Codexis (CDXS) 10-K 13 Mar 14 2013 FY Annual report Financial data

Document_and_Entity_Informatio

Document and Entity Information (USD $)	12 Months Ended
In Millions, except Share data, unless otherwise specified	Dec. 31, 2013	Feb. 28, 2014	Jun. 28, 2013
Document and Entity Information [Abstract]	'	'	'
Entity Registrant Name	'CODEXIS INC	'	'
Entity Central Index Key	'0001200375	'	'
Document Type	'10-K	'	'
Document Period End Date	31-Dec-13	'	'
Amendment Flag	'false	'	'
Document Fiscal Year Focus	'2013	'	'
Document Fiscal Period Focus	'FY	'	'
Current Fiscal Year End Date	'--12-31	'	'
Entity Filer Category	'Accelerated Filer	'	'
Entity Common Stock, Shares Outstanding	'	38,395,862	'
Entity Well-known Seasoned Issuer	'No	'	'
Entity Public Float	'	'	$61.20
Entity Current Reporting Status	'Yes	'	'
Entity Voluntary Filers	'No	'	'

Consolidated_Balance_Sheets

Consolidated Balance Sheets (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$22,130	$32,003
Marketable securities	3,005	13,524
Accounts receivable, net of allowances of $460 and $150 at December 31, 2013 and 2012, respectively	5,413	7,545
Inventories	1,487	1,302
Prepaid expenses and other current assets	1,567	5,395
Assets held for sale	2,179	0
Total current assets	35,781	59,769
Restricted cash	711	1,511
Non-current marketable securities	795	3,623
Property and equipment, net	8,446	16,650
Intangible assets, net	9,560	12,934
Goodwill	3,241	3,241
Other non-current assets	306	2,237
Total assets	58,840	99,965
Current liabilities:	'	'
Accounts payable	3,961	3,654
Accrued compensation	3,625	3,495
Other accrued liabilities	1,612	6,948
Deferred revenues	2,001	2,186
Total current liabilities	11,199	16,283
Deferred revenues, net of current portion	1,114	1,299
Lease incentive obligation	2,160	'
Other long-term liabilities	5,044	3,943
Commitments and contingencies	'	'
Stockholders’ equity:	'	'
Preferred stock, $0.0001 par value per share; 5,000 shares authorized at December 31, 2013 and 2012; None issued and outstanding at December 31, 2013 and 2012;	0	0
Common stock, $0.0001 par value per share; 100,000 shares authorized at December 31, 2013 and 2012; 38,351 and 37,692 shares issued and outstanding at December 31, 2013 and 2012, respectively;	4	4
Additional paid-in capital	298,370	294,128
Accumulated other comprehensive loss	-32	-136
Accumulated deficit	-256,859	-215,556
Total stockholders’ equity	41,483	78,440
Total liabilities and stockholders’ equity	$58,840	$99,965

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parenthetical) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, except Share data, unless otherwise specified
Statement of Financial Position [Abstract]	'	'
Accounts receivable, allowances	$460	$150
Preferred stock, par value	$0.00	$0.00
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$0.00	$0.00
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	38,351,000	37,692,000
Common stock, shares outstanding	38,351,000	37,692,000

Consolidated_Statements_of_Ope

Consolidated Statements of Operations (USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Revenues:	'	'	'
Product	$20,423	$35,924	$49,021
Collaborative research and development	6,868	49,977	70,918
Revenue sharing arrangement	4,631	150	450
Government awards	0	2,247	3,476
Total revenues	31,922	88,298	123,865
Costs and operating expenses:	'	'	'
Cost of product revenues	14,554	30,647	41,781
Research and development	31,606	56,785	61,049
Selling, general and administrative	26,908	31,379	36,942
Total costs and operating expenses	73,068	118,811	139,772
Loss from operations	-41,146	-30,513	-15,907
Interest income	60	252	273
Interest expense and other, net	-304	-326	-675
Loss before income taxes	-41,390	-30,587	-16,309
Provision for (benefit from) income taxes	-87	270	241
Net loss	($41,303)	($30,857)	($16,550)
Net loss per share of common stock, basic and diluted (dollars per share)	($1.08)	($0.84)	($0.46)
Weighted average common shares used in computing net loss per share of common stock, basic and diluted (shares)	38,231	36,768	35,674

Consolidated_Statements_of_Com

Consolidated Statements of Comprehensive Loss (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Statement of Other Comprehensive Income [Abstract]	'	'	'
Net loss	($41,303)	($30,857)	($16,550)
Other comprehensive income (loss):	'	'	'
Foreign currency translation adjustments	0	165	-3
Reclassification of other-than-temporary loss in marketable securities included in net loss	0	753	0
Unrealized gain (loss) on marketable securities, net of tax	104	-647	-370
Other comprehensive income (loss)	104	271	-373
Total comprehensive loss	($41,199)	($30,586)	($16,923)

Consolidated_Statements_Stockh

Consolidated Statements Stockholders' Equity (USD $)	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Accumulated Deficit [Member]
In Thousands
Beginning balance at Dec. 31, 2010	$107,361	$4	$275,540	($34)	($168,149)
Beginning balance (shares) at Dec. 31, 2010	'	34,829	'	'	'
Exercise of stock options	2,579	'	2,579	'	'
Exercise of stock options (shares)	'	1,167	'	'	'
Employee stock-based compensation	9,286	'	9,286	'	'
Non-employee stock-based compensation	387	'	387	'	'
Total comprehensive loss	-16,923	'	'	-373	-16,550
Ending balance at Dec. 31, 2011	102,690	4	287,792	-407	-184,699
Ending balance (shares) at Dec. 31, 2011	'	35,996	'	'	'
Exercise of common warrants (shares)	0	3	'	'	'
Exercise of stock options	1,257	'	1,257	'	'
Exercise of stock options (shares)	'	708	'	'	'
Cancellation of shares	-65	'	-65	'	'
Cancellation of shares (shares)	'	-17	'	'	'
Release of stock awards (shares)	'	982	'	'	'
Employee stock-based compensation	5,040	'	5,040	'	'
Non-employee stock-based compensation	104	'	104	'	'
Non-employee stock-based compensation (shares)	'	20	'	'	'
Total comprehensive loss	-30,586	'	'	271	-30,857
Ending balance at Dec. 31, 2012	78,440	4	294,128	-136	-215,556
Ending balance (shares) at Dec. 31, 2012	'	37,692	'	'	'
Exercise of stock options	318	'	318	'	'
Exercise of stock options (shares)	'	326	'	'	'
Cancellation of shares	-465	'	-465	'	'
Cancellation of shares (shares)	'	-75	'	'	'
Release of stock awards (shares)	'	408	'	'	'
Employee stock-based compensation	4,366	'	4,366	'	'
Non-employee stock-based compensation	23	'	23	'	'
Total comprehensive loss	-41,199	'	'	104	-41,303
Ending balance at Dec. 31, 2013	$41,483	$4	$298,370	($32)	($256,859)
Ending balance (shares) at Dec. 31, 2013	'	38,351	'	'	'

Consolidated_Statements_of_Cas

Consolidated Statements of Cash Flows (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Operating activities:	'	'	'
Net loss	($41,303)	($30,857)	($16,550)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'	'
Amortization of intangible assets	3,374	3,509	3,716
Depreciation and amortization of property and equipment	6,944	8,908	7,755
Loss on impairment and disposal of property and equipment	1,582	1,551	49
Allowance for bad debt	386	133	-41
Impairment of marketable securities	0	753	0
Gain from extinguishment of asset retirement obligation	0	-212	-124
Stock-based compensation	4,389	5,076	9,431
Common stock issuances for royalty payment to a licensor	0	68	0
Accretion of asset retirement obligation	0	30	39
Accretion of premium on marketable securities	42	697	771
Changes in operating assets and liabilities:	'	'	'
Accounts receivable	1,629	11,372	-3,583
Inventories	-185	3,186	-1,671
Prepaid expenses and other current assets	850	-3,051	-682
Other assets	337	-1,330	513
Accounts payable	308	-6,710	1,156
Accrued compensation	130	-3,290	-1,322
Other accrued liabilities	-2,724	197	4,351
Deferred revenues	1,629	-1,789	-4,339
Net cash used in operating activities	-22,998	-11,892	-490
Investing activities:	'	'	'
Decrease (increase) in restricted cash	800	0	-45
Purchase of property and equipment	-1,175	-2,933	-10,736
Purchase of marketable securities	0	-20,638	-52,564
Proceeds from sale of marketable securities	0	10,397	6,037
Proceeds from maturities of marketable securities	13,409	29,885	8,500
Proceeds from disposal of property and equipment	238	0	0
Net cash provided by (used in) investing activities	13,272	16,711	-48,808
Financing activities:	'	'	'
Proceeds from exercises of stock options	318	1,257	2,579
Taxes paid related to net share settlement of equity awards	-465	0	0
Net cash provided by (used in) financing activities	-147	1,257	2,579
Effect of exchange rate changes on cash and cash equivalents	0	165	85
Net increase (decrease) in cash and cash equivalents	-9,873	6,241	-46,634
Cash and cash equivalents at the beginning of the year	32,003	25,762	72,396
Cash and cash equivalents at the end of the year	22,130	32,003	25,762
Supplemental disclosures of cash flow information:	'	'	'
Cash paid for income taxes	103	126	89
Long term deposit in other assets transferred to property and equipment	1,857	0	0
Equipment in property and equipment transferred to assets held for sale	$2,179	$0	$0

Description_of_Business

Description of Business	12 Months Ended
	Dec. 31, 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 develops biocatalysts for the pharmaceutical and fine chemicals markets. Its proven technologies enable scale-up and implementation of biocatalytic solutions to meet customer needs for rapid, cost-effective and sustainable process development, from research to manufacturing.
	Biocatalysts are enzymes or microbes that initiate and/or accelerate chemical reactions. Manufacturers have historically used naturally occurring biocatalysts to produce many goods used in everyday life. However, inherent limitations in naturally occurring biocatalysts have restricted their commercial use. The Company’s proprietary technology platform is able to overcome many of these limitations, allowing us to evolve and optimize biocatalysts to perform specific and desired chemical reactions at commercial scale.
	The Company has commercialized its technology and products in the pharmaceuticals market, which is the Company’s primary business focus. The Company’s pharmaceutical customers, which include several of the largest global pharmaceutical companies, use the Company’s technology, products and services in their manufacturing process development, including in the production of some of the world's bestselling and fastest growing drugs.
	The Company has recently begun to use its technology to develop biocatalysts for use in the fine chemicals markets. The fine chemicals market is similar to the Company’s pharmaceutical business and consists of several large market segments, including food, animal feed, polymers, flavors and fragrances and agricultural chemicals, and so it is a natural fit for the Company’s technology.
	The Company creates its products by applying its CodeEvolver® directed evolution technology platform, which introduces genetic mutations into microorganisms, giving rise to changes in the enzymes that they produce. Once the Company identifies potentially beneficial mutations, it tests combinations of these mutations until it has created variant enzymes that exhibit marketable performance characteristics superior to competitive products. This process allows the Company to make continuous, efficient improvements to the performance of its enzymes.
	In these Notes to Consolidated Financial Statements, the “Company” refers to Codexis, Inc. and its subsidiaries on a consolidated basis.

Summary_of_Significant_Account

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2013

Accounting Policies [Abstract]

'

Summary of Significant Accounting Policies

'

Summary of Significant Accounting Policies

Basis of Presentation and Consolidation

The 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”) and include the accounts of Codexis, Inc. and its wholly-owned subsidiaries. The Company has subsidiaries in the United States, Brazil, Hungary, India, Mauritius, The Netherlands and Singapore. All significant intercompany balances and transactions have been eliminated in consolidation.

Significant Risks and Uncertainties

The Company incurred net losses of $41.3 million, $30.9 million and $16.6 million for the years ended December 31, 2013, 2012 and 2011, respectively. The Company used $23.0 million, $11.9 million and $0.5 million of cash in operating activities for the years ended December 31, 2013, 2012 and 2011, respectively. At December 31, 2013, the Company had an accumulated deficit of $256.9 million and unrestricted cash and cash equivalents of $22.1 million. The Company may be required to seek additional funds through collaborations or public or private debt or equity financings, and may also seek to reduce expenses related to its operations. There can be no assurance that any financing will be available or at terms acceptable to us.

Use of Estimates

The preparation of consolidated 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 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, stock awards and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the consolidated financial statements.

Concentrations of Credit Risk/Major Customers

Financial instruments that potentially subject us 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 full extent of amounts presented in the consolidated financial statements. The Company periodically requires collateral to support credit sales. 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 the Company's estimates and could be material to the Company's consolidated financial position, results of operations, and cash flows.

The Company's top five customers accounted for 81% and 83% of the Company's total revenues for the twelve months ended December 31, 2013 and 2012, respectively.

Customers with revenues of 10% or more of the Company's total revenues consist of the following:

Percentage of Total Revenues

For The Years Ended December  31,

2013

2012

2011

Customers:

Merck

39

%

13

%

10

%

Exela

15

%

—

%

—

%

Novartis

14

%

1

%

1

%

Shell

—

%

51

%

51

%

Novartis had a balance of 50% of the Company's accounts receivable as of December 31, 2013. Merck had a balance of 53% and Novartis had a balance of 11% of the Company’s accounts receivable as of December 31, 2012.

During 2013, the Company recorded an allowance for bad debt of approximately $387,000 due to a write-off of an accounts receivable from Arch Pharmalabs Limited ("Arch").

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, government-sponsored enterprise securities 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 1 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 the Company's current and forecasted liquidity requirements and its capital requirements. Based on the Company's evaluation, 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 deemed to be other-than-temporary and as a result, the Company recorded a $753,000 impairment charge in its consolidated statement of operations (see Note 8). As of December 31, 2013, there were no unrealized losses related to the Company's equity securities.

For the Company's investments in debt securities, the Company's management determines whether it intends to sell or if it is more-likely-than-not that it will be required to sell impaired securities. This determination considers the Company's current and forecasted liquidity requirements, its capital requirements and securities portfolio objectives. 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 December 31, 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 estimated fair value. Unrealized gains and losses are reported on the 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 interest expense and other, net. 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 years ended December 31, 2013, 2012, and 2011.

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, accounts payable, accrued compensation and other accrued liabilities 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.

Accounts Receivable

Accounts receivable represent amounts owed to the Company under its collaborative research and development agreements, product revenues and government awards. The Company records trade accounts receivable at invoiced amounts and maintains a valuation allowance for doubtful accounts.

The following is a summary of activity in the Company's allowance for doubtful accounts for the three years ended December 31, 2013, 2012 and 2011 (in thousands):

Years ended December 31,

2013

2012

2011

Allowance - beginning of period

$

(150

)

$

(17

)

$

(58

)

Provisions for doubtful accounts

(386

)

(133

)

41

Recoveries from bad debts

76

—

—

Write-off and other

—

—

—

Allowance - end of period

$

(460

)

$

(150

)

$

(17

)

Inventories

Inventories consist of biocatalysts and pharmaceutical intermediates. Internally produced biocatalysts only qualify as commercial inventory after they have achieved specifications that are required for selling the materials. Inventories held at the Company's contract manufacturers are accepted as finished goods after achieving specifications stated in its purchase orders. Inventories are carried at the lower of cost or market. Cost is determined using the first-in first-out method or the specific identification method depending on location. Inventories, based on demand and age, are written down as excess and obsolete materials, if necessary.

Prepaid Expenses and Other Current Assets

Included in prepaid expenses and other current assets as of December 31, 2012 was $1,100,000 in deferred cost of sales related to a sales arrangement with a customer that was deferred due to extended payment terms. Payment was received in 2013 and recorded in cost of sales.

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. During the year ended December 31, 2013, restricted cash decreased by $800,000 due to the termination of the Company's working capital line of credit. Restricted cash was unchanged during the year ended December 31, 2012.

Property and Equipment

Property and equipment, including the cost of purchased software, are stated at cost, less accumulated depreciation and amortization. Property and equipment also includes equipment that has been received but not yet placed in service. Normal repairs and maintenance costs are expensed as incurred. Depreciation is calculated using the straight-line method over the following estimated ranges of useful lives:

Asset classification

Estimated useful life

Laboratory equipment

5 years

Computer equipment and software

3 to 5 years

Office equipment and furniture

5 years

Leasehold improvements

Lesser of useful life or lease term

Assets Held for Sale

The Company reclassifies long-lived assets to Assets Held for Sale when all required criteria for such reclassification are met. The assets are recorded at the lower of the carrying value or fair value less costs to sell. Assets held for sale must meet the following conditions: (1) management, having authority to approve the action, commits to a plan to sell the asset, (2) the asset is available for immediate sale in its present condition, (3) an active program to locate a buyer and other actions required to complete the plan to sell the asset have been initiated, (4) the sale of the asset is probable, and transfer of the asset is expected to qualify for recognition as a completed sale, within one year, (5) the asset is being actively marketed for sale at a price that is reasonable in relation to its current fair value, and (6) actions required to complete the plan indicate that it is unlikely that significant changes to the plan will be made or that the plan will be withdrawn.

In determining the fair value of the assets less cost to sell, the Company considered factors including current sales prices for comparable assets, recent market analysis studies, appraisals and any recent legitimate offers. If the estimated fair value less cost to sell of an asset is less than its current carrying value, the asset is written down to its estimated fair value less cost to sell. The carrying value of assets, net of the impairment write-off, held for sale was $2,179,000 at December 31, 2013 (see Note 5). All these assets continue to be actively marketed for sale at December 31, 2013. Due to uncertainties in the estimation process, it is reasonably possible that actual results could differ from the estimates used in the Company's historical analyses. The assumptions about equipment sales prices require significant judgment related to equipment condition and certain selling costs. The Company calculated the estimated fair values of assets held for sale based on current market conditions and assumptions made by management, which may differ from actual results and may result in additional impairments if market conditions deteriorate.

Impairment of Long-Lived Assets and Intangible Assets

Long-lived and intangible assets with finite lives are reviewed for impairment whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of these assets is measured by comparison of their carrying amounts to future undiscounted cash flows the assets are expected to generate.

The Company's intangible assets with finite lives consist of customer relationships, developed core technology, trade names, and the intellectual property (“IP”) rights associated with the acquisition of Maxygen Inc.'s ("Maxygen") directed evolution technology in 2010. Intangible assets were recorded at their fair values at the date the Company acquired the assets and, for those assets having finite useful lives, are amortized using the straight-line method over their estimated useful lives. The Company's long-lived assets include property, plant and equipment, and other non-current assets.

The Company determined that it has a single entity wide asset group (“Asset Group”). The directed evolution technology patent portfolio acquired from Maxygen (“Core IP”) is the most significant component of the Asset Group since it is the base technology for all aspects of its research and development, and represents the basis for all of the Company's identifiable cash flow generating capacity. Consequently, the Company does not believe that identification of independent cash flows associated with its long-lived assets is currently possible at any lower level than the Asset Group.

The Core IP is the only finite-lived intangible asset on the Company's consolidated balance sheet as of December 31, 2013 and is considered the primary asset within the Asset Group. There has been no significant change in the utilization or estimated life of the Company's Core IP since the Company acquired the technology patent portfolio from Maxygen. The estimated remaining useful life of the Company's Core IP is not impacted by the termination of the Shell Research Agreement or its winding down of its CodeXyme® cellulase enzyme program.

The carrying value of the Company's long-lived assets in the Asset Group may not be recoverable based upon the existence of one or more indicators of impairment which could include: a significant decrease in the market price of the Company's common stock; current period cash flow losses or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the assets; slower growth rates in the Company's industry; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the assets; loss of significant customers or partners; or the current expectation that the assets will more likely than not be sold or disposed of significantly before the end of their estimated useful life.

The Company evaluates recoverability of its long-lived assets and intangible assets based on the sum of the undiscounted cash flows expected to result from the use, and the eventual disposal of, the Asset Group. The Company makes estimates and judgments about the future undiscounted cash flows over the remaining useful life of the Asset Group. The Company's anticipated future cash flows include its estimates of existing or in process product revenues, production and operating costs, future capital expenditures, working capital needs, and assumptions regarding the ultimate sale of the Asset Group at the end of the life of the primary asset. The useful life of the Asset Group was based on the estimated useful life of the Core IP, the primary asset at the time of acquisition. There has been no change in the estimated useful life of the Asset Group. Although the Company's cash flow forecasts are based on assumptions that are consistent with our plans, there is significant judgment involved in determining the cash flows attributable to the Asset Group over its estimated remaining useful life.

2012 Analysis

As of December 31, 2012 the Company determined that its continued operating losses and the termination of the Shell Research Agreement were indications of impairment.

As a result, in 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 undiscounted cash flows included revenue and expense from the Company's biocatalyst business, both from the pharmaceuticals market and from enzyme markets adjacent to its business in the pharmaceuticals market, including fine chemicals markets.

The Company typically receives revenues from the pharmaceuticals market and expect to receive revenues from other enzyme markets adjacent to its pharmaceutical business in the form of one or more of the following: up-front payments, milestone payments, payments based upon the number of FTEs engaged in related research and development activities and licensing fees and royalties. The Company's best estimate of future cash flows did not include any CodeXol® and CodeXyme® revenues associated with collaboration research and development agreements, but did include an estimate of cash flows from potential strategic transactions with respect to its CodeXyme® and CodeXol® programs, as described below.

In the Company's 2012 impairment analysis, approximately 69% and 31% of total Company revenues included in the estimated undiscounted cash flows (excluding cash flows from potential strategic transactions with respect to the Company's CodeXyme® and CodeXol® programs) over the remaining useful life of the Core IP were derived from the pharmaceuticals market and from adjacent enzyme market opportunities, respectively.

The Company's pharmaceuticals revenues were estimated based on existing commercial relationships, signed agreements or contracts, and conservative estimates for the capture of additional market share that management determined to be reasonably achievable. For existing and in process customer revenues the Company assumed a modest rate of growth based on its historical business model for the Company's core pharmaceutical business, including research and development services revenue from partners and customers, which management determined to be reasonably achievable. The Company has historically worked closely with its pharmaceutical partners to evolve, engineer and develop enzymes that meet their specific needs. The Company's business model is based on having its partners and customers pay in whole or in part for the research and development required to engineer the enzymes required.

In determining which adjacent enzyme markets to exploit, management assessed various segments of the large and growing enzyme markets and selected those adjacent markets where the Company already had entry points through its existing pharmaceutical business relationships, such as fine chemicals markets. Estimated revenues associated with these adjacent markets were based on market penetration and adoption rates that management determined to be reasonably achievable.

The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 18.0% (“Estimated Weighted-Average Cost of Capital”) and a long term growth rate of 2%. The 18.0% 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. Based on the results obtained, the Company determined there was no impairment of its intangible assets as of December 31, 2012.

The Company also included in the undiscounted cash flows an estimate of cash flows from potential strategic transactions with respect to the Company's existing CodeXyme® cellulase enzymes and CodeXol® detergent alcohol programs. The amount of estimated cash flows related to CodeXol® and CodeXyme® represented 38% of the total undiscounted cash flows associated with the Asset Group. These amounts were not based on any existing contracts or agreements.

The results of the Company's fourth quarter 2012 impairment analysis indicated that the undiscounted cash flows for the Asset Group were greater than the carrying value of the Asset Group by approximately 14%. Based on the results obtained, the Company determined there was no impairment of the Company's intangible assets as of December 31, 2012.

2013 Analysis

In the fourth quarter of 2013, the Company determined that its continued annual operating losses and a decline in market price of the Company’s common stock, reduced anticipated future cashflows related to potential CodeXyme® cellulase enzyme and CodeXol® detergent alcohols transactions and reduced future revenue growth to reflect the Company’s most recent outlook were indicators of impairment.

As a result, in the fourth quarter of 2013 the Company performed the recoverability test and calculated estimated cashflows through the remaining period of the estimated useful life of the Core IP. The undiscounted cash flows included revenue and expense from the Company's biocatalyst business, both from the pharmaceuticals market and from enzyme markets adjacent to its business in the pharmaceuticals market, including fine chemicals markets.

The methodology employed in the Company's 2013 analysis was consistent with that used in the Company's impairment analysis performed as of December 31, 2012, although certain assumptions changed in 2013 based on new developments, including reduced anticipated future cashflows related to potential strategic transactions with respect to the Company's CodeXyme® and CodeXol® programs, and reduced future revenue growth to reflect the Company’s most recent outlook and an increase in the Company's fine chemicals activities.

In the Company's 2013 impairment analysis, approximately 90% and 10% of total Company revenues included in its estimated undiscounted cash flows (excluding cash flows from potential strategic transactions with respect to its CodeXyme® and CodeXol® programs) through the estimated useful life of the Core IP were derived from the pharmaceuticals market and from adjacent enzyme market opportunities, respectively.

The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 19.5% (“Estimated Weighted-Average Cost of Capital”) and a long term growth rate of 2%. The 19.5% 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.

The Company also included in the undiscounted cash flows an estimate of cash flows from potential strategic transactions with respect to the Company’s CodeXyme® cellulase enzymes and CodeXol® detergent alcohol programs. The amount of estimated cash flows related to CodeXol® and CodeXyme® represented 7% of the total undiscounted cash flows associated with the Asset Group. These amounts are not based on any existing contracts or agreements.

The results of the Company's fourth quarter 2013 impairment analysis indicated that the undiscounted cash flows for the Asset Group were greater than the carrying value of the Asset Group by approximately 37%. Based on the results obtained, the Company determined there was no impairment of the Company's intangible assets as of December 31, 2013.

Although the Company's analysis indicated that the estimated future undiscounted cash flows exceeded the carrying value of the Asset Group, the Company performed a supplemental 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 consistent with the time period for final patent expiration from the Maxygen patent portfolio. The Company utilized the multi-period Excess Earnings model and obtained key financial inputs from a review of market participants, Company specific factors and generally accepted valuation methods. The Company utilized a discount rate of 19.5% 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 44% as of December 31, 2013.

Valuation of Goodwill

The Company reviews goodwill impairment annually in the fourth quarter of each of its fiscal years and whenever events or changes in circumstances indicate the carrying value of goodwill may not be recoverable.

The Company determined that it has only one operating segment and reporting unit under the criteria in ASC 280, Segment Reporting. Accordingly, the Company's review of goodwill impairment indicators is performed at the Company level.

The goodwill impairment test consists of a two-step process. The first step of the goodwill impairment test, used to identify potential impairment, compares the fair value of the reporting unit to its carrying value. If the fair value of the reporting unit exceeds its carrying amount, goodwill of the reporting unit is considered not impaired, and the second step of the impairment test is not required.

The Company uses its market capitalization as an indicator of fair value. The Company believes that since its reporting unit is publicly traded, the ability of a controlling shareholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of the Company's reporting unit as a whole to exceed its market capitalization. However, the Company believes that the fair value measurement need not be based solely on the quoted market price of an individual share of the Company's common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.

If the Company were to use an income approach it would establish a fair value by estimating the present value of its projected future cash flows expected to be generated from its business. The discount rate applied to the projected future cash flows to arrive at the present value would be intended to reflect all risks of ownership and the associated risks of realizing the stream of projected future cash flows. the Company's discounted cash flow methodology would consider projections of financial performance for a period of several years combined with an estimated residual value. The most significant assumptions it would use in a discounted cash flow methodology are the discount rate, the residual value and expected future revenues, gross margins and operating costs, along with considering any implied control premium.

Should the Company's market capitalization be less than the total stockholder's equity as of the Company's annual test date or as of any interim impairment testing date, the Company would also consider market comparables, recent trends in the Company's stock price over a reasonable period and, if appropriate, use an income approach to determine whether the fair value of its reporting unit is greater than the carrying amount.

The second step, if required, compares the implied fair value of the reporting unit goodwill with the carrying amount of that goodwill. If the carrying amount of the reporting unit's goodwill exceeds its implied fair value, an impairment charge is recognized in an amount equal to that excess. Implied fair value is the excess of the fair value of the reporting unit over the fair value of all identified assets and liabilities. The Company bases its fair value estimates on assumptions it believes to be reasonable. Actual future results may differ from those estimates.

Goodwill was tested for impairment in the fourth quarter of 2013. The Company concluded that the fair value of the reporting unit exceeded the carrying value and no impairment existed. No impairment charges were recorded during the years ended December 31, 2013, 2012 and 2011.

Revenue Recognition

Revenues are recognized when the four basic revenue recognition criteria are met: (1) persuasive evidence of an arrangement exists; (2) products have been delivered, transfer of technology has been completed or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured.

The Company's primary sources of revenues consist of product revenues, collaborative research and development agreements, revenue sharing arrangements 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 ("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.

For each source of collaborative research and development revenues, product revenues and award revenues, the Company applies the following revenue recognition criteria:

Product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria, if any, have been met, provided all other revenue recognition criteria have also been met. Product revenues consist of sales of biocatalysts, intermediates, active pharmaceutical ingredients and Codex Biocatalyst Panels and Kits. Cost of product revenues includes both internal and third party fixed and variable costs including amortization of purchased technology, materials and supplies, labor, facilities and other overhead costs associated with the Company's product revenues.

Revenue sharing arrangement revenues are recognized based upon sales of licensed products by the Company's revenue share partner Exela (see Note 9 "Related Party Transactions"). Revenue share amounts received are net of product and selling costs. The Company bases its estimates of earned revenue on notification from its revenue share partner of the Company’s share of net profit based on the contractual percentage from the sale of licensed product. The Company bases its estimates on notification of the sale of revenue sharing products and related costs by its revenue share partner.

Up-front fees received in connection with 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 related to the combined units of accounting appropriate for each customer arrangement.

Revenues related to FTE services recognized as research services are performed over the related performance periods for each contract. The Company is required to perform research and development activities as specified in each respective agreement. The payments received are not refundable and are based on a contractual reimbursement rate per FTE working on the project. When up-front payments are combined with FTE services in a single unit of accounting, the Company recognizes the up-front payments using the proportionate performance method of revenue recognition based upon the actual amount of research and development labor hours incurred relative to the amount of the total expected labor hours to be incurred by the Company, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, the Company is required to make estimates of the total hours required to perform the Company's obligations. Research and development expenses related to FTE services under the collaborative research and development agreements approximate the research funding over the term of the respective agreements.

A payment that is contingent upon the achievement of a substantive milestone is recognized in its entirety in the period in which the milestone is achieved. A milestone is an event (i) that can only be achieved based in whole or in part on either the Company's performance or on the occurrence of a specific outcome resulting from its performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved, and (iii) results in additional payments being due to the Company. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either the Company's performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from its performance, (ii) relates solely to past performance, and (iii) is reasonable relative to all deliverable and payment terms in the arrangement.

Other payments received for which such payments are contingent solely upon the passage of time or the result of a collaborative partner’s performance are recognized as revenue when earned in accordance with the contract terms and when such payments can be reasonably estimated and collectability is reasonably assured.

The Company recognizes revenues from royalties based on licensees’ sales of products using the Company's technologies. Royalties are recognized as earned in accordance with the contract terms when royalties from licensees can be reasonably estimated and collectability is reasonably assured. The Company bases its estimates on notification the sale of licensed products from licensees.

Through 2012, the Company received payments from government entities for work performed in the form of government awards. Government awards are agreements that generally provide the Company with cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government awards are recognized in the period during which the related costs are incurred, provided that the conditions under which the government awards were provided have been met and the Company has only perfunctory obligations outstanding.

Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in the Company's cost of product revenues. Such charges were not significant in any of the periods presented.

Concentrations of Supply Risk

The Company relies on a limited number of suppliers for its products. The Company believes that other vendors would be able to provide similar products; however, the qualification of such vendors may require substantial start-up time. In order to mitigate any adverse impacts from a disruption of supply, the Company attempts to maintain an adequate supply of critical single-sourced materials. For certain materials, the Company's vendors maintain a supply for the Company. The Company outsources the commercial scale manufacturing of its products to contract manufacturers with facilities in Austria, India and Italy.

Research and Development Expenses

Research and development expenses consist of costs incurred for internal projects as well as partner-funded collaborative research and development activities. These costs include direct and research-related overhead expenses, which include salaries, stock-based compensation and other personnel-related expenses, facility costs, supplies, depreciation of facilities and laboratory equipment, as well as research consultants and the cost of funding research at universities and other research institutions, and are expensed as incurred. Costs to acquire technologies that are utilized in research and development that have no alternative future use, are expensed when incurred.

Advertising

Advertising costs are expensed as incurred and included in selling, general and administrative expenses in the consolidated statements of operations. Advertising costs were $513,000, $351,000, and $113,000 for the years ended December 31, 2013, 2012, and 2011, respectively.

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.

Where the United States dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in interest expense and other, net in the accompanying consolidated statements of operations. Gains and losses realized from transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity’s functional currency, are included in interest expense and other, net in the accompanying consolidated statements of operations.

Income Taxes

The Company uses the liability method of accounting for income taxes, whereby deferred tax assets or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized.

The Company makes certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenues and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to the Company's tax provision in a subsequent period.

In assessing the realizability of deferred tax assets, the Company considers whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. The Company has recorded a deferred tax asset in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur.

The Company makes estimates and judgments about its future taxable income that are based on assumptions that are consistent with its plans and estimates. Should the actual amounts differ from its estimates, the amount of its valuation allowance could be materially impacted. Any adjustment to the deferred tax asset valuation allowance would be recorded in the income statement for the periods in which the adjustment is determined to be required.

The Company accounts for uncertainty in income taxes as required by the provisions of ASC Topic 740, Income Taxes, which clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the position will be sustained on audit, including resolution of related appeals or litigation processes, if any. The second step is to estimate and measure the tax benefit as the largest amount that is more than 50% likely of being realized upon ultimate settlement. It is inherently difficult and subjective to estimate such amounts, as this requires us to determine the probability of various possible outcomes. The Company considers many factors when evaluating and estimating the Company's tax positions and tax benefits, which may require periodic adjustments and may not accurately anticipate actual outcomes.

The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company should experience an ownership change, as defined, utilization of the Company's federal and state net operating loss carryforwards could be limited.

Stock-Based Compensation

The fair value of stock options is estimated at grant date using the Black-Scholes option pricing model. The Company’s determination of fair value of stock options on the date of grant, using an option pricing model, is affected by the Company’s stock price, as well as the assumptions regarding a number of highly complex and subjective variables. These variables include, but are not limited to, the Company’s expected stock price volatility over the term of the awards and projected employee stock option exercise behaviors. The fair value of each restricted stock unit grant, each restricted stock award unit and each performance stock unit grant is based on the underlying value of the Company’s common stock on the date of grant. In addition, the Company estimates the expected forfeiture rate and only recognizes expense for those awards expected to vest. The Company estimates the forfeiture rate based on historical experience and to the extent the actual forfeiture rate is different from the estimate, share-based compensation expense is adjusted accordingly. 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 Company accounts for stock awards issued to non-employees based on their estimated fair value determined using the Black-Scholes option-pricing model. Compensation expense for the stock awards granted to non-employees is recognized based on the fair value of awards as they vest, during the period the related services are rendered.

Net Loss per Share of Common Stock

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, less the weighted-average unvested common stock subject to repurchase. Diluted net loss per share of common stock is computed by giving effect to all potential common shares, consisting of stock options, restricted stock units, performance stock units and warrants , 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 table presents the calculation of basic and diluted net loss per share of common stock (in thousands, except per share amounts):

Years Ended December 31,

2013

2012

2011

Numerator:

Net loss

$

(41,303

)

$

(30,857

)

$

(16,550

)

Denominator:

Weighted-average shares of common stock outstanding

38,231

36,768

35,674

Weighted-average shares of common stock used in computing net loss per share, basic and diluted

38,231

36,768

35,674

Net loss per share, basic and diluted

$

(1.08

)

$

(0.84

)

$

(0.46

)

The following options to purchase common stock, restricted stock units, performance stock units and warrants to purchase common stock were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have had an anti-dilutive effect (in thousands):

Years Ended December 31,

2013

2012

2011

Options to purchase common stock

4,126

6,133

7,904

Restricted stock units

2,238

958

546

Performance stock units

358

—

—

Warrants to purchase common stock

75

260

266

Total

6,797

7,351

8,716

Restructuring Costs

The Company applies applicable accounting guidance on accounting for costs associated with restructuring costs, including exit or disposal activities, which requires that a liability for costs associated with an exit or disposal activity be recognized and measured initially at fair value when the liability is incurred. The Company's restructuring activities have primarily been related to severance, benefits and related personnel costs and facility closing costs. The Company determines the facility accrual based on expected cash payments, under the applicable facility lease, reduced by any estimated sublease rental income for such facility (see Note 17).

Reclassifications

From time to time the Company reclassifies certain prior period balances to conform to the current year presentation. These include revenue amounts reclassified and split out into additional categories. These reclassifications had no material impact on previously reported total assets, total liabilities, stockholders’ equity, results of operations or cash flows.

Accounting Guidance Update

Recently Adopted Accounting Guidance

In February 2013, the Financial Accounting Standards 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 Company's financial statements or disclosures.

Collaborative_Research_and_Dev

Collaborative Research and Development Agreements	12 Months Ended
	Dec. 31, 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 September 2012, the Company entered into an agreement with Shell (the “New Shell Agreement”) which among other things, terminated the Shell Research Agreement effective as of August 31, 2012, except for certain provisions of the Shell Research Agreement which will survive such termination, including provisions regarding intellectual property rights, patent prosecution and maintenance, confidentiality and indemnification. The New Shell Agreement required Shell to pay the Company approximately $7,500,000 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 us under the Shell Research Agreement. The $7,500,000 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.
	Beginning September 1, 2012, the Company has no further obligations to Shell under the Shell Research Agreement to provide any FTEs to perform work under or after the collaboration and Shell has no future obligations to us under the Shell Research Agreement to provide funding for FTEs to perform work under or after the collaboration. The Company remains eligible to receive a one-time $3,000,000 payment from Shell under the Shell Research Agreement upon the first sale by Shell of a product in the field of converting cellulosic biomass into fermentable sugars in Brazil, or in the fields of converting fermentable sugars derived from biomass into liquid fuel or liquid fuel additives or into lubricants.
	Under the New Shell Agreement, Shell granted the Company royalty-bearing, non-exclusive rights and licenses to develop, manufacture, use and sell enzymes 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 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. Following the date on which the Company's biocatalysts are used to produce sugars used in the Field of Use sufficient to produce 30.0 million gallons of liquid fuel, the Company will be required to pay Shell a royalty on the Company's sales to third parties of the Company's enzymes and microbes in the Field of Use, equal to a low single-digit percentage of net sales and the Company will also be required to pay Shell a royalty on the Company's use of biocatalysts in the Field of Use, equal to a low single-digit percentage of its applicable net sales of such enzymes or microbes. Shell is also entitled to discounted pricing under the New Shell Agreement for biocatalysts purchased from the Company by Shell for use in the Field of Use, but the Company is under no obligation to sell such biocatalysts to Shell.
	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 remains subject to existing royalty obligations to us for future sales of products covered by the intellectual property and technology that remain exclusively licensed to Shell under the License Agreement.
	Additionally, with respect to each invention relating to technology or materials regarding novel liquid fuel compounds, liquid fuel additives or lubricants, Shell will continue to be required to work exclusively with the Company, for a period of three years after the first nonprovisional patent application filing for such invention, to identify biological methods of synthesis of the compound(s) that are claimed, or whose use as a liquid fuel compound, additive or lubricant, is claimed, in such patent filing.
	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.
	In June 2011, Shell completed the transfer of all of its equity interests in us 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. Work under this joint development agreement was completed in 2012 and the Company does not expect this project to continue.
	Merck Research and Development Collaboration
	On February 1, 2012, the Company entered into a 5 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 one of its products, Januvia®. 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 December 31, 2013, the Company has a deferred revenue balance of $696,000 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 twelve months ended December 31, 2013, the Company recognized $1,804,000 of the license fee as collaborative research and development revenue and $1,004,000 in product revenue. Pursuant to the Sitagliptin Agreement, Merck may purchase substance from the Company for a fee based on contractually stated prices. No revenue was recognized under the Sitagliptin Agreement during the twelve months ended December 31, 2012.
	Arch Manufacturing Collaboration
	From 2006 through November 2012, Arch of Mumbai, India manufactured substantially all of the Company's commercialized intermediates and APIs for sale to generic and innovator pharmaceutical manufacturers. Prior to November 2012, Arch produced atorva-family API's and intermediates for the Company and it sold these directly to end customers primarily in India. In November 2012, the Company entered into a new commercial arrangement with Arch (the "New Arch Enzyme Supply Agreement") whereby it will supply Arch with enzymes for use in the manufacture of atorva family products and Arch will market these products directly to end customers. During 2013, Arch was unable to competitively supply these products to end customers, resulting in a significant decrease in revenues. For the twelve months ended December 31, 2013, the Company recognized $2,134,000 in product revenue for the sale of enzyme inventory to Arch pursuant to the New Arch Enzyme Supply Agreement. During 2013, the Company recorded an allowance for bad debt of approximately $387,000 due to a write-off of an accounts receivable from Arch.

Joint_Development_Agreement_wi

Joint Development Agreement with CO2 Solutions	12 Months Ended
	Dec. 31, 2013
Joint Development Agreement [Abstract]	'
Joint Development Agreement with CO2 Solutions	'
	Joint Development Agreement with CO2 Solutions
	On December 15, 2009, the Company entered into an exclusive joint development agreement with CO2 Solutions, a company based in Quebec City, Quebec, Canada, whose shares are publicly traded in Canada on TSX Venture Exchange. The joint development agreement expired in January 2011. In January 2011, the Company extended its joint development agreement with CO2 Solutions on essentially the same terms as the original agreement. This exclusive arrangement expired in February 2013 and has not been extended.
	Under the agreement, the Company obtained a research license to CO2 Solutions’s intellectual property and agreed to conduct research and development activities jointly with CO2 Solutions with the goal of advancing the development of carbon management technology. The Company also purchased 10,000,000 common shares (approximately 16.6% of the total common shares outstanding at the time of investment) of CO2 Solutions in a private placement subject to a four-month statutory resale restriction. This restriction expired on April 15, 2010. The Company concluded that it did not have the ability to exercise significant influence over CO2 Solutions’ operating and financial policies through December 31, 2013.
	The Company’s investment in CO2 Solutions is classified as available for sale and is recorded at its fair value. During the year ended December 31, 2012 the Company recorded an impairment charge of $753,000, as the decline in the fair value of the investment was deemed to be other-than-temporary.

Assets_Held_for_Sale

Assets Held for Sale	12 Months Ended
	Dec. 31, 2013
Assets Held for Sale [Abstract]	'
Assets Held for Sale	'
	Assets Held for Sale
	In the fourth quarter of 2013, the Company announced that it would begin winding down its CodeXyme® cellulase enzymes program. As a result of the termination of these research programs and corresponding reductions in headcount, the Company has concluded that certain excess research and development equipment is no longer held in use, and these assets were determined to meet the criteria to be classified as held for sale at December 31, 2013. The Company intends to sell the excess assets in an orderly manner, is conducting a program to actively market these assets and believes it will complete the sale within one year.
	The Company performed a detailed review of its excess research and development equipment with the assistance of a third party and determined that the estimated net sales price, less selling costs, is below the carrying value. The net carrying value of the excess research and development equipment totaled $3,750,000 and was reduced to an adjusted carrying value of $2,179,000 as of December 31, 2013 to reflect the estimated current fair value for these assets. A charge of $1,571,000 was recorded in the fourth quarter of 2013 to research and development expenses to reduce the value of held for sale assets to their estimated fair market value net of selling expenses. Any changes in the estimated net sale price prior to the sale of the asset will be recognized upon identification of changes in fair value. The Company reclassified the adjusted carrying value to Assets Held for Sale as of December 31, 2013.
	Total assets reclassified as Assets Held for Sale at December 31, 2013 along with the related expense to reduce carrying value to fair value were (in thousands):
	Held for Sale Assets	Net Carrying Value		Impairment Charge		Adjusted Carrying Value
	Excess research & development equipment	$	3,750	$	1,571	$	2,179

Balance_Sheets_and_Statements_

Balance Sheets and Statements of Operations Details	12 Months Ended
	Dec. 31, 2013
Balance Sheets Details [Abstract]	'
Balance Sheets and Statements of Operations Details	'
	Balance Sheets and Statements of Operations Details
	Inventories
	Inventories, net consisted of the following (in thousands):
		December 31,
		2013			2012
	Raw materials	$	763		$	588
	Work in process	31			52
	Finished goods	693			662
	Total inventories	$	1,487		$	1,302
	Property and Equipment, net
	Property and equipment consisted of the following (in thousands):
		December 31,
		2013			2012
	Laboratory equipment	$	23,949		$	33,776
	Leasehold improvements	9,493			4,388
	Computer equipment and software	3,196			11,099
	Office equipment and furniture	1,228			1,531
	Construction in progress (1)	41			28
		37,907			50,822
	Less: accumulated depreciation and amortization	(29,461		)	(34,172		)
	Property and equipment, net	$	8,446		$	16,650
	-1	Construction in progress includes equipment received but not yet placed into service pending installation.
	Intangible Assets
	Intangible assets consisted of the following (in thousands):
		31-Dec-13									31-Dec-12
		Gross			Accumulated			Net			Gross		Accumulated			Net		Weighted-
		Carrying			Amortization			Carrying			Carrying		Amortization			Carrying		Average
		Amount						Amount			Amount					Amount		Amortization
																		Period
																		(years)
	Customer relationships	$	3,098		$	(3,098	)	$	—		$	3,098	$	(3,098	)	$	—	5
	Developed and core technology	1,534			(1,534		)	—			1,534		(1,534		)	—		5
	Maxygen intellectual property	20,244			(10,684		)	9,560			20,244		(7,310		)	12,934		6
	Total	$	24,876		$	(15,316	)	$	9,560		$	24,876	$	(11,942	)	$	12,934	6
	The estimated future amortization expense to be charged to research and development through the year ending December 31, 2016 is as follows (in thousands):
	Year ending December 31:	Total
	2014	$	3,374
	2015	3,374
	2016	2,812
		$	9,560
	Goodwill
	There were no changes in the carrying value of goodwill of $3,241,000 during 2013 and 2012.
	Interest Expense and Other, Net
	Interest expense and other, net consisted of the following (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Interest expense	$	13		$	—		$	—
	Foreign exchange losses	305			348			706
	Other	(14		)	(22		)	(31		)
	Interest expense and other, net	$	304		$	326		$	675

Cash_Equivalents_Marketable_Se

Cash Equivalents, Marketable Securities and Other Investments (Notes)	12 Months Ended
	Dec. 31, 2013
Investments, Debt and Equity Securities [Abstract]	'
Cash Equivalents, Marketable Securities and Other Investments	'
	Cash Equivalents, Marketable Securities and Other Investments
	At December 31, 2013, cash equivalents, marketable securities and other investments consisted of the following (in thousands):
		31-Dec-13
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	16,089	$	—	$	—	$	16,089	n/a
	Corporate bonds	1,002		3		—		1,005		140
	U.S. Treasury obligations	2,000		—		—		2,000		59
	Common shares of CO2 Solutions	563		232		—		795		n/a
	Total	$	19,654	$	235	$	—	$	19,889
	The total cash and cash equivalents balance of $22,130,000 as of December 31, 2013 was comprised of money market funds of $16,089,000 and cash of $6,041,000 held with major financial institutions worldwide. At December 31, 2013, the Company had no marketable security in an unrealized loss position.
	At December 31, 2012, cash equivalents, marketable securities and other investments 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	9,512		10		—		9,522		156
	U.S. Treasury obligations	5,511		5		—		5,516		262
	Common shares of CO2 Solutions	563		47		—		610		n/a
	Total	$	41,874	$	63	$	—	$	41,937
	The total cash and cash equivalents balance of $32,003,000 as of December 31, 2012 was comprised of money market funds of $24,789,000 and $7,214,000 held as cash primarily with major financial institutions in North America. At December 31, 2012, the Company had no marketable security in an unrealized loss position.

Fair_Value

Fair Value	12 Months Ended
	Dec. 31, 2013
Fair Value, Assets and Liabilities Measured on Recurring Basis [Abstract]	'
Fair Value	'
	Fair Value
	Assets and liabilities recorded at fair value in the 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 investments, the Company's investment advisor provides the Company with monthly account statements documenting the value of each investment 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, the Company performs quarterly analyses using prices obtained from another independent provider of financial instrument valuations, to validate that the prices the Company has used are reasonable estimates of fair value.
	Fair Value of Financial Instruments
	The following table presents the Company's financial instruments that were measured at fair value on a recurring basis at December 31, 2013 by level within the fair value hierarchy (in thousands):
		31-Dec-13
		Level 1		Level 2		Level 3		Total
	Financial Assets
	Money market funds	$	16,089	$	—	$	—	$	16,089
	Corporate bonds	—		1,005		—		1,005
	U.S. Treasury obligations	—		2,000		—		2,000
	Common shares of CO2 Solutions			795		—		795
	Total	$	16,089	$	3,800	$	—	$	19,889
	The following table presents the Company's 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
	Financial Assets
	Money market funds	$	24,789	$	—	$	—	$	24,789
	Commercial paper	—		1,500		—		1,500
	Corporate bonds	—		9,522		—		9,522
	U.S. Treasury obligations	—		5,516		—		5,516
	Common shares of CO2 Solutions	610		—		—		610
	Total	$	25,399	$	16,538	$	—	$	41,937
	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 by trading on the TSX Venture Exchange. These securities have been reclassified to Level 2 at December 31, 2013 after further analysis of the fair value inputs available for this investment. The Company believes the fair value inputs do not meet all of the criteria for Level 1 classification primarily due to the low trading volume of the stock in 2013. As of December 31, 2013, the fair value of the Company's investment in CO2 Solutions’ common stock was $795,000 with an unrealized gain of $232,000. During 2012, the Company evaluated its investment in the common shares of CO2 Solutions and determined the impairment was other-than-temporary considering the length of time and extent to which the fair value has been less than its cost, the financial condition and near term prospects of CO2 Solutions, and its management’s ability and intent to hold the securities until fair value recovers. As a result of the above analysis, the Company recorded an impairment of $756,000 during the year ended December 31, 2012 as an expense in its consolidated statement of operations as selling, general and administrative expense. At December 31, 2012, the estimated fair value of its investment in CO2 Solutions' common stock was $610,000 and the unrealized gain was $47,000.
	The unrealized gain for the years ended December 31, 2013 and 2012, is reflected on the consolidated statements of comprehensive loss, net of a related tax expense of $66,000 and $69,000, respectively.
	Fair Value of Assets Held for Sale
	As of December 31, 2013, we had assets held for sale of $2,179,000 related to lab equipment located in the Unites States and Hungary. The fair value of these assets was determined based on Level 3 inputs, primarily sales data for similar properties. Losses recognized in fiscal year 2013 due to fair value remeasurements using Level 3 inputs were $1,571,000. The fair value of assets held for sale at December 31, 2013, measured on a nonrecurring basis, is as follows (in thousands):
		Level 1		Level 2		Level 3
		Inputs		Inputs		Inputs
	Assets held for sale	$	—	$	—	$	2,179

Related_Party_Transactions

Related Party Transactions	12 Months Ended
	Dec. 31, 2013
Related Party Transaction, Due from (to) Related Party [Abstract]	'
Related Party Transactions	'
	Related Party Transactions
	Shell and Raízen
	As discussed in Note 3, “Collaborative Research and Development Agreements,” Shell transferred full ownership of the Company's common stock to Raízen, Shell’s joint venture with Cosan S.A., ("Cosan"), in Brazil, in June 2011. Upon Shell’s transfer of ownership interest to Raízen in 2011, Raízen owned 5.6 million shares of the Company's common stock. In July 2011, the Company appointed Pedro Mizutani to the Board of Directors. Mr. Mizutani also serves as the Chief Operating Officer of Raízen S.A. and other affiliated companies as well as a director of Cosan. There were no related party transactions with either Raízen or Cosan for the years ended December 31, 2013, 2012 and 2011.
	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 agreed to pay to the Company a contractual percentage share of Exela’s net profit from the sales of licensed products.
	During the years ended December 31, 2013, 2012 and 2011, the Company recognized $4,631,000, $150,000 and $450,000 of revenue, respectively, related to this arrangement, shown in the Company's consolidated statement of operations as revenue sharing arrangement. As of December 31, 2013, the Company had $445,000 owed from Exela and as of December 31, 2012, the Company had no receivables from Exela.
	Alexander A. Karsner
	Alexander A. Karsner is a director of Codexis and provided consulting services to the Company during 2011, 2012 and 2013. Mr. Karsner was paid $120,000 for consulting services for the year ended December 31, 2013 and there was no amount owed as of December 31, 2013.

Commitments_and_Contingencies

Commitments and Contingencies	12 Months Ended
	Dec. 31, 2013
Loss Contingency [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 within the same business park from Metropolitan Life Insurance Company ("MetLife"). The Company entered into the initial lease with Met Life for a portion of this space in 2004 and the lease has been amended numerous times since then to add and subtract space and amend the terms of the lease, with the latest amendment being in 2012. The various terms for the spaces under the lease have expiration dates that range from January 2017 through January 2020. Annual lease payments for the Redwood City properties totaled $2,587,000 in 2013.
	As of December 31, 2012, we incurred $3,600,000 of capital improvement costs related to the facilities leased from MetLife. During 2011 and 2012, we requested and received $3,100,000 of reimbursements from the landlord out of the tenant improvement and HVAC allowances for the completed construction. The reimbursements were recorded once cash was received and is amortized on a straight line basis over the term of the lease as a reduction in rent expense. As of December 31, 2013, the lease incentive obligation remaining as a long-term liability on the Balance Sheet was $2,160,000.
	Rent expense for the Redwood City properties 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 its right to deliver a letter of credit in lieu of a security deposit. The letters of credit in the amount of $707,000 as of December 31, 2013 and 2012 are collateralized by deposit balances held by the bank. These deposits are recorded as restricted cash on the consolidated balance sheets.
	The Company also rents facilities in Hungary. Rent expense is being recognized on a straight-line basis over the respective terms of the lease. This lease requires annual lease payments of approximately $309,000 and expires in September 2016.
	The Company's leased facility in Singapore has been vacated, the lease terminated and the Company recorded a cease use liability of $354,000 representing the remaining six months lease term for the facility as an accrued expense at December 31, 2012, which was paid in 2013.
	As of December 31, 2013 and 2012, the Company had asset retirement obligations of $109,000 from operating leases, whereby the Company must restore the facilities that the Company is renting to their original form. The Company is expensing the asset retirement obligation over the terms of the respective leases. The Company reviews the estimated obligation each reporting period and makes adjustments if its estimates change.
	Future minimum payments under noncancellable operating leases are as follows at December 31, 2013 (in thousands):
		Lease Payments
	Years ending December 31,
	2014	$	2,968
	2015	3,053
	2016	3,063
	2017	2,677
	2018	2,736
	2019 and beyond	3,054
	Total	$	17,551
	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 Company's 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, Dyadic delivered notice to the Company alleging that it is in breach under the Dyadic license agreement and stating that Dyadic intended to terminate the Dyadic license agreement in 60 days if the alleged breach was not cured to Dyadic's satisfaction. This notice was subsequently withdrawn by Dyadic in February 2014 in light of the Company's decision to wind down its CodeXyme® cellulase enzyme program. Although the Company does not believe that the use of the licensed technology in its CodeXyme® cellulase enzyme program constituted a breach of the Dyadic license agreement , the Company can make no assurances that Dyadic will not make such allegations again in the future, or regarding the Company's ability to resolve any possible future disputes with Dyadic on commercially reasonable terms or the Company's ability to dispute with success, through legal action or otherwise, any possible future allegations by Dyadic that such use may have breached the Dyadic license agreement.
	In November 2009, one of the Company's foreign subsidiaries sold intellectual property to the Company. 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, have not recorded an accrual for this exposure. Should the sale be deemed a sale of research and development services, the Company could be obligated to pay an estimated amount of $0.6 million. No amount related to this contingency has been recorded as a payable as of December 31, 2013.

Warrants

Warrants	12 Months Ended
	Dec. 31, 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. During the year ended December 31, 2012, 6,066 warrants were exercised in a net share transaction to acquire 3,308 shares of the Company's common stock. No warrants were exercised during 2013.
	At December 31, 2013, the following warrants were issued and outstanding:
	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

Stockholders_Equity

Stockholders' Equity	12 Months Ended
	Dec. 31, 2013
Stockholders' Equity Attributable to Parent [Abstract]	'
Stockholders' Equity	'
	Stockholders' Equity
	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 its common stock held by stockholders of record as of September 18, 2012. Each right entitles 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 its common stock is announced or commenced. These 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.
	Accumulated Other Comprehensive Income (Loss)
	The components of accumulated other comprehensive income (loss), net of tax, and other comprehensive income (loss) are summarized as follows (in thousands):
		Net Unrealized Gains on Marketable Securities			Cumulative Translation Adjustment			Accumulated Other Comprehensive Income (Loss)
	Balance at December 31, 2010	$	128		$	(162	)	$	(34	)
	Other comprehensive loss	(370		)	(3		)	(373		)
	Balance at December 31, 2011	(242		)	(165		)	(407		)
	Other comprehensive loss	(647		)	165			(482		)
	Reclassification of Other-Than-Temporary Loss in Marketable Securities	753			—			753
	Balance at December 31, 2012	(136		)	—			(136		)
	Other comprehensive loss	104			—			104
	Balance at December 31, 2013	$	(32	)	$	—		$	(32	)

Stockbased_Compensation

Stock-based Compensation	12 Months Ended
	Dec. 31, 2013
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-based Compensation	'
	Stock-based Compensation
	Stock Plans
	In 2002, the Company adopted the 2002 Stock Plan (the “2002 Plan”), pursuant to which its board of directors issued incentive stock options, non-statutory stock options and stock purchase rights to its employees, officers, directors or consultants. In March 2010, the Company's board of directors and stockholders approved the 2010 Equity Incentive Award Plan (the “2010 Plan”), which became effective upon the completion of its IPO in April 2010. The 2010 Plan is similar to the 2002 Plan but allows for issuance of additional awards, such as a restricted stock unit (“RSU”), performance stock unit (“PSU”), deferred stock award and stock appreciation rights. A total of 1,100,000 shares of common stock were initially reserved for future issuance under the 2010 Plan and any shares of common stock reserved for future grant or issuance under the Company's 2002 Plan that remained unissued at the time of completion of the IPO became available for future grant or issuance under the 2010 Plan. In addition, the shares reserved for issuance pursuant to the exercise of any outstanding awards under the 2002 Plan that expire unexercised will also become available for future issuance under the 2010 Plan. The 2010 Plan also provides for automatic annual increases in the number of shares reserved for future issuance.
	A summary of share-based activity is as follows (in thousands):
		Shares
		Available
		for Grant
	31-Dec-12	3,767
	Annual increase in shares available for grant	1,507
	Option grants	(922	)
	RSU award grants	(2,101	)
	RSU award shares withheld for taxes	132
	RSA award grants	(216	)
	PSU award grants	(523	)
	Options forfeited, cancelled or expired	2,603
	RSU awards forfeited, cancelled or expired	165
	PSU awards forfeited, cancelled or expired	496
	31-Dec-13	4,908
	Stock Options
	Awards granted under the 2002 Plan and 2010 Plan expire no later than 10 years from the date of grant. For incentive stock options and nonstatutory stock options, the option price shall be at least 100% and 85%, respectively, of the fair value of the common stock on the date of grant, as determined by the board of directors. If, at the time of a grant, the optionee directly or by attribution owns stock possessing more than 10% of the total combined voting power of all of the Company's outstanding capital stock, the exercise price for these options must be at least 110% of the fair value of the underlying common stock. Options typically vest over a 4-year period at a rate of no less than 25% per year but may be granted with different vesting terms.
	A summary of stock option activity for the years ended December 31, 2011, 2012 and 2013 is as follows (in thousands, except per share amounts and years):
			Options Outstanding
			Number of			Weighted				Weighted Average Remaining Contractual Terms (years)		Aggregate Intrinsic Value
			Options			Average
						Exercise Price
						per Share
	31-Dec-10		7,796			$	6.27			6.57		$	34,228
	Grants		1,751			9.33
	Exercises		(1,167	)		2.21						9,077
	Early exercised options repurchased		(476	)		9.51
	Forfeited/Cancelled		—			—
	31-Dec-11		7,904			7.35				6.77		6,570
	Grants		1,521			3.42
	Exercises		(708	)		1.78						925
	Forfeited/Cancelled		(2,584	)		8.23
	31-Dec-12		6,133			6.65				4.91		657
	Grants		922			2.28
	Exercises		(326	)		0.98						409
	Forfeited/Cancelled		(2,603	)		7.35
	31-Dec-13		4,126			5.68				5.75		87
	Options vested and expected to vest at December 31, 2013		4,006			5.77				5.66		87
	Options exercisable at December 31, 2013		2,805			$	6.76			4.37		$	87
	The weighted-average grant date fair value of options granted during the years ended December 31, 2013, 2012 and 2011 was $1.34, $1.91, and $5.19, respectively.
	The intrinsic value of options outstanding, vested and expected to vest, and exercisable as of December 31, 2013 is calculated based on the difference between the exercise price and the fair value of the Company’s common stock as of December 31, 2013. The aggregate intrinsic value of exercised stock options is calculated based on the difference between the exercise price and the fair value of the Company’s common stock as of the exercise date.
	At December 31, 2013, there was $2,177,000 of unrecognized stock-based compensation cost for outstanding options which is expected to be recognized over an average period of 2.66 years.
	The following table summarizes information about stock options outstanding and exercisable at December 31, 2013 (amounts in thousands, except per share and years):
		Options Outstanding									Options Exercisable
	Exercise Prices	Number			Weighted		Weighted				Number			Weighted
		of			Average		Average				of			Average
		Options			Remaining		Exercise				Options			Exercise
					Contractual		Price per							Price per
					Term		Share							Share
					(Years)
	$0.68 - $2.32	869			7.3		$	1.96			199			$	0.96
	$2.34 - $3.46	971			6.5		2.93				561			2.76
	$3.56 - $7.40	719			5.3		5.31				595			5.6
	$7.41 - $9.81	721			4.36		8.38				673			8.34
	$9.82 - $11.87	846			4.88		10.66				777			10.67
		4,126			5.75		$	5.68			2,805			$	6.76
	Restricted stock units
	RSUs issued generally vest over four years with 25% of the RSUs vesting annually. The fair value of the RSUs 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 requisite service period.
	A summary of RSU activity for the years ended December 31, 2011, 2012 and 2013 is as follows (in thousands, except per share amounts and years):
			RSUs Outstanding
		Number of RSUs			Weighted Average Grant Date Fair Value Per Share				Weighted Average Remaining Contractual Terms (years)		Aggregate Intrinsic Value
31-Dec-10		—
Grants		578			$	9.54
Shares released		—
Forfeited/Cancelled		(32	)
31-Dec-11		546							1.66		$	2,895
Grants		1,148			$	3.54
Shares released		(167	)
Forfeited/Cancelled		(569	)
31-Dec-12		958							1.21		$	2,117
Grants		2,101			$	1.8
Shares released		(325	)
Forfeited/Cancelled		(496	)
31-Dec-13		2,238							1.1		$	3,133
RSUs vested and expected to vest at December 31, 2013		2,015									$	2,821
The intrinsic value of RSUs outstanding and vested and expected to vest as of December 31, 2013 is calculated based on the fair value of the Company’s common stock as of December 31, 2013. The aggregate intrinsic value of RSUs released is calculated based on the fair value of the Company’s common stock as of the vesting date.
The fair value of RSUs released during the years ended December 31, 2013 and 2012 was $726,000 and $591,000, respectively. The majority of RSUs that vested in 2013 and 2012 were net-share settled such that the Company withheld shares with value equivalent to the employees’ minimum statutory obligation for the applicable income and other employment taxes, and remitted the cash to the appropriate taxing authorities. The Company pays the taxes on behalf of the restricted stock unit holder, returns the withheld restricted stock units to the shares available for grant pool and did not represent an expense to the Company.
At December 31, 2013, there was $3,385,000 of unrecognized stock-based compensation cost for outstanding RSUs which is expected to be recognized over an average period of 1.81 years.
Performance Stock Units
PSUs awarded may be conditional upon the attainment of one or more performance objectives over a specified period. Total compensation expense for PSUs is determined by the product of the number of shares eligible to be awarded and expected to vest, and the market price of the Company's common stock, commencing at the inception of the requisite service period. During the performance period, the compensation expense for PSUs is re-computed using the market price and the performance modifier at the end of a reporting period. At the end of the performance period, if the goals are attained, the awards are granted. The Company recognizes compensation expense of these awards on a straight-line basis over the vesting period.
The Company awarded 523,048 PSUs under the 2010 Plan during the year ended December 31, 2013 based upon achieving certain cashflow criteria for 2013. A 100% achievement of the performance goal would result in one common share issued for each vested PSU. 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 $298,000 recorded on a year to date basis was fully reversed at September 30, 2013. At December 31, 2013, there were 358,308 PSUs outstanding, which were cancelled in February 2014 based on not attaining the performance target.
Restricted Stock Awards
In June 2012, the Company granted 750,000 restricted stock awards and 400,000 options, pursuant to the employment agreement with its new chief executive officer, Mr. John Nicols. The restricted stock award of 750,000 shares vests over four years with 25% of the award vesting on each annual anniversary of Mr. Nichols' start date such that the restricted stock award would be fully vested on June 13, 2016.
In September 2012, the Company granted 50,000 restricted stock awards and 200,000 options, pursuant to the offer letter agreement with its new chief financial officer, Mr. David O’Toole. The restricted stock award of 50,000 shares vest over four years with 25% of the awards vesting on each annual anniversary of Mr. O’Toole’s start date such that the restricted stock award would be fully vested on September 4, 2016.
In January 2013, the Company granted a total of 215,515 restricted stock awards to specific non-employee members of its board of directors with a total value of $500,000. These awards vest over three years with 33% of the awards vesting on each annual anniversary of the grant date.
At December 31, 2013, there was $1,714,000 of unrecognized stock-based compensation cost for outstanding restricted stock awards which is expected to be recognized over an average period of 2.36 years.
Stock-Based Compensation Expense
The following table presents stock-based compensation expense included in the consolidated statements of operations (in thousands):
	Years Ended December 31,
	2013				2012				2011
Research and development	$	1,201			$	2,334			$	3,311
Selling, general and administrative	3,188				2,742				6,120
	$	4,389			$	5,076			$	9,431
Stock-based compensation expense attributable to cost of goods sold was immaterial. Stock-based compensation costs capitalized during the years ended December 31, 2013, 2012, and 2011 were insignificant.
There were no stock-based compensation tax benefits during the years ended December 31, 2013, 2012, and 2011.
The Company estimates the fair value of stock-based awards granted to employees and directors using the Black- Scholes option-pricing model. The Black-Scholes option-pricing model requires the use of highly subjective and complex assumptions to determine the fair value of stock-based awards, including the expected life of the option and expected volatility of the underlying stock over the expected life of the related grants.
The Company used the following assumptions to estimate the fair value of its employee option grants:
	Years Ended December 31,
	2013			2012			2011
Weighted-average expected life (years)	6			6			6.1
Weighted-average expected volatility	65	%		61	%		58	%
Weighted-average risk free interest rate	1.2	%		1	%		2.2	%
Expected dividend yield	0	%		0	%		0	%
Since the Company was not a publicly traded entity prior to April 2010, sufficient company-specific historical volatility data was not available for reporting periods prior to the second quarter of 2012. As a result, for those periods, the Company estimated the expected volatility based on the historical volatility of a group of unrelated public companies within its industry. Effective for the second quarter of 2012, the Company determined it had sufficient company-specific historical volatility data. As a result, the Company estimates the expected volatility based on historical volatility of its common stock.
Due to the Company's limited history of grant activity, the expected life of options granted to employees is calculated using the “simplified method” permitted by the SEC as the average of the total contractual term of the option and its vesting period. The risk-free rate assumption was based on United States Treasury instruments whose terms were consistent with the terms of its stock options. The expected dividend assumption was based on the Company's history and expectation of dividend payouts.

Income_Taxes

Income Taxes	12 Months Ended
	Dec. 31, 2013
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	Income Taxes
	The Company's loss before provision for income taxes was as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	United States	$	(41,696	)	$	(30,743	)	$	(17,474	)
	Foreign	306			156			1,165
	Loss before provision for income taxes	$	(41,390	)	$	(30,587	)	$	(16,309	)
	The tax provision for the years ended December 31, 2013, 2012 and 2011 consists primarily of taxes attributable to foreign operations. The components of the provision for income taxes are as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Current provision (benefit):
	Federal	$	—		$	—		$	3
	State	5			7			7
	Foreign	(45		)	178			82
	Total current provision	(40		)	185			92
	Deferred provision (benefit):
	Federal	(59		)	(62		)	—
	State	(7		)	(7		)	—
	Foreign	19			154			149
	Total deferred provision	(47		)	85			149
	Total provision for (benefit from) income taxes	$	(87	)	$	270		$	241
	Reconciliation of the provision for income taxes calculated at the statutory rate to the Company's provision for (benefit from) income taxes is as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Tax benefit at federal statutory rate	$	(14,073	)	$	(10,399	)	$	(5,708	)
	State taxes	(1,948		)	(1,063		)	(1,421		)
	Research and development credits	(195		)	—			(83		)
	Foreign operations taxed at different rates	(108		)	7			(252		)
	Stock-based compensation	117			312			1,241
	Other nondeductible items	(1,272		)	204			650
	Change in federal statutory rate	—			1,493			—
	Change in valuation allowance	17,392			9,716			5,814
	Provision for (benefit from) income taxes	$	(87	)	$	270		$	241
	Deferred income taxes reflect the net tax effects of (a) temporary differences between the carrying amounts of assets and liabilities for financial reporting purposes and the amounts used for income tax purposes, and (b) operating losses and tax credit carryforwards.
	Significant components of the Company's deferred tax assets and liabilities are as follows (in thousands):
		December 31,
		2013			2012
	Deferred tax assets:
	Net operating losses	$	67,507		$	54,923
	Credits	4,194			3,329
	Deferred revenues	1,198			1,297
	Stock-based compensation	3,043			4,464
	Reserves and accruals	3,626			2,090
	Depreciation	2,247			1,746
	Intangible assets	4,208			3,556
	Unrealized gain/loss	112			166
	Other assets	159			141
	Total deferred tax assets:	86,294			71,712
	Deferred tax liabilities:
	Other	—			—
	Total deferred tax liabilities:	—			—
	Valuation allowance	(86,294		)	(71,692		)
	Net deferred tax assets	$	—		$	20
	ASC Topic 740 requires that the tax benefit of NOL, temporary differences and credit carryforwards are recorded as an asset to the extent that management assesses that realization is “more likely than not.” Realization of the future tax benefits is dependent on the Company's ability to generate sufficient taxable income within the carryforward period. Because of the Company's history of operating losses, management believes that recognition of the deferred tax assets arising from the above-mentioned future tax benefits is currently not more likely than not to be realized and, accordingly, has provided a valuation allowance against the Company's deferred tax assets. Accordingly, the net deferred tax assets in all the Company's jurisdictions have been fully reserved by a valuation allowance. The net valuation allowance increased by $14,600,000, $8,600,000 and $5,800,000 during the years ended December 31, 2013, 2012 and 2011, respectively. At such time as it is determined that it is more likely than not that the deferred tax assets are realizable, the valuation allowance will be reduced.
	The following table sets forth the Company's federal, state and foreign NOL carryforwards and federal research and development tax credits as of December 31, 2013 (in thousands):
		31-Dec-13
		Amount			Expiration
					Years
	Net operating losses, federal	$	184,818		2022-2033
	Net operating losses, state	148,325			2015-2033
	Tax credits, federal	5,138			2022-2033
	Tax credits, state	5,459			Do not expire
	Net operating losses, foreign	15,403			Various
Tax credits, foreign	$	16		Various
Current federal and California tax laws include substantial restrictions on the utilization of NOLs and tax credit carryforwards in the event of an ownership change of a corporation. Accordingly, the Company's ability to utilize NOLs and tax credit carryforwards may be limited as a result of such ownership changes. Such a limitation could result in the expiration of carryforwards before they are utilized.
Income tax expense or benefit from continuing operations is generally determined without regard to other categories of earnings, such as discontinued operations and other comprehensive income. An exception is provided in ASC 740 when there is aggregate income from categories other than continuing operations and a loss from continuing operations in the current year. In this case, the tax benefit allocated to continuing operations is the amount by which the loss from continuing operations reduces the tax expenses recorded with respect to the other categories of earnings, even when a valuation allowance has been established against the deferred tax assets. In instances where a valuation allowance is established against current year losses, income from other sources, including gain from available-for-sale securities recorded as a component of other comprehensive income, is considered when determining whether sufficient future taxable income exists to realize the deferred tax assets. As a result, for the year ended December 31, 2013, the Company recorded a tax expense of $66,000 in other comprehensive income related to the gain on available-for-sale securities, and recorded a corresponding tax benefit of $66,000 in continuing operations.
The Company has not provided for United States federal and state income taxes on all of the non-United States subsidiaries’ undistributed earnings as of December 31, 2013, because such earnings are intended to be indefinitely reinvested. As of December 31, 2013, cumulative unremitted foreign earnings that are considered to be permanently invested outside the United States and on which no United States taxes have been provided were approximately $1,300,000. The residual United States tax liability, if such amounts were remitted, would be nominal.
The Company adopted ASC's Topic 740's provision for accounting for uncertainty in income taxes on January 1, 2007. A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows (in thousands):
	December 31,
	2013			2012			2011
Balance at beginning of year	$	7,420		$	6,611		$	6,492
Additions based on tax positions related to current year	1,116			709			470
Additions to tax provision of prior years	6			263			4
Reductions to tax provision of prior years	(78		)	24			(262		)
Lapse of the applicable statute of limitations	(158		)	(187		)	(93		)
Balance at end of year	$	8,306		$	7,420		$	6,611
The Company recognizes interest and penalties as a component of the Company's income tax expense. Total interest and penalties recognized in the consolidated statement of operations was $29,000, $11,000 and $39,000, respectively, in 2013, 2012 and 2011. Total penalties and interest recognized in the balance sheet was $280,000 and $250,000, respectively, in 2013 and 2012. The total unrecognized tax benefits that, if recognized currently, would impact the Company's effective tax rate were $1,000,000 and $1,500,000 as of December 31, 2013 and 2012, respectively. The Company expects $663,000 of unrecognized tax benefits to be recognized within the next 12 months of which $439,000 will impact the Company's effective tax rate. The Company is not subject to examination by United States federal or state tax authorities for years prior to 2002 and foreign tax authorities for years prior to 2007.

401k_Plan

401(k) Plan	12 Months Ended
	Dec. 31, 2013
Compensation and Retirement Disclosure [Abstract]	'
401(k) Plan	'
	401(k) Plan
	In January 2005, the Company implemented a 401(k) Plan covering certain employees. Currently, all of the Company's United States based employees over the age of 18 are eligible to participate in the 401(k) Plan. Under the 401(k) Plan, eligible employees may elect to reduce their current compensation up to a certain annual limit and contribute these amounts to the 401(k) Plan. The Company may make matching or other contributions to the 401(k) Plan on behalf of eligible employees. During the year end December 31, 2013, the Company recorded $488,000 in expense for matching contributions to the 401(k) Plan. In the years ended December 31, 2012 and 2011, the Company did not make any contributions to the 401(k) Plan on behalf of eligible employees.

Segment_Reporting

Segment Reporting	12 Months Ended
	Dec. 31, 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 maker is its Chief Executive Officer. The Chief Executive Officer and the Company's board of directors review financial information presented on a consolidated basis, accompanied by information about revenues by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity and there are no segment managers who are held accountable for operations, operating results beyond revenue goals or plans for levels or components below the consolidated unit level. Accordingly, the Company has a single reporting segment. Operations outside of the United States consist principally of research and development and sales activities.
	Geographic revenues are identified by the location of the customer and consist of the following (in thousands):
		Years Ended December 31,
		2013		2012		2011
	Revenues
	United States	$	11,005	$	51,714	$	72,355
	Europe	9,568		11,150		16,751
	Asia
	India	3,099		16,813		21,063
	Singapore	7,220		7,507		12,008
	Others	1,030		1,114		1,688
		$	31,922	$	88,298	$	123,865
	Geographic presentation of identifiable long-lived assets below shows those assets that can be directly associated with a particular geographic area and consist of the following (in thousands):
		December 31,
		2013		2012		2011
	Long-lived assets
	United States	$	16,189	$	25,953	$	34,817
	Europe (1)	2,123		5,157		4,395
	Asia	—		711		2,380
		$	18,312	$	31,821	$	41,592
	-1	Primarily Hungary

Restructuring

Restructuring	12 Months Ended
	Dec. 31, 2013
Restructuring Costs [Abstract]	'
Restructuring	'
	Restructuring
	Q1 2012 Restructuring Plan
	During the first quarter of 2012, the Company's board of directors approved and committed to a restructuring plan (the “Q1 2012 Restructuring Plan”) to reduce its cost structure, which included a total of 13 employee terminations in Hungary, Singapore, and the United States. Costs of $572,000 were originally recognized in selling, general and administrative expenses during the year ended December 31, 2012, comprised of employee severance and other termination benefits. The Company made cash payments of $512,000 and recorded $60,000 of reductions to previously recorded charges during 2012 and have no further obligations under this restructuring plan.
	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 its 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 impacted the general and administrative functions.
	The Company's cost of the Q3 2012 Restructuring Plan was $2,418,000, comprised of $1,071,000 of leasehold improvement write down, $684,000 for employee severance and other termination benefits, $320,000 for facility lease termination costs and $342,000 for equipment disposal charges. For the twelve months ended December 31, 2012, costs of $1,470,000 have been recognized in selling, general and administrative expenses and $948,000 have been recognized in research and development on the Company's consolidated statements of operations. As of December 31, 2012, there was $68,000 recorded in accrued compensation and $352,000 recorded as accrued expenses on the Company's consolidated balance sheet and the remaining payments were made in 2013. The Company does not anticipate recording any further costs under this restructuring plan.
	Q4 2013 Restructuring Plan
	During the fourth quarter of 2013, the Company's board of directors approved and committed to a restructuring plan (the “Q4 2013 Restructuring Plan”) to reduce its cost structure resulting from the Company's decision to begin winding down its CodeXyme® cellulase enzymes program, which included a total of 15 employee terminations in the United States. For the year ended December 31, 2013, costs of $809,000 of employee severance and other termination benefits have been recognized, consisting of $573,000 in research and development expenses and $236,000 in selling, general and administrative expenses. As of December 31, 2013, there was $277,000 recorded in accrued compensation on the Company's consolidated balance sheet. Associated with the Q4 2013 Restructuring Plan, the Company announced it was selling certain R&D assets that have become excess to future requirements (see Note 5). The Company does not anticipate recording any further costs under this restructuring plan.
	The following table summarizes the activity in the restructuring accrual during the years ended December 31, 2013 and 2012 (in thousands):
		Q1 2012 Restructuring Plan			Q3 2012 Restructuring Plan			Q4 2013 Restructuring Plan			Total
	Restructuring charges	$	572		$	2,537		$	—		$	3,109
	Cash payments	(512		)	(611		)	—			(1,123		)
	Leasehold improvements write-down and equipment disposal charges	—			(1,413		)	—			(1,413		)
	Adjustments to previously accrued charges	(60		)	(93		)	—			(153		)
	Balance at December 31, 2012	—			420			—			420
	Restructuring charges	—						809			809
	Cash payments	—			(345		)	(532		)	(877		)
	Non-cash items	—			(49		)	—			(49		)
	Adjustments to previously accrued charges	—			(26		)	—			(26		)
	Balance at December 31, 2013	$	—		$	—		$	277		$	277

Selected_Quarterly_Financial_D

Selected Quarterly Financial Data (Unaudited)	12 Months Ended
	Dec. 31, 2013
Quarterly Financial Information Disclosure [Abstract]	'
Selected Quarterly Financial Data (Unaudited)	'
	Selected Quarterly Financial Data (Unaudited)
	The following table provides the selected quarterly financial data for 2013 and 2012 (in thousands):
	Condensed Consolidated Statements of Operations
	(In Thousands, Except Per Share Amounts)
		Quarter Ended
		December 31,			September 30,			June 30,			March 31,			December 31,			September 30,			June 30,			March 31,
		2013			2013			2013			2013			2012			2012			2012			2012
	Revenues:
	Product	$	5,263		$	1,076		$	4,948		$	9,136		$	6,834		$	7,140		$	6,783		$	15,167
	Collaborative research and development	1,931			2,028			1,609			1,300			1,078			18,569			15,868			14,362
	Revenue sharing arrangement	2,331			839			417			1,044			—			—			—			250
	Government awards	—			—			—			—			—			632			258			1,357
	Total revenues	9,525			3,943			6,974			11,480			7,912			26,341			22,909			31,136
	Costs and operating expenses:
	Cost of product revenues	4,764			494			3,631			5,665			5,779			6,397			5,829			12,642
	Research and development	8,829			6,831			8,624			7,322			10,594			14,191			15,650			16,349
	Selling, general and administrative	5,783			5,832			7,169			8,124			7,286			7,909			6,789			9,395
	Total costs and operating expenses	19,376			13,157			19,424			21,111			23,659			28,497			28,268			38,386
	Loss before income taxes	(9,858		)	(9,227		)	(12,617		)	(9,688		)	(15,711		)	(2,140		)	(5,442		)	(7,293		)
	Net loss	$	(9,813	)	$	(9,262	)	$	(12,605	)	$	(9,623	)	$	(15,538	)	$	(2,309	)	$	(5,519	)	$	(7,490	)
	Net loss per share, basic and diluted	$	(0.26	)	$	(0.24	)	$	(0.33	)	$	(0.25	)	$	(0.41	)	$	(0.06	)	$	(0.15	)	$	(0.21	)
	Weighted average common shares used in computing net loss per share, basic and diluted (1)	38,329			38,102			38,060			37,842			37,581			37,118			36,296			36,057
	-1	The full year net loss per share of common stock, basic and diluted, may not equal the sum of the quarters due to weighting of outstanding shares.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	12 Months Ended
	Dec. 31, 2013
Accounting Policies [Abstract]	'
Basis of Presentation and Consolidation	'
	Basis of Presentation and Consolidation
	The 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”) and include the accounts of Codexis, Inc. and its wholly-owned subsidiaries. The Company has 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 consolidated 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 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, stock awards and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the consolidated financial statements.
Concentration Risk	'
	Concentrations of Credit Risk/Major Customers
	Financial instruments that potentially subject us 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 full extent of amounts presented in the consolidated financial statements. The Company periodically requires collateral to support credit sales. 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 the Company's estimates and could be material to the Company's consolidated financial position, results of operations, and cash flows.
	The Company's top five customers accounted for 81% and 83% of the Company's total revenues for the twelve months ended December 31, 2013 and 2012, respectively.
	Customers with revenues of 10% or more of the Company's total revenues consist of the following:
		Percentage of Total Revenues
		For The Years Ended December  31,
		2013		2012		2011
	Customers:
	Merck	39	%	13	%	10	%
	Exela	15	%	—	%	—	%
	Novartis	14	%	1	%	1	%
	Shell	—	%	51	%	51	%
	Novartis had a balance of 50% of the Company's accounts receivable as of December 31, 2013. Merck had a balance of 53% and Novartis had a balance of 11% of the Company’s accounts receivable as of December 31, 2012.
	During 2013, the Company recorded an allowance for bad debt of approximately $387,000 due to a write-off of an accounts receivable from Arch Pharmalabs Limited ("Arch").
	Concentrations of Supply Risk
	The Company relies on a limited number of suppliers for its products. The Company believes that other vendors would be able to provide similar products; however, the qualification of such vendors may require substantial start-up time. In order to mitigate any adverse impacts from a disruption of supply, the Company attempts to maintain an adequate supply of critical single-sourced materials. For certain materials, the Company's vendors maintain a supply for the Company. The Company outsources the commercial scale manufacturing of its products to contract manufacturers with facilities in Austria, India and Italy.
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, government-sponsored enterprise securities 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 1 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 the Company's current and forecasted liquidity requirements and its capital requirements. Based on the Company's evaluation, 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 deemed to be other-than-temporary and as a result, the Company recorded a $753,000 impairment charge in its consolidated statement of operations (see Note 8). As of December 31, 2013, there were no unrealized losses related to the Company's equity securities.
	For the Company's investments in debt securities, the Company's management determines whether it intends to sell or if it is more-likely-than-not that it will be required to sell impaired securities. This determination considers the Company's current and forecasted liquidity requirements, its capital requirements and securities portfolio objectives. 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 December 31, 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 estimated fair value. Unrealized gains and losses are reported on the 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 interest expense and other, net. 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 years ended December 31, 2013, 2012, and 2011.
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, accounts payable, accrued compensation and other accrued liabilities 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.
Accounts Receivable	'
	Accounts Receivable
	Accounts receivable represent amounts owed to the Company under its collaborative research and development agreements, product revenues and government awards. The Company records trade accounts receivable at invoiced amounts and maintains a valuation allowance for doubtful accounts.
Inventories	'
	Inventories
	Inventories consist of biocatalysts and pharmaceutical intermediates. Internally produced biocatalysts only qualify as commercial inventory after they have achieved specifications that are required for selling the materials. Inventories held at the Company's contract manufacturers are accepted as finished goods after achieving specifications stated in its purchase orders. Inventories are carried at the lower of cost or market. Cost is determined using the first-in first-out method or the specific identification method depending on location. Inventories, based on demand and age, are written down as excess and obsolete materials, if necessary.
Prepaid Expenses and Other Current Assets	'
	Prepaid Expenses and Other Current Assets
	Included in prepaid expenses and other current assets as of December 31, 2012 was $1,100,000 in deferred cost of sales related to a sales arrangement with a customer that was deferred due to extended payment terms. Payment was received in 2013 and recorded in cost of sales.
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.
Property and Equipment	'
	Property and Equipment
	Property and equipment, including the cost of purchased software, are stated at cost, less accumulated depreciation and amortization. Property and equipment also includes equipment that has been received but not yet placed in service. Normal repairs and maintenance costs are expensed as incurred. Depreciation is calculated using the straight-line method over the following estimated ranges of useful lives:
		Asset classification	Estimated useful life
		Laboratory equipment	5 years
		Computer equipment and software	3 to 5 years
		Office equipment and furniture	5 years
		Leasehold improvements	Lesser of useful life or lease term
Assets Held for Sale	'
	Assets Held for Sale
	The Company reclassifies long-lived assets to Assets Held for Sale when all required criteria for such reclassification are met. The assets are recorded at the lower of the carrying value or fair value less costs to sell. Assets held for sale must meet the following conditions: (1) management, having authority to approve the action, commits to a plan to sell the asset, (2) the asset is available for immediate sale in its present condition, (3) an active program to locate a buyer and other actions required to complete the plan to sell the asset have been initiated, (4) the sale of the asset is probable, and transfer of the asset is expected to qualify for recognition as a completed sale, within one year, (5) the asset is being actively marketed for sale at a price that is reasonable in relation to its current fair value, and (6) actions required to complete the plan indicate that it is unlikely that significant changes to the plan will be made or that the plan will be withdrawn.
	In determining the fair value of the assets less cost to sell, the Company considered factors including current sales prices for comparable assets, recent market analysis studies, appraisals and any recent legitimate offers. If the estimated fair value less cost to sell of an asset is less than its current carrying value, the asset is written down to its estimated fair value less cost to sell. The carrying value of assets, net of the impairment write-off, held for sale was $2,179,000 at December 31, 2013 (see Note 5). All these assets continue to be actively marketed for sale at December 31, 2013. Due to uncertainties in the estimation process, it is reasonably possible that actual results could differ from the estimates used in the Company's historical analyses. The assumptions about equipment sales prices require significant judgment related to equipment condition and certain selling costs. The Company calculated the estimated fair values of assets held for sale based on current market conditions and assumptions made by management, which may differ from actual results and may result in additional impairments if market conditions deteriorate.
Impairment of Intangible Assets and other Long-Lived Assets	'
	Impairment of Long-Lived Assets and Intangible Assets
	Long-lived and intangible assets with finite lives are reviewed for impairment whenever events or changes in circumstances indicate the carrying amount of an asset may not be recoverable. Recoverability of these assets is measured by comparison of their carrying amounts to future undiscounted cash flows the assets are expected to generate.
	The Company's intangible assets with finite lives consist of customer relationships, developed core technology, trade names, and the intellectual property (“IP”) rights associated with the acquisition of Maxygen Inc.'s ("Maxygen") directed evolution technology in 2010. Intangible assets were recorded at their fair values at the date the Company acquired the assets and, for those assets having finite useful lives, are amortized using the straight-line method over their estimated useful lives. The Company's long-lived assets include property, plant and equipment, and other non-current assets.
	The Company determined that it has a single entity wide asset group (“Asset Group”). The directed evolution technology patent portfolio acquired from Maxygen (“Core IP”) is the most significant component of the Asset Group since it is the base technology for all aspects of its research and development, and represents the basis for all of the Company's identifiable cash flow generating capacity. Consequently, the Company does not believe that identification of independent cash flows associated with its long-lived assets is currently possible at any lower level than the Asset Group.
	The Core IP is the only finite-lived intangible asset on the Company's consolidated balance sheet as of December 31, 2013 and is considered the primary asset within the Asset Group. There has been no significant change in the utilization or estimated life of the Company's Core IP since the Company acquired the technology patent portfolio from Maxygen. The estimated remaining useful life of the Company's Core IP is not impacted by the termination of the Shell Research Agreement or its winding down of its CodeXyme® cellulase enzyme program.
	The carrying value of the Company's long-lived assets in the Asset Group may not be recoverable based upon the existence of one or more indicators of impairment which could include: a significant decrease in the market price of the Company's common stock; current period cash flow losses or operating losses combined with a history of losses or a forecast of continuing losses associated with the use of the assets; slower growth rates in the Company's industry; significant adverse changes in the business climate or legal factors; accumulation of costs significantly in excess of the amount originally expected for the acquisition or construction of the assets; loss of significant customers or partners; or the current expectation that the assets will more likely than not be sold or disposed of significantly before the end of their estimated useful life.
	The Company evaluates recoverability of its long-lived assets and intangible assets based on the sum of the undiscounted cash flows expected to result from the use, and the eventual disposal of, the Asset Group. The Company makes estimates and judgments about the future undiscounted cash flows over the remaining useful life of the Asset Group. The Company's anticipated future cash flows include its estimates of existing or in process product revenues, production and operating costs, future capital expenditures, working capital needs, and assumptions regarding the ultimate sale of the Asset Group at the end of the life of the primary asset. The useful life of the Asset Group was based on the estimated useful life of the Core IP, the primary asset at the time of acquisition. There has been no change in the estimated useful life of the Asset Group. Although the Company's cash flow forecasts are based on assumptions that are consistent with our plans, there is significant judgment involved in determining the cash flows attributable to the Asset Group over its estimated remaining useful life.
	2012 Analysis
	As of December 31, 2012 the Company determined that its continued operating losses and the termination of the Shell Research Agreement were indications of impairment.
	As a result, in 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 undiscounted cash flows included revenue and expense from the Company's biocatalyst business, both from the pharmaceuticals market and from enzyme markets adjacent to its business in the pharmaceuticals market, including fine chemicals markets.
	The Company typically receives revenues from the pharmaceuticals market and expect to receive revenues from other enzyme markets adjacent to its pharmaceutical business in the form of one or more of the following: up-front payments, milestone payments, payments based upon the number of FTEs engaged in related research and development activities and licensing fees and royalties. The Company's best estimate of future cash flows did not include any CodeXol® and CodeXyme® revenues associated with collaboration research and development agreements, but did include an estimate of cash flows from potential strategic transactions with respect to its CodeXyme® and CodeXol® programs, as described below.
	In the Company's 2012 impairment analysis, approximately 69% and 31% of total Company revenues included in the estimated undiscounted cash flows (excluding cash flows from potential strategic transactions with respect to the Company's CodeXyme® and CodeXol® programs) over the remaining useful life of the Core IP were derived from the pharmaceuticals market and from adjacent enzyme market opportunities, respectively.
	The Company's pharmaceuticals revenues were estimated based on existing commercial relationships, signed agreements or contracts, and conservative estimates for the capture of additional market share that management determined to be reasonably achievable. For existing and in process customer revenues the Company assumed a modest rate of growth based on its historical business model for the Company's core pharmaceutical business, including research and development services revenue from partners and customers, which management determined to be reasonably achievable. The Company has historically worked closely with its pharmaceutical partners to evolve, engineer and develop enzymes that meet their specific needs. The Company's business model is based on having its partners and customers pay in whole or in part for the research and development required to engineer the enzymes required.
	In determining which adjacent enzyme markets to exploit, management assessed various segments of the large and growing enzyme markets and selected those adjacent markets where the Company already had entry points through its existing pharmaceutical business relationships, such as fine chemicals markets. Estimated revenues associated with these adjacent markets were based on market penetration and adoption rates that management determined to be reasonably achievable.
	The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 18.0% (“Estimated Weighted-Average Cost of Capital”) and a long term growth rate of 2%. The 18.0% 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. Based on the results obtained, the Company determined there was no impairment of its intangible assets as of December 31, 2012.
	The Company also included in the undiscounted cash flows an estimate of cash flows from potential strategic transactions with respect to the Company's existing CodeXyme® cellulase enzymes and CodeXol® detergent alcohol programs. The amount of estimated cash flows related to CodeXol® and CodeXyme® represented 38% of the total undiscounted cash flows associated with the Asset Group. These amounts were not based on any existing contracts or agreements.
	The results of the Company's fourth quarter 2012 impairment analysis indicated that the undiscounted cash flows for the Asset Group were greater than the carrying value of the Asset Group by approximately 14%. Based on the results obtained, the Company determined there was no impairment of the Company's intangible assets as of December 31, 2012.
	2013 Analysis
	In the fourth quarter of 2013, the Company determined that its continued annual operating losses and a decline in market price of the Company’s common stock, reduced anticipated future cashflows related to potential CodeXyme® cellulase enzyme and CodeXol® detergent alcohols transactions and reduced future revenue growth to reflect the Company’s most recent outlook were indicators of impairment.
	As a result, in the fourth quarter of 2013 the Company performed the recoverability test and calculated estimated cashflows through the remaining period of the estimated useful life of the Core IP. The undiscounted cash flows included revenue and expense from the Company's biocatalyst business, both from the pharmaceuticals market and from enzyme markets adjacent to its business in the pharmaceuticals market, including fine chemicals markets.
	The methodology employed in the Company's 2013 analysis was consistent with that used in the Company's impairment analysis performed as of December 31, 2012, although certain assumptions changed in 2013 based on new developments, including reduced anticipated future cashflows related to potential strategic transactions with respect to the Company's CodeXyme® and CodeXol® programs, and reduced future revenue growth to reflect the Company’s most recent outlook and an increase in the Company's fine chemicals activities.
	In the Company's 2013 impairment analysis, approximately 90% and 10% of total Company revenues included in its estimated undiscounted cash flows (excluding cash flows from potential strategic transactions with respect to its CodeXyme® and CodeXol® programs) through the estimated useful life of the Core IP were derived from the pharmaceuticals market and from adjacent enzyme market opportunities, respectively.
	The expected residual value was determined by applying a Gordon Growth Model to normalized net cash flows using a discount rate of 19.5% (“Estimated Weighted-Average Cost of Capital”) and a long term growth rate of 2%. The 19.5% 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.
	The Company also included in the undiscounted cash flows an estimate of cash flows from potential strategic transactions with respect to the Company’s CodeXyme® cellulase enzymes and CodeXol® detergent alcohol programs. The amount of estimated cash flows related to CodeXol® and CodeXyme® represented 7% of the total undiscounted cash flows associated with the Asset Group. These amounts are not based on any existing contracts or agreements.
	The results of the Company's fourth quarter 2013 impairment analysis indicated that the undiscounted cash flows for the Asset Group were greater than the carrying value of the Asset Group by approximately 37%. Based on the results obtained, the Company determined there was no impairment of the Company's intangible assets as of December 31, 2013.
	Although the Company's analysis indicated that the estimated future undiscounted cash flows exceeded the carrying value of the Asset Group, the Company performed a supplemental 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 consistent with the time period for final patent expiration from the Maxygen patent portfolio. The Company utilized the multi-period Excess Earnings model and obtained key financial inputs from a review of market participants, Company specific factors and generally accepted valuation methods. The Company utilized a discount rate of 19.5% 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 44% as of December 31, 2013.
Valuation of Goodwill	'
	Valuation of Goodwill
	The Company reviews goodwill impairment annually in the fourth quarter of each of its fiscal years and whenever events or changes in circumstances indicate the carrying value of goodwill may not be recoverable.
	The Company determined that it has only one operating segment and reporting unit under the criteria in ASC 280, Segment Reporting. Accordingly, the Company's review of goodwill impairment indicators is performed at the Company level.
	The goodwill impairment test consists of a two-step process. The first step of the goodwill impairment test, used to identify potential impairment, compares the fair value of the reporting unit to its carrying value. If the fair value of the reporting unit exceeds its carrying amount, goodwill of the reporting unit is considered not impaired, and the second step of the impairment test is not required.
	The Company uses its market capitalization as an indicator of fair value. The Company believes that since its reporting unit is publicly traded, the ability of a controlling shareholder to benefit from synergies and other intangible assets that arise from control might cause the fair value of the Company's reporting unit as a whole to exceed its market capitalization. However, the Company believes that the fair value measurement need not be based solely on the quoted market price of an individual share of the Company's common stock, but also can consider the impact of a control premium in measuring the fair value of its reporting unit.
	If the Company were to use an income approach it would establish a fair value by estimating the present value of its projected future cash flows expected to be generated from its business. The discount rate applied to the projected future cash flows to arrive at the present value would be intended to reflect all risks of ownership and the associated risks of realizing the stream of projected future cash flows. the Company's discounted cash flow methodology would consider projections of financial performance for a period of several years combined with an estimated residual value. The most significant assumptions it would use in a discounted cash flow methodology are the discount rate, the residual value and expected future revenues, gross margins and operating costs, along with considering any implied control premium.
	Should the Company's market capitalization be less than the total stockholder's equity as of the Company's annual test date or as of any interim impairment testing date, the Company would also consider market comparables, recent trends in the Company's stock price over a reasonable period and, if appropriate, use an income approach to determine whether the fair value of its reporting unit is greater than the carrying amount.
	The second step, if required, compares the implied fair value of the reporting unit goodwill with the carrying amount of that goodwill. If the carrying amount of the reporting unit's goodwill exceeds its implied fair value, an impairment charge is recognized in an amount equal to that excess. Implied fair value is the excess of the fair value of the reporting unit over the fair value of all identified assets and liabilities. The Company bases its fair value estimates on assumptions it believes to be reasonable. Actual future results may differ from those estimates.
Revenue Recognition	'
	Revenue Recognition
	Revenues are recognized when the four basic revenue recognition criteria are met: (1) persuasive evidence of an arrangement exists; (2) products have been delivered, transfer of technology has been completed or services have been rendered; (3) the fee is fixed or determinable; and (4) collectability is reasonably assured.
	The Company's primary sources of revenues consist of product revenues, collaborative research and development agreements, revenue sharing arrangements 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 ("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.
	For each source of collaborative research and development revenues, product revenues and award revenues, the Company applies the following revenue recognition criteria:
	Product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria, if any, have been met, provided all other revenue recognition criteria have also been met. Product revenues consist of sales of biocatalysts, intermediates, active pharmaceutical ingredients and Codex Biocatalyst Panels and Kits. Cost of product revenues includes both internal and third party fixed and variable costs including amortization of purchased technology, materials and supplies, labor, facilities and other overhead costs associated with the Company's product revenues.
	Revenue sharing arrangement revenues are recognized based upon sales of licensed products by the Company's revenue share partner Exela (see Note 9 "Related Party Transactions"). Revenue share amounts received are net of product and selling costs. The Company bases its estimates of earned revenue on notification from its revenue share partner of the Company’s share of net profit based on the contractual percentage from the sale of licensed product. The Company bases its estimates on notification of the sale of revenue sharing products and related costs by its revenue share partner.
	Up-front fees received in connection with 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 related to the combined units of accounting appropriate for each customer arrangement.
	Revenues related to FTE services recognized as research services are performed over the related performance periods for each contract. The Company is required to perform research and development activities as specified in each respective agreement. The payments received are not refundable and are based on a contractual reimbursement rate per FTE working on the project. When up-front payments are combined with FTE services in a single unit of accounting, the Company recognizes the up-front payments using the proportionate performance method of revenue recognition based upon the actual amount of research and development labor hours incurred relative to the amount of the total expected labor hours to be incurred by the Company, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, the Company is required to make estimates of the total hours required to perform the Company's obligations. Research and development expenses related to FTE services under the collaborative research and development agreements approximate the research funding over the term of the respective agreements.
	A payment that is contingent upon the achievement of a substantive milestone is recognized in its entirety in the period in which the milestone is achieved. A milestone is an event (i) that can only be achieved based in whole or in part on either the Company's performance or on the occurrence of a specific outcome resulting from its performance, (ii) for which there is substantive uncertainty at the date the arrangement is entered into that the event will be achieved, and (iii) results in additional payments being due to the Company. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either the Company's performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from its performance, (ii) relates solely to past performance, and (iii) is reasonable relative to all deliverable and payment terms in the arrangement.
	Other payments received for which such payments are contingent solely upon the passage of time or the result of a collaborative partner’s performance are recognized as revenue when earned in accordance with the contract terms and when such payments can be reasonably estimated and collectability is reasonably assured.
	The Company recognizes revenues from royalties based on licensees’ sales of products using the Company's technologies. Royalties are recognized as earned in accordance with the contract terms when royalties from licensees can be reasonably estimated and collectability is reasonably assured. The Company bases its estimates on notification the sale of licensed products from licensees.
	Through 2012, the Company received payments from government entities for work performed in the form of government awards. Government awards are agreements that generally provide the Company with cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenues from government awards are recognized in the period during which the related costs are incurred, provided that the conditions under which the government awards were provided have been met and the Company has only perfunctory obligations outstanding.
	Shipping and handling costs charged to customers are recorded as revenues. Shipping costs are included in the Company's cost of product revenues. Such charges were not significant in any of the periods presented.
Research and Development Expenses	'
	Research and Development Expenses
	Research and development expenses consist of costs incurred for internal projects as well as partner-funded collaborative research and development activities. These costs include direct and research-related overhead expenses, which include salaries, stock-based compensation and other personnel-related expenses, facility costs, supplies, depreciation of facilities and laboratory equipment, as well as research consultants and the cost of funding research at universities and other research institutions, and are expensed as incurred. Costs to acquire technologies that are utilized in research and development that have no alternative future use, are expensed when incurred.
Advertising	'
	Advertising
	Advertising costs are expensed as incurred and included in selling, general and administrative expenses in the consolidated statements of operations.
Foreign Currency Translation	'
	Foreign Currency Translation
	The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into United States dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates during the period.
	Where the United States dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in interest expense and other, net in the accompanying consolidated statements of operations. Gains and losses realized from transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity’s functional currency, are included in interest expense and other, net in the accompanying consolidated statements of operations.
Income Taxes	'
	Income Taxes
	The Company uses the liability method of accounting for income taxes, whereby deferred tax assets or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized.
	The Company makes certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenues and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to the Company's tax provision in a subsequent period.
	In assessing the realizability of deferred tax assets, the Company considers whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. The Company has recorded a deferred tax asset in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur.
	The Company makes estimates and judgments about its future taxable income that are based on assumptions that are consistent with its plans and estimates. Should the actual amounts differ from its estimates, the amount of its valuation allowance could be materially impacted. Any adjustment to the deferred tax asset valuation allowance would be recorded in the income statement for the periods in which the adjustment is determined to be required.
	The Company accounts for uncertainty in income taxes as required by the provisions of ASC Topic 740, Income Taxes, which clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the position will be sustained on audit, including resolution of related appeals or litigation processes, if any. The second step is to estimate and measure the tax benefit as the largest amount that is more than 50% likely of being realized upon ultimate settlement. It is inherently difficult and subjective to estimate such amounts, as this requires us to determine the probability of various possible outcomes. The Company considers many factors when evaluating and estimating the Company's tax positions and tax benefits, which may require periodic adjustments and may not accurately anticipate actual outcomes.
	The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event the Company should experience an ownership change, as defined, utilization of the Company's federal and state net operating loss carryforwards could be limited.
Stock-Based Compensation	'
	Stock-Based Compensation
	The fair value of stock options is estimated at grant date using the Black-Scholes option pricing model. The Company’s determination of fair value of stock options on the date of grant, using an option pricing model, is affected by the Company’s stock price, as well as the assumptions regarding a number of highly complex and subjective variables. These variables include, but are not limited to, the Company’s expected stock price volatility over the term of the awards and projected employee stock option exercise behaviors. The fair value of each restricted stock unit grant, each restricted stock award unit and each performance stock unit grant is based on the underlying value of the Company’s common stock on the date of grant. In addition, the Company estimates the expected forfeiture rate and only recognizes expense for those awards expected to vest. The Company estimates the forfeiture rate based on historical experience and to the extent the actual forfeiture rate is different from the estimate, share-based compensation expense is adjusted accordingly. 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 Company accounts for stock awards issued to non-employees based on their estimated fair value determined using the Black-Scholes option-pricing model. Compensation expense for the stock awards granted to non-employees is recognized based on the fair value of awards as they vest, during the period the related services are rendered.
Net Loss per Share of Common Stock	'
	Net Loss per Share of Common Stock
	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, less the weighted-average unvested common stock subject to repurchase. Diluted net loss per share of common stock is computed by giving effect to all potential common shares, consisting of stock options, restricted stock units, performance stock units and warrants , 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.
Restructuring Costs	'
	Restructuring Costs
	The Company applies applicable accounting guidance on accounting for costs associated with restructuring costs, including exit or disposal activities, which requires that a liability for costs associated with an exit or disposal activity be recognized and measured initially at fair value when the liability is incurred. The Company's restructuring activities have primarily been related to severance, benefits and related personnel costs and facility closing costs. The Company determines the facility accrual based on expected cash payments, under the applicable facility lease, reduced by any estimated sublease rental income for such facility (see Note 17).
Reclassifications	'
	Reclassifications
	From time to time the Company reclassifies certain prior period balances to conform to the current year presentation. These include revenue amounts reclassified and split out into additional categories. These reclassifications had no material impact on previously reported total assets, total liabilities, stockholders’ equity, results of operations or cash flows.
Accounting Guidance Update	'
	Accounting Guidance Update
	Recently Adopted Accounting Guidance
	In February 2013, the Financial Accounting Standards 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 Company's financial statements or disclosures.

Summary_of_Significant_Account2

Summary of Significant Accounting Policies (Tables)	12 Months Ended
	Dec. 31, 2013
Accounting Policies [Abstract]	'
Schedules of concentration of risk	'
	Customers with revenues of 10% or more of the Company's total revenues consist of the following:
		Percentage of Total Revenues
		For The Years Ended December  31,
		2013			2012			2011
	Customers:
	Merck	39	%		13	%		10	%
	Exela	15	%		—	%		—	%
	Novartis	14	%		1	%		1	%
	Shell	—	%		51	%		51	%
Schedule of allowance for doubtful accounts	'
	The following is a summary of activity in the Company's allowance for doubtful accounts for the three years ended December 31, 2013, 2012 and 2011 (in thousands):
			Years ended December 31,
			2013				2012				2011
	Allowance - beginning of period		$	(150	)		$	(17	)		$	(58	)
	Provisions for doubtful accounts		(386		)		(133		)		41
	Recoveries from bad debts		76				—				—
	Write-off and other		—				—				—
	Allowance - end of period		$	(460	)		$	(150	)		$	(17	)
Schedule of estimated ranges of useful lives of property and equipment	'
	Depreciation is calculated using the straight-line method over the following estimated ranges of useful lives:
		Asset classification	Estimated useful life
		Laboratory equipment	5 years
		Computer equipment and software	3 to 5 years
		Office equipment and furniture	5 years
		Leasehold improvements	Lesser of useful life or lease term
	Property and Equipment, net
	Property and equipment consisted of the following (in thousands):
		December 31,
		2013				2012
	Laboratory equipment	$	23,949			$	33,776
	Leasehold improvements	9,493				4,388
	Computer equipment and software	3,196				11,099
	Office equipment and furniture	1,228				1,531
	Construction in progress (1)	41				28
		37,907				50,822
	Less: accumulated depreciation and amortization	(29,461		)		(34,172		)
	Property and equipment, net	$	8,446			$	16,650
	-1	Construction in progress includes equipment received but not yet placed into service pending installation.
Schedule of calculation of basic and diluted net loss per share of common stock	'
	The following table presents the calculation of basic and diluted net loss per share of common stock (in thousands, except per share amounts):
		Years Ended December 31,
		2013				2012				2011
	Numerator:
	Net loss	$	(41,303	)		$	(30,857	)		$	(16,550	)
	Denominator:
	Weighted-average shares of common stock outstanding	38,231				36,768				35,674
	Weighted-average shares of common stock used in computing net loss per share, basic and diluted	38,231				36,768				35,674
	Net loss per share, basic and diluted	$	(1.08	)		$	(0.84	)		$	(0.46	)
Securities not included in the net loss per common share calculations	'
	The following options to purchase common stock, restricted stock units, performance stock units and warrants to purchase common stock were excluded from the computation of diluted net loss per share of common stock for the periods presented because including them would have had an anti-dilutive effect (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Options to purchase common stock	4,126			6,133			7,904
	Restricted stock units	2,238			958			546
	Performance stock units	358			—			—
	Warrants to purchase common stock	75			260			266
	Total	6,797			7,351			8,716

Assets_Held_for_Sale_Tables

Assets Held for Sale (Tables)	12 Months Ended
	Dec. 31, 2013
Property, Plant and Equipment [Abstract]	'
Disclosure of Long Lived Assets Held-for-sale	'
	Total assets reclassified as Assets Held for Sale at December 31, 2013 along with the related expense to reduce carrying value to fair value were (in thousands):
	Held for Sale Assets	Net Carrying Value		Impairment Charge		Adjusted Carrying Value
	Excess research & development equipment	$	3,750	$	1,571	$	2,179

Balance_Sheets_and_Statements_1

Balance Sheets and Statements of Operations Details (Tables)	12 Months Ended
	Dec. 31, 2013
Balance Sheets Details [Abstract]	'
Schedule of inventory components	'
	Inventories
	Inventories, net consisted of the following (in thousands):
		December 31,
		2013			2012
	Raw materials	$	763		$	588
	Work in process	31			52
	Finished goods	693			662
	Total inventories	$	1,487		$	1,302
Property and Equipment, net	'
	Depreciation is calculated using the straight-line method over the following estimated ranges of useful lives:
		Asset classification	Estimated useful life
		Laboratory equipment	5 years
		Computer equipment and software	3 to 5 years
		Office equipment and furniture	5 years
		Leasehold improvements	Lesser of useful life or lease term
	Property and Equipment, net
	Property and equipment consisted of the following (in thousands):
		December 31,
		2013			2012
	Laboratory equipment	$	23,949		$	33,776
	Leasehold improvements	9,493			4,388
	Computer equipment and software	3,196			11,099
	Office equipment and furniture	1,228			1,531
	Construction in progress (1)	41			28
		37,907			50,822
	Less: accumulated depreciation and amortization	(29,461		)	(34,172		)
	Property and equipment, net	$	8,446		$	16,650
	-1	Construction in progress includes equipment received but not yet placed into service pending installation.
Intangible Assets	'
	Intangible Assets
	Intangible assets consisted of the following (in thousands):
		31-Dec-13									31-Dec-12
		Gross			Accumulated			Net			Gross		Accumulated			Net		Weighted-
		Carrying			Amortization			Carrying			Carrying		Amortization			Carrying		Average
		Amount						Amount			Amount					Amount		Amortization
																		Period
																		(years)
	Customer relationships	$	3,098		$	(3,098	)	$	—		$	3,098	$	(3,098	)	$	—	5
	Developed and core technology	1,534			(1,534		)	—			1,534		(1,534		)	—		5
	Maxygen intellectual property	20,244			(10,684		)	9,560			20,244		(7,310		)	12,934		6
	Total	$	24,876		$	(15,316	)	$	9,560		$	24,876	$	(11,942	)	$	12,934	6
Estimate intangible asset future amortization expense	'
	The estimated future amortization expense to be charged to research and development through the year ending December 31, 2016 is as follows (in thousands):
	Year ending December 31:	Total
	2014	$	3,374
	2015	3,374
	2016	2,812
		$	9,560
Components of Interest Expense and Other, Net	'
	Interest Expense and Other, Net
	Interest expense and other, net consisted of the following (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Interest expense	$	13		$	—		$	—
	Foreign exchange losses	305			348			706
	Other	(14		)	(22		)	(31		)
	Interest expense and other, net	$	304		$	326		$	675

Cash_Equivalents_Marketable_Se1

Cash Equivalents, Marketable Securities and Other Investments (Tables)	12 Months Ended
	Dec. 31, 2013
Investments, Debt and Equity Securities [Abstract]	'
Available-for-sale Securities	'
	At December 31, 2013, cash equivalents, marketable securities and other investments consisted of the following (in thousands):
		31-Dec-13
		Adjusted Cost		Gross		Gross		Estimated		Average
				Unrealized		Unrealized		Fair Value		Contractual
				Gains		Losses				Maturities
										(in days)
	Money market funds	$	16,089	$	—	$	—	$	16,089	n/a
	Corporate bonds	1,002		3		—		1,005		140
	U.S. Treasury obligations	2,000		—		—		2,000		59
	Common shares of CO2 Solutions	563		232		—		795		n/a
	Total	$	19,654	$	235	$	—	$	19,889
	At December 31, 2012, cash equivalents, marketable securities and other investments 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	9,512		10		—		9,522		156
	U.S. Treasury obligations	5,511		5		—		5,516		262
	Common shares of CO2 Solutions	563		47		—		610		n/a
	Total	$	41,874	$	63	$	—	$	41,937

Fair_Value_Tables

Fair Value (Tables)	12 Months Ended
	Dec. 31, 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 Company's financial instruments that were measured at fair value on a recurring basis at December 31, 2013 by level within the fair value hierarchy (in thousands):
		31-Dec-13
		Level 1		Level 2		Level 3		Total
	Financial Assets
	Money market funds	$	16,089	$	—	$	—	$	16,089
	Corporate bonds	—		1,005		—		1,005
	U.S. Treasury obligations	—		2,000		—		2,000
	Common shares of CO2 Solutions			795		—		795
	Total	$	16,089	$	3,800	$	—	$	19,889
	The following table presents the Company's 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
	Financial Assets
	Money market funds	$	24,789	$	—	$	—	$	24,789
	Commercial paper	—		1,500		—		1,500
	Corporate bonds	—		9,522		—		9,522
	U.S. Treasury obligations	—		5,516		—		5,516
	Common shares of CO2 Solutions	610		—		—		610
	Total	$	25,399	$	16,538	$	—	$	41,937

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	12 Months Ended
	Dec. 31, 2013
Loss Contingency [Abstract]	'
Schedule of future minimum payments under non-cancellable operating leases	'
	Future minimum payments under noncancellable operating leases are as follows at December 31, 2013 (in thousands):
		Lease Payments
	Years ending December 31,
	2014	$	2,968
	2015	3,053
	2016	3,063
	2017	2,677
	2018	2,736
	2019 and beyond	3,054
	Total	$	17,551

Warrants_Tables

Warrants (Tables)	12 Months Ended
	Dec. 31, 2013
Warrants and Rights Note Disclosure [Abstract]	'
Schedule of common stock warrants issued and outstanding	'
	At December 31, 2013, the following warrants were issued and outstanding:
	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

Stockholders_Equity_Tables

Stockholders' Equity (Tables)	12 Months Ended
	Dec. 31, 2013
Equity [Abstract]	'
Schedule of Accumulated Other Comprehensive Income (Loss) [Table Text Block]	'
	Accumulated Other Comprehensive Income (Loss)
	The components of accumulated other comprehensive income (loss), net of tax, and other comprehensive income (loss) are summarized as follows (in thousands):
		Net Unrealized Gains on Marketable Securities			Cumulative Translation Adjustment			Accumulated Other Comprehensive Income (Loss)
	Balance at December 31, 2010	$	128		$	(162	)	$	(34	)
	Other comprehensive loss	(370		)	(3		)	(373		)
	Balance at December 31, 2011	(242		)	(165		)	(407		)
	Other comprehensive loss	(647		)	165			(482		)
	Reclassification of Other-Than-Temporary Loss in Marketable Securities	753			—			753
	Balance at December 31, 2012	(136		)	—			(136		)
	Other comprehensive loss	104			—			104
	Balance at December 31, 2013	$	(32	)	$	—		$	(32	)

Stockbased_Compensation_Tables

Stock-based Compensation (Tables)	12 Months Ended
	Dec. 31, 2013
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Summary of Share Based Award Activity	'
	A summary of share-based activity is as follows (in thousands):
		Shares
		Available
		for Grant
	31-Dec-12	3,767
	Annual increase in shares available for grant	1,507
	Option grants	(922	)
	RSU award grants	(2,101	)
	RSU award shares withheld for taxes	132
	RSA award grants	(216	)
	PSU award grants	(523	)
	Options forfeited, cancelled or expired	2,603
	RSU awards forfeited, cancelled or expired	165
	PSU awards forfeited, cancelled or expired	496
	31-Dec-13	4,908
Summary of stock option activity	'
	A summary of stock option activity for the years ended December 31, 2011, 2012 and 2013 is as follows (in thousands, except per share amounts and years):
			Options Outstanding
			Number of			Weighted				Weighted Average Remaining Contractual Terms (years)		Aggregate Intrinsic Value
			Options			Average
						Exercise Price
						per Share
	31-Dec-10		7,796			$	6.27			6.57		$	34,228
	Grants		1,751			9.33
	Exercises		(1,167	)		2.21						9,077
	Early exercised options repurchased		(476	)		9.51
	Forfeited/Cancelled		—			—
	31-Dec-11		7,904			7.35				6.77		6,570
	Grants		1,521			3.42
	Exercises		(708	)		1.78						925
	Forfeited/Cancelled		(2,584	)		8.23
	31-Dec-12		6,133			6.65				4.91		657
	Grants		922			2.28
	Exercises		(326	)		0.98						409
	Forfeited/Cancelled		(2,603	)		7.35
	31-Dec-13		4,126			5.68				5.75		87
	Options vested and expected to vest at December 31, 2013		4,006			5.77				5.66		87
	Options exercisable at December 31, 2013		2,805			$	6.76			4.37		$	87
Information about stock options outstanding and exercisable by exercise price range	'
	The following table summarizes information about stock options outstanding and exercisable at December 31, 2013 (amounts in thousands, except per share and years):
		Options Outstanding									Options Exercisable
	Exercise Prices	Number			Weighted		Weighted				Number			Weighted
		of			Average		Average				of			Average
		Options			Remaining		Exercise				Options			Exercise
					Contractual		Price per							Price per
					Term		Share							Share
					(Years)
	$0.68 - $2.32	869			7.3		$	1.96			199			$	0.96
	$2.34 - $3.46	971			6.5		2.93				561			2.76
	$3.56 - $7.40	719			5.3		5.31				595			5.6
	$7.41 - $9.81	721			4.36		8.38				673			8.34
	$9.82 - $11.87	846			4.88		10.66				777			10.67
		4,126			5.75		$	5.68			2,805			$	6.76
Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity	'
	A summary of RSU activity for the years ended December 31, 2011, 2012 and 2013 is as follows (in thousands, except per share amounts and years):
			RSUs Outstanding
			Number of RSUs			Weighted Average Grant Date Fair Value Per Share				Weighted Average Remaining Contractual Terms (years)		Aggregate Intrinsic Value
	31-Dec-10		—
	Grants		578			$	9.54
	Shares released		—
	Forfeited/Cancelled		(32	)
	31-Dec-11		546							1.66		$	2,895
	Grants		1,148			$	3.54
	Shares released		(167	)
	Forfeited/Cancelled		(569	)
	31-Dec-12		958							1.21		$	2,117
	Grants		2,101			$	1.8
	Shares released		(325	)
	Forfeited/Cancelled		(496	)
	31-Dec-13		2,238							1.1		$	3,133
	RSUs vested and expected to vest at December 31, 2013		2,015									$	2,821
Schedule of stock-based compensation expense	'
	The following table presents stock-based compensation expense included in the consolidated statements of operations (in thousands):
		Years Ended December 31,
		2013				2012				2011
	Research and development	$	1,201			$	2,334			$	3,311
	Selling, general and administrative	3,188				2,742				6,120
		$	4,389			$	5,076			$	9,431
Assumptions used to estimate the fair value of option grants	'
	The Company used the following assumptions to estimate the fair value of its employee option grants:
		Years Ended December 31,
		2013			2012			2011
	Weighted-average expected life (years)	6			6			6.1
	Weighted-average expected volatility	65	%		61	%		58	%
	Weighted-average risk free interest rate	1.2	%		1	%		2.2	%
	Expected dividend yield	0	%		0	%		0	%

Income_Taxes_Tables

Income Taxes (Tables)	12 Months Ended
	Dec. 31, 2013
Income Tax Disclosure [Abstract]	'
Schedule of loss before income taxes, domestic and foreign	'
	The Company's loss before provision for income taxes was as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	United States	$	(41,696	)	$	(30,743	)	$	(17,474	)
	Foreign	306			156			1,165
	Loss before provision for income taxes	$	(41,390	)	$	(30,587	)	$	(16,309	)
Components of provision for income taxes	'
	The components of the provision for income taxes are as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Current provision (benefit):
	Federal	$	—		$	—		$	3
	State	5			7			7
	Foreign	(45		)	178			82
	Total current provision	(40		)	185			92
	Deferred provision (benefit):
	Federal	(59		)	(62		)	—
	State	(7		)	(7		)	—
	Foreign	19			154			149
	Total deferred provision	(47		)	85			149
	Total provision for (benefit from) income taxes	$	(87	)	$	270		$	241
Reconciliation of provision for income taxes calculated at the statutory rate to provision for income taxes	'
	Reconciliation of the provision for income taxes calculated at the statutory rate to the Company's provision for (benefit from) income taxes is as follows (in thousands):
		Years Ended December 31,
		2013			2012			2011
	Tax benefit at federal statutory rate	$	(14,073	)	$	(10,399	)	$	(5,708	)
	State taxes	(1,948		)	(1,063		)	(1,421		)
	Research and development credits	(195		)	—			(83		)
	Foreign operations taxed at different rates	(108		)	7			(252		)
	Stock-based compensation	117			312			1,241
	Other nondeductible items	(1,272		)	204			650
	Change in federal statutory rate	—			1,493			—
	Change in valuation allowance	17,392			9,716			5,814
	Provision for (benefit from) income taxes	$	(87	)	$	270		$	241
Significant components of our deferred tax assets and liabilities	'
	Significant components of the Company's deferred tax assets and liabilities are as follows (in thousands):
		December 31,
		2013			2012
	Deferred tax assets:
	Net operating losses	$	67,507		$	54,923
	Credits	4,194			3,329
	Deferred revenues	1,198			1,297
	Stock-based compensation	3,043			4,464
	Reserves and accruals	3,626			2,090
	Depreciation	2,247			1,746
	Intangible assets	4,208			3,556
	Unrealized gain/loss	112			166
	Other assets	159			141
	Total deferred tax assets:	86,294			71,712
	Deferred tax liabilities:
	Other	—			—
	Total deferred tax liabilities:	—			—
	Valuation allowance	(86,294		)	(71,692		)
	Net deferred tax assets	$	—		$	20
Summary of federal, state and foreign NOL carryforwards and federal research and development tax credits	'
	The following table sets forth the Company's federal, state and foreign NOL carryforwards and federal research and development tax credits as of December 31, 2013 (in thousands):
		31-Dec-13
		Amount			Expiration
					Years
	Net operating losses, federal	$	184,818		2022-2033
	Net operating losses, state	148,325			2015-2033
	Tax credits, federal	5,138			2022-2033
	Tax credits, state	5,459			Do not expire
	Net operating losses, foreign	15,403			Various
	Tax credits, foreign	$	16		Various
Reconciliation of the beginning and ending amount of unrecognized tax benefits	'
	A reconciliation of the beginning and ending amount of unrecognized tax benefits is as follows (in thousands):
		December 31,
		2013			2012			2011
	Balance at beginning of year	$	7,420		$	6,611		$	6,492
	Additions based on tax positions related to current year	1,116			709			470
	Additions to tax provision of prior years	6			263			4
	Reductions to tax provision of prior years	(78		)	24			(262		)
	Lapse of the applicable statute of limitations	(158		)	(187		)	(93		)
	Balance at end of year	$	8,306		$	7,420		$	6,611

Segment_Reporting_Tables

Segment Reporting (Tables)	12 Months Ended
	Dec. 31, 2013
Segment Reporting Information, Operating Income (Loss) [Abstract]	'
Schedule of revenues by geographical area	'
	Geographic revenues are identified by the location of the customer and consist of the following (in thousands):
		Years Ended December 31,
		2013		2012		2011
	Revenues
	United States	$	11,005	$	51,714	$	72,355
	Europe	9,568		11,150		16,751
	Asia
	India	3,099		16,813		21,063
	Singapore	7,220		7,507		12,008
	Others	1,030		1,114		1,688
		$	31,922	$	88,298	$	123,865
Schedule of long-lived assets by geographical area	'
	Geographic presentation of identifiable long-lived assets below shows those assets that can be directly associated with a particular geographic area and consist of the following (in thousands):
		December 31,
		2013		2012		2011
	Long-lived assets
	United States	$	16,189	$	25,953	$	34,817
	Europe (1)	2,123		5,157		4,395
	Asia	—		711		2,380
		$	18,312	$	31,821	$	41,592
	-1	Primarily Hungary

Restructuring_Tables

Restructuring (Tables)	12 Months Ended
	Dec. 31, 2013
Restructuring Costs [Abstract]	'
Summary of changes in restructuring accrual	'
	The following table summarizes the activity in the restructuring accrual during the years ended December 31, 2013 and 2012 (in thousands):
		Q1 2012 Restructuring Plan			Q3 2012 Restructuring Plan			Q4 2013 Restructuring Plan			Total
	Restructuring charges	$	572		$	2,537		$	—		$	3,109
	Cash payments	(512		)	(611		)	—			(1,123		)
	Leasehold improvements write-down and equipment disposal charges	—			(1,413		)	—			(1,413		)
	Adjustments to previously accrued charges	(60		)	(93		)	—			(153		)
	Balance at December 31, 2012	—			420			—			420
	Restructuring charges	—						809			809
	Cash payments	—			(345		)	(532		)	(877		)
	Non-cash items	—			(49		)	—			(49		)
	Adjustments to previously accrued charges	—			(26		)	—			(26		)
	Balance at December 31, 2013	$	—		$	—		$	277		$	277

Selected_Quarterly_Financial_D1

Selected Quarterly Financial Data (Unaudited) (Tables)	12 Months Ended
	Dec. 31, 2013
Quarterly Financial Information Disclosure [Abstract]	'
Selected Quarterly Financial Data	'
	The following table provides the selected quarterly financial data for 2013 and 2012 (in thousands):
	Condensed Consolidated Statements of Operations
	(In Thousands, Except Per Share Amounts)
		Quarter Ended
		December 31,			September 30,			June 30,			March 31,			December 31,			September 30,			June 30,			March 31,
		2013			2013			2013			2013			2012			2012			2012			2012
	Revenues:
	Product	$	5,263		$	1,076		$	4,948		$	9,136		$	6,834		$	7,140		$	6,783		$	15,167
	Collaborative research and development	1,931			2,028			1,609			1,300			1,078			18,569			15,868			14,362
	Revenue sharing arrangement	2,331			839			417			1,044			—			—			—			250
	Government awards	—			—			—			—			—			632			258			1,357
	Total revenues	9,525			3,943			6,974			11,480			7,912			26,341			22,909			31,136
	Costs and operating expenses:
	Cost of product revenues	4,764			494			3,631			5,665			5,779			6,397			5,829			12,642
	Research and development	8,829			6,831			8,624			7,322			10,594			14,191			15,650			16,349
	Selling, general and administrative	5,783			5,832			7,169			8,124			7,286			7,909			6,789			9,395
	Total costs and operating expenses	19,376			13,157			19,424			21,111			23,659			28,497			28,268			38,386
	Loss before income taxes	(9,858		)	(9,227		)	(12,617		)	(9,688		)	(15,711		)	(2,140		)	(5,442		)	(7,293		)
	Net loss	$	(9,813	)	$	(9,262	)	$	(12,605	)	$	(9,623	)	$	(15,538	)	$	(2,309	)	$	(5,519	)	$	(7,490	)
	Net loss per share, basic and diluted	$	(0.26	)	$	(0.24	)	$	(0.33	)	$	(0.25	)	$	(0.41	)	$	(0.06	)	$	(0.15	)	$	(0.21	)
	Weighted average common shares used in computing net loss per share, basic and diluted (1)	38,329			38,102			38,060			37,842			37,581			37,118			36,296			36,057
	-1	The full year net loss per share of common stock, basic and diluted, may not equal the sum of the quarters due to weighting of outstanding shares.

Summary_of_Significant_Account3

Summary of Significant Accounting Policies (Textual) (Details) (USD $)

3 Months Ended

12 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2010

operating_segment

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Additional Cash and Cash Equivalent Related Text

'

'

'

'

'

'

'

'

'3 months

'

'

'

Assets Held-for-sale, Current

$2,179,000

'

'

'

$0

'

'

'

$2,179,000

$0

'

'

Investment Maturity Date

'

'

'

'

'

'

'

'

'1 year

'

'

'

Other than Temporary Impairment Losses, Investments

'

'

'

'

'

'

'

'

'

753,000

'

'

Entity-Wide Revenue, Major Customer, Percentage

'

'

'

'

'

'

'

'

10.00%

'

'

'

Number of Operating Segments

'

'

'

'

'

'

'

1

1

'

'

'

Net income (loss)

9,813,000

9,262,000

12,605,000

9,623,000

15,538,000

2,309,000

5,519,000

7,490,000

41,303,000

30,857,000

16,550,000

'

Net cash provided by (used in) operating activities

'

'

'

'

'

'

'

'

22,998,000

11,892,000

490,000

'

Accumulated deficit

256,859,000

'

'

'

215,556,000

'

'

'

256,859,000

215,556,000

'

'

Cash and cash equivalents

22,130,000

'

'

'

32,003,000

'

'

'

22,130,000

32,003,000

25,762,000

72,396,000

Cash, Cash Equivalents and Marketable Securities [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Recorded impairment in condensed consolidated statement of operations as sales, general and administrative expenses

'

'

'

'

'

'

'

'

0

'

'

'

Decrease (increase) in restricted cash

'

'

'

'

'

'

'

'

800,000

0

-45,000

'

Accounts Receivable, Net

'

'

'

'

'

'

'

'

'

'

'

'

Write-off and other

'

'

'

'

'

'

'

'

0

0

0

'

Advertising

'

'

'

'

'

'

'

'

'

'

'

'

Advertising Expense

'

'

'

'

'

'

'

'

513,000

351,000

113,000

'

Intangible Assets, Net (Excluding Goodwill) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Asset Impairment Charges

'

'

'

'

'

'

'

'

1,571,000

'

'

'

Sales Revenue, Services, Net [Member] | Exela [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

15.00%

0.00%

0.00%

'

Sales Revenue, Services, Net [Member] | Shell [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

0.00%

51.00%

51.00%

'

Sales Revenue, Services, Net [Member] | Merck [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

39.00%

13.00%

10.00%

'

Sales Revenue, Services, Net [Member] | Novartis [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

14.00%

1.00%

1.00%

'

Prepaid Expenses and Other Current Assets [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Deferred cost of sales

'

'

'

'

1,100,000

'

'

'

'

1,100,000

'

'

Core IP [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Intangible Assets, Net (Excluding Goodwill) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Undiscounted cash flows, discount rate (percent)

'

'

'

'

'

'

'

'

19.50%

18.00%

'

'

Undiscounted cash flows, long-term growth rate (percent)

'

'

'

'

'

'

'

'

2.00%

2.00%

'

'

Fair value in excess of carrying value (percent)

44.00%

'

'

'

'

'

'

'

44.00%

'

'

'

Percentage of undiscounted cash flows per product (percent)

7.00%

'

'

'

38.00%

'

'

'

7.00%

38.00%

'

'

Percentage of undiscounted cash flows greater than the carrying value of the asset group (percent)

37.00%

'

'

'

14.00%

'

'

'

37.00%

14.00%

'

'

Customer relationships [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Entity-Wide Revenue, Major Customer, Percentage

'

'

'

'

'

'

'

'

81.00%

83.00%

'

'

Novartis [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

50.00%

11.00%

'

'

Merck [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Concentration of Credit Risk

'

'

'

'

'

'

'

'

'

'

'

'

Customer concentration risk (percentage)

'

'

'

'

'

'

'

'

'

53.00%

'

'

Arch [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Accounts Receivable, Net

'

'

'

'

'

'

'

'

'

'

'

'

Write-off and other

'

'

'

'

'

'

'

'

387,000

'

'

'

Debt Securities [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Cash, Cash Equivalents and Marketable Securities [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Recorded impairment in condensed consolidated statement of operations as sales, general and administrative expenses

'

'

'

'

'

'

'

'

0

'

'

'

Available-for-sale Securities [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Cash, Cash Equivalents and Marketable Securities [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Realized gains (losses) from sales of marketable securities

'

'

'

'

'

'

'

'

0

0

0

'

Impairment of Goodwill [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Intangible Assets, Net (Excluding Goodwill) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

Asset Impairment Charges

'

'

'

'

'

'

'

'

$0

$0

$0

'

Enzyme Opportunities [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Undiscounted cash flows, expected percentage of revenue (percent)

'

'

'

'

31.00%

'

'

'

'

31.00%

'

'

Entity-Wide Revenue, Major Customer, Percentage

'

'

'

'

'

'

'

'

10.00%

'

'

'

Core Pharmaceutical Business [Member]

'

'

'

'

'

'

'

'

'

'

'

'

Accounting Policies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Undiscounted cash flows, expected percentage of revenue (percent)

'

'

'

'

69.00%

'

'

'

'

69.00%

'

'

Entity-Wide Revenue, Major Customer, Percentage

'

'

'

'

'

'

'

'

90.00%

'

'

'

Summary_of_Significant_Account4

Summary of Significant Accounting Policies (Accounts Receivable) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Receivables [Abstract]	'	'	'
Allowance - beginning of period	($150)	($17)	($58)
Allowance for bad debt	-386	-133	41
Recoveries from bad debts	76	0	0
Write-off and other	0	0	0
Allowance - end of period	($460)	($150)	($17)

Summary_of_Significant_Account5

Summary of Significant Accounting Policies (Plant, Property, and Equipment) (Details)	12 Months Ended
	Dec. 31, 2013
Laboratory equipment [Member]	'
Property, Plant and Equipment [Line Items]	'
Estimated useful life (years)	'5 years
Computer equipment and software [Member] | Minimum [Member]	'
Property, Plant and Equipment [Line Items]	'
Estimated useful life (years)	'3 years
Computer equipment and software [Member] | Maximum [Member]	'
Property, Plant and Equipment [Line Items]	'
Estimated useful life (years)	'5 years
Office equipment and furniture [Member]	'
Property, Plant and Equipment [Line Items]	'
Estimated useful life (years)	'5 years

Summary_of_Significant_Account6

Summary of Significant Accounting Policies (Earnings Per Share) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Numerator [Abstract]	'	'	'	'	'	'	'	'	'	'	'
Net loss	($9,813)	($9,262)	($12,605)	($9,623)	($15,538)	($2,309)	($5,519)	($7,490)	($41,303)	($30,857)	($16,550)
Denominator [Abstract]	'	'	'	'	'	'	'	'	'	'	'
Weighted-average shares of common stock outstanding (shares)	'	'	'	'	'	'	'	'	38,231	36,768	35,674
Weighted-average shares of common stock used in computing net loss per share of common stock, basic and diluted (shares)	'	'	'	'	'	'	'	'	38,231	36,768	35,674
Net loss per share of common stock, basic and diluted (dollars per share)	($0.26)	($0.24)	($0.33)	($0.25)	($0.41)	($0.06)	($0.15)	($0.21)	($1.08)	($0.84)	($0.46)

Summary_of_Significant_Account7

Summary of Significant Accounting Policies (Anti-Dilutive Securities) (Details)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Total	6,797	7,351	8,716
Options to purchase common stock [Member]	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Total	4,126	6,133	7,904
Restricted stock units [Member]	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Total	2,238	958	546
Performance Stock Units [Member]	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Total	358	0	'
Warrants to purchase common stock [Member]	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'
Total	75	260	266

Collaborative_Research_and_Dev1

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

3 Months Ended

12 Months Ended

1 Months Ended

3 Months Ended

12 Months Ended

60 Months Ended

12 Months Ended

Dec. 31, 2013

Sep. 30, 2013

Jun. 30, 2013

Mar. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Jun. 30, 2012

Mar. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Sep. 30, 2012

Nov. 30, 2007

Sep. 30, 2012

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Jan. 31, 2017

Dec. 31, 2013

Shell [Member]

Shell [Member]

Shell [Member]

Shell [Member]

Arch [Member]

Merck [Member]

Merck [Member]

Arch [Member]

gal

Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Sales Revenue, Services, Net

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$1,804,000

'

'

Collaborative Research and Development Agreements (Textual) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Term of collaborative research and development agreement (in years)

'

'

'

'

'

'

'

'

'

'

'

'

'5 years

'

'

'

'

'5 years

'

Amount of new shell agreement requires Shell pay

'

'

'

'

'

'

'

'

'

'

'

7,500,000

'

'

'

'

'

'

'

Collection of agreement

'

'

'

'

'

'

'

'

'

'

'

'

'

7,500,000

'

'

'

'

'

Milestone payment under Shell Research Agreement

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,000,000

'

'

'

'

Liquid fuel (gallons)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

30,000,000

'

'

'

'

Period of research agreement with shell (years)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'10 years

'

'

'

'

Collaborative agreements exclusively right period (years)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'3 years

'

'

'

'

Revenue sharing arrangement

2,331,000

839,000

417,000

1,044,000

0

0

0

250,000

4,631,000

150,000

450,000

'

'

'

'

'

'

'

'

Sales revenue

5,263,000

1,076,000

4,948,000

9,136,000

6,834,000

7,140,000

6,783,000

15,167,000

20,423,000

35,924,000

49,021,000

'

'

'

'

'

'

'

'

Deferred Revenue

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

696,000

'

'

Sales Revenue, Goods, Net

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2,134,000

1,004,000

'

'

Write-off and other

'

'

'

'

'

'

'

'

$0

$0

$0

'

'

'

'

'

'

'

$387,000

Joint_Development_Agreement_wi1

Joint Development Agreement with CO2 Solutions (Details) (USD $)	12 Months Ended	0 Months Ended	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2012	Dec. 15, 2009	Dec. 31, 2013
		CO2 Solutions [Member]	CO2 Solutions [Member]
Joint Development Agreement with CO2 solutions (Textual) [Abstract]	'	'	'
Number of shares acquired in joint venture (shares)	'	10,000,000	'
Percentage of common shares outstanding at the time of investment (percent)	'	16.60%	'
Statutory resale restriction, expiry period (months)	'	'4 months	'
Statutory resale restriction, expiry date	'	15-Apr-10	'
Expiration period of original joint development agreement	'	'	'2011-01
Other than Temporary Impairment Losses, Investments	$753	'	'

Assets_Held_for_Sale_Narrative

Assets Held for Sale (Narrative) (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Long Lived Assets Held-for-sale [Line Items]	'	'
Property, Plant and Equipment, Net	$8,446,000	$16,650,000
Assets Held-for-sale, at Carrying Value	2,179,000	'
Asset Impairment Charges	1,571,000	'
Assets Held-for-sale [Member]	'	'
Long Lived Assets Held-for-sale [Line Items]	'	'
Property, Plant and Equipment, Net	$3,750,000	'

Balance_Sheets_and_Statements_2

Balance Sheets and Statements of Operations Details (Schedule of Inventory Components) (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Schedule of Inventory Components	'	'
Raw materials	$763	$588
Work in process	31	52
Finished goods	693	662
Total inventories	$1,487	$1,302

Balance_Sheets_and_Statements_3

Balance Sheets and Statements of Operations Details (Property and Equipment, net) (Details) (USD $)	Dec. 31, 2013		Dec. 31, 2012
In Thousands, unless otherwise specified
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	$37,907		$50,822
Less: accumulated depreciation and amortization	-29,461		-34,172
Property and equipment, net	8,446		16,650
Laboratory equipment [Member]	'		'
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	23,949		33,776
Leasehold improvements [Member]	'		'
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	9,493		4,388
Computer equipment and software [Member]	'		'
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	3,196		11,099
Office equipment and furniture [Member]	'		'
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	1,228		1,531
Construction in progress [Member]	'		'
Property, Plant and Equipment, Net, by Type [Abstract]	'		'
Property and Equipment, Gross	$41	[1]	$28	[1]
[1]	Construction in progress includes equipment received but not yet placed into service pending installation.

Balance_Sheets_and_Statements_4

Balance Sheets and Statements of Operations Details (Intangible Assets) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	$24,876	$24,876
Accumulated Amortization	-15,316	-11,942
Net Carrying Amount	9,560	12,934
Weighted- Average Amortization Period (years)	'6 years	'
Customer relationships [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	3,098	3,098
Accumulated Amortization	-3,098	-3,098
Net Carrying Amount	0	0
Weighted- Average Amortization Period (years)	'5 years	'
Developed and core technology [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	1,534	1,534
Accumulated Amortization	-1,534	-1,534
Net Carrying Amount	0	0
Weighted- Average Amortization Period (years)	'5 years	'
Maxygen intellectual property [Member]	'	'
Finite-Lived Intangible Assets [Line Items]	'	'
Gross Carrying Amount	20,244	20,244
Accumulated Amortization	-10,684	-7,310
Net Carrying Amount	$9,560	$12,934
Weighted- Average Amortization Period (years)	'6 years	'

Balance_Sheets_and_Statements_5

Balance Sheets and Statements of Operations Details (Intangible Asset Future Amortization Expense) (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Finite-Lived Intangible Assets, Net, Amortization Expense, Fiscal Year Maturity [Abstract]	'	'
2014	$3,374	'
2015	3,374	'
2016	2,812	'
Net Carrying Amount	$9,560	$12,934

Balance_Sheets_and_Statements_6

Balance Sheets and Statements of Operations Details (Interest Expense and Other, Net) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Other Income and Expenses [Abstract]	'	'	'
Interest expense	$13	$0	$0
Foreign exchange losses	305	348	706
Other	-14	-22	-31
Interest expense and other, net	$304	$326	$675

Balance_Sheets_and_Statements_7

Balance Sheets and Statements of Operations Details (Textual) (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Balance Sheets Details [Abstract]	'	'
Goodwill	$3,241	$3,241

Cash_Equivalents_Marketable_Se2

Cash Equivalents, Marketable Securities and Other Investments (Details) (USD $)

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2010

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

In Thousands, unless otherwise specified

securities

securities

Corporate Debt Securities [Member]

Corporate Debt Securities [Member]

Money Market Funds [Member]

Money Market Funds [Member]

Commercial Paper [Member]

US Treasury Securities [Member]

US Treasury Securities [Member]

Common Shares of Co Two Solution [Member]

Common Shares of Co Two Solution [Member]

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

'

'

'

'

'

'

'

'

'

'

'

'

'

Amortized Cost Basis

$19,654

$41,874

'

'

$1,002

$9,512

$16,089

$24,789

$1,499

$2,000

$5,511

$563

$563

Gross Unrealized Gains

235

63

'

'

3

10

0

0

1

0

5

232

47

Available-for-sale Securities, Gross Unrealized Losses

0

0

'

'

0

0

0

0

0

0

0

0

0

Available-for-sale Securities, Fair Value Disclosure

19,889

41,937

'

'

1,005

9,522

16,089

24,789

1,500

2,000

5,516

795

610

Average Contractual Maturities

'

'

'

'

'140 days

'156 days

'

'

'70 days

'59 days

'262 days

'

'

Cash and cash equivalents

22,130

32,003

25,762

72,396

'

'

'

'

'

'

'

'

'

Money Market Funds, at Carrying Value

16,089

24,789

'

'

'

'

'

'

'

'

'

'

'

Cash

$6,041

$7,214

'

'

'

'

'

'

'

'

'

'

'

Number of Marketable Securities

0

0

'

'

'

'

'

'

'

'

'

'

'

Fair_Value_Financial_Assets_me

Fair Value (Financial Assets measured at Fair Value on a Recurring Basis) (Details) (USD $)	Dec. 31, 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	$19,889	$41,937
Level 1	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	16,089	25,399
Level 2	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	3,800	16,538
Level 3	'	'
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	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	16,089	24,789
Money market funds | Level 1	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	16,089	24,789
Money market funds | Level 2	'	'
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 | Level 3	'	'
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	'	'
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 | Level 1	'	'
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 | Level 2	'	'
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 | Level 3	'	'
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	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	1,005	9,522
Corporate bonds | Level 1	'	'
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 | Level 2	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	1,005	9,522
Corporate bonds | Level 3	'	'
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	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	2,000	5,516
U.S. Treasury obligations | Level 1	'	'
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 | Level 2	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	2,000	5,516
U.S. Treasury obligations | Level 3	'	'
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 Solutions	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	795	610
Common shares of CO2 Solutions | Level 1	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	'	610
Common shares of CO2 Solutions | Level 2	'	'
Summary of financial instruments measured at fair value on a recurring basis	'	'
Total financial assets measured at fair value on a recurring basis	795	0
Common shares of CO2 Solutions | Level 3	'	'
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_Assets_Held_for_Sal

Fair Value Assets Held for Sale (Details) (USD $)	Dec. 31, 2013
In Thousands, unless otherwise specified
Fair Value Disclosures [Abstract]	'
Assets Held-for-sale, at Carrying Value	$2,179

Fair_Value_Textual_Details

Fair Value (Textual) (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Fair Value (Textual) [Abstract]	'	'	'
Impairment of marketable securities	$0	$753,000	$0
Income Tax Expense (Benefit)	-87,000	270,000	241,000
Assets Held-for-sale, at Carrying Value	2,179,000	'	'
Asset Impairment Charges	1,571,000	'	'
Co Two Solutions [Member]	'	'	'
Fair Value (Textual) [Abstract]	'	'	'
Number of common shares fair value (shares)	10,000,000	'	'
Estimated fair value of investment in common stock	795,000	610,000	'
Unrealized gain on investment	232,000	47,000	'
Impairment of marketable securities	'	756,000	'
Income Tax Expense (Benefit)	$66,000	$69,000	'

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Related Party Transaction [Line Items]	'	'	'
Common Stock, Value, Issued	$4,000	$4,000	'
Accounts Receivable, Net, Current	5,413,000	7,545,000	'
Raizen [Member]	'	'	'
Related Party Transaction [Line Items]	'	'	'
Common Stock, Value, Issued	5,600,000	'	'
Exela PharmaSci, Inc [Member]	'	'	'
Related Party Transaction [Line Items]	'	'	'
Revenue from exclusivity fee	4,631,000	150,000	450,000
Exela [Member]	'	'	'
Related Party Transaction [Line Items]	'	'	'
Accounts Receivable, Net, Current	445,000	0	'
Director [Member]	'	'	'
Related Party Transaction [Line Items]	'	'	'
Accounts Receivable, Net, Current	0	'	'
Related Party Transaction, Expenses from Transactions with Related Party	$120,000	'	'

Commitments_and_Contingencies_1

Commitments and Contingencies (Future Minimum Payments Under Operating Leases) (Details) (USD $)	Dec. 31, 2013
In Thousands, unless otherwise specified
Future minimum payments under non-cancellable operating leases	'
2014	$2,968
2015	3,053
2016	3,063
2017	2,677
2018	2,736
2019 and beyond	3,054
Total	$17,551

Commitments_and_Contingencies_2

Commitments and Contingencies (Textual) (Details) (USD $)	12 Months Ended			12 Months Ended			12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2013
		Fifth Amendment [Member]	Fifth Amendment [Member]	Penobscot Space, Building 2 Space, and Saginaw Space [Member]	MTS HUNGARY [Member]	Headquarters, Redwood City [Member]	Chesapeake Space [Member]	Singapore [Member]
				Fifth Amendment [Member]		Fifth Amendment [Member]
						sqft
Commitments and Contingencies (Textual) [Abstract]	'	'	'	'	'	'	'	'
Lease area space occupancy (in square feet)	'	'	'	'	'	107,000	'	'
Payments for Rent	$2,587,000	'	'	'	'	'	'	'
Expiration date of lease	'	'	'	31-Jan-20	30-Sep-16	'	31-Jan-17	'
Amount spent for capital improvements	'	3,600,000	'	'	'	'	'	'
Reimbursements from landlord	'	3,100,000	'	'	'	'	'	'
Incentive from Lessor	2,160,000	'	'	'	'	'	'	'
Letters of credit	'	707,000,000	707,000	'	'	'	'	'
Operating Leases, Rent Expense, Minimum Rentals	309,000	'	'	'	'	'	'	'
Remaining minimum lease payments	17,551,000	'	'	'	'	'	'	354,000
Facility lease term (months)	'	'	'	'	'	'	'	'6 months
Asset retirement obligations	109,000	'	'	'	'	'	'	'
Estimated obligation payable	$600,000	'	'	'	'	'	'	'

Warrants_Details

Warrants (Details)	12 Months Ended
	Dec. 31, 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	2,384
Exercise Price 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	72,727
Exercise Price per Share	8.25
Expiration	28-Sep-17

Warrants_Textual_Details

Warrants (Textual) (Details)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012
Warrant (Textual) [Abstract]	'	'
Warrants in a net exercise transaction	0	6,066
Common shares issued	3,308	'

Stockholders_Equity_Details

Stockholders' Equity (Details) (USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Class of Stock [Line Items]	'	'	'
Preferred stock, par value	$0.00	$0.00	'
Noncontrolling Interest, Ownership Percentage by Noncontrolling Owners	15.00%	'	'
Tender Offer Portion of Common Stock	15.00%	'	'
Accumulated Other Comprehensive Income (Loss) [Roll Forward]	'	'	'
Accumulated Other Comprehensive Income (Loss), Available-for-sale Securities Adjustment, Net of Tax, Beginning of Period	($136)	($242)	$128
Other Comprehensive Income (Loss), Unrealized Holding Gain (Loss) on Securities Arising During Period, Net of Tax	104	-647	-370
Other Comprehensive Income (Loss), Reclassification Adjustment for Write-down of Securities Included in Net Income, Net of Tax	'	753	'
Accumulated Other Comprehensive Income (Loss), Available-for-sale Securities Adjustment, Net of Tax, End of Period	-32	-136	-242
Accumulated Other Comprehensive Income (Loss), Foreign Currency Translation Adjustment, Net of Tax, Beginning of Period	0	-165	-162
Other Comprehensive Income (Loss), Foreign Currency Transaction and Translation Adjustment, Net of Tax	0	165	-3
Accumulated Other Comprehensive Income (Loss), Foreign Currency Translation Adjustment, Net of Tax, End of Period	0	0	-165
Accumulated Other Comprehensive Income (Loss), Net of Tax, Beginning of Period	-136	-407	-34
Other Comprehensive Income (Loss), Net of Tax, Portion Attributable to Parent	104	271	-373
Other Comprehensive Income (Loss), Net of Tax, Portion Attributable to Parent, Before Reclassifications	'	-482	'
Other Comprehensive Income (Loss), Available-for-sale Securities Adjustment, Net of Tax, Portion Attributable to Parent, Reclassification of Losses Included Net Loss	0	753	0
Accumulated Other Comprehensive Income (Loss), Net of Tax, End of Period	($32)	($136)	($407)
Series A Preferred Stock [Member]	'	'	'
Class of Stock [Line Items]	'	'	'
Preferred stock, par value	$0.00	'	'
Share Price	$11.35	'	'
Series A Preferred Stock [Member]	'	'	'
Class of Stock [Line Items]	'	'	'
Preferred Stock, Participation Rights	'one	'	'
Warrants and Rights Outstanding	0.001	'	'

Stockbased_Compensation_ShareB

Stock-based Compensation (Share-Based Award Activity) (Details)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013
Shares Available For Grant [Roll Forward]	'
Shares Available for Grant, beginning of period (shares)	3,767
Shares Available for Grant, authorized (shares)	1,507
Shares Available for Grant, end of period (shares)	4,908
Stock Options [Member]	'
Shares Available For Grant [Roll Forward]	'
Shares Available for Grant, granted (shares)	-922
Shares Available for Grant, Forfeited/Cancelled (shares)	2,603
Restricted stock units [Member]	'
Shares Available For Grant [Roll Forward]	'
Shares Available for Grant, granted (shares)	-2,101
Shares Paid for Tax Withholding for Share Based Compensation	-132
Shares Available for Grant, Forfeited/Cancelled (shares)	165
Restricted Stock Award [Member]	'
Shares Available For Grant [Roll Forward]	'
Shares Available for Grant, granted (shares)	-216
Performance Stock Units [Member]	'
Shares Available For Grant [Roll Forward]	'
Shares Available for Grant, granted (shares)	-523
Shares Available for Grant, Forfeited/Cancelled (shares)	496

Stockbased_Compensation_Stock_

Stock-based Compensation (Stock Option Activity) (Details) (Stock Options [Member], USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Stock Options [Member]	'	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]	'	'	'	'
Outstanding, beginning of period (number of options)	6,133	7,904	7,796	'
Grants (number of options)	922	1,521	1,751	'
Exercises (number of options)	-326	-708	-1,167	'
Early exercised options repurchased (number of options)	'	'	-476	'
Forfeited/Cancelled (number of options)	-2,603	-2,584	0	'
Outstanding, end of period (number of options)	4,126	6,133	7,904	7,796
Options Vested and Expected to Vest (shares)	4,006	'	'	'
Options Exercisable (number of options)	2,805	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]	'	'	'	'
Outstanding, beginning of period, weighted average exercise price per share (dollars per option)	$6.65	$7.35	$6.27	'
Grants, weighted average exercise price per share (dollars per option)	$2.28	$3.42	$9.33	'
Exercises, weighted average exercise price per share (dollars per option)	$0.98	$1.78	$2.21	'
Early exercised option repurchased, weighted average exercise price per share (dollars per option)	'	'	$9.51	'
Forfeited/Cancelled, weighted average exercise price per share (dollars per option)	$7.35	$8.23	$0	'
Outstanding, end of period, weighted average exercise price per share (dollars per option)	$5.68	$6.65	$7.35	$6.27
Options Vested and Expected to Vest (dollars per option)	$5.77	'	'	'
Options Exercisable (dollars per option)	$6.76	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Options, Additional Disclosures [Abstract]	'	'	'	'
Options Outstanding, Weighted Average Remaining Contractual Terms (years)	'5 years 9 months	'4 years 10 months 27 days	'6 years 9 months 7 days	'6 years 6 months 25 days
Options Outstanding, Aggregate Intrinsic Value	$87	$657	$6,570	$34,228
Options Exercised, Aggregate Intrinsic Value	409	925	9,077	'
Options Vested and Expected to Vest, Weighted Average Remaining Contractual Term (years)	'5 years 7 months 27 days	'	'	'
Options Vested and Expected to Vest, Aggregate Intrinsic Value	87	'	'	'
Options Exercisable, Weighted Average Remaining Contractual Terms (years)	'4 years 4 months 13 days	'	'	'
Options Exercisable, Aggregate Intrinsic Value	$87	'	'	'

Stockbased_Compensation_Stock_1

Stock-based Compensation (Stock Option Exercise Price Range) (Details) (Stock Options [Member], USD $)	12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	4,126
Weighted Average Remaining Contractual Term (years)	'5 years 9 months
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$5.68
Number of Options Exercisable (number of options)	2,805
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$6.76
$0.68 - $2.32	'
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	869
Weighted Average Remaining Contractual Term (years)	'7 years 3 months 18 days
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$1.96
Number of Options Exercisable (number of options)	199
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$0.96
Exercise price range, lower range limit (dollars per share)	$0.68
Exercise price range, upper range limit (dollars per share)	$2.32
$2.34 - $3.46	'
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	971
Weighted Average Remaining Contractual Term (years)	'6 years 6 months
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$2.93
Number of Options Exercisable (number of options)	561
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$2.76
Exercise price range, lower range limit (dollars per share)	$2.34
Exercise price range, upper range limit (dollars per share)	$3.46
$3.56 - $7.40	'
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	719
Weighted Average Remaining Contractual Term (years)	'5 years 3 months 18 days
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$5.31
Number of Options Exercisable (number of options)	595
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$5.60
Exercise price range, lower range limit (dollars per share)	$3.56
Exercise price range, upper range limit (dollars per share)	$7.40
$7.41 - $9.81	'
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	721
Weighted Average Remaining Contractual Term (years)	'4 years 4 months 9 days
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$8.38
Number of Options Exercisable (number of options)	673
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$8.34
Exercise price range, lower range limit (dollars per share)	$7.41
Exercise price range, upper range limit (dollars per share)	$9.81
$9.82 - $11.87	'
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]	'
Number of Outstanding Options (options)	846
Weighted Average Remaining Contractual Term (years)	'4 years 10 months 17 days
Options Outstanding, Weighted Average Exercise Price Per Share (dollars per share)	$10.66
Number of Options Exercisable (number of options)	777
Options Exercisable, Weighted Average Exercise Price Per Share (dollars per share)	$10.67
Exercise price range, lower range limit (dollars per share)	$9.82
Exercise price range, upper range limit (dollars per share)	$11.87

Stockbased_Compensation_Restri

Stock-based Compensation (Restricted Stock Activity) (Details) (Restricted stock units [Member], USD $)	12 Months Ended
In Thousands, except Share data, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Restricted stock units [Member]	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]	'	'	'
Outstanding, Beginning of Period (shares)	958,000	546,000	0
Stock units granted (shares)	2,101,000	1,148,000	578,000
Stock units released (shares)	-325,000	-167,000	0
Stock units forfeited or cancelled (shares)	-496,000	-569,000	-32,000
Outstanding, Ending of Period (shares)	2,238,000	958,000	546,000
Stock units granted, weighted average grant date fair value (dollars per share)	$1.80	$3.54	$9.54
Stock units, Outstanding, Weighted Average Remaining Contractual Terms (in years)	'1 year 1 month 6 days	'1 year 2 months 15 days	'1 year 7 months 27 days
Stock units, Aggregate Intrinsic Value, Outstanding	$3,133	$2,117	$2,895
Stock Units Vested and Expected to Vest (shares)	2,000	'	'
Stock Units Vested and Expected to Vest, Aggregate Intrinsic Value	$2,821	'	'

Stockbased_Compensation_StockB

Stock-based Compensation (Stock-Based Compensation Expense) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Schedule of stock-based compensation expense	'	'	'
Stock-based compensation	$4,389	$5,076	$9,431
Research and Development [Member]	'	'	'
Schedule of stock-based compensation expense	'	'	'
Stock-based compensation	1,201	2,334	3,311
Sales, general and administrative [Member]	'	'	'
Schedule of stock-based compensation expense	'	'	'
Stock-based compensation	$3,188	$2,742	$6,120

Stockbased_Compensation_Stock_2

Stock-based Compensation (Stock Option Assumptions) (Details) (Employee Stock Option [Member], Stock Options [Member])	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Employee Stock Option [Member] | Stock Options [Member]	'	'	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'	'	'
Weighted-average expected life (years)	'6 years	'6 years	'6 years 1 month 6 days
Weighted-average expected volatility (percent)	65.00%	61.00%	58.00%
Weighted-average risk free interest rate (percent)	1.20%	1.00%	2.20%
Expected dividend yield (percent)	0.00%	0.00%	0.00%

Stockbased_Compensation_Textua

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

12 Months Ended

12 Months Ended

1 Months Ended

In Thousands, except Share data, unless otherwise specified

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Mar. 31, 2010

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2011

Jul. 31, 2012

Jul. 31, 2012

Sep. 30, 2012

Sep. 30, 2012

Jan. 31, 2014

Jan. 31, 2013

Jan. 31, 2014

2010 Plan [Member]

Incentive Stock Options [Member]

Restricted stock units [Member]

Restricted stock units [Member]

Restricted stock units [Member]

Performance Stock Units [Member]

Restricted Stock [Member]

Non-Statutory Stock Options [Member]

Stock Options [Member]

Stock Options [Member]

Stock Options [Member]

Chief Executive Officer [Member]

Chief Executive Officer [Member]

Chief Financial Officer [Member]

Chief Financial Officer [Member]

Director [Member]

Director [Member]

Subsequent Event [Member]

Restricted Stock [Member]

Stock Options [Member]

Restricted Stock [Member]

Stock Options [Member]

Restricted Stock [Member]

Restricted Stock [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 option expiration period (in years)

'10 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Option price as a percent of common stock (percent)

'

'

'

'

100.00%

'

'

'

'

'

85.00%

'

'

'

'

'

'

'

'

'

'

Percent of voting interests (percent)

'

'

'

'

'

'

'

'

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

Purchase price of common stock when voting percent is above minimum threshold (percent)

'

'

'

'

'

'

'

'

'

'

'

110.00%

'

'

'

'

'

'

'

'

'

Vesting period of units granted

'

'

'

'

'

'4 years

'

'

'

'

'

'4 years

'

'

'4 years

'

'4 years

'

'3 years

'

'

Annual stock option vesting percentage (percent)

'

'

'

'

'

25.00%

'

'

'

'

'

25.00%

'

'

25.00%

'

25.00%

'

33.00%

'

'

Stock options granted, weighted average grant date fair value (dollars per share)

'

'

'

'

'

$1.80

$3.54

$9.54

'

'

'

$1.34

$1.91

$5.19

'

'

'

'

'

'

'

Unamortized compensation cost

$2,177

'

'

'

'

$3,385

'

'

'

$1,714

'

'

'

'

'

'

'

'

'

'

'

Unrecognized compensation cost, period for recognition (in years)

'2 years 7 months 27 days

'

'

'

'

'1 year 9 months 21 days

'

'

'

'2 years 4 months 9 days

'

'

'

'

'

'

'

'

'

'

'

Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period, Total Fair Value

'

'

'

'

'

726

591

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock units granted (shares)

'

'

'

'

'

2,101,000

1,148,000

578,000

523,048

'

'

'

'

'

750,000

400,000

50,000

200,000

'

215,515

'

Estimated Performance Goal Percentage

'

'

'

'

'

'

'

'

100.00%

'

'

'

'

'

'

'

'

'

'

'

'

Share-based Compensation

4,389

5,076

9,431

'

'

'

'

'

298

'

'

'

'

'

'

'

'

'

'

'

'

Stock units canceled (shares)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

358,308

Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number

'

'

'

'

'

'

'

'

358,308

'

'

'

'

'

'

'

'

'

'

'

'

Employee Service Share-based Compensation, Nonvested Awards, Total Compensation Cost Not yet Recognized, Share-based Awards Other than Options

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$500

'

Income_Taxes_Components_of_Los

Income Taxes (Components of Loss Before Provision for Income Taxes) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Tax Disclosure [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Loss before provision for income taxes	($9,858)	($9,227)	($12,617)	($9,688)	($15,711)	($2,140)	($5,442)	($7,293)	($41,390)	($30,587)	($16,309)
United States	'	'	'	'	'	'	'	'	'	'	'
Income Tax Disclosure [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Loss before provision for income taxes	'	'	'	'	'	'	'	'	-41,696	-30,743	-17,474
Foreign	'	'	'	'	'	'	'	'	'	'	'
Income Tax Disclosure [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Loss before provision for income taxes	'	'	'	'	'	'	'	'	$306	$156	$1,165

Income_Taxes_Components_of_Pro

Income Taxes (Components of Provision for Income Taxes) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Current provision (benefit):	'	'	'
Federal	$0	$0	$3
State	5	7	7
Foreign	-45	178	82
Total current provision	-40	185	92
Deferred provision (benefit):	'	'	'
Federal	-59	-62	0
State	-7	-7	0
Foreign	19	154	149
Total deferred provision	-47	85	149
Total provision for (benefit from) income taxes	($87)	$270	$241

Income_Taxes_Tax_Rate_Reconcil

Income Taxes (Tax Rate Reconciliation) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Income Tax Rate Reconciliation	'	'	'
Tax benefit at federal statutory rate	($14,073)	($10,399)	($5,708)
State taxes	-1,948	-1,063	-1,421
Research and development credits	-195	0	-83
Foreign operations taxed at different rates	-108	7	-252
Stock-based compensation	117	312	1,241
Other nondeductible items	-1,272	204	650
Change in federal statutory rate	0	1,493	0
Change in valuation allowance	17,392	9,716	5,814
Total provision for (benefit from) income taxes	($87)	$270	$241

Income_Taxes_Components_of_Def

Income Taxes (Components of Deferred Tax Assets and Liabilities) (Details) (USD $)	Dec. 31, 2013	Dec. 31, 2012
In Thousands, unless otherwise specified
Deferred tax assets:	'	'
Net operating losses	$67,507	$54,923
Credits	4,194	3,329
Deferred revenues	1,198	1,297
Stock-based compensation	3,043	4,464
Reserves and accruals	3,626	2,090
Depreciation	2,247	1,746
Intangible assets	4,208	3,556
Unrealized gain/loss	112	166
Other assets	159	141
Total deferred tax assets:	86,294	71,712
Deferred tax liabilities:	'	'
Other	0	0
Total deferred tax liabilities:	0	0
Valuation allowance	-86,294	-71,692
Net deferred tax assets	$0	$20

Income_Taxes_NOL_and_Tax_Credi

Income Taxes (NOL and Tax Credit Carryforward) (Details) (USD $)	Dec. 31, 2013
In Thousands, unless otherwise specified
Federal	'
Net Operating Losses and Tax Credit Carryforwards	'
Net operating losses, amount	$184,818
Tax credits, amount	5,138
State	'
Net Operating Losses and Tax Credit Carryforwards	'
Net operating losses, amount	148,325
Tax credits, amount	5,459
Foreign	'
Net Operating Losses and Tax Credit Carryforwards	'
Net operating losses, amount	15,403
Tax credits, amount	$16

Income_Taxes_Unrecognized_Tax_

Income Taxes (Unrecognized Tax Benefit Rollforward) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Unrecognized Tax Benefits, Excluding Amounts Pertaining to Examined Tax Returns [Roll Forward]	'	'	'
Balance at beginning of year	$7,420	$6,611	$6,492
Additions based on tax positions related to current year	1,116	709	470
Additions to tax provision of prior years	6	263	4
Reductions to tax provision of prior years	-78	24	-262
Lapse of the applicable statute of limitations	-158	-187	-93
Balance at end of year	$8,306	$7,420	$6,611

Income_Taxes_Textual_Details

Income Taxes (Textual) (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Subsidiary or Equity Method Investee [Line Items]	'	'	'
Income Tax Expense (Benefit)	($87,000)	$270,000	$241,000
Increase in deferred tax asset valuation allowance	14,600,000	8,600,000	5,800,000
Unremitted foreign earnings	1,300,000	'	'
Interest and penalties recognize in income tax expense	29,000	11,000	39,000
Interest and penalties recognized on the balance sheet	280,000	250,000	'
Unrecognized Tax Benefits that Would Impact Effective Tax Rate	1,000,000	1,500,000	'
Unrecognized tax benefits expected to be recognized during the next twelve months	663,000	'	'
Unrecognized tax benefits expected to be recognized during the next twelve months	439,000	'	'
Co Two Solutions [Member]	'	'	'
Subsidiary or Equity Method Investee [Line Items]	'	'	'
Income Tax Expense (Benefit)	$66,000	$69,000	'

401k_Plan_Details

401(k) Plan (Details) (USD $)	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Compensation and Retirement Disclosure [Abstract]	'	'	'
Employer contributions to 401(k) plan	$488,000	$0	$0
Minimum employee eligibility age (years)	'18 years	'	'

Segment_Reporting_Revenues_Det

Segment Reporting (Revenues) (Details) (USD $)	3 Months Ended								12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	$9,525	$3,943	$6,974	$11,480	$7,912	$26,341	$22,909	$31,136	$31,922	$88,298	$123,865
United States	'	'	'	'	'	'	'	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	'	'	'	'	'	'	'	'	11,005	51,714	72,355
Europe	'	'	'	'	'	'	'	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	'	'	'	'	'	'	'	'	9,568	11,150	16,751
India	'	'	'	'	'	'	'	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	'	'	'	'	'	'	'	'	3,099	16,813	21,063
Singapore	'	'	'	'	'	'	'	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	'	'	'	'	'	'	'	'	7,220	7,507	12,008
Others	'	'	'	'	'	'	'	'	'	'	'
Schedule of revenues by geographical area	'	'	'	'	'	'	'	'	'	'	'
Revenues	'	'	'	'	'	'	'	'	$1,030	$1,114	$1,688

Segment_Reporting_Longlived_as

Segment Reporting (Long-lived assets) (Details) (USD $)	Dec. 31, 2013		Dec. 31, 2012		Dec. 31, 2011
In Thousands, unless otherwise specified
Schedule of long-lived assets by geographical area	'		'		'
Long-lived assets	$18,312		$31,821		$41,592
United States	'		'		'
Schedule of long-lived assets by geographical area	'		'		'
Long-lived assets	16,189		25,953		34,817
Europe	'		'		'
Schedule of long-lived assets by geographical area	'		'		'
Long-lived assets	2,123	[1]	5,157	[1]	4,395	[1]
Asia	'		'		'
Schedule of long-lived assets by geographical area	'		'		'
Long-lived assets	$0		$711		$2,380
[1]	Primarily Hungary

Segment_Reporting_Segment_Repo

Segment Reporting Segment Reporting (Details)	3 Months Ended	12 Months Ended
	Mar. 31, 2012	Dec. 31, 2013
	operating_segment
Segment Reporting [Abstract]	'	'
Number of Operating Segments	1	1

Restructuring_Reserve_Rollforw

Restructuring (Reserve Rollforward) (Details) (USD $)	12 Months Ended
In Thousands, unless otherwise specified	Dec. 31, 2013	Dec. 31, 2012
Summary of changes in restructuring accrual	'	'
Beginning balance	$420	'
Restructuring charges	809	3,109
Cash payments	-877	-1,123
Non-cash items	-49	-1,413
Adjustments to previously accrued charges	-26	-153
Ending balance	277	420
Q1 2012 Restructuring Plan [Member]	'	'
Summary of changes in restructuring accrual	'	'
Beginning balance	0	'
Restructuring charges	0	572
Cash payments	0	-512
Non-cash items	0	0
Adjustments to previously accrued charges	0	-60
Ending balance	0	0
Q3 2012 Restructuring Plan [Member]	'	'
Summary of changes in restructuring accrual	'	'
Beginning balance	420	'
Restructuring charges	'	2,537
Cash payments	-345	-611
Non-cash items	-49	-1,413
Adjustments to previously accrued charges	-26	-93
Ending balance	0	420
Q4 2013 Restructuring Plan [Member]	'	'
Summary of changes in restructuring accrual	'	'
Beginning balance	0	'
Restructuring charges	809	0
Cash payments	-532	0
Non-cash items	0	0
Adjustments to previously accrued charges	0	0
Ending balance	$277	$0

Restructuring_Textual_Details

Restructuring (Textual) (Details) (USD $)

12 Months Ended

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

3 Months Ended

12 Months Ended

In Thousands, unless otherwise specified

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Sep. 30, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2012

Sep. 30, 2012

Sep. 30, 2012

Dec. 31, 2012

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2013

Dec. 31, 2012

Dec. 31, 2012

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]

Q4 2013 Restructuring Plan [Member]

Q4 2013 Restructuring Plan [Member]

Q4 2013 Restructuring Plan [Member]

Employee Severance [Member]

Facility Closing [Member]

Leasehold Improvement Write Down [Member]

Equipment Disposal Charges [Member]

Research and Development Functions [Member]

General and Administrative Functions [Member]

Selling, General and Administrative [Member]

Selling, General and Administrative [Member]

Selling, General and Administrative [Member]

Research and Development [Member]

Research and Development [Member]

Accrued Compensation [Member]

Accrued Expenses [Member]

employee

employee

employee

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]

Q3 2012 Restructuring Plan [Member]

Q4 2013 Restructuring Plan [Member]

Q3 2012 Restructuring Plan [Member]

Q4 2013 Restructuring Plan [Member]

Q3 2012 Restructuring Plan [Member]

Q3 2012 Restructuring Plan [Member]

employee

employee

Restructuring (Textual) [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Number of positions eliminated (employee)

'

'

'

13

173

'

'

15

'

'

'

'

'

'

150

23

'

'

'

'

'

'

'

Restructuring charges adjusted

'

'

'

'

'

'

$2,418

'

'

'

$684

'

$1,071

'

'

'

$572

'

'

$948

'

'

'

Restructuring charges

809

3,109

0

572

'

'

2,537

'

809

0

'

320

'

342

'

'

'

1,470

236

'

573

'

'

Cash payments

877

1,123

0

512

'

345

611

'

532

0

'

'

'

'

'

'

'

'

'

'

'

'

'

Adjustment to previously accrued charges

26

153

0

60

'

26

93

'

0

0

'

'

'

'

'

'

'

'

'

'

'

'

'

Restructuring reserve

$277

$420

$0

$0

'

$0

$420

$277

$277

$0

'

'

'

'

'

'

'

'

'

'

'

$68

$352

Selected_Quarterly_Financial_D2

Selected Quarterly Financial Data (Unaudited) (Details) (USD $)	3 Months Ended																12 Months Ended
In Thousands, except Per Share data, unless otherwise specified	Dec. 31, 2013		Sep. 30, 2013		Jun. 30, 2013		Mar. 31, 2013		Dec. 31, 2012		Sep. 30, 2012		Jun. 30, 2012		Mar. 31, 2012		Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Revenues:	'		'		'		'		'		'		'		'		'	'	'
Product	$5,263		$1,076		$4,948		$9,136		$6,834		$7,140		$6,783		$15,167		$20,423	$35,924	$49,021
Collaborative research and development	1,931		2,028		1,609		1,300		1,078		18,569		15,868		14,362		6,868	49,977	70,918
Revenue sharing arrangement	2,331		839		417		1,044		0		0		0		250		4,631	150	450
Government awards	0		0		0		0		0		632		258		1,357		0	2,247	3,476
Total revenues	9,525		3,943		6,974		11,480		7,912		26,341		22,909		31,136		31,922	88,298	123,865
Costs and operating expenses:	'		'		'		'		'		'		'		'		'	'	'
Cost of product revenues	4,764		494		3,631		5,665		5,779		6,397		5,829		12,642		14,554	30,647	41,781
Research and development	8,829		6,831		8,624		7,322		10,594		14,191		15,650		16,349		31,606	56,785	61,049
Selling, general and administrative	5,783		5,832		7,169		8,124		7,286		7,909		6,789		9,395		26,908	31,379	36,942
Total costs and operating expenses	19,376		13,157		19,424		21,111		23,659		28,497		28,268		38,386		73,068	118,811	139,772
Loss before income taxes	-9,858		-9,227		-12,617		-9,688		-15,711		-2,140		-5,442		-7,293		-41,390	-30,587	-16,309
Net loss	($9,813)		($9,262)		($12,605)		($9,623)		($15,538)		($2,309)		($5,519)		($7,490)		($41,303)	($30,857)	($16,550)
Net loss per share of common stock, basic and diluted (dollars per share)	($0.26)		($0.24)		($0.33)		($0.25)		($0.41)		($0.06)		($0.15)		($0.21)		($1.08)	($0.84)	($0.46)
Weighted average common shares used in computing net loss per share of common stock, basic and diluted (shares)	38,329	[1]	38,102	[1]	38,060	[1]	37,842	[1]	37,581	[1]	37,118	[1]	36,296	[1]	36,057	[1]	38,231	36,768	35,674
[1]	The full year net loss per share of common stock, basic and diluted, may not equal the sum of the quarters due to weighting of outstanding shares.