10-Q/A

SECURITIES AND EXCHANGE COMMISSION

Washington, D.C. 20549

FORM 10-Q/A

(Amendment No. 1)

x QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

For the Quarterly period ended June 30, 2012

¨ TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934

Commission File Number: 001-34705

Codexis Inc.

(Exact name of registrant as specified in its charter)

Delaware	71-0872999
(State or other jurisdiction of incorporation or organization)	(I.R.S. Employer Identification No.)
200 Penobscot Drive, Redwood City	94063
(Address of principal executive offices)	(Zip Code)

650 421 8100

(Registrant’s telephone number, including area code)

Check whether the issuer: (1) filed all reports required to be filed by Section 13 or 15(d) of the Exchange Act during the past 12 months (or for such shorter period that the registrant was required to file such reports); and (2) has been subject to such filing requirements for the past 90 days.    Yes  x    No  ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate Web site, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (Section 232.405 of this chapter) during the preceding 12 months (or such shorter period that the registrant was required to submit and post such files.    Yes  x    No  ¨

Indicate by check mark whether the registrant is a large accelerated filer, a non-accelerated filer, or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “small reporting company” in Rule 12b-2 of the Exchange Act.

Large accelerated filer	¨	Accelerated filer	x
Non-accelerated filer	¨  (Do not check if a smaller reporting company)	Smaller reporting company	¨

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Exchange Act)    Yes  ¨    No  x

As of July 31, 2012, there were 37,057,772 shares of the registrant’s Common Stock, par value $0.0001 per share, outstanding.

Explanatory Note

The purpose of this Amendment No. 1 to Codexis Inc. Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2012, filed with the Securities and Exchange Commission on August 9, 2012 (the “Form 10-Q”), is solely to furnish Exhibit 101 to the Form 10-Q in accordance with Rule 405 of Regulation S-T. Exhibit 101 to this report provides the consolidated financial statements and related notes from the Form 10-Q formatted in XBRL (eXtensible Business Reporting Language).

No other changes have been made to the Form 10-Q. This Amendment No. 1 to the Form 10-Q speaks as of the original filing date of the Form 10-Q, does not reflect events that may have occurred subsequent to the original filing date, and does not modify or update in any way disclosures made in the original Form 10-Q.

Pursuant to Rule 406T of Regulation S-T, the interactive data files on Exhibit 101 hereto are deemed not filed or part of a registration statement or prospectus for purposes of Sections 11 or 12 of the Securities Act of 1933, as amended, are deemed not filed for purposes of Section 18 of the Securities Exchange Act of 1934, as amended, and otherwise are not subject to liability under those sections.

Item 6. Exhibits

31.1*	Certification of CEO/CFO pursuant to Sec. 302
32.1*	Certification of CEO/CFO pursuant to Sec. 906
101.DEF	XBRL Taxonomy Extension Definition Linkbase Document
101.INS	XBRL Instance Document
101SCH	XBRL Taxonomy Extension Schema Document
101.CAL	XBRL Taxonomy Extension Calculation Linkbase Document
101.LAB	XBRL Taxonomy Extension Label Linkbase Document
101.PRE	XBRL Taxonomy Extension Presentation Linkbase Document
101.DEF	XBRL Taxonomy Extension Definition Linkbase Document

* These exhibits were previously included or incorporated by reference in Codexis Inc. Quarterly Report on Form 10-Q for the quarterly period ended June 30, 2012, filed with the Securities and Exchange Commission on August 9, 2012.

SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this Report to be signed on its behalf by the undersigned, thereunto duly authorized.

	Codexis Inc.
Date: September 7, 2012	By:	/s/ David O’Toole
		David O’Toole
		SVP & CFO

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Commitments and Contingencies (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012
Future minimum payments under non-cancellable operating leases
Lease payments, 6 months ending December 31, 2012	$ 1,641
Lease payments, Year ending December 31, 2013	2,905
Lease payments, Year ending December 31, 2014	2,722
Lease payments, Year ending December 31, 2015	2,799
Lease payments, Year ending December 31, 2016	2,805
Lease payments, Year ending December 31, 2017 and beyond	8,447
Lease payments, Total	$ 21,319

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Restructuring (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Mar. 31, 2012	Jun. 30, 2012
Summary of changes in restructuring accrual
Restructuring charges	$ 53	$ 510
Cash payments	422	(24)	422
Balance at March 31, 2012	486
Adjustment to previously accrued charges	(49)		(49)
Balance at June 30, 2012	$ 68	$ 486	$ 68

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Balance Sheets and Statements of Operations Details (Details) (USD $) In Thousands, unless otherwise specified	6 Months Ended	12 Months Ended
	Jun. 30, 2012	Dec. 31, 2011
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	$ 54,076	$ 57,090
Gross Unrealized Gains	34	45
Gross Unrealized Losses	(782)	(200)
Estimated Fair Value	53,328	56,935
Money market funds [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	12,093	18,866
Estimated Fair Value	12,093	18,866
Commercial paper [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	3,997	1,999
Estimated Fair Value	3,997	1,999
Average Contractual Maturities (in days)	8	55
Corporate bonds [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	26,148	30,908
Gross Unrealized Gains	26	29
Gross Unrealized Losses	(4)	(45)
Estimated Fair Value	26,170	30,892
Average Contractual Maturities (in days)	193	270
U.S. Treasury obligations [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	6,521	998
Gross Unrealized Gains	1	4
Estimated Fair Value	6,522	1,002
Average Contractual Maturities (in days)	102	274
Government-sponsored enterprise securities [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	4,001	3,003
Gross Unrealized Gains	7	12
Estimated Fair Value	4,008	3,015
Average Contractual Maturities (in days)	40	373
Common shares of CO2 Solution [Member]
Schedule of cash equivalents and marketable securities
Cost or Amortized Cost	1,316	1,316
Gross Unrealized Losses	(778)	(155)
Estimated Fair Value	$ 538	$ 1,161

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Stockholders' Equity (Tables)

6 Months Ended

Jun. 30, 2012

Stockholders' Equity [Abstract]

Schedule of stock-based compensation expense

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Research and development	$	779	$	951	$	1,433	$	1,801
Sales, general and administrative		1,060		1,597		1,576		3,056
	$	1,839	$	2,548	$	3,009	$	4,857

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Stockholders' Equity (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Schedule of stock-based compensation expense
Stock-based compensation	$ 1,839	$ 2,548	$ 3,077	$ 4,856
Research and development [Member]
Schedule of stock-based compensation expense
Stock-based compensation	779	951	1,433	1,801
Sales, general and administrative [Member]
Schedule of stock-based compensation expense
Stock-based compensation	$ 1,060	$ 1,597	$ 1,576	$ 3,056

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Fair Value (Details Textual) (USD $)	6 Months Ended	12 Months Ended
	Jun. 30, 2012	Dec. 31, 2011
Fair Value (Textual) [Abstract]
Number of common shares fair value	10,000,000
Estimated fair value of investment in common stock	$ 538,000	$ 1,200,000
Unrealized loss on investment	$ 778,000	$ 155,000

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Restructuring (Details Textual) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Mar. 31, 2012	Jun. 30, 2012
Restructuring (Textual) [Abstract]
Estimated cost of restructuring plan			$ 567,000
Restructuring revised estimated cost	563,000		563,000
Cash payments	422,000	(24,000)	422,000
Adjustment to previously accrued charges	(49,000)		(49,000)
Restructuring planned cost other accrued liabilities	$ 68,000		$ 68,000

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Collaborative Research and Development Agreements

6 Months Ended

Jun. 30, 2012

Collaborative Research and Development Agreements [Abstract]

Collaborative Research and Development Agreements

3. Collaborative Research and Development Agreements

Shell and Raízen

In November 2006, we 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, we entered into a new and expanded five-year collaborative research agreement and a license agreement with Shell. In connection with the expanded collaborative research agreement and license agreement, Shell agreed to pay us (1) research funding at specified rates per FTE working on the project during the research term, (2) milestone payments upon the achievement of milestones and (3) royalties on future product sales. The agreement also specifies certain minimum levels of FTE services that we must allocate to the collaboration efforts that increase over the term of the agreement.

The term of the agreement ends on November 1, 2012, unless extended further by the parties. During the term of the agreement, we are required to act exclusively with Shell as it relates to the rights and research described in the arrangement and may not conduct research or contract to conduct research, for another party in the field of use. Under this agreement, we also have a right of first negotiation but not an obligation to manufacture any biocatalysts developed under the collaborative research agreement if Shell decides to out-source the manufacture of such biocatalysts. Although we have not received formal notice from Shell, we do not currently expect any continued Shell FTE funding after November 1, 2012.

In March 2009, we amended our collaborative research agreement and license agreement with Shell to further expand the scope of the collaboration and allow for additional purchases of the Company’s preferred stock by Shell. In connection with the amended collaborative research agreement and license agreement, Shell agreed to pay us (1) additional research funding at specified rates per FTE working on the project during the research term and (2) additional milestone payments upon the achievement of milestones. Shell has the right to reduce the number of funded FTEs, subject to certain limitations, with a required advance notice period ranging from 30 to 270 days and a subsequent period ranging from 90 to 360 days during which notices of further FTE reductions cannot be made by Shell. The length of these periods varies dependent on the number of funded FTEs reduced. Effective August 2011, Shell reduced the number of funded FTEs engaged in our research and development collaboration from 128 to 116 FTEs.

In July 2012, we signed an Exclusive Negotiation Agreement with Shell, pursuant to which Shell has agreed to negotiate exclusively with us through September 1, 2012 the terms of a new agreement under which Shell would grant us certain rights and licenses in the biofuels field to develop and sell cellulase enzymes to third parties on a worldwide basis, except Brazil. We also agreed with Shell under the Exclusive Negotiation Agreement that, beginning on August 31, 2012, Shell can elect to reduce between 13 and 48 FTEs under the collaborative research agreement with one day of notice. Previously, the required notice period for this type of FTE reduction was 90 days. We have not received any notice of FTE reduction below the current 116 FTEs as of the date of filing of this Quarterly Report on Form 10-Q; however we expect Shell to deliver notice of a reduction by 48 FTEs effective September 1, 2012.

In accordance with our revenue recognition policy, the $20.0 million up-front exclusivity fee and the research funding fees to be received for FTE services are recognized in proportion to the actual research efforts incurred relative to the amount of total expected effort to be incurred by us over the five-year research period commencing November 2007. Milestones payments to be earned under this agreement have been determined to be at risk at the inception of the arrangement and substantive and are expected to be recognized upon achievement of the applicable milestone and when collectability of such payment is reasonably assured. We did not record any milestone revenues during the three and six months ended June 30, 2012 and 2011, respectively. For the three months ended June 30, 2012 and 2011, our collaborative research and development revenue from Shell was $13.9 million and $14.8 million, respectively. For the six months ended June 30, 2012 and 2011, our collaborative research and development revenue from Shell was $27.8 million and $29.7 million, respectively

Under the agreements with Shell, we have the right to license technology from third parties that will assist us in meeting objectives under the collaboration. If third-party technology to be licensed is identified and mutually agreed upon by both parties, Shell is obligated to reimburse us for the licensing costs of the technology. Payments made by us to the third-party providers were recorded as research and development expenses related to our collaborative research agreement with Shell. None of the acquired licenses are expected to be used in products that will be sold within the next year and the phase of the project has not reached technological feasibility. Shell reimbursed us for licensing costs of $39,000 and $0 for the three months ended June 30, 2012 and 2011, respectively. Shell reimbursed us for licensing costs of $272,000 and $65,000 for the six months ended June 30, 2012 and 2011, respectively. We recorded these reimbursements against the costs incurred.

In June 2011, Shell completed the transfer of all of its equity interests in us, together with the associated right to appoint one member to our board of directors, to Raízen Energia Participações S.A. (“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 our collaborative research agreement to Raízen and we continue to collaborate with Shell. Additionally in September 2011, we entered into a joint development agreement directly with Raízen. Under the agreement, we will deploy our CodeEvolver^™ directed evolution technology platform to develop an improved process for producing first generation ethanol made from sugar. There has been no material financial activity with Raízen through June 30, 2012.

Manufacturing Collaboration

Arch

In February 2010, we consolidated certain of the contractual terms in our then-existing agreements with Arch Pharmalabs, Ltd. (“Arch”) by simultaneously terminating all of our existing agreements with Arch, other than the Master Services Agreement with Arch entered into as of August 1, 2006, and entering into new agreements with Arch. The new agreements, among other things, provide for biocatalyst supply from us to Arch and intermediate supply from Arch to us. We sell the biocatalysts to Arch at an agreed upon price, and Arch manufactures the intermediates on our behalf. Arch sells the intermediates to us at a formula-based or agreed upon price. We then directly market and sell the intermediates to a specified group of customers in the generic pharmaceutical industry. Under the new agreements, Arch may also sell intermediates directly to other customers, and a license royalty is owed by Arch to us based on the volume of product they sell to us and their other customers. Royalties earned from Arch under this arrangement were $22,000 and $37,000 for the three months ended June 30, 2012 and 2011, respectively and are reflected in collaborative research and development revenue on our condensed consolidated statement of operations. Royalties earned from Arch under this arrangement were $70,000 and $40,000 for the six months ended June 30, 2012 and 2011, respectively.

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Stockholders' Equity (Details Textual) (USD $) In Millions, except Share data, unless otherwise specified	3 Months Ended	6 Months Ended	3 Months Ended		3 Months Ended			3 Months Ended	6 Months Ended	3 Months Ended
	Jun. 30, 2012	Jun. 30, 2012	Jun. 30, 2012 Chief Executive Officer [Member]	Jun. 30, 2012 2002 Plan [Member]	Mar. 31, 2012 2010 Plan [Member]	Jun. 30, 2012 2010 Plan [Member]	Mar. 31, 2010 2010 Plan [Member]	Jun. 30, 2012 Restricted stock units [Member]	Jun. 30, 2012 Restricted stock units [Member]	Jun. 30, 2012 Restricted Stock [Member]
Stockholders' Equity (Textual) [Abstract]
Shares reserved for future issuance				0		11,551,638	1,100,000
Additional shares reserved for future issuance					1,439,827
Stock units granted								750,000	767,953	13,133
Vesting period of units granted								4 years		4 years
Vesting rate of stock units on each annual anniversary								25.00%		25.00%
Common shares issued for stock options exercised	81,154	147,185						33,750	98,144
Options awarded to new chief executive officer			400,000
Stock units granted to new chief executive office	750,000
Per share exercise price			$ 3.46
vesting period of options granted after first year of vesting			36 months
vesting rate of options granted for the first year			25.00%
Stockholders' Equity (Additional Textual) [Abstract]
Common shares issued for stock options exercised	81,154	147,185						33,750	98,144
Accrued bonus to settled stock award		$ 0.5

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Summary of Significant Accounting Policies (Details) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Securities not included in the net loss per common share calculations
Total	9,365	8,841	9,365	8,841
Options to purchase common stock [Member]
Securities not included in the net loss per common share calculations
Total	8,092	8,020	8,092	8,020
Unvested restricted stock units [Member]
Securities not included in the net loss per common share calculations
Total	1,007	555	1,007	555
Warrants to purchase common stock [Member]
Securities not included in the net loss per common share calculations
Total	266	266	266	266

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Description of Business (Details)	6 Months Ended
	Jun. 30, 2012 Entity
Description of Business (Textual) [Abstract]
Number of pharmaceutical firms using technology	50

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Segment Reporting (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Schedule of revenues by geographical area
Revenues	$ 22,909	$ 26,055	$ 54,045	$ 57,089
Americas [Member]
Schedule of revenues by geographical area
Revenues	16,914	17,417	32,543	35,135
Europe [Member]
Schedule of revenues by geographical area
Revenues	2,445	3,721	7,930	5,356
Asia [Member]
Schedule of revenues by geographical area
Revenues	$ 3,550	$ 4,917	$ 13,572	$ 16,598

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Summary of Significant Accounting Policies (Details Textual) (USD $)	3 Months Ended			6 Months Ended
	Jun. 30, 2012	Mar. 31, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Summary of Significant Accounting Policies (Additional Textual) [Abstract]
Significant realized gains or losses from sales of marketable securities	$ 0		$ 0	$ 0	$ 0
Additional grant revenue		530,000
Decrease in net loss from operations		530,000
Milestone revenues recognized	1,000,000
Reduction in basic and diluted net loss per share of common stock		$ 0.01
Maturity of grant agreement				2012-06
Revenue from grant	258,000		273,000	1,616,000	889,000
Change in accounting estimate				530,000
Restricted cash was unchanged				$ 0	$ 46,000
Minimum [Member]
Summary of Significant Accounting Policies (Textual) [Abstract]
Marketable securities included in non-current asset				1 year

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Collaborative Research and Development Agreements (Details) (USD $)	3 Months Ended		1 Months Ended	3 Months Ended		6 Months Ended		1 Months Ended		29 Months Ended	1 Months Ended		11 Months Ended	6 Months Ended	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Aug. 31, 2011	Nov. 30, 2007 Shell [Member]	Jun. 30, 2012 Shell [Member]	Jun. 30, 2011 Shell [Member]	Jun. 30, 2012 Shell [Member]	Jun. 30, 2011 Shell [Member]	Aug. 31, 2011 Shell [Member] Maximum [Member] FundedFTEs	Mar. 31, 2009 Shell [Member] Maximum [Member]	Jul. 31, 2011 Shell [Member] Maximum [Member] FundedFTEs	Aug. 31, 2011 Shell [Member] Minimum [Member] FundedFTEs	Mar. 31, 2009 Shell [Member] Minimum [Member]	Jun. 30, 2012 Shell [Member] Minimum [Member] FundedFTEs	Jun. 30, 2012 Raizen [Member]	Jun. 30, 2012 Arch [Member]	Jun. 30, 2011 Arch [Member]	Jun. 30, 2012 Arch [Member]	Jun. 30, 2011 Arch [Member]
Collaborative Research and Development Agreements (Textual) [Abstract]
Term of collaborative research and development agreement (in years)			5 years
Revenue from exclusivity fee			$ 20,000,000
Advance notice period to be provided for non-eligibility of further reductions in funds of FTEs, days									270 days			30 days
Subsequent notice period to be provided for non-eligibility of further reductions in funds of FTEs, days									360 days			90 days
Number of funded FTEs allowed to be reduced under agreement								48			13
Number of funded FTEs engaged in research and development collaboration										128			116
Period of notice to reduce FTEs		1 day
Previous period of notice to reduce FTEs		90 days
Milestone revenues recognized	1,000,000			0	0	0	0
Research and development revenue				13,900,000	14,800,000	27,800,000	29,700,000
Reimbursements of licensing costs				39,000	0	272,000	65,000
Royalties earned															22,000	37,000	70,000	40,000
Maturity date of collaborative research agreement and license agreement	2012-11
Material financial activity														$ 0

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Summary of Significant Accounting Policies

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation and Consolidation

The accompanying condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”) and the applicable rules and regulations of the Securities and Exchange Commission (“SEC”) for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K filed with the SEC on March 5, 2012. The December 31, 2011 condensed consolidated balance sheet included herein was derived from the audited financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of June 30, 2012 and results of our operations for the three and six months ended June 30, 2012 and 2011, and cash flows for the six months ended June 30, 2012 and 2011. The interim results are not necessarily indicative of the results that may be expected for the year ending December 31, 2012.

The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly-owned subsidiaries. Codexis, Inc. 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

The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements.

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 U.S. dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the condensed consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates for each period. Where the U.S. dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in U.S. 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 U.S. dollars at the exchange rates in effect at the balance sheet date. Foreign currency transaction gains and losses are not material for any period presented.

Fair Value of Financial Instruments

The carrying amounts of certain of our financial instruments, including cash and cash equivalents, restricted cash, accounts receivable and accounts payable, approximate fair value due to their short maturities.

Fair value is considered to be the price at which an asset could be exchanged or a liability transferred (an exit price) in an orderly transaction between knowledgeable, willing parties in the principal or most advantageous market for the asset or liability. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

Cash, Cash Equivalents and Marketable Securities

We consider 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 U.S. Treasury obligations. Marketable securities included in non-current assets are comprised of corporate bonds and U.S. Treasury obligations that have a maturity date greater than 1 year. Our investment in common shares of CO ₂ Solutions Inc. (“CO ₂ Solutions”) is included in non-current marketable securities.

We perform 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 (“OTTI”).

For our investments in equity securities, our 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 our 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 our current and forecasted liquidity requirements, our capital requirements and securities portfolio objectives. Based on our evaluation, we concluded that as of June 30, 2012, the unrealized losses related to equity securities are temporary.

For our investments in debt securities, our management determines whether we intend to sell or if it is more-likely-than-not that we will be required to sell impaired securities. This determination considers our current and forecasted liquidity requirements, our 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. We conduct a regular assessment of our 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. Based on our evaluation, we concluded that as of June 30, 2012, the unrealized losses related to debt securities are temporary.

Our 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 condensed consolidated statement of comprehensive loss. 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 three and six months ended June 30, 2012 and 2011.

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 our Redwood City, California facility lease agreement and for the purpose of securing a working capital line of credit. Restricted cash was unchanged during the three and six months ended June 30, 2012.

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.

Our primary sources of revenues consist of collaborative research and development agreements, product revenues and government awards. Collaborative research and development agreements typically provide us with multiple revenue streams, including up-front fees for licensing, exclusivity and technology access, fees for full-time employee equivalent (“FTE”) services and the potential to earn milestone payments upon achievement of contractual criteria and royalty fees based on future product sales or cost savings by our customers. Our collaborative research and development revenues consist of revenues from Shell and revenues from other collaborative research and development agreements. For each source of collaborative research and development revenues, product revenues and award revenues, we apply the following revenue recognition criteria:

• 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.

• Revenues related to FTE services are recognized as research services are performed over the related performance periods for each contract. We are 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, we recognize 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 us, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, we are required to make estimates of the total hours required to perform our 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 our performance or on the occurrence of a specific outcome resulting from our 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 us. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either our performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from our 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.

• We recognize revenues from royalties based on licensees’ sales of products using our 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.

• Product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria 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 our product revenues.

• We license mutually agreed upon third party technology for use in our research and development collaboration with Shell. We record the license payments to research and development expense and offset related reimbursements received from Shell. These payments made by Shell to us are direct reimbursements of our costs. We account for these direct reimbursable costs as a net amount, whereby no expense or revenue is recorded for the costs reimbursed by Shell. For any payments not reimbursed by Shell, we recognize these as expenses in the statement of operations. We elected to present the reimbursement from Shell as a component of our research and development expense since presenting the receipt of payment from Shell as revenues does not reflect the substance of the arrangement.

• We receive payments from government entities in the form of government awards. Government awards are agreements that generally provide us 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 we have only perfunctory obligations outstanding.

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

Milestone revenue

During the three months ended June 30, 2012, we recognized in collaborative research and development revenue $1 million of milestone revenue from one of our pharmaceutical partners related to the use of our enzymes in its manufacturing processes.

We evaluated the nature of the milestone triggering the contingent payment, and concluded that the amount can be recognized as a milestone payment based on the facts that (i) the milestone was achieved through successful performance by us, (ii) the milestone was at risk at the inception of the arrangement, (iii) the milestone was substantive in nature and is non-refundable, (iv) substantial effort was required by us to complete the milestone, (v) the amount of milestone payment is reasonable in relation to the value created in achieving the milestone, and (vi) the milestone payment relates solely to past performance. No further milestones payments are expected under this arrangement from this pharmaceutical partner.

Change in accounting estimate - U.S. Government awards

We recognize U.S. Government award revenue based on reimbursable costs incurred. Reimbursable costs include only allocable, allowable and reasonable costs, as determined in accordance with the Federal Acquisition Regulations and the related Cost Accounting Standards as applicable to the U.S. Government award. Costs incurred include direct labor and materials that are directly associated with the individual award plus indirect overhead and general and administrative type costs based upon our provisional indirect billing rates submitted by us to the U.S. Department of Energy (“DOE”). Our provisional indirect billing rates are subject to audit by the DOE. Changes in estimates affecting reimbursable costs are recognized in the period in which the change becomes known.

During 2011, our provisional indirect billing rates for the award from the DOE under the ARPA-E Recovery Act were audited by the DOE resulting in a revision to our provisional indirect billing rates. The revised indirect rates were subsequently approved by the DOE during the first quarter of 2012. As a result of this change in accounting estimate, we invoiced and recognized $530,000 of additional award revenue during the three months ended March 31, 2012 for reimbursable costs incurred by us in 2010 and 2011. The impact on our condensed consolidated statement of operations for the three months ended March 31, 2012 was a $530,000 decrease to our net loss and loss from operations and $0.01 reduction to our basic and diluted net loss per share of common stock. Our revenue from this award for the three months ended June 30, 2012 was $258,000 which represents the final funds available under the award. The $530,000 would have been recognized in the second quarter of 2012 had the change in accounting estimate not occured. The term of the award agreement ended in June 2012.

Income Taxes

We use the liability method of accounting for income taxes. Deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the consolidated financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets are recognized for deductible temporary differences, along with net operating loss (“NOL”) carryforwards, if it is more likely than not that the tax benefits will be realized. To the extent a deferred tax asset cannot be recognized under the preceding criteria, a valuation allowance is established. Deferred tax assets and liabilities are measured using enacted tax rates in effect for the year in which those temporary differences are expected to be recovered or settled.

We recognize the financial statement effects of an uncertain tax position when it is more likely than not, based on the technical merits, that the position will be sustained upon examination.

Stock-Based Compensation

We recognize compensation expense related to share-based transactions, including the awarding of employee stock options, based on the estimated fair value of the awards granted. All awards granted, modified or settled after January 1, 2006 have been accounted for based on the fair value of the awards granted. We generally use 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.

We account for stock options issued to non-employees based on their estimated fair value determined using the Black-Scholes option-pricing model. The fair value of the options granted to non-employees is remeasured as they vest, and the resulting change in value, if any, is recognized as an increase or decrease in stock compensation expense during the period the related services are rendered.

Net Loss per Share of Common Stock

Basic and diluted 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. Basic and diluted net loss per share of common stock was the same for each period presented, because inclusion of all potential common shares outstanding was anti-dilutive. The following table presents the securities not included in the net loss per common share calculations for the three and six months ended June 30, 2012 and 2011 (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Options to purchase common stock		8,092		8,020		8,092		8,020
Unvested restricted stock units		1,007		555		1,007		555
Warrants to purchase common stock		266		266		266		266
Total		9,365		8,841		9,365		8,841

Reclassifications

Certain amounts in prior period financial statements related to Shell including related party collaboration revenue (see Note 3), related party receivable, and related party deferred revenue have been reclassified to the corresponding non-related party accounts, since effective July 1, 2011, Shell is no longer considered a related party (see Note 7).

Recent Accounting Pronouncements

In June 2011, the FASB issued ASU 2011-05 that eliminates the option to present items of other comprehensive income (“OCI”) as part of the statement of changes in stockholders’ equity, and instead requires either, OCI presentation and net loss in a single continuous statement in the statement of operations, or as a separate statement of comprehensive loss. This new guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011, with early adoption permitted. We adopted this update in the fourth quarter of 2011 and have presented a separate condensed consolidated statement of comprehensive loss. The adoption of this accounting guidance did not have a material financial impact on our financial statements.

In May 2011, the FASB issued ASU 2011-04 that clarifies and changes some fair value measurement principles and disclosure requirements. Among them is the clarification that the concepts of highest and best use and valuation premise in a fair value measurement, should only be applied when measuring the fair value of nonfinancial assets. Additionally, the new guidance requires quantitative information about unobservable inputs, and disclosure of the valuation processes used and narrative descriptions with regard to fair value measurements within the Level 3 categorization of the fair value hierarchy. We adopted this accounting standard January 1, 2012. The adoption of this new guidance did not have a material impact on our financial statements or disclosures.

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Joint Development Agreement with CO2 Solutions (Details) (CO2 Solutions [Member])	0 Months Ended	6 Months Ended
	Dec. 15, 2009	Jun. 30, 2012
CO2 Solutions [Member]
Joint Development Agreement with CO2 solutions (Textual) [Abstract]
Number of shares acquired in joint venture	10,000,000
Percentage of common shares outstanding at the time of investment	16.60%
Statutory resale restriction, expiry date	Apr. 15, 2010
Statutory resale restriction, expiry period	4 months
Expiration period of original joint development agreement		2011-01
Expiration period of extended joint development agreement		later of June 30, 2012, or six months after the expiryof any third party collaborations

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Commitments and Contingencies (Details Textual) (USD $)	6 Months Ended		12 Months Ended	3 Months Ended		6 Months Ended	12 Months Ended	6 Months Ended			6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011	Jun. 30, 2012 Fifth Amendment [Member]	Mar. 31, 2011 Fifth Amendment [Member]	Jun. 30, 2012 Fifth Amendment [Member]	Dec. 31, 2011 Fifth Amendment [Member]	Jun. 30, 2012 Penobscot Space, Building 2 Space, and Saginaw Space [Member] Fifth Amendment [Member] extensions	Jun. 30, 2012 Headquarters, Redwood City [Member] Fifth Amendment [Member] sqft	Mar. 16, 2011 Saginaw Space [Member] Fifth Amendment [Member] sqft	Jun. 30, 2012 Chesapeake Space [Member]
Commitments and Contingencies (Textual) [Abstract]
Lease area space occupancy (in square feet)									107,000	29,921
Number of extensions available on lease								2
Extended term of lease								5 years			2 years
Expiration date of lease								Jan. 31, 2020			Jan. 31, 2013
Initial time period for forgiveness of rent payments (in months)						2 months
Tenant improvement allowances						$ 2,400,000
Special allowances for costs						800,000
Amount spent for capital improvements						3,600,000
Reimbursements from landlord				1,400,000			1,800,000
Decrease in asset retirement obligation					300,000
Gain on extinguishment of asset retirement obligations					100,000
Letter of credit				707,000		707,000	707,000
Commitments and Contingencies (Additional Textual) [Abstract]
Estimated obligation payable	600,000
Asset retirement obligations	594000		580000
Accretion of asset retirement obligations	$ 15,000	$ 29,000

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Condensed Consolidated Balance Sheets (Unaudited) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Current assets:
Cash and cash equivalents	$ 16,693	$ 25,762
Marketable securities	34,671	27,720
Accounts receivable, net of allowances of $17 at June 30, 2012 and December 31, 2011, respectively	8,124	18,917
Inventories	4,201	4,488
Prepaid expenses and other current assets	5,144	2,345
Total current assets	68,833	79,232
Restricted cash	1,511	1,511
Non-current marketable securities	6,062	10,348
Property and equipment, net	22,073	24,176
Intangible assets, net	14,636	16,442
Goodwill	3,241	3,241
Other non-current assets	1,316	972
Total assets	117,672	135,922
Current liabilities:
Accounts payable	4,313	10,364
Accrued compensation	4,189	6,785
Other accrued liabilities	7,496	7,354
Deferred revenues	3,647	3,789
Total current liabilities	19,645	28,292
Deferred revenues, net of current portion	1,393	1,485
Other long-term liabilities	4,126	3,455
Commitments and contingencies
Stockholders' equity:
Common stock	4	4
Additional paid-in capital	291,090	287,792
Accumulated other comprehensive loss	(878)	(407)
Accumulated deficit	(197,708)	(184,699)
Total stockholders' equity	92,508	102,690
Total liabilities and stockholders' equity	$ 117,672	$ 135,922

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Segment Reporting (Details 1) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Schedule of long-lived assets by geographical area
Long-lived assets	$ 38,025	$ 41,592
Americas [Member]
Schedule of long-lived assets by geographical area
Long-lived assets	31,699	34,817
Europe [Member]
Schedule of long-lived assets by geographical area
Long-lived assets	4,763	4,395
Asia [Member]
Schedule of long-lived assets by geographical area
Long-lived assets	$ 1,563	$ 2,380

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Condensed Consolidated Statements of Cash Flows (Unaudited) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011
Operating activities:
Net loss	$ (13,009)	$ (8,511)
Adjustments to reconcile net loss to net cash used in operating activities:
Amortization of intangible assets	1,806	1,858
Depreciation and amortization of property and equipment	4,544	3,760
Loss on disposal of property and equipment	109	59
Gain from extinguishment of asset retirement obligation		(124)
Stock-based compensation	3,077	4,856
Accretion of asset retirement obligation	15	29
Amortization of premium on marketable securities	377	51
Changes in operating assets and liabilities:
Accounts receivable	10,793	4,027
Inventories	287	(1,370)
Prepaid expenses and other current assets	(2,799)	(735)
Other assets	(409)	(13)
Accounts payable	(6,051)	(1,493)
Accrued compensation	(2,596)	(3,088)
Other accrued liabilities	798	2,554
Deferred revenues	(234)	(2,203)
Net cash used in operating activities	(3,292)	(343)
Investing activities:
Increase in restricted cash	0	(46)
Purchase of property and equipment	(2,551)	(4,187)
Purchase of marketable securities	(19,141)	(38,152)
Proceeds from sale of marketable securities	10,500
Proceeds from maturities of marketable securities	4,964
Net cash used in investing activities	(6,228)	(42,385)
Financing activities:
Proceeds from exercises of stock options	287	2,390
Net cash provided by financing activities	287	2,390
Effect of exchange rate changes on cash and cash equivalents	164	24
Net decrease in cash and cash equivalents	(9,069)	(40,314)
Cash and cash equivalents at the beginning of the period	25,762	72,396
Cash and cash equivalents at the end of the period	$ 16,693	$ 32,082

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Balance Sheets and Statements of Operations Details (Details Textual) (USD $)	Jun. 30, 2012 Securities	Dec. 31, 2011 Securities	Jun. 30, 2011	Dec. 31, 2010
Balance Sheets and Statements of Operations Details (Textual) [Abstract]
Cash and cash equivalents	$ 16,693,000	$ 25,762,000	$ 32,082,000	$ 72,396,000
Money market funds	12,100,000	18,900,000
Corporate bonds in settlement with major financial institutions	500,000
Cash with major financial institutions	4,100,000	6,900,000
Fair value of marketable securities	14,900,000	18,500,000
Aggregated unrealized loss amount	$ 5,000	$ 46,000
Marketable securities	11	14
Unrealized loss position period	Less than 12 months	Less than 12 months

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Fair Value (Tables)

6 Months Ended

Jun. 30, 2012

Fair Value [Abstract]

Summary of financial instruments measured at fair value on a recurring basis

	June 30, 2012
	Level 1		Level 2		Level 3		Total
Financial Assets
Money market funds	$	12,093	$	—	$	—	$	12,093
Commercial paper		—		3,997		—		3,997
Corporate bonds		—		26,170		—		26,170
U.S. Treasury obligations		—		6,522		—		6,522
Government-sponsored enterprise securities		—		4,008		—		4,008
Common shares of CO 2 Solutions		538		—		—		538
Total	$	12,631	$	40,697	$	—	$	53,328

	December 31, 2011
	Level 1		Level 2		Level 3		Total
Financial Assets
Money market funds	$	18,866	$	—	$	—	$	18,866
Commercial paper		—		1,999		—		1,999
Corporate bonds		—		30,892		—		30,892
U.S. Treasury obligations		—		1,002		—		1,002
Government-sponsored enterprise securities		—		3,015		—		3,015
Common shares of CO 2 Solutions		1,161		—		—		1,161
Total	$	20,027	$	36,908	$	—	$	56,935

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Fair Value (Details) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	$ 53,328	$ 56,935
Level 1 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	12,631	20,027
Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	40,697	36,908
Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
Money market funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	12,093	18,866
Money market funds [Member] | Level 1 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	12,093	18,866
Money market funds [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
Commercial paper [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	3,997	1,999
Commercial paper [Member] | Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	3,997	1,999
Commercial paper [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
Corporate bonds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	26,170	30,892
Corporate bonds [Member] | Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	26,170	30,892
Corporate bonds [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
U.S. Treasury obligations [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	6,522	1,002
U.S. Treasury obligations [Member] | Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	6,522	1,002
U.S. Treasury obligations [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
Government-sponsored enterprise securities [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	4,008	3,015
Government-sponsored enterprise securities [Member] | Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	4,008	3,015
Government-sponsored enterprise securities [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis
Common shares of CO2 Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	538	1,161
Common shares of CO2 Solution [Member] | Level 1 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis	538	1,161
Common shares of CO2 Solution [Member] | Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Total financial assets measured at fair value on a recurring basis

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Warrants (Tables)

6 Months Ended

Jun. 30, 2012

Warrants [Abstract]

Schedule of common stock warrants issued and outstanding

June 30, 2012
Issue Date	Shares Subject to  warrants		Exercise Price per Share		Expiration
October 25, 2005		6,066	$	1.05	October 25, 2012
May 25, 2006		184,895	$	5.96	May 25, 2013
July 17, 2007		2,384	$	12.45	February 9, 2016
September 28, 2007		72,727	$	8.25	September 28, 2017

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Description of Business

6 Months Ended

Jun. 30, 2012

Description of Business [Abstract]

Description of Business

1. Description of Business

Codexis, Inc. (together with its subsidiaries, “we,” “Codexis” or the “Company”) is a producer of custom industrial enzymes. Our products enable novel, sustainable processes for the manufacture of biofuels, chemicals, and pharmaceutical ingredients.

We are developing our flagship CodeXyme^™ cellulase enzymes to convert non-food plant material, which we call cellulosic biomass, into affordable sugars, which can then be converted into renewable fuels and chemicals. We have been developing these cellulase enzymes with Equilon Enterprises LLC dba Shell Oil Products US, or Shell, since 2006 for applications in the biofuels markets. We intend to market CodeXyme^™ cellulase enzymes to chemicals manufacturers worldwide. We are also developing our own novel processes to manufacture certain specialty and commodity bio-based chemicals, which we intend to commercialize with strategic partners. The first of these products is CodeXol^™ detergent alcohols. Detergent alcohols are used to manufacture surfactants, which are key, active cleaning ingredients in consumer products such as shampoos, liquid soaps and laundry detergents.

We have commercialized our technology, products and services in the pharmaceuticals market. There are currently over 50 pharmaceutical firms using or evaluating our technology in their manufacturing process development, including the production of some of the world’s bestselling and fastest growing drugs.

We create our products by applying our CodeEvolver ^™ directed evolution technology platform which introduces genetic mutations into microorganisms, giving rise to changes in the enzymes which they produce. Once we identify potentially beneficial mutations, we test combinations of these mutations until we have created variant enzymes that exhibit marketable performance characteristics superior to competitive products. This process allows us to make continuous, efficient improvements to the performance of our enzymes.

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Condensed Consolidated Balance Sheets (Parenthetical) (Unaudited) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Condensed Consolidated Balance Sheets [Abstract]
Accounts receivable, net of allowances	$ 17	$ 17

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Segment Reporting

6 Months Ended

Jun. 30, 2012

Segment Reporting [Abstract]

Segment Reporting

11. 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. Our chief operating decision makers are our Chief Executive Officer and our board of directors. The Chief Executive Officer and our 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. We have one business activity and there are no segment managers who are held accountable for operations, operating results beyond revenue goals or gross margins, or plans for levels or components below the consolidated unit level. Accordingly, we have 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):

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Revenues
Americas(1)	$	16,914	$	17,417	$	32,543	$	35,135
Asia		3,550		4,917		13,572		16,598
Europe		2,445		3,721		7,930		5,356
	$	22,909	$	26,055	$	54,045	$	57,089

(1) Primarily United States

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):

	June 30,		December 31,
	2012		2011
Long-lived assets
Americas(1)	$	31,699	$	34,817
Europe		4,763		4,395
Asia		1,563		2,380
	$	38,025	$	41,592

(1) Primarily United States

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Document and Entity Information	6 Months Ended
	Jun. 30, 2012	Jul. 31, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	CODEXIS INC
Entity Central Index Key	0001200375
Document Type	10-Q
Document Period End Date	Jun. 30, 2012
Amendment Flag	false
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	Q2
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		37,057,772

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Restructuring

6 Months Ended

Jun. 30, 2012

Restructuring Costs [Abstract]

Restructuring

12. Restructuring

During the first quarter of 2012, our board of directors approved and committed to a restructuring plan (“2012 restructuring plan”) to reduce our cost structure which included employee terminations in Hungary and the United States. The total estimated cost of the 2012 restructuring plan was $567,000 comprised of employee severance and other termination benefits. As of June 30, 2012, planned costs of $563,000 have been recognized in selling, general and administrative expenses on our condensed consolidated statements of operations. We have made cash payments of $446,000 and recorded $49,000 of reductions to previously recorded charges with the remaining $68,000 recorded in other accrued liabilities on our condensed consolidated balance sheet as of June 30, 2012. We do not anticipate recording any further charges under this restructuring plan. We anticipated that all costs under the 2012 restructuring plan will be paid by December 31, 2012.

The table below summarizes the changes in our restructuring accrual:

(in thousands)	Severance, benefits and related personal costs
	2012 Plan
Restructuring charges	$	510
Cash payments		(24	)
Balance at March 31, 2012		486
Restructuring charges		53
Adjustments to previously accrued charges		(49	)
Cash payments		(422	)
Balance at June 30, 2012	$	68

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Condensed Consolidated Statements of Operations (Unaudited) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Revenues:
Product	$ 6,783	$ 8,397	$ 21,949	$ 21,329
Collaborative research and development	15,868	17,385	30,480	34,871
Government awards	258	273	1,616	889
Total revenues	22,909	26,055	54,045	57,089
Costs and operating expenses:
Cost of product revenues	5,829	7,106	18,471	18,756
Research and development	15,650	14,965	31,999	28,715
Selling, general and administrative	6,789	9,276	16,184	18,289
Total costs and operating expenses	28,268	31,347	66,654	65,760
Loss from operations	(5,359)	(5,292)	(12,609)	(8,671)
Interest income	74	71	149	120
Interest expense and other, net	(157)	16	(275)	34
Loss before provision (benefit) for income taxes	(5,442)	(5,205)	(12,735)	(8,517)
Provision (benefit) for income taxes	77	(165)	274	(6)
Net loss	$ (5,519)	$ (5,040)	$ (13,009)	$ (8,511)
Net loss per share of common stock, basic and diluted	$ (0.15)	$ (0.14)	$ (0.36)	$ (0.24)
Weighted average common shares used in computing net loss per share of common stock, basic and diluted	36,296	35,685	36,177	35,402

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Fair Value

6 Months Ended

Jun. 30, 2012

Fair Value [Abstract]

Fair Value

6. Fair Value

Assets and liabilities recorded at fair value in the condensed consolidated financial statements are categorized based upon the level of judgment associated with the inputs used to measure their fair value. Hierarchical levels which are directly related to the amount of subjectivity associated with the inputs to the valuation of these assets or liabilities are as follows:

Level 1 — Inputs that are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date.

Level 2 — Inputs (other than quoted prices included in Level 1) that are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life.

Level 3 — Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities and which reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date.

For Level 2 financial investments, our investment advisor provides us 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 our 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 we are ultimately responsible for the determination of the fair value of these instruments, we perform quarterly analyses using prices obtained from another independent provider of financial instrument valuations, to validate that the prices we have used are reasonable estimates of fair value.

The following table presents our financial instruments that were measured at fair value on a recurring basis at June 30, 2012 by level within the fair value hierarchy (in thousands):

	June 30, 2012
	Level 1		Level 2		Level 3		Total
Financial Assets
Money market funds	$	12,093	$	—	$	—	$	12,093
Commercial paper		—		3,997		—		3,997
Corporate bonds		—		26,170		—		26,170
U.S. Treasury obligations		—		6,522		—		6,522
Government-sponsored enterprise securities		—		4,008		—		4,008
Common shares of CO 2 Solutions		538		—		—		538
Total	$	12,631	$	40,697	$	—	$	53,328

The following table presents our financial instruments that were measured at fair value on a recurring basis at December 31, 2011 by level within the fair value hierarchy (in thousands):

	December 31, 2011
	Level 1		Level 2		Level 3		Total
Financial Assets
Money market funds	$	18,866	$	—	$	—	$	18,866
Commercial paper		—		1,999		—		1,999
Corporate bonds		—		30,892		—		30,892
U.S. Treasury obligations		—		1,002		—		1,002
Government-sponsored enterprise securities		—		3,015		—		3,015
Common shares of CO 2 Solutions		1,161		—		—		1,161
Total	$	20,027	$	36,908	$	—	$	56,935

We estimated the fair value of our investment in 10,000,000 common shares of CO₂ Solutions using the fair value of common shares as determined by trading on TSX Venture Exchange. Accordingly, we have classified our investment in CO₂ Solutions as a level 1 investment. At June 30, 2012, the estimated fair value of our investment in CO ₂ Solutions common stock was $538,000 and the unrealized loss was $778,000. At December 31, 2011, the estimated fair value of our investment in CO₂ Solutions common stock was $1.2 million and the unrealized loss was $155,000.

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Balance Sheets and Statements of Operations Details

6 Months Ended

Jun. 30, 2012

Balance Sheets and Statements of Operations Details [Abstract]

Balance Sheets and Statements of Operations Details

5. Balance Sheets and Statements of Operations Details

Cash Equivalents and Marketable Securities At June 30, 2012, cash equivalents and marketable securities consisted of the following (in thousands):

	June 30, 2012									Average Contractual Maturities
	Cost or Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
										(in days)
Money market funds	$	12,093	$	—	$	—		$	12,093		n/a
Commercial paper		3,997		—		—			3,997		8
Corporate bonds		26,148		26		(4	)		26,170		193
U.S. Treasury obligations		6,521		1		—			6,522		102
Government-sponsored enterprise securities		4,001		7		—			4,008		40
Common shares of CO 2 Solutions		1,316		—		(778	)		538		n/a
Total	$	54,076	$	34	$	(782	)	$	53,328

The total cash and cash equivalents balance of $16.7 million as of June 30, 2012 was comprised of money market funds of $12.1 million, $0.5 million of corporate bonds in settlement and $4.1 million held as cash, primarily with major financial institutions in North America. At June 30, 2012 we had 11 marketable securities, including corporate bonds and government-sponsored enterprise securities in a loss position for less than 12 months with an aggregated unrealized loss of $5,000 and an aggregated fair value of $14.9 million.

At December 31, 2011, cash equivalents and marketable securities consisted of the following (in thousands):

	December 31, 2011									Average Contractual Maturities
	Cost or Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
										(in days)
Money market funds	$	18,866	$	—	$	—		$	18,866		n/a
Commercial paper		1,999		—		—			1,999		55
Corporate bonds		30,908		29		(45	)		30,892		270
U.S. Treasury obligations		998		4		—			1,002		274
Government-sponsored enterprise securities		3,003		12		—			3,015		373
Common shares of CO 2 Solutions		1,316		—		(155	)		1,161		n/a
Total	$	57,090	$	45	$	(200	)	$	56,935

The total cash and cash equivalents balance of $25.8 million as of December 31, 2011 was comprised of money market funds of $18.9 million and $6.9 million held as cash, primarily with major financial institutions in North America. At December 31, 2011, we had 14 marketable securities, including corporate bonds and government-sponsored enterprise securities in a loss position for less than 12 months with an aggregated unrealized loss of $46,000 and an aggregated fair value of $18.5 million.

Inventories

Inventories consisted of the following (in thousands):

	June 30, 2012		December 31, 2011
Raw materials	$	1,947	$	2,779
Work in process		48		54
Finished goods		2,206		1,655
Total inventories	$	4,201	$	4,488

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Commitments and Contingencies (Tables)

6 Months Ended

Jun. 30, 2012

Commitments and Contingencies [Abstract]

Schedule of future minimum payments under non-cancellable operating leases

	Lease payments
6 months ending December 31,
2012	$	1,641
Years ending December 31,
2013		2,905
2014		2,722
2015		2,799
2016		2,805
2017 and beyond		8,447
Total	$	21,319

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Summary of Significant Accounting Policies (Policies)

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies [Abstract]

Basis of Presentation and Consolidation

Basis of Presentation and Consolidation

The accompanying condensed consolidated financial statements have been prepared in accordance with accounting principles generally accepted in the United States of America (“GAAP”) and the applicable rules and regulations of the Securities and Exchange Commission (“SEC”) for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K filed with the SEC on March 5, 2012. The December 31, 2011 condensed consolidated balance sheet included herein was derived from the audited financial statements as of that date, but does not include all disclosures including notes required by GAAP for complete financial statements.

The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of June 30, 2012 and results of our operations for the three and six months ended June 30, 2012 and 2011, and cash flows for the six months ended June 30, 2012 and 2011. The interim results are not necessarily indicative of the results that may be expected for the year ending December 31, 2012.

The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly-owned subsidiaries. Codexis, Inc. 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 financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements.

Foreign Currency Translation

Foreign Currency Translation

The assets and liabilities of foreign subsidiaries, where the local currency is the functional currency, are translated from their respective functional currencies into U.S. dollars at the exchange rates in effect at the balance sheet date, with resulting foreign currency translation adjustments recorded in the condensed consolidated statement of comprehensive loss. Revenue and expense amounts are translated at average rates for each period. Where the U.S. dollar is the functional currency, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in U.S. 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 U.S. dollars at the exchange rates in effect at the balance sheet date. Foreign currency transaction gains and losses are not material for any period presented.

Fair Value of Financial Instruments

Fair Value of Financial Instruments

The carrying amounts of certain of our financial instruments, including cash and cash equivalents, restricted cash, accounts receivable and accounts payable, approximate fair value due to their short maturities.

Fair value is considered to be the price at which an asset could be exchanged or a liability transferred (an exit price) in an orderly transaction between knowledgeable, willing parties in the principal or most advantageous market for the asset or liability. Where available, fair value is based on or derived from observable market prices or other observable inputs. Where observable prices or inputs are not available, valuation models are applied. These valuation techniques involve some level of management estimation and judgment, the degree of which is dependent on the price transparency for the instruments or market and the instruments’ complexity.

Cash, Cash Equivalents and Marketable Securities

Cash, Cash Equivalents and Marketable Securities

We consider 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 U.S. Treasury obligations. Marketable securities included in non-current assets are comprised of corporate bonds and U.S. Treasury obligations that have a maturity date greater than 1 year. Our investment in common shares of CO ₂ Solutions Inc. (“CO ₂ Solutions”) is included in non-current marketable securities.

We perform 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 (“OTTI”).

For our investments in equity securities, our 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 our 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 our current and forecasted liquidity requirements, our capital requirements and securities portfolio objectives. Based on our evaluation, we concluded that as of June 30, 2012, the unrealized losses related to equity securities are temporary.

For our investments in debt securities, our management determines whether we intend to sell or if it is more-likely-than-not that we will be required to sell impaired securities. This determination considers our current and forecasted liquidity requirements, our 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. We conduct a regular assessment of our 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. Based on our evaluation, we concluded that as of June 30, 2012, the unrealized losses related to debt securities are temporary.

Our 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 condensed consolidated statement of comprehensive loss. 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 three and six months ended June 30, 2012 and 2011.

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 our Redwood City, California facility lease agreement and for the purpose of securing a working capital line of credit. Restricted cash was unchanged during the three and six months ended June 30, 2012.

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.

Our primary sources of revenues consist of collaborative research and development agreements, product revenues and government awards. Collaborative research and development agreements typically provide us with multiple revenue streams, including up-front fees for licensing, exclusivity and technology access, fees for full-time employee equivalent (“FTE”) services and the potential to earn milestone payments upon achievement of contractual criteria and royalty fees based on future product sales or cost savings by our customers. Our collaborative research and development revenues consist of revenues from Shell and revenues from other collaborative research and development agreements. For each source of collaborative research and development revenues, product revenues and award revenues, we apply the following revenue recognition criteria:

• 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.

• Revenues related to FTE services are recognized as research services are performed over the related performance periods for each contract. We are 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, we recognize 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 us, up to the amount of cash received. In cases where the planned levels of research services fluctuate substantially over the research term, we are required to make estimates of the total hours required to perform our 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 our performance or on the occurrence of a specific outcome resulting from our 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 us. Milestones are considered substantive when the consideration earned from the achievement of the milestone (i) is commensurate with either our performance to achieve the milestone or the enhancement of value of the item delivered as a result of a specific outcome resulting from our 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.

• We recognize revenues from royalties based on licensees’ sales of products using our 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.

• Product revenues are recognized once passage of title and risk of loss has occurred and contractually specified acceptance criteria 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 our product revenues.

• We license mutually agreed upon third party technology for use in our research and development collaboration with Shell. We record the license payments to research and development expense and offset related reimbursements received from Shell. These payments made by Shell to us are direct reimbursements of our costs. We account for these direct reimbursable costs as a net amount, whereby no expense or revenue is recorded for the costs reimbursed by Shell. For any payments not reimbursed by Shell, we recognize these as expenses in the statement of operations. We elected to present the reimbursement from Shell as a component of our research and development expense since presenting the receipt of payment from Shell as revenues does not reflect the substance of the arrangement.

• We receive payments from government entities in the form of government awards. Government awards are agreements that generally provide us 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 we have only perfunctory obligations outstanding.

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

Change in accounting estimate - U.S. Government grants

Change in accounting estimate - U.S. Government awards

We recognize U.S. Government award revenue based on reimbursable costs incurred. Reimbursable costs include only allocable, allowable and reasonable costs, as determined in accordance with the Federal Acquisition Regulations and the related Cost Accounting Standards as applicable to the U.S. Government award. Costs incurred include direct labor and materials that are directly associated with the individual award plus indirect overhead and general and administrative type costs based upon our provisional indirect billing rates submitted by us to the U.S. Department of Energy (“DOE”). Our provisional indirect billing rates are subject to audit by the DOE. Changes in estimates affecting reimbursable costs are recognized in the period in which the change becomes known.

During 2011, our provisional indirect billing rates for the award from the DOE under the ARPA-E Recovery Act were audited by the DOE resulting in a revision to our provisional indirect billing rates. The revised indirect rates were subsequently approved by the DOE during the first quarter of 2012. As a result of this change in accounting estimate, we invoiced and recognized $530,000 of additional award revenue during the three months ended March 31, 2012 for reimbursable costs incurred by us in 2010 and 2011. The impact on our condensed consolidated statement of operations for the three months ended March 31, 2012 was a $530,000 decrease to our net loss and loss from operations and $0.01 reduction to our basic and diluted net loss per share of common stock. Our revenue from this award for the three months ended June 30, 2012 was $258,000 which represents the final funds available under the award. The $530,000 would have been recognized in the second quarter of 2012 had the change in accounting estimate not occured. The term of the award agreement ended in June 2012.

Income Taxes

Income Taxes

We use the liability method of accounting for income taxes. Deferred tax assets and liabilities are recognized for the estimated future tax consequences attributable to differences between the consolidated financial statement carrying amounts of existing assets and liabilities and their respective tax bases. Deferred tax assets are recognized for deductible temporary differences, along with net operating loss (“NOL”) carryforwards, if it is more likely than not that the tax benefits will be realized. To the extent a deferred tax asset cannot be recognized under the preceding criteria, a valuation allowance is established. Deferred tax assets and liabilities are measured using enacted tax rates in effect for the year in which those temporary differences are expected to be recovered or settled.

We recognize the financial statement effects of an uncertain tax position when it is more likely than not, based on the technical merits, that the position will be sustained upon examination.

Stock-Based Compensation

Stock-Based Compensation

We recognize compensation expense related to share-based transactions, including the awarding of employee stock options, based on the estimated fair value of the awards granted. All awards granted, modified or settled after January 1, 2006 have been accounted for based on the fair value of the awards granted. We generally use 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.

We account for stock options issued to non-employees based on their estimated fair value determined using the Black-Scholes option-pricing model. The fair value of the options granted to non-employees is remeasured as they vest, and the resulting change in value, if any, is recognized as an increase or decrease in stock compensation expense during the period the related services are rendered.

Net Loss per Share of Common Stock

Net Loss per Share of Common Stock

Basic and diluted 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. Basic and diluted net loss per share of common stock was the same for each period presented, because inclusion of all potential common shares outstanding was anti-dilutive. The following table presents the securities not included in the net loss per common share calculations for the three and six months ended June 30, 2012 and 2011 (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Options to purchase common stock		8,092		8,020		8,092		8,020
Unvested restricted stock units		1,007		555		1,007		555
Warrants to purchase common stock		266		266		266		266
Total		9,365		8,841		9,365		8,841

Reclassifications

Reclassifications

Certain amounts in prior period financial statements related to Shell including related party collaboration revenue (see Note 3), related party receivable, and related party deferred revenue have been reclassified to the corresponding non-related party accounts, since effective July 1, 2011, Shell is no longer considered a related party (see Note 7).

Recent Accounting Pronouncements

Recent Accounting Pronouncements

In June 2011, the FASB issued ASU 2011-05 that eliminates the option to present items of other comprehensive income (“OCI”) as part of the statement of changes in stockholders’ equity, and instead requires either, OCI presentation and net loss in a single continuous statement in the statement of operations, or as a separate statement of comprehensive loss. This new guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011, with early adoption permitted. We adopted this update in the fourth quarter of 2011 and have presented a separate condensed consolidated statement of comprehensive loss. The adoption of this accounting guidance did not have a material financial impact on our financial statements.

In May 2011, the FASB issued ASU 2011-04 that clarifies and changes some fair value measurement principles and disclosure requirements. Among them is the clarification that the concepts of highest and best use and valuation premise in a fair value measurement, should only be applied when measuring the fair value of nonfinancial assets. Additionally, the new guidance requires quantitative information about unobservable inputs, and disclosure of the valuation processes used and narrative descriptions with regard to fair value measurements within the Level 3 categorization of the fair value hierarchy. We adopted this accounting standard January 1, 2012. The adoption of this new guidance did not have a material impact on our financial statements or disclosures.

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Warrants

6 Months Ended

Jun. 30, 2012

Warrants [Abstract]

Warrants

9. Warrants

No warrants were exercised during the three and six months months ending June 30, 2012. At June 30, 2012, the following common stock warrants were issued and outstanding:

June 30, 2012
Issue Date	Shares Subject to  warrants		Exercise Price per Share		Expiration
October 25, 2005		6,066	$	1.05	October 25, 2012
May 25, 2006		184,895	$	5.96	May 25, 2013
July 17, 2007		2,384	$	12.45	February 9, 2016
September 28, 2007		72,727	$	8.25	September 28, 2017

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Related Party Transactions

6 Months Ended

Jun. 30, 2012

Related Party Transactions [Abstract]

Related Party Transactions

7. Related Party Transactions

Maxygen

Maxygen, Inc. (“Maxygen”) was one of our stockholders until it distributed its holdings to its stockholders in December 2010, and so transactions between us and Maxygen prior to that time were considered related party transactions. In October of 2010, we acquired Maxygen’s directed evolution technology patent portfolio for net consideration of $20.2 million including $20.0 million paid to Maxygen, transaction costs of $0.7 million and a royalty payable extinguishment of $0.5 million. We recorded an intangible asset for $20.2 million. In conjunction with this transaction, we terminated our existing license agreement with Maxygen including terminating our obligation to pay biofuels royalties to Maxygen.

Shell and Raízen

Prior to June 2011, Shell was considered a related party due to the size of its ownership interest. As discussed in Note 3, “Collaborative Research and Development Agreements”, Shell transferred full ownership of our common stock to Raízen, Shell’s joint venture with Cosan in Brazil. Based on our analysis and effective as of July 1, 2011, Shell was no longer considered a related party. Before June 30, 2011, related party receivables, related party deferred revenue, and related party collaboration research and development revenue were primarily comprised of transactions under our five-year collaborative research agreement (currently set to expire on November 1 2012, unless extended by the parties) and a license agreement with Shell. The revenues earned from Shell are included in the collaborative research and development line on our consolidated statement of operations. Collaborative research and development revenue received from Shell accounted for 51%, 62% and 76% of our revenues for the years ended December 31, 2011, 2010 and 2009, respectively. Collaborative research and development revenue received from Shell accounted for 61% and 57% of our revenues for the three months ended June 30, 2012 and 2011, respectively. Collaborative research and development revenue received from Shell accounted for 51% and 52% of our revenues for the six months ended June 30, 2012 and 2011, respectively.

At the time of the transfer, Raízen owned 5.6 million shares of our common stock and has the right to appoint a member to our board of directors. In September 2011, we entered into a joint development agreement with Raízen to develop an improved first generation ethanol process with enhanced economics. There has been no material financial activity with Raízen through June 30, 2012.

Exela PharmaSci, Inc.

We signed a license agreement with Exela PharmaSci, Inc. (“Exela”) in 2007. A member of our board of directors is also on the board of directors of Exela. Under the terms of the agreement, Exela would pay us a royalty based on their achievement of certain commercial goals.

During the three months ended June 30, 2012 and 2011, we recognized zero and $105,000, respectively, of revenue related to this arrangement shown in our consolidated statement of operations as collaborative research and development revenue. During the six months ended June 30, 2012 and 2011, we recognized $150,000 and $330,000, respectively, of revenue related to this arrangement. We did not recognize any revenue from Exela prior to 2011. As of June 30, 2012 and December 31, 2011, we had no amounts owed from Exela.

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Commitments and Contingencies

6 Months Ended

Jun. 30, 2012

Commitments and Contingencies [Abstract]

Commitments and Contingencies

8. Commitments and Contingencies

Operating Leases

Our headquarters are located in Redwood City, California where we occupy approximately 107,000 square feet of office and laboratory space in four buildings. On March 16, 2011, we entered into a Fifth Amendment to Lease (the “Fifth Amendment”) with Metropolitan Life Insurance Company (“MetLife”) with respect to our offices located at 200 and 220 Penobscot Drive, Redwood City, California, (the “Penobscot Space”), 400 Penobscot Drive, Redwood City, California (the “Building 2 Space”) and 640 Galveston Drive, Redwood City, California (the “Galveston Space”), and with respect to approximately 29,921 square feet of additional space located at 101 Saginaw Drive, Redwood City, California (the “Saginaw Space”). Under the Fifth Amendment, the term of the lease of the Penobscot Space, the Building 2 Space and the Saginaw Space lasts until January 31, 2020, and we have options to extend for two additional five year periods. Pursuant to the Fifth Amendment, we surrendered the Galveston Space in August 2011. The Fifth Amendment provides a number of incentives to us including forgiveness of rent payments for the initial two months of the extended lease term for certain buildings, a tenant improvement allowance (“TIA”) of $2.4 million and an additional $0.8 million special allowances for certain HVAC costs. We applied the TIA funds toward capital improvements to the expanded facility as well as upgrades and reconfiguration of existing lab and office space. A portion of the TIA may be utilized by us to pay costs for furniture, furnishings and equipment.

As of June 30, 2012, we had completed the capital improvements to the expanded facilities and incurred $3.6 million of capital improvement costs related to the facilities. During 2011, we requested and received $1.8 million of reimbursements from the landlord out of the TIA for the completed construction. We requested and received reimbursement of the remaining $1.4 million of TIA and special HVAC allowance during the second quarter of 2012. The TIA is recorded once cash is received and is amortized on a straight-line basis over the term of the lease as a reduction in rent expense. Additionally, the Fifth Amendment waived our existing asset retirement obligations for the impacted buildings, resulting in a $0.3 million decrease of our obligation which in turn resulted in $0.1 million gain on extinguishment of asset retirement obligations recorded for the quarter ended March 31, 2011 in our condensed consolidated statement of operation as sales, general and administrative expenses.

We also lease space in 501 Chesapeake Drive, Redwood City, California (the “501 Chesapeake Space”). The lease for the 501 Chesapeake Space was not extended with the Fifth Amendment and will expire as per the original agreement in January 2013, with an option for an additional term of up to two years.

Rent expense is recognized on a straight-line basis over the term of the lease. In accordance with the terms of the lease agreement, we exercised our right to deliver a letter of credit in lieu of a security deposit. The letters of credit in the amounts of $707,000 and $707,000 as of June 30, 2012 and December 31, 2011, respectively, are collateralized by deposit balances held by the bank. These deposits are recorded as restricted cash on the consolidated balance sheets.

As of June 30, 2012 and December 31, 2011 we had asset retirement obligations of $594,000 and $580,000, respectively from operating leases, whereby we must restore the facilities that we are renting to their original form. We incurred $15,000 and $29,000 of accretion expense related to our asset retirement obligations during the six months ended June 30, 2012 and 2011, respectively. We are expensing the asset retirement obligation over the terms of the respective leases. We review the estimated obligation each period and we make adjustments if our estimates change.

Future minimum payments under noncancellable operating leases are as follows at June 30, 2012 (in thousands):

	Lease payments
6 months ending December 31,
2012	$	1,641
Years ending December 31,
2013		2,905
2014		2,722
2015		2,799
2016		2,805
2017 and beyond		8,447
Total	$	21,319

Litigation

We have 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, we have 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 our consolidated financial position, results of operations or cash flows.

Indemnifications

We have certain agreements with licensors, licensees and collaborators that contain indemnification provisions. In such provisions, we typically agree to indemnify the licensor, licensee and collaborator against certain types of third party claims. The maximum amount of the indemnifications is not limited. We accrue for known indemnification issues when a loss is probable and can be reasonably estimated. There were no accruals related to indemnification issues for any periods presented.

Other contingencies

In November 2009, one of our foreign subsidiaries sold intellectual property to us. 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. We believe 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, we could be obligated to pay an estimated amount of $0.6 million.

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Stockholders' Equity

6 Months Ended

Jun. 30, 2012

Stockholders' Equity [Abstract]

Stockholders' Equity

10. Stockholders’ Equity

In 2002, we adopted the 2002 Stock Plan (the “2002 Plan”), pursuant to which our board of directors issued incentive stock options, non-statutory stock options (options that do not qualify as incentive stock options) and restricted stock to our employees, officers, directors or consultants. In March, 2010, our board of directors and stockholders approved the 2010 Equity Incentive Award Plan (the “2010 Plan”), which became effective upon the completion of our IPO in April 2010. A total of 1,100,000 shares of common stock were initially reserved for future issuance under the 2010 Plan and any shares of common stock reserved for future grant or issuance under our 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, and during the three months ended March 31 2012 an additional 1,439,827 shares were reserved under the 2010 plan as a result of this provision. As of June 30, 2012, we had a total of 11,551,638 shares of common stock reserved for issuance under our Plans and no shares available for issuance under the 2002 Plan.

Additionally during the three months ended June 30, 2012, we granted 400,000 options and 750,000 restricted stock awards pursuant to the employment agreement with our new chief executive officer, Mr. John Nicols. The option award has a per share exercise price equal to $3.46 per share, which was the closing price of the Company’s common stock on June 13, 2012. Mr Nicols will vest 25% of the option award on June 13, 2013 with the remaining shares vesting ratably on a monthly basis over a period of 36 months thereafter, such that the option award would be fully vested and exercisable on June 13, 2016. The restricted stock award of 750,000 shares vest over four years with 25% of the awards vesting on each annual anniversary such that the restricted stock award would be fully vested on June 13, 2016.

We awarded 13,133 and 767,953 restricted stock units during the three and six months ended June 30, 2012, respectively. These stock awards vest over four years with 25% of the awards vesting on each annual anniversary. The fair value of the awards was calculated based the NASDAQ quoted stock price on the date of the grant with the expense recognized over the vesting period.

We issued 81,154 and 147,185 common shares for stock options exercised during the three and six months ended June 30, 2012, respectively.

We issued 33,750 and 98,144 common shares for restricted stock units which vested during the three and six months ended June 30, 2012, respectively.

Stock-Based Compensation Expense

We estimate 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. Since we were not a publicly traded entity prior to April 2010, sufficient company-specific historical volatility data was not available for reporting periods prior to the three months ended June 30, 2012. As a result, for those prior periods, we we estimated the expected volatility based on the historical volatility of a group of unrelated public companies within our industry. Effective for the quarter ended June 30, 2012, we determined we had sufficient company-specific historical volatility data As a result, for the three months ended June 30, 2012, we estimate the expected volatility based on the historical volatility of our common stock.

Due to our 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 U.S. Treasury instruments whose terms were consistent with the terms of our stock options. The expected dividend assumption was based on our history and expectation of dividend payouts.

The following table presents total stock-based compensation expense included in the condensed consolidated statements of operations (in thousands):

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Research and development	$	779	$	951	$	1,433	$	1,801
Sales, general and administrative		1,060		1,597		1,576		3,056
	$	1,839	$	2,548	$	3,009	$	4,857

During the second quarter of 2012, certain members of our executive team were informed that their annual bonus for 2012 would be paid in the form of common stock awards rather than cash payments. We expect to pay the 2012 annual bonus in the first quarter of 2013. Through June 30, 2012 we have accrued $0.5 million in bonuses to be settled in common stock awards. This amount is included in the above stock-based compensation expense table and on our balance sheet as additional paid in capital.

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Balance Sheets and Statements of Operations Details (Details 1) (USD $) In Thousands, unless otherwise specified	Jun. 30, 2012	Dec. 31, 2011
Schedule of Inventory Components
Raw materials	$ 1,947	$ 2,779
Work in process	48	54
Finished goods	2,206	1,655
Total inventories	$ 4,201	$ 4,488

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Balance Sheets and Statements of Operations Details (Tables)

6 Months Ended

Jun. 30, 2012

Balance Sheets and Statements of Operations Details [Abstract]

Schedule of cash equivalents and marketable securities

	June 30, 2012									Average Contractual Maturities
	Cost or Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
										(in days)
Money market funds	$	12,093	$	—	$	—		$	12,093		n/a
Commercial paper		3,997		—		—			3,997		8
Corporate bonds		26,148		26		(4	)		26,170		193
U.S. Treasury obligations		6,521		1		—			6,522		102
Government-sponsored enterprise securities		4,001		7		—			4,008		40
Common shares of CO 2 Solutions		1,316		—		(778	)		538		n/a
Total	$	54,076	$	34	$	(782	)	$	53,328

	December 31, 2011									Average Contractual Maturities
	Cost or Amortized Cost		Gross Unrealized Gains		Gross Unrealized Losses			Estimated Fair Value
										(in days)
Money market funds	$	18,866	$	—	$	—		$	18,866		n/a
Commercial paper		1,999		—		—			1,999		55
Corporate bonds		30,908		29		(45	)		30,892		270
U.S. Treasury obligations		998		4		—			1,002		274
Government-sponsored enterprise securities		3,003		12		—			3,015		373
Common shares of CO 2 Solutions		1,316		—		(155	)		1,161		n/a
Total	$	57,090	$	45	$	(200	)	$	56,935

Schedule of inventory components

	June 30, 2012		December 31, 2011
Raw materials	$	1,947	$	2,779
Work in process		48		54
Finished goods		2,206		1,655
Total inventories	$	4,201	$	4,488

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Segment Reporting (Tables)

6 Months Ended

Jun. 30, 2012

Segment Reporting [Abstract]

Schedule of revenues by geographical area

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Revenues
Americas(1)	$	16,914	$	17,417	$	32,543	$	35,135
Asia		3,550		4,917		13,572		16,598
Europe		2,445		3,721		7,930		5,356
	$	22,909	$	26,055	$	54,045	$	57,089

(1) Primarily United States

Schedule of long-lived assets by geographical area

	June 30,		December 31,
	2012		2011
Long-lived assets
Americas(1)	$	31,699	$	34,817
Europe		4,763		4,395
Asia		1,563		2,380
	$	38,025	$	41,592

(1) Primarily United States

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Warrants (Details)	6 Months Ended
	Jun. 30, 2012
Warrants Issued on October 25, 2005 and Expiring on October 25, 2012 [Member]
Schedule of common stock warrants issued and outstanding
Issue Date	Oct. 25, 2005
Shares Subject to warrants	6,066
Exercise Price per Share	1.05
Expiration	Oct. 25, 2012
Warrants Issued on May 25, 2006 and Expiring on May 25, 2013 [Member]
Schedule of common stock warrants issued and outstanding
Issue Date	May 25, 2006
Shares Subject to warrants	184,895
Exercise Price per Share	5.96
Expiration	May 25, 2013
Warrants Issued on July 17, 2007 and Expiring on February 9, 2016 [Member]
Schedule of common stock warrants issued and outstanding
Issue Date	Jul. 17, 2007
Shares Subject to warrants	2,384
Exercise Price per Share	12.45
Expiration	Feb. 09, 2016
Warrants Issued on September 28, 2007 and Expiring on September 28, 2017 [Member]
Schedule of common stock warrants issued and outstanding
Issue Date	Sep. 28, 2007
Shares Subject to warrants	72,727
Exercise Price per Share	8.25
Expiration	Sep. 28, 2017

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Condensed Consolidated Statements of Comprehensive Loss (Unaudited) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Jun. 30, 2012	Jun. 30, 2011
Condensed Consolidated Statements of Comprehensive Loss [Abstract]
Net loss	$ (5,519)	$ (5,040)	$ (13,009)	$ (8,511)
Other comprehensive income (loss):
Foreign currency translation adjustments		8	165	44
Unrealized gain (loss) on marketable securities, net of tax	(337)	358	(636)	405
Other comprehensive income (loss)	(337)	366	(471)	449
Total comprehensive loss	$ (5,856)	$ (4,674)	$ (13,480)	$ (8,062)

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Joint Development Agreement with CO2 Solutions

6 Months Ended

Jun. 30, 2012

Joint Development Agreement with CO2 Solutions [Abstract]

Joint Development Agreement with CO2 Solutions

4. Joint Development Agreement with CO ₂ Solutions

On December 15, 2009, we entered into an exclusive joint development agreement with CO ₂ 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. Under the agreement, we obtained a research license to CO ₂ Solutions’s intellectual property and agreed to conduct research and development activities jointly with CO ₂ Solutions with the goal of advancing the development of carbon capture technology. We also purchased 10,000,000 common shares (approximately 16.6% of the total common shares outstanding at the time of investment) of CO ₂ Solutions in a private placement subject to a four-month statutory resale restriction. This restriction expired on April 15, 2010. In July 2012, Alan Shaw, our former Chief Executive Officer and currently an advisor to our board of directors, resigned from the board of directors of CO ₂ Solutions and we are currently considering potential replacements to this designated board seat.

In January 2011, we extended our joint development agreement with CO ₂ Solutions on essentially the same terms as the original agreement. The extended agreement expires six months after the expiry of any third party collaborations. We expect this agreement to expire during the first half of 2013.

We concluded that through June 30, 2012, we did not have the ability to exercise significant influence over CO₂ Solutions’s operating and financial policies. We consider our investment in CO ₂ Solutions’s common shares as an investment in a marketable security that is available for sale, and carry it at fair value in non-current marketable securities, with changes in fair value recognized in the Statement of Comprehensive Income (loss). We have estimated the fair value of common shares as of June 30, 2012, as determined by trading on TSX Venture Exchange. Accordingly, we have classified our investment in CO₂ Solutions as a level 1 investment as discussed in Note 6.

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Restructuring (Tables)

6 Months Ended

Jun. 30, 2012

Restructuring Costs [Abstract]

Summary of changes in restructuring accrual

(in thousands)	Severance, benefits and related personal costs
	2012 Plan
Restructuring charges	$	510
Cash payments		(24	)
Balance at March 31, 2012		486
Restructuring charges		53
Adjustments to previously accrued charges		(49	)
Cash payments		(422	)
Balance at June 30, 2012	$	68

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Related Party Transactions (Details) (USD $) Share data in Millions, unless otherwise specified	3 Months Ended			1 Months Ended	3 Months Ended		6 Months Ended		12 Months Ended		1 Months Ended	6 Months Ended		12 Months Ended
	Jun. 30, 2012	Jun. 30, 2011	Dec. 31, 2011	Oct. 31, 2010 Maxygen [Member]	Jun. 30, 2012 Exela PharmaSci, Inc [Member]	Jun. 30, 2011 Exela PharmaSci, Inc [Member]	Jun. 30, 2012 Exela PharmaSci, Inc [Member]	Jun. 30, 2011 Exela PharmaSci, Inc [Member]	Dec. 31, 2011 Exela PharmaSci, Inc [Member]	Jun. 30, 2012 Raizen [Member]	Nov. 30, 2007 Shell [Member]	Jun. 30, 2012 Shell [Member]	Jun. 30, 2011 Shell [Member]	Dec. 31, 2011 Shell [Member]	Dec. 31, 2010 Shell [Member]	Dec. 31, 2009 Shell [Member]
Related Party Transactions (Textual) [Abstract]
Acquisition of technology patent portfolio				$ 20,200,000
Term of collaborative research and development agreement (in years)											5 years
Collaborative research and development agreement, expiration period													Nov. 01, 2012
Shells percentage of total Collaborative R&D revenue	61.00%	57.00%										51.00%	52.00%	51.00%	62.00%	76.00%
Shares held by collaboration company										5.6
Collaborative research and development					0	105,000	150,000	330,000			20,000,000
Payment made to related party				20,000,000
Transaction costs				700,000
Royalty payable extinguishment				500,000
Intangible asset	14,636,000		16,442,000	20,200,000
Recognize revenue									0
Amounts owed					$ 0		$ 0		$ 0

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Summary of Significant Accounting Policies (Tables)

6 Months Ended

Jun. 30, 2012

Summary of Significant Accounting Policies [Abstract]

Securities not included in the net loss per common share calculations

	Three Months Ended June 30,				Six Months Ended June 30,
	2012		2011		2012		2011
Options to purchase common stock		8,092		8,020		8,092		8,020
Unvested restricted stock units		1,007		555		1,007		555
Warrants to purchase common stock		266		266		266		266
Total		9,365		8,841		9,365		8,841