shares, consisting of stock options, warrants and redeemable convertible preferred stock, to the extent dilutive. Basic and diluted net loss per share of common stock was the same for each period presented as the inclusion of all potential common shares outstanding was anti-dilutive.
	The following options to purchase common stock, restricted stock units and warrants to purchase common stock were excluded from the computation of diluted net loss per share of common stock for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,		Nine Months Ended September 30,
		2013	2012	2013	2012
	Options to purchase common stock	4,805	7,228	4,805	7,228
	Restricted stock units	1,665	839	1,665	839
	Warrants to purchase common stock	75	260	75	260
	Total	6,545	8,327	6,545	8,327
	Recently Issued and Adopted Accounting Guidance
	In February 2013, the Financial Accounting Standard Board ("FASB") issued ASU 2013-02 related to the reporting of amounts reclassified out of accumulated other comprehensive income that requires entities to report, either on their income statement or in a footnote to their financial statements, the effects on earnings from items that are reclassified out of other comprehensive income. The Company adopted this accounting standard on January 1, 2013, and the adoption of this guidance did not have a material impact on the financial statements.

Collaborative_Research_and_Dev

Collaborative Research and Development Agreements	9 Months Ended
	Sep. 30, 2013
Collaborative Research and Development Agreements [Abstract]	'
Collaborative Research and Development Agreements	'
	Collaborative Research and Development Agreements
	Shell and Raízen
	In November 2006, the Company entered into a collaborative research agreement and a license agreement with Shell to develop biocatalysts and associated processes that use such biocatalysts.
	In November 2007, the Company entered into a new and expanded five-year collaborative research agreement (“Shell Research Agreement”) and a license agreement (the “Shell License Agreement”) with Shell. In connection with the Shell Research Agreement, the Company agreed to use its proprietary technology platform to discover and develop enzymes and microorganisms for use in converting cellulosic biomass into biofuels and related products and Shell agreed to pay (i) research funding at specified rates per FTE working on the project during the research term, (ii) payments upon the achievement of milestones, and (iii) royalties on future product sales. The Shell Research Agreement also specified certain minimum levels of FTE services that the Company was required to allocate to the collaboration efforts that increased over the term of the agreement, which was originally set to expire on November 1, 2012.
	In September 2012, the Company entered into an agreement with Shell (the “New Shell Agreement”) which among other things, terminated the Shell Research Agreement effective August 31, 2012, except for certain provisions of the Shell Research Agreement which survived such termination, including provisions regarding intellectual property rights, patent prosecution and maintenance, confidentiality and indemnification. The New Shell Agreement required Shell to pay approximately $7.5 million as full, complete and final satisfaction of amounts that Shell may have owed the Company under the Shell Research Agreement with respect to (i) FTEs assigned to the Shell Research Agreement and (ii) milestones achieved or achievable by the Company under the Shell Research Agreement. The $7.5 million was recognized as revenue during the third quarter of 2012 when all of the Company's obligations were fulfilled under the New Shell Agreement and was collected during the fourth quarter of 2012.
	Under the New Shell Agreement, Shell granted the Company royalty-bearing, non-exclusive rights and licenses to develop, manufacture, use and sell biocatalysts and microbes in the field of converting cellulosic biomass into fermentable sugars on a worldwide basis, except for Brazil, where such sugars are converted into liquid fuels, fuel additives or lubricants (the “Field of Use”). Raízen Energia S.A. (“Raízen”) holds the exclusive rights to use the Company's enzymes and microbes for converting cellulosic biomass into fermentable sugars in Brazil, where such sugars are converted into ethanol.
	Under the New Shell Agreement, the Company also granted to Shell a non-exclusive, royalty-free license to manufacture, use and import, solely for the use of Shell and its affiliates, (i) enzymes developed by the Company during the ten year period following August 31, 2012 outside of the Shell Research Agreement for use in the Field of Use and (ii) improvements to any microbe developed by the Company during the ten year period following August 31, 2012 outside of the Shell Research Agreement that is derivative of an identified microbe for use in the Field of Use. Shell remained subject to existing royalty obligations to the Company for future sales of products covered by the intellectual property and technology that remained exclusively licensed to Shell under the License Agreement.
	The New Shell Agreement has a term that commences on August 31, 2012 and continues until the later of August 31, 2032 or the date of the last to expire patent rights included in the Company's collaboration that claim a biocatalyst or a microbe for use in the Field of Use.
	Research and Development Collaboration
	On February 1, 2012, the Company entered into a five year Sitagliptin Catalyst Supply Agreement ("Sitagliptin Agreement") whereby Merck Sharp and Dohme Corp. ("Merck") may obtain commercial scale substance for their use in the manufacture of their products. Merck may extend the term of the Sitagliptin Agreement for an additional five years at its sole discretion.
	The Sitagliptin 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 Agreement. As of September 30, 2013, the Company has a deferred revenue balance of $1.2 million from Merck related to the license fee. The license fee is being recognized as collaborative research and development revenue ratably over the five year term of the Sitagliptin Agreement. During the three and nine months ended September 30, 2013, the Company recognized $0.5 million and $1.3 million of the license fee as collaborative research and development revenue. Pursuant to the Sitagliptin Agreement, Merck may purchase substance from the Company for a fee based on contractually stated prices. No product revenue was recognized during the three months ended September 30, 2013 under the Sitagliptin Agreement. During the nine months ended September 30, 2013, the Company recognized $0.5 million in product revenue related to the agreement. No revenue was recognized under the Sitagliptin Agreement during the three and nine months ended September 30, 2012.
	Manufacturing Collaboration
	In November 2012, the Company entered into a commercial arrangement with Arch Pharmalabs Limited ("Arch") by simultaneously terminating all of the Company's existing supply agreements with Arch and entering into the New Arch Enzyme Supply Agreement pursuant to which Arch agreed to exclusively purchase enzymes from the Company for use in the manufacture of certain of Arch's products and the Company agreed to exclusively supply, with limited exceptions, certain of the Company's enzymes to Arch at an agreed upon price for use in such manufacture. Under the New Arch Enzyme Supply Agreement, Arch will no longer produce atorva-family active pharmaceutical ingredients (“APIs”) and intermediates for the Company. Arch will instead market these products directly to end customers, and as a result Arch will no longer pay the Company royalties on their sale of such APIs and intermediates to customers and the Company will no longer have exclusive rights to market such APIs and intermediates in certain markets. No revenue was recognized under the New Arch Enzyme Supply Agreement during the three months ended September 30, 2013. For the nine months ended September 30, 2013, the Company recognized $2.1 million in product revenue for the sale of enzyme inventory to Arch pursuant to the agreement. Royalty revenues earned from Arch under the prior agreements were $0.05 million and $0.1 million for the three and nine months ended September 30, 2012 and are reflected in collaborative research and development revenue on the condensed consolidated statement of operations.

Balance_Sheets_Details

Balance Sheets Details	9 Months Ended
	Sep. 30, 2013
Balance Sheets Details [Abstract]	'
Balance Sheets Details	'
	Balance Sheets Details
	Inventory, net
	Inventory, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Raw materials	$	802		$	588
	Work in process	235			52
	Finished goods	1,064			662
	Inventory, net	$	2,101		$	1,302
	Property and Equipment, net
	Property and equipment, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Laboratory equipment	$	35,311		$	33,776
	Leasehold improvements	11,108			11,099
	Computer equipment	3,419			4,388
	Office furniture and equipment	1,503			1,531
		51,341			50,794
	Less: accumulated depreciation	(37,780		)	(34,172		)
		13,561			16,622
	Construction in progress	248			28
	Property and equipment, net	$	13,809		$	16,650
	Accumulated Other Comprehensive Income (Loss)
	The changes in accumulated other comprehensive income (loss) by component and related tax effects were as follows (in thousands):
	Balance as of December 31, 2012	$	(136	)
	Unrealized gains (losses) on available-for-sale securities	447
	Tax effects	(172		)
	Balance as of September 30, 2013	$	139

Cash_Equivalents_and_Marketabl

Cash Equivalents and Marketable Securities	9 Months Ended
	Sep. 30, 2013
Cash Equivalents and Marketable Securities [Abstract]	'
Cash Equivalents and Marketable Securities	'
	Cash Equivalents and Marketable Securities
	At September 30, 2013, cash equivalents and marketable securities consisted of the following (in thousands):
		September 30, 2013
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	21,079	$	—	$	—	$	21,079	n/a
	Corporate bonds (unamortized cost)	1,004		3		—		1,007		151
	U.S. Treasury obligations (unamortized cost)	2,000		2		—		2,002		232
	Common shares of CO2 Solutions	563		$	504	$	—	1,067		n/a
	Total	$	24,646	$	509	$	—	$	25,155
	The total cash and cash equivalents balance of $26.9 million as of September 30, 2013 was comprised of money market funds of $21.1 million, and $5.8 million held as cash, primarily with major financial institutions in North America. At September 30, 2013, we had no marketable securities in an unrealized loss position.
	At December 31, 2012, cash equivalents and marketable securities consisted of the following (in thousands):
		31-Dec-12
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	24,789	$	—	$	—	$	24,789	n/a
	Commercial paper	1,499		1		—		1,500		70
	Corporate bonds (unamortized cost)	9,512		10		—		9,522		156
	U.S. Treasury obligations (unamortized cost)	5,510		5		—		5,515		262
	Common shares of CO2 Solutions	563		47		—		610		n/a
	Total	$	41,873	$	63	$	—	$	41,936
	The total cash and cash equivalents balance of $32.0 million as of December 31, 2012, was comprised of money market funds of $24.8 million and $7.2 million held as cash, primarily with major financial institutions in North America. At December 31, 2012, we had no marketable securities in an unrealized loss position.

Fair_Value_Measurements

Fair Value Measurements	9 Months Ended
	Sep. 30, 2013
Fair Value, Assets and Liabilities 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.
	The following table presents the financial instruments that were measured at fair value on a recurring basis at September 30, 2013 by level within the fair value hierarchy (in thousands):
		30-Sep-13
		Level 1		Level 2		Level 3		Total
	Money market funds	$	21,079	$	—	$	—	$	21,079
	Corporate bonds	—		1,007		—		1,007
	U.S. Treasury obligations	—		2,002		—		2,002
	Common shares of CO2 Solutions	—		1,067		—		1,067
	Total	$	21,079	$	4,076	$	—	$	25,155
	The following table presents the financial instruments that were measured at fair value on a recurring basis at December 31, 2012 by level within the fair value hierarchy (in thousands):
		31-Dec-12
		Level 1		Level 2		Level 3		Total
	Money market funds	$	24,789	$	—	$	—	$	24,789
	Commercial paper	—		1,500		—		1,500
	Corporate bonds	—		9,522		—		9,522
	U.S. Treasury obligations	—		5,515		—		5,515
	Common shares of CO2 Solutions	610		—		—		610
	Total	$	25,399	$	16,537	$	—	$	41,936
	Cash balances at financial institutions of $5.8 million and $7.2 million as of September 30, 2013 and December 31, 2012, respectively, are not included in the above tables as they are not considered financial instruments. The Company estimated the fair value of its investment in 10,000,000 common shares of CO2 Solutions using the market value of common shares as determined based upon quoted prices on the TSX Venture Exchange. There were no other-than-temporary impairments noted as of September 30, 2013.

Related_Party_Transactions

Related Party Transactions	9 Months Ended
	Sep. 30, 2013
Related Party Transaction, Due from (to) Related Party [Abstract]	'
Related Party Transactions	'
	Related Party Transactions
	Shell and Raízen
	In June 2011, Shell completed the transfer of all of its equity interests in the Company, together with the associated right to appoint one member to the Company's board of directors, to Raízen, Shell's joint venture with Cosan S.A. Indústria e Comércio, (“Cosan”) in Brazil. As a result, Shell is no longer considered a related party. Notwithstanding the above, Shell did not transfer the Shell Research Agreement to Raízen. Additionally in September 2011, the Company entered into a joint development agreement directly with Raízen. The work under this joint development agreement has been completed and we do not expect this project to continue.
	As of September 30, 2013, Raízen owns 5.6 million shares of the Company's common stock. During the three and nine months ended September 30, 2013, there was no material financial activity with Raízen.
	Raízen has exclusive rights to market and use CodeXyme® in Brazil. The Company is engaged in discussions with Raízen about obtaining rights to market CodeXyme® to all ethanol producers in Brazil.
	Exela PharmaSci, Inc.
	The Company signed a license agreement with Exela PharmaSci, Inc. (“Exela”) in 2007. A member of the Company's board of directors is also on the board of directors of Exela. Under the terms of the agreement, Exela would pay the Company a royalty based on their achievement of certain commercial goals. During the nine months ended September 30, 2013 and 2012, the Company recognized $2.3 million and $0.2 million of revenue, respectively, related to this arrangement, in the condensed consolidated statements of operations as collaborative research and development revenue.

Commitments_and_Contingencies

Commitments and Contingencies	9 Months Ended
	Sep. 30, 2013
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 occupies approximately 107,000 square feet of office and laboratory space in four buildings. On March 16, 2011, the Company entered into a lease with Metropolitan Life Insurance Company (“MetLife”) with respect to the Company's offices located at 200 and 220 Penobscot Drive, Redwood City, California, (the “Penobscot Space”), 400 Penobscot Drive, Redwood City, California (the “Building 2 Space”), and 101 Saginaw Drive, Redwood City, California (the “Saginaw Space”). Under the terms of the agreement, the leases for the Penobscot Space, the Building 2 Space and the Saginaw Space expire on January 31, 2020, and the Company has options to extend for two additional five-year periods.
	The Company also leases space with MetLife at 501 Chesapeake Drive, Redwood City, California (the “501 Chesapeake Space”). In September 2012, the Company extended the term of the lease, which would have otherwise expired on January 31, 2013, to January 31, 2017. Pursuant to this extension, the Company has two consecutive options to extend the term of the lease for the 501 Chesapeake Space for an additional five-year period per option.
	As part of the Q3 2012 Restructuring Plan, the Company has vacated the Saginaw Space and the Company has begun marketing the facility for sublease (see Note 12).
	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 $0.7 million as of September 30, 2013 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 September 30, 2013, the Company had estimated asset retirement obligations of approximately $0.1 million from operating leases, requiring the Company to restore the facilities that the Company is renting to their original form. The Company expenses 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 September 30, 2013 (in thousands):
		Lease payments
	3 months ending December 31,
	2013	$	719
	Years ending December 31,
	2014	2,947
	2015	3,031
	2016	3,047
	2017	2,677
	2018 and beyond	5,790
	Total	$	18,211
	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.
	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.
	Other Contingencies
	On July 30, 2013, the Company received notice (the “Dyadic notice”) from Dyadic International, Inc. (“Dyadic”) alleging that the Company is in breach under the License Agreement, dated as of November 14, 2008, by and among the Company, Dyadic International (USA), Inc. and Dyadic (the “Dyadic License Agreement”), and that Dyadic intended to terminate the contract in 60 days if the breach was not cured to Dyadic’s satisfaction. On September 10, 2013, the Company reached agreement with Dyadic to extend the Company's time for response to the allegations until November 15, 2013 as part of ongoing negotiations between the Company and Dyadic to resolve the matter. Pursuant to the Dyadic License Agreement, the Company obtained a non-exclusive license relating to Dyadic's C1-based proprietary fungal expression technology for the production of enzymes.The Dyadic notice does not seek damages or allege any underpayment of fees or royalties. The Company has concluded that the extension of the Dyadic negotiation period does not result in any impact to the financial statement as of September 30, 2013.
	In November 2009, one of the Company's foreign subsidiaries sold intellectual property to the Company's U.S. entity. Under the local laws, the sale of intellectual property to a nonresident legal entity is deemed an export and is not subject to value added tax. However, there is uncertainty regarding whether the items sold represented intellectual property or research and development services, which would subject the sale to value added tax. The Company believes that the uncertainty results in an exposure to pay value added tax 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 $0.6 million.

Warrants

Warrants	9 Months Ended
	Sep. 30, 2013
Warrants and Rights Note Disclosure [Abstract]	'
Warrants	'
	Warrants
	The Company's outstanding warrants are exercisable for common stock at any time during their respective terms. As of September 30, 2013, the following warrants remain outstanding:
	30-Sep-13
	Issue Date	Shares Subject	Exercise Price		Expiration
		to warrants	per Share
	July 17, 2007	2,384	$	12.45	February 9, 2016
	September 28, 2007	72,727	$	8.25	September 28, 2017

StockBased_Compensation

Stock-Based Compensation	9 Months Ended
	Sep. 30, 2013
Stockholders' Equity Note [Abstract]	'
Stock-Based Compensation	'
	Stock-Based Compensation
	In 2002, the Company adopted the 2002 Stock Plan (the “2002 Plan”), pursuant to which the Company's board of directors issued incentive stock options, non-statutory stock options (options that do not qualify as incentive stock options) and restricted stock to our employees, officers, directors or consultants. In March 2010, the board of directors and stockholders approved the 2010 Equity Incentive Award Plan (the “2010 Plan”), which became effective upon the completion of the Company's IPO in April 2010. 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.
	The following table presents the shares available for grant as of September 30, 2013 (in thousands):
		Shares available for grant
	31-Dec-12	3,767
	Annual increase in shares available for grant	1,507
	Option grants	(922	)
	Restricted stock unit award grants	(1,367	)
	Restricted stock unit award shares withheld for taxes	132
	Options forfeited	1,968
	Restricted stock unit awards forfeited	335
	30-Sep-13	5,420
	Stock-Based Compensation Expense
	The Company recognizes compensation expense related to share-based transactions, including the awarding of employee stock options, based on the estimated fair value of the awards granted. All awards granted, modified or settled after January 1, 2006 have been accounted for based on the fair value of the awards granted. The Company generally uses the straight-line method to allocate stock-based compensation expense to the appropriate reporting periods. Some awards are accounted for using the accelerated method as appropriate for the terms of the awards.
	The following table presents total stock-based compensation expense by functional areas included in the condensed consolidated statements of operations for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,					Nine Months Ended September 30,
		2013			2012		2013		2012
	Research and development	$	97		$	682	$	989	$	2,183
	Selling, general and administrative	529			784		2,372		2,360
	Total	$	626		$	1,466	$	3,361	$	4,543
	The following table presents total stock-based compensation expense by security types included in the condensed consolidated statements of operations for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,					Nine Months Ended September 30,
		2013			2012		2013		2012
	Stock options	$	397		$	900	$	1,538	$	3,255
	Restricted stock units	527			566		1,823		1,288
	Performance stock units	(298		)	—		—		—
	Total	$	626		$	1,466	$	3,361	$	4,543
	Stock Options
	The fair value of the options granted is estimated on the date of grant using the Black-Scholes option-pricing model. The fair value of the options granted to non-employees is remeasured as they vest, and the resulting change in value, if any, is recognized as an increase or decrease in stock-based compensation expense during the period the related services are rendered. The stock options are generally scheduled to vest over four years and all options expire no later than ten years from the date of grant.
	Restricted Stock Units
	The Company awarded 843,698 restricted stock units (“RSUs”) under the 2010 Plan during the nine months ended September 30, 2013. The fair value of the RSU awards was calculated based on the NASDAQ quoted stock price on the date of the grant with the expense recognized over the vesting period. The RSUs are generally scheduled to vest over four years.
	Performance Stock Units
	The Company awarded 523,048 performance stock units ("PSU") under the 2010 Plan during the nine months ended September 30, 2013. The number of shares of common stock to be issued for each vested performance stock unit ("PSU") will range between zero and two, depending on the level of performance against the criteria set by the Company's board of directors with respect to the Company's annual cash burn for the year ending December 31, 2013. A 100% achievement of the performance goal would result in one common share issued for each vested PSU. The PSU awards vest in equal installments on March 5, 2014 and March 5, 2015. The fair value of the PSU awards was calculated based on the NASDAQ quoted stock price on the date of the grant with the expense recognized on a straight-line basis over the vesting period. In the third quarter of 2013, the Company revised its estimate of forecasted performance criteria and concluded that the performance target would not likely be achieved in 2013. As a result of the revised estimate of the performance goal, the PSU-related compensation expense of $0.3 million recorded on a year to date basis was fully reversed at September 30, 2013.
	Stockholder Rights Plan
	In August 2012, the Company's board of directors adopted a stockholder rights plan and declared a dividend of one preferred share purchase right for each share of the Company's common stock held by stockholders of record as of September 18, 2012. Each right entitled stockholders, after the rights become exercisable, to purchase one one-thousandth of a share of the Company's Series A Junior Participating Preferred Stock, par value $0.0001, at a purchase price of $11.35 per one thousandth of a share of Series A Junior Participating Preferred Stock. In general, the rights become exercisable when a person or group acquires 15% or more of the Company's common stock or a tender offer for 15% or more of the Company's common stock is announced or commenced. The rights expired in accordance with the terms of the stockholder rights plan on September 2, 2013. Therefore, the shares of the Company's common stock are no longer accompanied by the rights, and the plan is of no further force or effect. As a result of the expiration, the Company recorded a related expense of $0.3 million in the third quarter of 2013.

Segment_Reporting

Segment Reporting	9 Months Ended
	Sep. 30, 2013
Segment Reporting Information, Operating Income (Loss) [Abstract]	'
Segment Reporting	'
	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 makers are its Chief Executive Officer and the board of directors. The Chief Executive Officer and 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. As such, the Company has determined that it operates in one segment because operating results are reported only on an aggregate basis to the Company's chief operating decision makers. Operations outside of the United States consist principally of research and development and sales activities.
	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 September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	Revenues
	Americas (1)	$	2,764	$	18,324	$	7,065	$	50,867
	Europe	757		1,056		5,139		8,986
	Asia
	India	213		5,800		2,721		15,761
	Singapore	—		631		6,721		3,884
	Others	209		530		751		888
		$	3,943	$	26,341	$	22,397	$	80,386
	-1	Primarily United States
	The following table represents identifiable long-lived assets in the corresponding regions (in thousands):
		September 30,		December 31,
		2013		2012
	Long-lived assets
	Americas (1)	$	19,863	$	25,953
	Europe (2)	4,391		5,157
	Asia	319		711
		$	24,573	$	31,821
	-1	Primarily United States
	-2	Primarily Hungary

Restructuring

Restructuring	9 Months Ended
	Sep. 30, 2013
Restructuring Costs [Abstract]	'
Restructuring	'
	Restructuring
	Q3 2012 Restructuring Plan
	As a result of the termination of the Shell Research Agreement, the Company initiated a series of cost reduction measures. During the third quarter of 2012, the Company's board of directors approved and committed to a restructuring plan ("the Q3 2012 Restructuring Plan”) to reduce the Company's cost structure which included approximately 173 employee terminations in the United States and Singapore and the closing of the Company's Singapore facility. Approximately 150 of the total 173 employee terminations impacted the research and development functions with the remaining 23 employees impacting the selling, general and administrative functions. The cost of the Q3 2012 Restructuring Plan was $2.4 million, comprised of $1.1 million of leasehold improvements write down, $0.7 million for employee severance and other termination benefits, $0.3 million for facility lease termination costs, and $0.3 million for equipment disposal charges.
	The remaining balance of $0.05 million related to facility closing costs under the Q3 2012 Restructuring Plan was paid in full in the third quarter of 2013.
	The table below summarizes the changes in the restructuring accrual for the Q3 2012 Restructuring Plan as of September 30, 2013 (in thousands):
		Severance, benefits			Facility closing costs			Total
		and related
		personnel costs
	Balance at December 31, 2012	$	100		$	320		$	420
	Cash payments	(74		)	(320		)	(394		)
	Adjustments to restructuring charges	(26		)	—			(26		)
	Balance at September 30, 2013	$	—		$	—		$	—
	Q1 2012 Restructuring Plan
	During the first quarter of 2012, the Company's board of directors approved and committed to a restructuring plan ("Q1 2012 Restructuring Plan") to reduce the Company's cost structure which included approximately 13 employees terminations in Hungary and the United States. The total cost of the Q1 2012 Restructuring Plan was $0.6 million comprised of employee severance and other termination benefits. During the nine months ended September 30, 2012, we made cash payments of $0.5 million related to these expenses. All remaining costs under the Q1 2012 Restructuring Plan were paid by December 31, 2012.

Subsequent_Events

Subsequent Events	9 Months Ended
	Sep. 30, 2013
Subsequent Events [Abstract]	'
Subsequent Events	'
	Subsequent Events
	On November 12, 2013, the Company announced that it will begin immediately to wind down its CodeXyme® cellulase enzymes program.  As a result, the Company has committed to a restructuring plan to reduce the cost structure to align with the Company's projected future revenues from its pharmaceutical business. The restructuring plan includes a reduction of approximately 16 employees in the United States.  The Company expects to record a charge of approximately $0.7 million in the fourth quarter of 2013, consisting primarily of employee severance and related benefits. Cash payments for restructuring related costs are expected to be completed by the end of the first quarter of 2014.

Basis_of_Presentation_and_Summ1

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	9 Months Ended
	Sep. 30, 2013
Accounting Policies [Abstract]	'
Basis of Presentation and 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, 2012. The condensed consolidated balance sheet at December 31, 2012 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 September 30, 2013 and results of its operations, comprehensive loss and cash flows for the three and nine months ended September 30, 2013 and 2012. 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, 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, intangible assets, goodwill arising out of business acquisitions, inventories, accrued liabilities, common stock, and stock options 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.
Concentrations of Credit Risk	'
	Concentrations of Credit Risk
	Financial instruments that potentially subject the Company to significant concentrations of credit risk consist primarily of cash and cash equivalents, marketable securities, accounts receivable and restricted cash. Cash and cash equivalents, marketable securities and restricted cash are invested through banks and other financial institutions in the United States, as well as in other foreign countries. Such deposits may be in excess of insured limits.
	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, Cash Equivalents and Marketable Securities
	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. Marketable securities included in current assets are comprised of corporate bonds, commercial paper, and United States Treasury obligations. Marketable securities included in non-current assets are comprised of corporate bonds and United States Treasury obligations that have a maturity date greater than one year. 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. Based on these evaluation criteria, the Company concluded during the third quarter of 2012 the unrealized losses related to its equity investment in the common shares of CO2 Solutions were other-than-temporary and as a result, the Company recorded $0.8 million as a selling, general and administrative expense in its condensed consolidated statement of operations (see Note 6). As of September 30, 2013, 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 September 30, 2013, 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 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, and represents the basis for all of its identifiable cash flow generating capacity. The Core IP consist of 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.
	The Core IP is the only finite-lived intangible asset on the balance sheet as of September 30, 2013 and is considered the primary asset within the Asset Group. The Core IP is being amortized ratably over the six years from the acquisition date. There has been no significant change in the utilization of the Core IP since the Company acquired the technology patent portfolio from Maxygen. 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 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 anticipated future cash flows include the Company's 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.
	As of September 30, 2013, the Company determined that its projected annual operating losses, the potential impact of the Dyadic notice from Dyadic International, Inc. (see Note 8), and the decreasing market price of the Company’s common stock were indicators of impairment. Consequently, the Company tested its long-lived assets and intangible assets for impairment as of September 30, 2013. This approach is consistent with the Company’s impairment analysis performed as of December 31, 2012, as described in the Company's Annual Report on Form 10-K for the year ended December 31, 2012.
	The Company performed the recoverability test and calculated estimated cashflows through the remaining period of the estimated useful life of the Core IP. The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 18% (“Estimated Weighted-Average Cost of Capital”), long term growth rate of 2%, and a capitalization factor of 6.25. The 18% discount rate reflects the nature and the risk of the underlying forecast, and includes such financial components as the risk free rate, systemic stock price risk based on an evaluation with peer companies (“beta”), equity risk premium, size premium, and company specific risk. The long term growth rate of 2% reflects projected inflation and general economic conditions. While the methodology for determining recoverability was consistent with that used in the Company's impairment analysis performed as of December 31, 2012, certain assumptions changed in the third quarter based on activity within the quarter, including reduced anticipated future cashflows related to potential CodeXyme® and CodeXol® transactions and reduced future revenue growth to reflect the Company’s most recent outlook. Following this analysis, the Company determined that its estimated future undiscounted cash flows for the Asset Group are greater than the carrying value of the Asset Group Core IP asset fair value as of September 30, 2013.
	The Company supplementally performed an analysis to determine the fair value of the Core IP. In determining the fair value, the Company prepared cash flow forecasts over the remaining economic life of the Core IP primarily related to final patent expiration from the Maxygen patent portfolio. The Company utilized the multi-period Excess Earnings model and obtained key financial inputs from review of market participants, Company specific factors and generally accepted valuation methods. The Company utilized a discount rate of 19% which reflects the nature and the risk of the underlying forecast and includes other financial components.
	Based on these estimates, judgments and factors, the Company has determined that the fair value of the Core IP exceeded its carrying value by 38% as of September 30, 2013. No impairment loss was recorded as of September 30, 2013.
Valuation of Goodwill	'
	Valuation of Goodwill
	The Company reviews goodwill impairment annually 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, and accordingly, all of the goodwill is associated with the Company. 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 shareholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of our 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 our common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.
	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 as of October 1, 2012, the date of the Company's annual impairment review. The Company concluded that the fair value of the reporting unit exceeded the carrying value and no impairment existed. No impairment charges were recorded through September 30, 2013.
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 and for the purpose of securing a working capital line of credit.
Revenue Recognition	'
	Revenue Recognition
	The Company has generally recognized revenue from multiple element arrangements under collaborative research agreements, including license payments, research and development services, milestones, and royalties. Revenue arrangements with multiple deliverables are divided into separate units of accounting if certain criteria are met.
	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 product revenues, collaborative research and development agreements and government awards. Collaborative 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 equivalent (“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 by the Company's customers.
	Up-front fees received in connection with collaborative 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.
Income Taxes	'
	Income Taxes
	The Company uses the liability method of accounting for income taxes. Deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the consolidated financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets are recognized for deductible temporary differences, along with net operating loss (“NOL”) carry forwards, if it is more likely than not that the tax benefits will be realized. To the extent a deferred tax asset cannot be recognized under the preceding criteria, a valuation allowance is established. Deferred tax assets and liabilities are measured using enacted tax rates in effect for the year in which those temporary differences are expected to be recovered or settled. The Company recognizes the financial statement effects of an uncertain tax position when it is more likely than not, based on the technical merits, that the position will be sustained upon examination.
Net Loss per Share	'
	Net Loss per Share
	Basic net loss per share of common stock is computed by dividing the net loss by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potential common shares, consisting of stock options, warrants and redeemable convertible preferred stock, to the extent dilutive. Basic and diluted net loss per share of common stock was the same for each period presented as the inclusion of all potential common shares outstanding was anti-dilutive.
Recently Issued and Adopted Accounting Guidance	'
	Recently Issued and Adopted Accounting Guidance
	In February 2013, the Financial Accounting Standard Board ("FASB") issued ASU 2013-02 related to the reporting of amounts reclassified out of accumulated other comprehensive income that requires entities to report, either on their income statement or in a footnote to their financial statements, the effects on earnings from items that are reclassified out of other comprehensive income. The Company adopted this accounting standard on January 1, 2013, and the adoption of this guidance did not have a material impact on the financial statements.

Basis_of_Presentation_and_Summ2

Basis of Presentation and Summary of Significant Accounting Policies (Tables)	9 Months Ended
	Sep. 30, 2013
Accounting Policies [Abstract]	'
Securities not included in the net loss per common share calculations	'
	The following options to purchase common stock, restricted stock units and warrants to purchase common stock were excluded from the computation of diluted net loss per share of common stock for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,		Nine Months Ended September 30,
		2013	2012	2013	2012
	Options to purchase common stock	4,805	7,228	4,805	7,228
	Restricted stock units	1,665	839	1,665	839
	Warrants to purchase common stock	75	260	75	260
	Total	6,545	8,327	6,545	8,327

Balance_Sheets_Details_Tables

Balance Sheets Details (Tables)	9 Months Ended
	Sep. 30, 2013
Balance Sheets Details [Abstract]	'
Schedule of inventory components	'
	Inventory, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Raw materials	$	802		$	588
	Work in process	235			52
	Finished goods	1,064			662
	Inventory, net	$	2,101		$	1,302
Schedule of property and equipment, net	'
	Property and equipment, net consisted of the following (in thousands):
		September 30,			December 31,
		2013			2012
	Laboratory equipment	$	35,311		$	33,776
	Leasehold improvements	11,108			11,099
	Computer equipment	3,419			4,388
	Office furniture and equipment	1,503			1,531
		51,341			50,794
	Less: accumulated depreciation	(37,780		)	(34,172		)
		13,561			16,622
	Construction in progress	248			28
	Property and equipment, net	$	13,809		$	16,650
Schedule of changes in accumulated other comprehensive income (loss) by components	'
	The changes in accumulated other comprehensive income (loss) by component and related tax effects were as follows (in thousands):
	Balance as of December 31, 2012	$	(136	)
	Unrealized gains (losses) on available-for-sale securities	447
	Tax effects	(172		)
	Balance as of September 30, 2013	$	139

Cash_Equivalents_and_Marketabl1

Cash Equivalents and Marketable Securities (Tables)	9 Months Ended
	Sep. 30, 2013
Cash Equivalents and Marketable Securities [Abstract]	'
Schedule of cash equivalents and marketable securities	'
	At September 30, 2013, cash equivalents and marketable securities consisted of the following (in thousands):
		September 30, 2013
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	21,079	$	—	$	—	$	21,079	n/a
	Corporate bonds (unamortized cost)	1,004		3		—		1,007		151
	U.S. Treasury obligations (unamortized cost)	2,000		2		—		2,002		232
	Common shares of CO2 Solutions	563		$	504	$	—	1,067		n/a
	Total	$	24,646	$	509	$	—	$	25,155
	At December 31, 2012, cash equivalents and marketable securities consisted of the following (in thousands):
		31-Dec-12
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	24,789	$	—	$	—	$	24,789	n/a
	Commercial paper	1,499		1		—		1,500		70
	Corporate bonds (unamortized cost)	9,512		10		—		9,522		156
	U.S. Treasury obligations (unamortized cost)	5,510		5		—		5,515		262
	Common shares of CO2 Solutions	563		47		—		610		n/a
	Total	$	41,873	$	63	$	—	$	41,936

Fair_Value_Measurements_Tables

Fair Value Measurements (Tables)	9 Months Ended
	Sep. 30, 2013
Fair Value, Assets and Liabilities 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 September 30, 2013 by level within the fair value hierarchy (in thousands):
		30-Sep-13
		Level 1		Level 2		Level 3		Total
	Money market funds	$	21,079	$	—	$	—	$	21,079
	Corporate bonds	—		1,007		—		1,007
	U.S. Treasury obligations	—		2,002		—		2,002
	Common shares of CO2 Solutions	—		1,067		—		1,067
	Total	$	21,079	$	4,076	$	—	$	25,155
	The following table presents the financial instruments that were measured at fair value on a recurring basis at December 31, 2012 by level within the fair value hierarchy (in thousands):
		31-Dec-12
		Level 1		Level 2		Level 3		Total
	Money market funds	$	24,789	$	—	$	—	$	24,789
	Commercial paper	—		1,500		—		1,500
	Corporate bonds	—		9,522		—		9,522
	U.S. Treasury obligations	—		5,515		—		5,515
	Common shares of CO2 Solutions	610		—		—		610
	Total	$	25,399	$	16,537	$	—	$	41,936

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2013
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 September 30, 2013 (in thousands):
		Lease payments
	3 months ending December 31,
	2013	$	719
	Years ending December 31,
	2014	2,947
	2015	3,031
	2016	3,047
	2017	2,677
	2018 and beyond	5,790
	Total	$	18,211

Warrants_Tables

Warrants (Tables)	9 Months Ended
	Sep. 30, 2013
Warrants and Rights Note Disclosure [Abstract]	'
Schedule of common stock warrants issued and outstanding	'
	As of September 30, 2013, the following warrants remain outstanding:
	30-Sep-13
	Issue Date	Shares Subject	Exercise Price		Expiration
		to warrants	per Share
	July 17, 2007	2,384	$	12.45	February 9, 2016
	September 28, 2007	72,727	$	8.25	September 28, 2017

StockBased_Compensation_Tables

Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2013
Stockholders' Equity Note [Abstract]	'
Schedule of stock options available for grant	'
	The following table presents the shares available for grant as of September 30, 2013 (in thousands):
		Shares available for grant
	31-Dec-12	3,767
	Annual increase in shares available for grant	1,507
	Option grants	(922	)
	Restricted stock unit award grants	(1,367	)
	Restricted stock unit award shares withheld for taxes	132
	Options forfeited	1,968
	Restricted stock unit awards forfeited	335
	30-Sep-13	5,420
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 nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,					Nine Months Ended September 30,
		2013			2012		2013		2012
	Research and development	$	97		$	682	$	989	$	2,183
	Selling, general and administrative	529			784		2,372		2,360
	Total	$	626		$	1,466	$	3,361	$	4,543
	The following table presents total stock-based compensation expense by security types included in the condensed consolidated statements of operations for the three and nine months ended September 30, 2013 and 2012 (in thousands):
		Three Months Ended September 30,					Nine Months Ended September 30,
		2013			2012		2013		2012
	Stock options	$	397		$	900	$	1,538	$	3,255
	Restricted stock units	527			566		1,823		1,288
	Performance stock units	(298		)	—		—		—
	Total	$	626		$	1,466	$	3,361	$	4,543

Segment_Reporting_Tables

Segment Reporting (Tables)	9 Months Ended
	Sep. 30, 2013
Segment Reporting Information, Operating Income (Loss) [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 September 30,				Nine Months Ended September 30,
		2013		2012		2013		2012
	Revenues
	Americas (1)	$	2,764	$	18,324	$	7,065	$	50,867
	Europe	757		1,056		5,139		8,986
	Asia
	India	213		5,800		2,721		15,761
	Singapore	—		631		6,721		3,884
	Others	209		530		751		888
		$	3,943	$	26,341	$	22,397	$	80,386
	-1	Primarily United States
Schedule of long-lived assets by geographical area	'
	The following table represents identifiable long-lived assets in the corresponding regions (in thousands):
		September 30,		December 31,
		2013		2012
	Long-lived assets
	Americas (1)	$	19,863	$	25,953
	Europe (2)	4,391		5,157
	Asia	319		711
		$	24,573	$	31,821
	-1	Primarily United States
	-2	Primarily Hungary

Restructuring_Tables

Restructuring (Tables)	9 Months Ended
	Sep. 30, 2013
Restructuring Costs [Abstract]	'
Summary of changes in restructuring accrual	'
	The table below summarizes the changes in the restructuring accrual for the Q3 2012 Restructuring Plan as of September 30, 2013 (in thousands):
		Severance, benefits			Facility closing costs			Total
		and related
		personnel costs
	Balance at December 31, 2012	$	100		$	320		$	420
	Cash payments	(74		)	(320		)	(394		)
	Adjustments to restructuring charges	(26		)	—			(26		)
	Balance at September 30, 2013	$	—		$	—		$	—

Description_of_Business_Detail

Description of Business (Details)	9 Months Ended
	Sep. 30, 2013
	pharmaceutical_firm
Description of Business [Abstract]	'
Number of pharmaceutical firms using technology (more than)	50

Basis_of_Presentation_and_Summ3

Basis of Presentation and Summary of Significant Accounting Policies (Textual) (Details) (USD $)

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

12 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

Sep. 30, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

reporting_unit

Total revenues [Member]

Total revenues [Member]

Accounts Receivable [Member]

Accounts Receivable [Member]

Equity Securities [Member]

Debt Securities [Member]

Customer A [Member]

Customer A [Member]

Customer B [Member]

Customer B [Member]

operating_segment

Customer concentration risk [Member]

Customer concentration risk [Member]

Customer concentration risk [Member]

Customer concentration risk [Member]

Total revenues [Member]

Total revenues [Member]

Total revenues [Member]

Total revenues [Member]

Criteria

customer

customer

customer

customer

Customer concentration risk [Member]

Customer concentration risk [Member]

Customer concentration risk [Member]

Customer concentration risk [Member]

Schedule of Available-for-sale Securities [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of major customers (customer)

'

'

'

5

5

5

5

'

'

'

'

'

'

Major customers, concentration risk percentage (percent)

'

'

'

59.00%

81.00%

89.00%

84.00%

'

'

34.00%

47.00%

21.00%

10.00%

Maturity date of highly liquid investments (months)

'

'3 months

'

'

'

'

'

'

'

'

'

'

'

Maturity period of marketable securities included in non-current asset (years)

'

'1 year

'

'

'

'

'

'

'

'

'

'

'

OTTI recorded in selling, general and administrative expenses

$800,000

'

'

'

'

'

'

'

'

'

'

'

'

Gross unrealized losses

'

$0

$0

'

'

'

'

$0

$0

'

'

'

'

Number of operating segments (operating segment)

'

1

'

'

'

'

'

'

'

'

'

'

'

Number of reportable units (reportable unit)

'

1

'

'

'

'

'

'

'

'

'

'

'

Number revenue recognition criteria (criteria)

'

4

'

'

'

'

'

'

'

'

'

'

'

Basis_of_Presentation_and_Summ4

Basis of Presentation and Summary of Significant Accounting Policies (Impairment of Long-Lived Assets and Intangible Assets) (Details) (Intellectual Property [Member])	3 Months Ended	9 Months Ended
	Sep. 30, 2013	Sep. 30, 2013
Intellectual Property [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Amortization period from acquisition date	'	'6 years
Gordon Growth Model, discount rate	18.00%	'
Gordon Growth Model, long-term revenue growth rate	2.00%	'
Gordon Growth Model, capitalization factor	625.00%	'
Excess Earnings Model, discount rate	19.00%	'
Fair value, percent over carrying value	38.00%	'

Basis_of_Presentation_and_Summ5

Basis of Presentation and Summary of Significant Accounting Policies (Anti-Dilutive Securities) (Details)	3 Months Ended		9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total	6,545	8,327	6,545	8,327
Options to purchase common stock [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total	4,805	7,228	4,805	7,228
Restricted stock units [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total	1,665	839	1,665	839
Warrants to purchase common stock [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Total	75	260	75	260

Collaborative_Research_and_Dev1

Collaborative Research and Development Agreements (Details) (USD $)

3 Months Ended

9 Months Ended

1 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Nov. 30, 2007

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2012

Shell [Member]

Shell [Member]

Shell [Member]

Merck [Member]

Merck [Member]

Merck [Member]

Merck [Member]

New Arch Enzyme Supply Agreement [Member]

New Arch Enzyme Supply Agreement [Member]

Previous Arch Agreement [Member]

Previous Arch Agreement [Member]

Collaborative research and development [Member]

Collaborative research and development [Member]

Arch [Member]

Arch [Member]

Arch [Member]

Arch [Member]

Collaborative Research and Development Agreements (Textual) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Term of collaborative research and development agreement (years)

'

'

'

'

'5 years

'

'

'

'5 years

'

'

'

'

'

'

Amount of New Shell Agreement requires Shell pay

'

'

'

'

'

$7,500,000

'

'

'

'

'

'

'

'

'

Period of research agreement with shell (years)

'

'

'

'

'

'

'10 years

'

'

'

'

'

'

'

'

License fee recognized as revenue

'

'

'

'

'

'

'

'

'

500,000

1,300,000

'

'

'

'

One year license fee paid

'

'

'

'

'

'

'

'

1,200,000

'

'

'

'

'

'

Royalties earned

'

'

'

'

'

'

'

500,000

'

'

'

'

'

'

'

Product revenue

$2,867,000

$18,569,000

$7,236,000

$49,049,000

'

'

'

'

'

'

'

$0

$2,100,000

$50,000

$100,000

Balance_Sheets_Details_Invento

Balance Sheets Details (Inventory) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Schedule of Inventory Components	'	'
Raw materials	$802	$588
Work in process	235	52
Finished goods	1,064	662
Inventory, net	$2,101	$1,302	[1]
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Balance_Sheets_Details_Propert

Balance Sheets Details (Property and Equipment) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	$51,341	$50,794
Less: accumulated depreciation	-37,780	-34,172
Property and equipment, net, excluding construction in progress	13,561	16,622
Property and equipment, net	13,809	16,650	[1]
Laboratory equipment [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	35,311	33,776
Leasehold Improvements [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	11,108	11,099
Computer equipment [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	3,419	4,388
Office equipment and furniture [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	1,503	1,531
Construction in Progress [Member]	'	'
Property, Plant and Equipment [Line Items]	'	'
Property and equipment, gross	$248	$28
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Balance_Sheets_Details_Accumul

Balance Sheets Details (Accumulated Other Comprehensive Income (Loss)) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012		Sep. 30, 2013
In Thousands, unless otherwise specified				Unrealized gains (losses) on available-for-sale securities [Member]
Accumulated Other Comprehensive Income (Loss) [Roll Forward]	'	'		'
Beginning balance	$139	($136)	[1]	($136)
Unrealized gains (losses) on available-for-sale securities	'	'		447
Tax effects	'	'		-172
Ending balance	$139	($136)	[1]	$139
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Cash_Equivalents_and_Marketabl2

Cash Equivalents and Marketable Securities (Components of Cash Equivalents and Marketable Securities) (Details) (USD $)	9 Months Ended	12 Months Ended
	Sep. 30, 2013	Dec. 31, 2012
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	$24,646,000	$41,873,000
Gross Unrealized Gains	509,000	63,000
Gross Unrealized Losses	0	0
Estimated Fair Value	25,155,000	41,936,000
Money market funds [Member]	'	'
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	21,079,000	24,789,000
Gross Unrealized Gains	0	0
Gross Unrealized Losses	0	0
Estimated Fair Value	21,079,000	24,789,000
Commercial paper [Member]	'	'
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	'	1,499,000
Gross Unrealized Gains	'	1,000
Gross Unrealized Losses	'	0
Estimated Fair Value	'	1,500,000
Average Contractual Maturities (in days)	'	'70 days
Corporate bonds (unamortized cost) [Member]	'	'
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	1,004,000	9,512,000
Gross Unrealized Gains	3,000	10,000
Gross Unrealized Losses	0	0
Estimated Fair Value	1,007,000	9,522,000
Average Contractual Maturities (in days)	'151 days	'156 days
U.S. Treasury obligations (unamortized cost) [Member]	'	'
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	2,000,000	5,510,000
Gross Unrealized Gains	2,000	5,000
Gross Unrealized Losses	0	0
Estimated Fair Value	2,002,000	5,515,000
Average Contractual Maturities (in days)	'232 days	'262 days
Common shares of CO2 Solution [Member]	'	'
Cash Equivalents and Marketable Securities [Line Items]	'	'
Adjusted Cost	563,000	563,000
Gross Unrealized Gains	504,000	47,000
Gross Unrealized Losses	0	0
Estimated Fair Value	$1,067,000	$610,000

Cash_Equivalents_and_Marketabl3

Cash Equivalents and Marketable Securities (Textual) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012		Sep. 30, 2012	Dec. 31, 2011
	security	security
Cash Equivalents and Marketable Securities [Abstract]	'	'		'	'
Cash and cash equivalents	$26,911,000	$32,003,000	[1]	$25,573,000	$25,762,000
Money market funds	21,100,000	24,800,000		'	'
Cash	$5,800,000	$7,200,000		'	'
Number of marketable securities in a loss position (securities)	0	0		'	'
[1]	The Condensed Consolidated Balance Sheet as of December 31, 2012 has been derived from the audited consolidated financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

Fair_Value_Measurements_Schedu

Fair Value Measurements (Schedule of Financial Instruments Measured at Fair Value on Recurring Basis) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012
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	$25,155	$41,936
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	21,079	25,399
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	4,076	16,537
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
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	21,079	24,789
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	21,079	24,789
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
Commercial paper [Member]	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	'	1,500
Commercial paper [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
Commercial paper [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	'	1,500
Commercial paper [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
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	1,007	9,522
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	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	1,007	9,522
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	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	2,002	5,515
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	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	2,002	5,515
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	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	1,067	610
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	610
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	1,067	0
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

Fair_Value_Measurements_Textua

Fair Value Measurements (Textual) (Details) (USD $)	Sep. 30, 2013	Dec. 31, 2012	Sep. 30, 2013
In Millions, except Share data, unless otherwise specified			CO2 Solutions [Member]
Subsidiary or Equity Method Investee [Line Items]	'	'	'
Cash	$5.80	$7.20	'
Number of common shares fair value (shares)	'	'	10,000,000

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)	3 Months Ended	9 Months Ended
Share data in Millions, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2013	Sep. 30, 2013	Sep. 30, 2012
	Raizen [Member]	Raizen [Member]	Exela PharmaSci, Inc [Member]	Exela PharmaSci, Inc [Member]
Related Party Transaction [Line Items]	'	'	'	'
Shares held by collaboration company (shares)	5.6	5.6	'	'
Material financial activity	$0	$0	'	'
Collaborative research and development revenue	'	'	$2,300,000	$200,000

Commitments_and_Contingencies_1

Commitments and Contingencies (Textual) (Details) (USD $)	9 Months Ended
In Millions, unless otherwise specified	Sep. 30, 2013
	extension
Commitments and Contingencies [Line Items]	'
Asset retirement obligations	0.1
Estimated obligation payable	0.6
Sixth Amendment [Member]	'
Commitments and Contingencies [Line Items]	'
Letters of credit	0.7
Headquarters, Redwood City [Member] | Fifth Amendment [Member]	'
Commitments and Contingencies [Line Items]	'
Lease area space occupancy (square feet)	107,000
Penobscot Space, Building 2 Space, and Saginaw Space [Member] | Fifth Amendment [Member]	'
Commitments and Contingencies [Line Items]	'
Expiration date of lease	31-Jan-20
Number of extensions available on lease (extension)	2
Extended term of lease (years)	'5 years
Chesapeake Space [Member] | Sixth Amendment [Member]	'
Commitments and Contingencies [Line Items]	'
Expiration date of lease	31-Jan-13
Number of extensions available on lease (extension)	2
Extended term of lease (years)	'5 years
Extended expiration date of lease	31-Jan-17
Dyadic [Member]	'
Commitments and Contingencies [Line Items]	'
Contract termination period (days)	'60 days

Commitments_and_Contingencies_2

Commitments and Contingencies (Future Minimum Lease Payments) (Details) (USD $)	Sep. 30, 2013
In Thousands, unless otherwise specified
Future minimum payments under non-cancellable operating leases	'
Lease payments, 3 months ending December 31, 2013	$719
Lease payments, Year ending December 31, 2014	2,947
Lease payments, Year ending December 31, 2015	3,031
Lease payments, Year ending December 31, 2016	3,047
Lease payments, Year ending December 31, 2017	2,677
Lease payments, Year ending December 31, 2018 and beyond	5,790
Lease payments, Total	$18,211

Warrants_Details

Warrants (Details)	9 Months Ended
	Sep. 30, 2013
Warrants Issued on July 17, 2007 and Expiring on February 9, 2016 [Member]	'
Schedule of common stock warrants issued and outstanding	'
Issue Date	17-Jul-07
Shares subject to warrants (shares)	2,384
Exercise Price per Share (dollars per share)	12.45
Expiration	9-Feb-16
Warrants Issued on September 28, 2007 and Expiring on September 28, 2017 [Member]	'
Schedule of common stock warrants issued and outstanding	'
Issue Date	28-Sep-07
Shares subject to warrants (shares)	72,727
Exercise Price per Share (dollars per share)	8.25
Expiration	28-Sep-17

StockBased_Compensation_Textua

Stock-Based Compensation (Textual) (Details) (USD $)

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

3 Months Ended

9 Months Ended

In Thousands, except Share data, unless otherwise specified

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Sep. 18, 2012

Mar. 31, 2010

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2013

Series A Preferred Stock [Member]

Series A Preferred Stock [Member]

Series A Preferred Stock [Member]

2010 Plan [Member]

Restricted stock units [Member]

Restricted stock units [Member]

Restricted stock units [Member]

Restricted stock units [Member]

Performance stock units [Member]

Performance stock units [Member]

Performance stock units [Member]

Performance stock units [Member]

Minimum [Member]

Maximum [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

'

'

'

'

'

'

'

'

'

'

Stock units granted (shares)

'

'

'

'

'

'

'

'

'

'

843,698

'

'

'

523,048

'

'

'

Conversion of convertible securities per share (shares)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1

'

0

2

Share-based Compensation

$626

$1,466

$3,361

$4,543

$300

'

'

'

$527

$566

$1,823

$1,288

($298)

$0

$0

$0

'

'

Estimated performance goal percentage (percent)

'

'

'

'

'

'

'

'

'

'

'

'

100.00%

'

100.00%

'

'

'

Common stock dividend paid in kind (shares)

'

'

'

'

'

1

'

'

'

'

'

'

'

'

'

'

'

'

Preferred stock par value of one thousandth of a share (dollars per share)

'

'

'

'

'

'

$0.00

'

'

'

'

'

'

'

'

'

'

'

Preferred stock purchase price of one thousandth of a share (dollars per share)

'

'

'

'

'

'

$11.35

'

'

'

'

'

'

'

'

'

'

'

Shares subject to warrants (shares)

'

'

'

'

0.001

0.001

'

'

'

'

'

'

'

'

'

'

'

'

Tender offer portion of common stock (percent)

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

Portion of common stock (percent)

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

StockBased_Compensation_Shares

Stock-Based Compensation (Shares Available For Grant) (Details)	9 Months Ended
	Sep. 30, 2013
Stock options [Member]	'
Shares Available For Grant [Roll Forward]	'
Beginning balance (shares)	3,767
Annual increase in shares available for grant (shares)	1,507
Grants (shares)	-922
Forfeited / cancelled (shares)	1,968
Ending balance (shares)	5,420
Restricted stock units [Member]	'
Shares Available For Grant [Roll Forward]	'
Grants (shares)	-1,367
Award shares withheld for taxes (shares)	132
Forfeited / cancelled (shares)	335

StockBased_Compensation_StockB

Stock-Based Compensation (Stock-Based Compensation Expense) (Details) (USD $)	3 Months Ended		9 Months Ended
In Thousands, except Share data, unless otherwise specified	Sep. 30, 2013	Sep. 30, 2012	Sep. 30, 2013	Sep. 30, 2012
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	$626	$1,466	$3,361	$4,543
Research and development [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	97	682	989	2,183
Selling, general and administrative [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	529	784	2,372	2,360
Stock options [Member]	'	'	'	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	397	900	1,538	3,255
Restricted stock units [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	'	'	843,698	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	527	566	1,823	1,288
Performance stock units [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period	'	'	523,048	'
Schedule of stock-based compensation expense	'	'	'	'
Stock-based compensation	($298)	$0	$0	$0

Revenues_by_Geographic_Area_De

(Revenues by Geographic Area) (Details) (USD $)	3 Months Ended				9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013		Sep. 30, 2012		Sep. 30, 2013		Sep. 30, 2012
Schedule of revenues by geographical area	'		'		'		'
Revenues	$3,943		$26,341		$22,397		$80,386
Americas [Member]	'		'		'		'
Schedule of revenues by geographical area	'		'		'		'
Revenues	2,764	[1]	18,324	[1]	7,065	[1]	50,867	[1]
Europe [Member]	'		'		'		'
Schedule of revenues by geographical area	'		'		'		'
Revenues	757		1,056		5,139		8,986
India [Member]	'		'		'		'
Schedule of revenues by geographical area	'		'		'		'
Revenues	213		5,800		2,721		15,761
Singapore [Member]	'		'		'		'
Schedule of revenues by geographical area	'		'		'		'
Revenues	0		631		6,721		3,884
Other [Member]	'		'		'		'
Schedule of revenues by geographical area	'		'		'		'
Revenues	$209		$530		$751		$888
[1]	Primarily United States

LongLived_Assets_by_Geographic

(Long-Lived Assets by Geographic Area) (Details) (USD $)	Sep. 30, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified
Schedule of long-lived assets by geographical area	'		'
Long-lived assets	$24,573		$31,821
Americas [Member]	'		'
Schedule of long-lived assets by geographical area	'		'
Long-lived assets	19,863	[1]	25,953	[1]
Europe [Member]	'		'
Schedule of long-lived assets by geographical area	'		'
Long-lived assets	4,391	[2]	5,157	[2]
Asia [Member]	'		'
Schedule of long-lived assets by geographical area	'		'
Long-lived assets	$319		$711
[1]	Primarily United States
[2]	Primarily Hungary

Restructuring_Changes_in_Restr

Restructuring (Changes in Restructuring Accrual) (Details) (Q3 2012 Restructuring Plan[Member], USD $)	9 Months Ended
In Thousands, unless otherwise specified	Sep. 30, 2013
Summary of changes in restructuring accrual	'
Beginning balance	$420
Cash payments	-394
Adjustments to restructuring charges	-26
Ending balance	0
Employee severance, benefits and related personnel costs [Member]	'
Summary of changes in restructuring accrual	'
Beginning balance	100
Cash payments	-74
Adjustments to restructuring charges	-26
Ending balance	0
Facility closing costs [Member]	'
Summary of changes in restructuring accrual	'
Beginning balance	320
Cash payments	-320
Adjustments to restructuring charges	0
Ending balance	$0

Restructuring_Textual_Details

Restructuring (Textual) (Details) (USD $)

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2012

Sep. 30, 2013

Sep. 30, 2012

Sep. 30, 2012

Mar. 31, 2012

Sep. 30, 2013

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Mar. 31, 2012

Sep. 30, 2012

Sep. 30, 2013

Dec. 31, 2012

Sep. 30, 2013

Jun. 30, 2013

Sep. 30, 2013

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q1 2012 Restructuring Plan [Member]

Leasehold improvement write down [Member]

Employee severance, benefits and related personnel costs [Member]

Employee severance, benefits and related personnel costs [Member]

Employee severance, benefits and related personnel costs [Member]

Employee severance, benefits and related personnel costs [Member]

Employee severance, benefits and related personnel costs [Member]

Facility closing costs [Member]

Facility closing costs [Member]

Facility closing costs [Member]

Facility closing costs [Member]

Equipment Disposal [Member]

United States and Singapore [Member]

United States and Singapore [Member]

United States and Singapore [Member]

United States and Singapore [Member]

Hungary and United States [Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q1 2012 Restructuring Plan [Member]

Q1 2012 Restructuring Plan [Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

Q3 2012 Restructuring Plan[Member]

employee

Research and development functions [Member]

General and administrative functions [Member]

employee

United States and Singapore [Member]

United States and Singapore [Member]

Hungary and United States [Member]

Hungary and United States [Member]

United States and Singapore [Member]

United States and Singapore [Member]

United States and Singapore [Member]

employee

employee

Restructuring Cost and Reserve [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Employee terminations (employee)

'

'

173

'

150

23

13

'

'

'

'

'

'

'

'

'

'

'

Estimated cost of restructuring plan

'

'

'

$2,400,000

'

'

'

$1,100,000

'

'

$700,000

$600,000

'

'

'

$300,000

'

$300,000

Restructuring accrual

0

420,000

'

'

'

'

'

'

0

100,000

'

'

'

0

320,000

'

50,000

'

Cash payments for restructuring

'

'

'

'

'

'

'

'

'

'

'

'

$500,000

'

'

'

'

'

Subsequent_Events_Details

Subsequent Events (Details) (Q4 2013 Restructuring Plan [Member], United States [Member], Subsequent Event [Member], USD $)	0 Months Ended
In Millions, unless otherwise specified	Nov. 12, 2013
	employee
Subsequent Event [Line Items]	'
Employee terminations (employee)	16
Employee severance, benefits and related personnel costs [Member]	'
Subsequent Event [Line Items]	'
Estimated cost of restructuring plan	0.7