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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2013	Mar. 21, 2014	Jun. 30, 2013
Document and Entity Information
Entity Registrant Name	METABOLIX, INC.
Entity Central Index Key	0001121702
Document Type	10-K
Document Period End Date	Dec. 31, 2013
Amendment Flag	false
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Smaller Reporting Company
Entity Public Float			$ 34,313,662
Entity Common Stock, Shares Outstanding		34,889,055
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	FY

CONSOLIDATED BALANCE SHEETS - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Current Assets:
Cash and cash equivalents	$ 7,698	$ 14,572
Short-term investments	11,511	29,201
Inventory	4,074	3,204
Accounts receivable	997	839
Due from related parties	51	75
Unbilled receivables	187	372
Prepaid expenses and other current assets	713	692
Total current assets	25,231	48,955
Restricted cash	619	594
Property and equipment, net	793	1,358
Long-term investments		2,508
Other assets	95	95
Total assets	26,738	53,510
Current Liabilities:
Accounts payable	579	1,233
Accrued expenses	4,892	3,519
Current portion of deferred rent	55	165
Short-term deferred revenue	669	1,067
Total current liabilities	6,195	5,984
Deferred rent, net of current portion		55
Other long-term liabilities	145	131
Total liabilities	6,340	6,170
Commitments and contingencies (Note 9)
Stockholders' Equity:
Preferred stock ($0.01 par value per share); 5,000,000 shares authorized; no shares issued or outstanding
Common stock ($0.01 par value per share); 100,000,000 shares authorized at December 31, 2013 and 2012, 34,581,449 and 34,306,570 shares issued and outstanding at December 31, 2013 and 2012, respectively	346	343
Additional paid-in capital	292,661	289,050
Accumulated other comprehensive loss	(71)	(21)
Accumulated deficit	(272,538)	(242,032)
Total stockholders' equity	20,398	47,340
Total liabilities and stockholders' equity	$ 26,738	$ 53,510

CONSOLIDATED BALANCE SHEETS (Parenthetical) - $ / shares	Dec. 31, 2013	Dec. 31, 2012
CONSOLIDATED BALANCE SHEETS
Preferred stock, par value per share (in dollars per share)	$ 0.01	$ 0.01
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value per share (in dollars per share)	$ 0.01	$ 0.01
Common stock, shares authorized	100,000,000	100,000,000
Common stock, shares issued	34,581,449	34,306,570
Common stock, shares outstanding	34,581,449	34,306,570

CONSOLIDATED STATEMENTS OF OPERATIONS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Revenue:
Revenue from termination of ADM collaboration		$ 38,885
Product revenue	$ 2,067	1,211
Grant revenue	2,490	1,971	$ 918
Research and development revenue	618
License fee and royalty revenue	219	249	507
Total revenue	5,394	42,316	1,425
Costs and expenses:
Cost of product revenue	3,026	1,426
Research and development	19,127	23,177	24,445
Selling, general, and administrative	13,743	14,110	15,841
Total costs and expenses	35,896	38,713	40,286
Income (loss) from operations	(30,502)	3,603	(38,861)
Other income (net):
Interest income, net	51	124	156
Other expense, net	(55)	(97)	(80)
Total other income (expense), net	(4)	27	76
Net income (loss)	$ (30,506)	$ 3,630	$ (38,785)
Net income (loss) per share:
Basic (in dollars per share)	$ (0.88)	$ 0.11	$ (1.24)
Diluted (in dollars per share)	$ (0.88)	$ 0.11	$ (1.24)
Number of shares used in per share calculations:
Basic (in shares)	34,471,301	34,217,298	31,257,376
Diluted (in shares)	34,471,301	34,279,779	31,257,376

CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
CONSOLIDATED STATEMENTS OF COMPREHENSIVE INCOME (LOSS)
Net income (loss):	$ (30,506)	$ 3,630	$ (38,785)
Other comprehensive income (loss)
Change in unrealized gain (loss) on investments	(12)	(3)	20
Change in foreign currency translation adjustment	(38)	(6)	(17)
Total other comprehensive income (loss)	(50)	(9)	3
Comprehensive income (loss)	$ (30,556)	$ 3,621	$ (38,782)

- Definition

The change in equity [net assets] of a business enterprise during a period from transactions and other events and circumstances from non-owner sources which are attributable to the reporting entity. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, but excludes any and all transactions which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

+ References + Details

- Definition

Amount after tax and reclassification adjustments, resulting from the process of expressing in the reporting currency of the reporting entity those amounts that are denominated or measured in a different currency, and from transactions whose terms are denominated in a currency other than the entity's functional currency, which is attributable to the parent entity.

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+ Details

- Definition

Net of tax amount of other comprehensive income (loss) attributable to the parent entity.

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- Definition

Net of tax amount of unrealized holding gain (loss) before reclassification adjustments and transfers on available-for-sale securities.

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+ Details

CONSOLIDATED STATEMENTS OF CASH FLOWS - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Cash flows from operating activities
Net income (loss)	$ (30,506)	$ 3,630	$ (38,785)
Adjustments to reconcile net income (loss) to cash used in operating activities:
Depreciation	928	1,298	1,507
Charge for 401(k) company common stock match	397	408	529
Stock-based compensation	3,193	3,807	4,633
Inventory impairment	818	138
Changes in operating assets and liabilities:
Inventory	(1,688)	(3,342)
Accounts receivable	(158)	(693)	(146)
Unbilled receivable	185	(68)	(296)
Due from related parties	24	236	(71)
Prepaid expenses and other assets	(21)	108	68
Accounts payable	(654)	721	273
Accrued expenses	1,383	(34)	(623)
Deferred rent and long-term liabilities	(151)	(154)	(153)
Deferred revenue	(398)	(37,791)	1,333
Net cash used in operating activities	(26,648)	(31,736)	(31,731)
Cash flows from investing activities
Purchase of property and equipment	(373)	(392)	(895)
Proceeds from sale of equipment		12
Change in restricted cash	(25)	28
Purchase of investments	(16,635)	(58,933)	(107,477)
Proceeds from sale and maturity of short-term investments	36,821	84,303	99,464
Net cash provided by (used in) investing activities	19,788	25,018	(8,908)
Cash flows from financing activities
Proceeds from options exercised	14	19	74
Proceeds from public stock offering, net of issuance costs			49,333
Net cash provided by financing activities	14	19	49,407
Effect of exchange rate changes on cash and cash equivalents	(28)	(6)	(17)
Net increase (decrease) in cash and cash equivalents	(6,874)	(6,705)	8,751
Cash and cash equivalents at beginning of period	14,572	21,277	12,526
Cash and cash equivalents at end of period	$ 7,698	$ 14,572	$ 21,277

CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-In Capital	Accumulated other Comprehensive Income (loss)	Accumulated Deficit
Balance at Dec. 31, 2010	$ 23,676	$ 269	$ 230,299	$ (15)	$ (206,877)
Balance (in shares) at Dec. 31, 2010		26,895,389
Increase (decrease) in stockholders' equity
Exercise of common stock options	74		74
Exercise of common stock options (in shares)		21,851
Non-cash stock-based compensation expense	4,633		4,633
Issuance of common stock for 401k match	$ 529	$ 1	528
Issuance of common stock for 401k match (in shares)	68,558	68,558
Issuance of common stock upon public offering, net of offering costs of $2,360	$ 49,333	$ 71	49,262
Issuance of common stock upon public offering, net of offering costs of $2,360 (in shares)		7,130,000
Change in unrealized gain (loss) on investments	20			20
Effect of foreign currency translation	(17)			(17)
Net income (loss)	(38,785)				(38,785)
Balance at Dec. 31, 2011	39,463	$ 341	284,796	(12)	(245,662)
Balance (in shares) at Dec. 31, 2011		34,115,798
Increase (decrease) in stockholders' equity
Exercise of common stock options	19		19
Exercise of common stock options (in shares)		11,436
Non-cash stock-based compensation expense	3,807		3,807
Issuance of common stock for 401k match	$ 430	$ 2	428
Issuance of common stock for 401k match (in shares)	179,336	179,336
Change in unrealized gain (loss) on investments	$ (3)			(3)
Effect of foreign currency translation	(6)			(6)
Net income (loss)	3,630				3,630
Balance at Dec. 31, 2012	$ 47,340	$ 343	289,050	(21)	(242,032)
Balance (in shares) at Dec. 31, 2012	34,306,570	34,306,570
Increase (decrease) in stockholders' equity
Exercise of common stock options	$ 14		14
Exercise of common stock options (in shares)		7,550
Non-cash stock-based compensation expense	3,193		3,193
Issuance of common stock for 401k match	$ 407	$ 3	404
Issuance of common stock for 401k match (in shares)	267,329	267,329
Change in unrealized gain (loss) on investments	$ (12)			(12)
Effect of foreign currency translation	(38)			(38)
Net income (loss)	(30,506)				(30,506)
Balance at Dec. 31, 2013	$ 20,398	$ 346	$ 292,661	$ (71)	$ (272,538)
Balance (in shares) at Dec. 31, 2013	34,581,449	34,581,449

CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY (Parenthetical) $ in Thousands	12 Months Ended
	Dec. 31, 2011 USD ($)
CONSOLIDATED STATEMENTS OF STOCKHOLDERS' EQUITY
Issuance of common stock upon public offering, offering costs	$ 2,360

Nature of Business	12 Months Ended
Nature of Business	Dec. 31, 2013
Nature of Business
Nature of Business	1. Nature of Business Metabolix, Inc. (the "Company") is an innovation-driven bioscience company which is focused on delivering sustainable solutions to the plastics and chemicals industries. The Company has core capabilities in microbial genetics, fermentation process engineering, chemical engineering, polymer science, plant genetics and botanical science, and has assembled these capabilities in a way that has allowed the integration of biotechnology with chemical engineering and industrial practice. The Company is subject to risks common to companies in the biotechnology industry including, but not limited to, development by the Company's competitors of new technological innovations, dependence on key personnel, protection of proprietary technology, the need to obtain additional funding, and compliance with government regulations. The accompanying consolidated financial statements have been prepared on a basis which assumes that the Company will continue as a going concern and which contemplates the realization of assets and satisfaction of liabilities and commitments in the normal course of business. However, with the exception of 2012, when the Company recognized $38,885 of deferred revenue from the terminated Telles joint venture, it has recorded losses since its inception, including its fiscal year ended December 31, 2013. As of December 31, 2013, the Company held unrestricted cash, cash equivalents and investments of $19,209. The Company's present capital resources are not sufficient to fund its planned operations for a twelve month period, and therefore, raise substantial doubt about its ability to continue as a going concern. The Company will, during 2014, require significant additional funding to continue its operations. Based on current plans and projections, which remain subject to numerous uncertainties, the Company anticipates raising additional funds over the next 12-15 months. The timing, structure and vehicles for obtaining this level of financing are under consideration by the Company and may be accomplished in stages. The Company's goal, however, is to use this capital to build an intermediate scale specialty materials business based on PHA additives that serves as the foundation for its longer range plans and future growth of its biopolymers business. Failure to receive additional funding will force the Company to delay, scale back or otherwise modify its business and its manufacturing plans, its sales and marketing efforts, research and development activities and other operations, and/or seek strategic alternatives. The consolidated financial statements do not include any adjustments that may result from the outcome of these uncertainties. The Company believes that its existing resources and the cash to be generated from existing grants and expected product sales will be sufficient to meet its projected operating requirements into the third quarter of 2014. However, any significant costs incurred to establish a commercial biopolymer manufacturing facility will shorten this liquidity horizon. The Company continues to face significant challenges and uncertainties and, as a result, its available capital resources may be consumed more rapidly than currently expected due to (a) lower than expected sales of its biopolymer products as a result of slow market adoption; (b) increases in capital costs and operating expenses related to the establishment and start-up of commercial manufacturing operations either on its own or with third parties; (c) changes the Company may make to the business that affect ongoing operating expenses; (d) changes the Company may make to its business strategy; (e) changes in the Company's research and development spending plans; and (f) other items affecting the Company's forecasted level of expenditures and use of cash resources. In any event, the Company will, during 2014, require significant additional financing to continue to fund its operations and to support its capital needs. Management of the Company will attempt to obtain additional funding through public or private financing, collaborative arrangements with strategic partners, or through additional credit lines or other debt financing sources. However, there is uncertainty regarding whether the Company can successfully execute these actions, and it can provide no assurance that it will. Furthermore, if the Company issues equity or debt securities to raise additional funds, its existing stockholders may experience dilution, and the new equity or debt securities may have rights, preferences and privileges senior to those of the Company's existing stockholders. If the Company raises additional funds through collaboration, licensing or other similar arrangements, it may be necessary to relinquish valuable rights to its potential products or proprietary technologies, or grant licenses on terms that are not favorable to the Company.

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2013

Summary of Significant Accounting Policies

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Principles of Consolidation

The consolidated financial statements include the accounts of the Company and its wholly-owned subsidiaries. All significant intercompany transactions were eliminated, including transactions with Metabolix GmbH, the Company's wholly-owned subsidiary that became operational in Germany during early 2013. Telles, LLC ("Telles"), the Company's former joint venture with Archer Daniels Midland Company ("ADM") that terminated in early 2012, was not consolidated by the Company.

Use of Estimates

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

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original maturity date of ninety days or less at the date of purchase to be cash equivalents.

Investments

The Company considers all highly liquid investments purchased with an original maturity date of ninety days or less at the date of purchase to be cash equivalents, and all investments purchased with an original maturity date of ninety days or more at the date of purchase and a maturity date of one year or less at the balance sheet date to be short-term investments. All other investments are classified as long-term. At December 31, 2013 and December 31, 2012, investments consisted of U.S. Treasury securities and debt securities of the U.S. government. All investments were classified as available for sale as of December 31, 2013 and 2012. See Note 5 for further discussion on investments.

Unrealized gains and temporary losses on investments are included in accumulated other comprehensive income (loss) as a separate component of stockholders' equity. Realized gains and losses, dividends, interest income and declines in value judged to be other-than-temporary credit losses are included in other income (expense). Any premium or discount arising at purchase is amortized and/or accreted to interest income.

Restricted Cash

The Company had restricted cash in the amount of $619 and $594 at December 31, 2013 and 2012, respectively. At December 31, 2013, restricted cash consisted of $494 held in connection with the lease agreement for the Company's Cambridge, Massachusetts facility and $125 held in connection with the Company's corporate credit card programs. At December 31, 2012, restricted cash consisted of $494 held in connection with the lease agreement for the Company's Cambridge, Massachusetts facility and $100 held in connection with the Company's corporate credit card program.

Foreign Currency Translation

Foreign denominated assets and liabilities of the Company's wholly-owned foreign subsidiaries are translated into U.S. dollars at the prevailing exchange rates in effect on the balance sheet date. Revenues and expenses are translated at average exchange rates prevailing during the period. Any resulting translation gains or losses are recorded in the accumulated other comprehensive income (loss) in the consolidated balance sheet.

Comprehensive Income (Loss)

Comprehensive income (loss) is comprised of net income (loss) and certain changes in stockholders' equity that are excluded from net income (loss). The Company includes unrealized gains and losses on marketable securities and foreign currency translation adjustments in other comprehensive income (loss).

Concentration of Credit Risk

Financial instruments that potentially subject the Company to concentrations of credit risk primarily consist of cash and cash equivalents and short-term investments. The Company primarily invests its excess cash and cash equivalents in money market funds, corporate debt, federal agency notes and U.S. Treasury notes. Investments are acquired in accordance with the Company's investment policy which establishes a concentration limit per issuer.

The Company provides credit to customers in the normal course of business. The Company performs ongoing credit evaluations of its customers' financial condition and limits the amount of credit extended when deemed necessary. At December 31, 2013, the Company's worldwide accounts and unbilled receivables include $552 or 46% from government grants and $528 or 44% from customer product sales. At December 31, 2013, the Company's REFABB grant with the Department of Energy represented 56% of billed and unbilled receivables from government grants and no single product customer represented more than 23% of total product receivables. At December 31, 2012, the Company's worldwide accounts and unbilled receivables included $561 or 46% from government grants and $535 or 44% from customer product sales. At December 31, 2012, one customer represented 41% of accounts receivable due from product sales.

Fair Value Measurements

The carrying amounts of the Company's financial instruments as of December 31, 2013 and 2012, which include cash equivalents, investments, accounts receivable, unbilled receivables, due from related parties, accounts payable, and accrued expenses, approximate their fair values due to the short-term nature of these instruments. See Note 6 for further discussion on fair value measurements.

Segment Information

The accounting guidance for segment reporting establishes standards for reporting information on operating segments in annual financial statements. The Company operates in one segment, which is the business of developing and commercializing technologies for the production of polymers and chemicals in plants and in microbes. The Company's chief operating decision-maker does not manage any part of the Company separately, and the allocation of resources and assessment of performance are based on the Company's consolidated operating results. As of December 31, 2013 and 2012, less than 10% of the Company's combined total assets were located outside of the United States. In addition, the reported net income (loss) outside of the United States was less than 10% of the combined net income (loss) of the consolidated Company.

Inventory

The Company's adopted inventory policies are to state inventory at the lower of cost or market and to value inventory using the average cost method. The Company analyzes its inventory levels quarterly and writes down, to cost of product revenue, inventory it considers to be in excess of expected sales requirements, fails to meet commercial sales specifications or that has become obsolete.

Property and Equipment

Property and equipment are stated at cost less accumulated depreciation. Repairs and maintenance are charged to operations as incurred. Gains and losses on the disposition of equipment are recorded in net income or loss and the related cost and accumulated depreciation are removed from the respective accounts. Depreciation is computed using the straight-line method over the estimated useful lives as follows:

Asset Description		Estimated Useful Life

Equipment		2.5 - 3 years
Furniture and Fixtures		5
Software		3
Leasehold improvements		Shorter of useful life or term of lease

The Company accounts for operating lease incentive payments received from a lessor in accordance with the accounting standard on accounting for leases. The Company records incentive payments received from its landlords as deferred rent and amortizes these amounts as reductions to lease expense over the lease term.

Impairment of Long-Lived Assets

The Company accounts for the impairment and disposal of long-lived assets in accordance with accounting guidance on accounting for the impairment or disposal of long-lived assets. The guidance requires that long-lived assets, such as property and equipment be reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. The guidance further requires that companies recognize an impairment loss only if the carrying amount of a long-lived asset is not recoverable based on its undiscounted future cash flows and measure an impairment loss as the difference between the carrying amount and fair value of the asset.

Revenue Recognition

The Company recognizes revenue in accordance with accounting standards on revenue recognition. Principal sources of revenue are government research grants, product sales, license fees, royalty revenues and research and development payments that are primarily derived from collaborative agreements with other companies.

During March 2012, the Company initiated biopolymer product sales to customers for the first time. The Company's policy is to recognize revenue when evidence of an arrangement exists, title has passed or services have been rendered, the selling price is fixed or determinable and collectability is reasonably assured. Revenue from product sales to customers is recognized when all elements of the sale have been delivered. The Company's product return policy provides for discretion in accepting customer product returns during a period of sixty days after product delivery. Until sufficient experience is developed on which to base an estimate of product returns, the Company defers recognition of product revenue and related costs until the later of (i) the end of the sixty day period or (ii) when the customer payment has been received. The Company includes deferred cost of product revenue in inventory. As of December 31, 2013 and December 31, 2012, the Company's deferred product revenue and associated cost of product revenue are shown below:

	Year ended December 31,

	2013		2012
Deferred product revenue	$	537	$	786
Deferred cost of product revenue	$	476	$	219

Fees to license the Company's proprietary and licensed technologies are recognized only after both the license period has commenced and the technology has been delivered. Royalty revenue is recognized when it becomes determinable and collectability is reasonably assured; otherwise the Company recognizes royalty revenue upon receipt of payment.

The Company follows authoritative guidance on revenue recognition for multiple-element arrangements entered into or materially modified on or after January 1, 2011. The guidance amends the criteria for separating and allocating consideration in a multiple-element arrangement by modifying the fair value requirements for revenue recognition and eliminating the use of the residual method. The fair value of deliverables under the arrangement may be derived using a "best estimate of selling price" if vendor-specific objective evidence and third-party evidence is not available. Deliverables under the arrangement will be separate units of accounting, provided (i) a delivered item has value to the customer on a standalone basis; and (ii) if the arrangement includes a general right of return relative to the delivered item, delivery or performance of the undelivered item is considered probable and substantially within the Company's control.

The Company recognizes funds received from contractual research and development services and from government grants as revenue. These contracts and grants are considered an ongoing major and central operation of the Company's business. For government grants, revenue is earned as research expenses related to the grants are incurred.

Research and Development Expenses

All costs associated with internal research and development as well as research and development services conducted for others are expensed as incurred. Research and development expenses include direct costs for salaries, employee benefits, subcontractors, facility related expenses, depreciation and stock-based compensation related to employees and non-employees involved in the Company's research and development. Costs related to revenue-producing grants are also recorded as research and development expenses.

Selling, General, and Administrative Expenses

The Company's selling, general and administrative expense line item includes costs for salaries, employee benefits, facilities expenses, consulting fees, travel expenses, depreciation expenses, and office related expenses incurred to support the selling and administrative operations of the Company.

Intellectual Property Costs

The Company includes all costs associated with the prosecution and maintenance of patents within selling, general and administrative expenses in the consolidated statement of operations.

Stock-Based Compensation

The Company accounts for stock-based compensation costs in accordance with the accounting standards for stock-based compensation, which require that all share-based payments to employees and members of the Board of Directors, be recognized in the statement of operations based on their fair values. Compensation cost is based on the grant-date fair value of the award, adjusted for estimated forfeitures, and is recognized on a straight-line basis over the period during which the recipient is required to provide service in exchange for the award. See Note 14 for a description of the types of stock-based awards granted, the compensation expense related to such awards and detail of equity-based awards outstanding.

Basic and Diluted Net Loss per Share

Basic net income (loss) per share is computed by dividing net income (loss) by the weighted-average number of common shares outstanding. Common stock equivalents include stock options and warrants. Diluted net loss per share is computed by dividing net income by the weighted-average number of dilutive common shares outstanding during the period. Diluted shares outstanding is calculated by adding to the weighted shares outstanding any potential (unissued) shares of common stock from outstanding stock options and warrants based on the treasury stock method. In periods when a net loss is reported, all common stock equivalents are excluded from the calculation because they would have an anti-dilutive effect, meaning the loss per share would be reduced. Therefore, in periods when a loss is reported, there is no difference in basic and dilutive loss per share.

Shares used to calculate diluted earnings per share for the three years ended December 31, 2013, 2012 and 2011, respectively, are shown below:

	Year Ended December 31,

	2013			2012		2011
Numerator:
Net income (loss)	$	(30,506	)	$	3,630	$	(38,785	)
Denominator:
Weighted average number of common shares outstanding		34,471,301			34,217,298		31,257,376
Effect of dilutive securities:
Stock options		—			62,481		—


Dilutive potential common shares		—			62,481		—


Shares used in calculating diluted earnings per share		34,471,301			34,279,779		31,257,376

The number of shares of potentially dilutive common stock related to options and warrants that were excluded from the calculation of dilutive shares since the inclusion of such shares would be anti-dilutive for the years ended December 31, 2013, 2012 and 2011, respectively, are shown below:

	Year ended December 31,

	2013		2012		2011
Options		6,201,429		5,579,042		3,858,685
Warrants		4,086		4,086		4,086


Total		6,205,515		5,583,128		3,862,771

Income Taxes

The Company follows the accounting guidance on accounting for income taxes which requires recognition of deferred tax assets and liabilities for the expected future tax consequences of events that have been included in the financial statements or tax returns. Under this method, deferred tax assets and liabilities are determined based on the difference between the financial statement and tax basis of assets and liabilities using enacted tax rates in effect for the year in which the differences are expected to reverse. A valuation allowance is provided to reduce the deferred tax asset to a level which, more likely than not, will be realized. See Note 15 for further discussion of income taxes.

Recent Accounting Standards Changes

In July 2013, the Financial Accounting Standards Board, or FASB, issued updated accounting guidance for the presentation of an unrecognized tax benefit when a net operating loss carryforward, a similar tax loss, or a tax credit carryforward exists. The updated guidance requires the netting of unrecognized tax benefits against a deferred tax asset for a loss or other carryforward that would apply in settlement of the uncertain tax position. In addition, unrecognized tax benefits will be netted against all available same-jurisdiction loss or other tax carryforwards that would be utilized, rather than only against carryforwards that are created by unrecognized tax benefits. The update is effective prospectively for reporting periods beginning after December 15, 2013, and early adoption is permitted. The adoption of this guidance is not expected to have an impact on the Company's consolidated financial statements.

In February 2013, the FASB issued ASU No. 2013-02, Comprehensive Income (Topic 220): Reporting of Amounts Reclassified out of Accumulated Other Comprehensive Income (ASU 2013-02). This newly issued accounting standard requires an entity to provide information about the amounts reclassified out of accumulated other comprehensive income by component. In addition, an entity is required to present, either on the face of the statement where net income is presented or in the notes, significant amounts reclassified out of accumulated other comprehensive income by the respective line items of net income but only if the amount reclassified is required under U.S. GAAP to be reclassified to net income in its entirety in the same reporting period. For other amounts that are not required under U.S. GAAP to be reclassified in their entirety to net income, an entity is required to cross-reference to other disclosures required under U.S. GAAP that provide additional detail about those amounts. This ASU is effective for reporting periods beginning after December 15, 2012. The adoption of this standard did not have an impact on the Company's financial position or results of operations. Reclassification adjustments were insignificant for all periods presented.

Reclassifications

Certain amounts reported in the prior year financial statements have been reclassified for comparative purposes to conform with the presentation in the current year consolidated financial statements.

Significant Collaborations

12 Months Ended

Dec. 31, 2013

Significant Collaborations

Significant Collaborations

3. Significant Collaborations

The Company follows the accounting guidance for collaborative arrangements which require that certain transactions between collaborators be recorded in the income statement on either a gross or net basis, depending on the characteristics of the collaboration relationship, and provides for enhanced disclosure of collaborative relationships. The Company evaluates its collaborative agreements for proper income statement classification based on the nature of the underlying activity. If payments to and from collaborative partners are not within the scope of other authoritative accounting literature, the income statement classification for the payments is based on a reasonable, rational analogy to authoritative accounting literature that is applied in a consistent manner. During the three years ended December 31, 2013, the Company had one significant collaboration arrangement with Archer Daniels Midland Company whereby the Company received payments and applied revenue recognition accounting guidance to the payments received and recorded corresponding costs as operating expenses. This arrangement ended in February 2012.

We are not currently participating in any collaborative arrangements. Our historical strategy for collaborative arrangements has been to retain substantial participation in the future economic value of our technology while receiving current cash payments to offset research and development costs and working capital needs. By their nature, our collaborative agreements have been complex, containing multiple elements covering a variety of present and future activities.

ADM Collaboration

From 2004 through 2011, the Company developed and began commercialization of its PHA biopolymers through a technology alliance and subsequent commercial alliance with ADM Polymer Corporation, a wholly-owned subsidiary of ADM, one of the largest agricultural processors in the world. The Commercial Alliance Agreement between Metabolix and ADM Polymer specified the terms and structure of the alliance. The agreement governed the activities and obligations of the parties to commercialize PHA biopolymers, which have been marketed under the brand names Mirel™ and Mvera™. These activities included the establishment of a joint venture company, Telles, LLC ("Telles"), to market and sell PHA biopolymers, the construction of a manufacturing facility capable of producing 110 million pounds of material annually (the "Commercial Manufacturing Facility"), the licensing of technology to Telles and to ADM, and the conducting of various research, development, manufacturing, sales and marketing, compounding and administrative services by the parties.

Telles was formed to: (i) serve as the commercial entity to establish and develop the commercial market for PHA biopolymers, and conduct the marketing and sales in accordance with the goals of the commercial alliance, (ii) assist in the coordination and integration of the manufacturing, compounding and marketing activities, and (iii) administer and account for financial matters on behalf of the parties. Metabolix and ADM each had a 50% ownership and voting interest in Telles.

Under the Commercial Alliance Agreement ADM was permitted, under limited circumstances, to terminate the alliance if a change in circumstances that was not reasonably within the control of ADM made the anticipated financial return from the project inadequate or too uncertain. The agreement provided that, upon termination by ADM due to a change in circumstances, Metabolix would be permitted to continue to produce and sell PHA biopolymers, and ADM would be required to perform manufacturing services for the Company for a period of time following the termination (subject to certain payment obligations to ADM). On January 9, 2012, ADM notified Metabolix that it was terminating the commercial alliance effective February 8, 2012. ADM had undertaken a strategic review of its business investments and activities and made the decision to focus resources outside of Telles. As the basis for the decision, ADM indicated to the Company that the projected financial returns from the alliance were too uncertain.

The Commercial Alliance Agreement with ADM limited the rights of both ADM and Metabolix to work with other parties or alone in developing or commercializing certain PHAs produced through fermentation. These exclusivity obligations ended upon termination of the alliance. Also, upon termination of the alliance, Metabolix intellectual property licenses to ADM Polymer and Telles ended, with Metabolix retaining all rights to its intellectual property. ADM retained its Commercial Manufacturing Facility located in Clinton, Iowa, previously used to produce PHA biopolymers for Telles.

Under the Technology Alliance and Option Agreement and Commercial Alliance Agreement, various payments were made to Metabolix by ADM as shown in the table below. All of these payments were recorded as deferred revenue on the Company's balance sheet and were expected to be recognized on a straight line basis over a period of approximately ten years in which Metabolix would fulfill its contractual obligations during the Commercial Phase of the Commercial Alliance Agreement.


Upfront payment	$	3,000
Milestone payments		2,000
Support payments		22,050
Cost sharing payments for pre-commercial manufacturing plant construction and operations		11,835


Total	$	38,885

The Company had no further performance obligations in connection with the commercial alliance after its termination, and as a result, the entire $38,885 of deferred revenue was recognized by the Company during its fiscal quarter ended March 31, 2012.

After termination of the Commercial Alliance Agreement, the parties entered into a Settlement Agreement in which the parties agreed to specific terms related to the winding up and dissolution of Telles. Under this Settlement Agreement, Metabolix purchased certain assets of the joint venture for $2,982 including Telles's entire inventory, exclusive and perpetual rights to all of Telles's trademarks, and all product registrations, certifications and approvals for Telles's PHA biopolymers. Pursuant to the Settlement Agreement, ADM relinquished any claims with respect to certain co-funded equipment previously acquired by Metabolix and situated at locations other than the Clinton, Iowa Commercial Manufacturing Facility, and Metabolix and Telles waived any rights to post-termination manufacturing and fermentation services under the Commercial Alliance Agreement.

Pursuant to the Settlement Agreement, Telles paid to ADM an amount equal to the aggregate cash balances of Telles totaling $3,778 on the date of the Settlement Agreement, minus $100 retained by Telles to settle any remaining trade obligations. The remaining trade obligations of Telles at the date of execution of the Settlement Agreement did not exceed $100. In the event that ADM is required to repay to Telles or to pay to any creditor of Telles any amounts included in the $2,982 purchase price or the $3,678 distributed to ADM by Telles pursuant to the Settlement Agreement, Metabolix is obligated to reimburse ADM in an amount equal to 50% of such payments, provided that in no event would the amount to be so paid by Metabolix exceed the total of the $2,982 purchase price and the $3,678 Telles cash required to be so repaid or reimbursed by ADM. In February 2013, ADM notified the Company that Telles had been formally dissolved and that no third party creditor trade obligations had been paid. As a result, the Company believes that it is no longer contingently liable for any third party obligations stemming from its former ADM collaboration.

Inventory

12 Months Ended

Dec. 31, 2013

Inventory

Inventory

4. Inventory

The components of the Company's biopolymer inventories are as follows:

	Year ended December 31

	2013		2012
Raw materials	$	537	$	640
Work-in-process		—		2
Finished goods		3,537		2,562


Total inventory	$	4,074	$	3,204

Included within finished goods at December 31, 2013 and December 31, 2012, are $476 and $257, respectively, of inventory that the Company has sold and shipped to customers for which the Company has not yet recognized revenue under its product revenue recognition policy. During the years ended December 31, 2013 and 2012, the Company recorded impairment charges to cost of product revenue of $818 and $138, respectively, for raw material and finished goods inventory that it determined was unlikely to be sold or converted to future sellable product based on quality, customer demand and current sales forecasts.

Investments

12 Months Ended

Dec. 31, 2013

Investments

Investments

5. Investments

Investments consist of the following:

			Unrealized

	Amortized Cost		Unrealized				Market Value
	Amortized Cost		Gain		(Loss)		Market Value
December 31, 2013
Short-term investments
Government-sponsored enterprises	$	11,510	$	1	$	—	$	11,511


Total	$	11,510	$	1	$	—	$	11,511




December 31, 2012
Short-term investments
Government sponsored enterprises	$	29,189	$	12	$	—	$	29,201
Long-term investments
Government-sponsored enterprises		2,507		1		—		2,508


Total	$	31,696	$	13	$	—	$	31,709

The average maturity of our marketable securities available-for-sale as of December 31, 2013 and 2012 was two and four months, respectively.

- Definition

The entire disclosure for investments in certain debt and equity securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Debt Security
-URI http://asc.fasb.org/extlink&oid=6509901

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 310
-SubTopic 30
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6379141&loc=d3e15032-111544

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-Glossary Equity Security
-URI http://asc.fasb.org/extlink&oid=6511694

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
-Section 50
-Paragraph 5
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27232-111563

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-SubTopic 10
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
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-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27161-111563

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
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-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27405-111563

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 3, 19, 20, 21, 22, 137
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Fair Value Measurements

12 Months Ended

Dec. 31, 2013

Fair Value Measurements

Fair Value Measurements

6. Fair Value Measurements

The Company has certain financial assets recorded at fair value which have been classified as Level 1or 2 within the fair value hierarchy as described in the accounting standards for fair value measurements. Fair value is the price that would be received from the sale of an asset or the price paid to transfer a liability in an orderly transaction between independent market participants at the measurement date. Fair values determined by Level 1 inputs utilize observable data such as quoted prices in active markets for identical instruments. Fair values determined by Level 2 inputs utilize data points other than quoted prices in active markets that are observable either directly or indirectly. Fair values determined by Level 3 inputs utilize unobservable data points in which there is little or no market data, which require the reporting entity to develop its own assumptions. The fair value hierarchy level is determined by the lowest level of significant input.

The Company's financial assets classified as Level 2 have been initially valued at the transaction price and subsequently valued typically utilizing third party pricing services. Because the Company's investment portfolio may include securities that do not always trade on a daily basis, the pricing services use many observable market inputs to determine value including reportable trades, benchmark yields and benchmarking of like securities. The Company validates the prices provided by the third party pricing services by reviewing their pricing methods and obtaining market values from other pricing sources. After completing the validation procedures, the Company did not adjust or override any fair value measurements provided by these pricing services as of December 31, 2013 and 2012.

The tables below present information about the Company's assets that are measured at fair value on a recurring basis as of December 31, 2013 and December 31, 2012 and indicate the fair value hierarchy of the valuation techniques utilized to determine such fair value.

	Fair value measurements at reporting date using

Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2013
Cash equivalents:
Money market funds	$	6,332	$	—	$	—	$	6,332
Short-term investments:
Government securities		—		11,511		—		11,511


Total	$	6,332	$	11,511	$	—	$	17,843

	Fair value measurements at reporting date using

Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2012
Cash equivalents:
Money market funds	$	11,157	$	—	$	—	$	11,157
Government securities		—		2,015		—		2,015
Short-term investments:
Government securities		—		29,201		—		29,201
Long-term investments:
Government securities		—		2,508		—		2,508


	$	11,157	$	33,724	$	—	$	44,881

- Definition

The entire disclosure for the fair value of financial instruments (as defined), including financial assets and financial liabilities (collectively, as defined), and the measurements of those instruments as well as disclosures related to the fair value of non-financial assets and liabilities. Such disclosures about the financial instruments, assets, and liabilities would include: (1) the fair value of the required items together with their carrying amounts (as appropriate); (2) for items for which it is not practicable to estimate fair value, disclosure would include: (a) information pertinent to estimating fair value (including, carrying amount, effective interest rate, and maturity, and (b) the reasons why it is not practicable to estimate fair value; (3) significant concentrations of credit risk including: (a) information about the activity, region, or economic characteristics identifying a concentration, (b) the maximum amount of loss the entity is exposed to based on the gross fair value of the related item, (c) policy for requiring collateral or other security and information as to accessing such collateral or security, and (d) the nature and brief description of such collateral or security; (4) quantitative information about market risks and how such risks are managed; (5) for items measured on both a recurring and nonrecurring basis information regarding the inputs used to develop the fair value measurement; and (6) for items presented in the financial statement for which fair value measurement is elected: (a) information necessary to understand the reasons for the election, (b) discussion of the effect of fair value changes on earnings, (c) a description of [similar groups] items for which the election is made and the relation thereof to the balance sheet, the aggregate carrying value of items included in the balance sheet that are not eligible for the election; (7) all other required (as defined) and desired information.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=7578670&loc=d3e19207-110258

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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Reference 5: http://www.xbrl.org/2003/role/presentationRef
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-URI http://asc.fasb.org/extlink&oid=7491637&loc=d3e13504-108611

Reference 6: http://www.xbrl.org/2003/role/presentationRef
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Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15B
-Subparagraph a, b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
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-Name Statement of Financial Accounting Standard (FAS)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 159
-Paragraph 17-22, 27, 28
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 15A
-Subparagraph a-d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 107
-Paragraph 3, 10, 14, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Property and Equipment, Net

12 Months Ended

Dec. 31, 2013

Property and Equipment, Net

Property and Equipment, Net

7. Property and Equipment, Net

Property and equipment consisted of the following:

	Year ended December 31,

	2013			2012
Equipment	$	4,868		$	5,151
Furniture and fixtures		227			227
Leasehold improvements		2,652			2,641
Software		381			381


Total property and equipment, at cost		8,128			8,400
Less: Accumulated depreciation		(7,335	)		(7,042	)


Property and equipment, net	$	793		$	1,358

Depreciation expense for the years ended December 31, 2013, 2012, and 2011 was $928, $1,298 and $1,507 respectively. The Company had no equipment under capital leases as of December 31, 2013 or 2012.

- Definition

The entire disclosure for long-lived, physical assets that are used in the normal conduct of business to produce goods and services and not intended for resale. Examples include land, buildings, machinery and equipment, and other types of furniture and equipment including, but not limited to, office equipment, furniture and fixtures, and computer equipment and software. This disclosure may include property plant and equipment accounting policies and methodology, a schedule of property, plant and equipment gross, additions, deletions, transfers and other changes, depreciation, depletion and amortization expense, net, accumulated depreciation, depletion and amortization expense and useful lives, income statement disclosures, assets held for sale and public utility disclosures.

+ References + Details

Accrued Expenses

12 Months Ended

Dec. 31, 2013

Accrued Expenses

Accrued Expenses

8. Accrued Expenses

Accrued expenses consist of the following:

	Year ended December 31,

	2013		2012
Employee compensation and benefits	$	2,595	$	2,379
Commercial manufacturing		815		229
Professional services		578		301
Other		904		610


Total accrued expenses	$	4,892	$	3,519

Commitments and Contingencies

12 Months Ended

Dec. 31, 2013

Commitments and Contingencies

Commitments and Contingencies

9. Commitments and Contingencies

Leases

The Company rents its facilities under operating leases, which expire through May 2020. Rental payments under operating leases for the years ended December 31, 2013, 2012 and 2011 were $1,662, $1,814 and $1,808, respectively. The deferred rent liability recorded on the Company's balance sheet at December 31, 2013 and 2012 includes the unamortized balance of the landlord incentive payments and the cumulative difference between actual facility lease payments and lease expense recognized ratably over the operating lease period. At December 31, 2013, the Company's future minimum payments required under operating leases are as follows:

Year ended December 31,	Minimum lease payment

2014	$	1,449
2015		1,383
2016		1,419
2017		1,454
2018 and thereafter		3,576


Total	$	9,281

Litigation

On March 7, 2012, a purported derivative lawsuit, Childs v. Kouba et al., Civil Action 12-0892 (the "Derivative Action"), was filed in Massachusetts Superior Court for Middlesex County, on behalf of the Company against members of the Company's Board of Directors for alleged breaches of their fiduciary duties. The parties transferred the case to the Business Litigation Session of Massachusetts Superior Court for Suffolk County, where it is now pending under Civil Action No. 13-4406-BLS2. The Derivative Action seeks compensatory damages in an unspecified amount, plaintiff's costs and attorneys' fees, and unspecified equitable or injunctive relief, based on a nearly identical set of alleged facts to those that were asserted in a purported shareholder class action, Hilary Coyne v. Metabolix, Inc., Richard P. Eno, and Joseph Hill, Civil Action 1:12-cv-10318 (the "Class Action"). On September 20, 2013, the United States District Court for the District of Massachusetts dismissed the Class Action in full and with prejudice. The defendants currently expect to file their motion to dismiss the Derivative Action on April 21, 2014.

The Company is currently unable to assess the probability of loss or estimate a range of potential loss, if any, associated with the Derivative Action because it is at an early stage.

From time to time, the Company may be subject to other legal proceedings and claims in the ordinary course of business. The Company is not currently aware of any such other proceedings or claims that it believes will have, individually or in the aggregate, a material adverse effect on the business, financial condition or the results of operations.

- Definition

The entire disclosure for commitments and contingencies.

+ References

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-Name Accounting Standards Codification
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-Name FASB Interpretation (FIN)
-Number 14
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-Name Statement of Financial Accounting Standard (FAS)
-Number 5
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+ Details

Related Party Transactions	12 Months Ended
Related Party Transactions	Dec. 31, 2013
Related Party Transactions
Related Party Transactions	10. Related Party Transactions Tepha Inc. During 1999 and 2003, the Company entered into sublicense agreements with Tepha Inc. ("Tepha"), to sublicense technology to Tepha. The Company's directors, Matthew Strobeck and Anthony J. Sinskey, serve on the Board of Directors of Tepha. Under the agreement, the Company also receives royalties on net sales of licensed products and sublicensing revenues received by Tepha, subject to a minimum payment each year. The Company engaged in various transactions with Tepha, and recognized license and royalty revenues of $149, $149 and $444, from Tepha for the years ended December 31, 2013, 2012, and 2011, respectively. The Company had outstanding receivable balances of $51 and $75 at December 31, 2013 and 2012, respectively.

- Definition

The entire disclosure for related party transactions. Examples of related party transactions include transactions between (a) a parent company and its subsidiary; (b) subsidiaries of a common parent; (c) and entity and its principal owners; and (d) affiliates.

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+ Details

Preferred Stock	12 Months Ended
Preferred Stock	Dec. 31, 2013
Preferred Stock
Preferred Stock	11. Preferred Stock The Company's certificate of incorporation, as amended and restated, authorizes it to issue up to 5,000,000 shares of $0.01 par value preferred stock. As of December 31, 2013 and 2012, no preferred stock was issued or outstanding.

Common Stock	12 Months Ended
Common Stock	Dec. 31, 2013
Common Stock
Common Stock	12. Common Stock Common Stock Issuances During May 2011, the Company completed a public offering of 7,130,000 shares of its common stock at a price of $7.25 per share. Net proceeds were $49,333 after deducting underwriting discounts, commissions and offering costs of $2,360. The Company used the proceeds from the offering for working capital and other general corporate purposes. Warrants In connection with signing a lease agreement in 2004, the Company issued the landlord warrants to purchase 4,086 shares of common stock at an exercise price of $3.30 per share. The warrants expire ten years from the lease term commencement date. The fair value of these warrants is immaterial. At December 31, 2013, these warrants remained outstanding and exercisable.

- Definition

The entire disclosure for shareholders' equity, comprised of portions attributable to the parent entity and noncontrolling interest, if any, including other comprehensive income (as applicable). Including, but not limited to: (1) balances of common stock, preferred stock, additional paid-in capital, other capital and retained earnings; (2) accumulated balance for each classification of other comprehensive income and total amount of comprehensive income; (3) amount and nature of changes in separate accounts, including the number of shares authorized and outstanding, number of shares issued upon exercise and conversion, and for other comprehensive income, the adjustments for reclassifications to net income; (4) rights and privileges of each class of stock authorized; (5) basis of treasury stock, if other than cost, and amounts paid and accounting treatment for treasury stock purchased significantly in excess of market; (6) dividends paid or payable per share and in the aggregate for each class of stock for each period presented; (7) dividend restrictions and accumulated preferred dividends in arrears (in aggregate and per share amount); (8) retained earnings appropriations or restrictions, such as dividend restrictions; (9) impact of change in accounting principle, initial adoption of new accounting principle and correction of an error in previously issued financial statements; (10) shares held in trust for Employee Stock Ownership Plan (ESOP); (11) deferred compensation related to issuance of capital stock; (12) note received for issuance of stock; (13) unamortized discount on shares; (14) description, terms, and number of warrants or rights outstanding; (15) shares under subscription and subscription receivables, effective date of new retained earnings after quasi-reorganization and deficit eliminated by quasi-reorganization and, for a period of at least ten years after the effective date, the point in time from which the new retained dates; and (16) retroactive effective of subsequent change in capital structure.

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+ Details

Shareholder Rights Plan	12 Months Ended
Shareholder Rights Plan	Dec. 31, 2013
Shareholder Rights Plan
Shareholder Rights Plan	13. Shareholder Rights Plan On July 7, 2009, the Company adopted a Shareholder Rights Plan, the purpose of which is, among other things, to enhance the Board's ability to protect shareholder interests and to ensure that shareholders receive fair treatment in the event any coercive takeover attempt of the Company is made in the future. The Shareholder Rights Plan could make it more difficult for a third party to acquire, or could discourage a third party from acquiring, the Company or a large block of the Company's common stock. In connection with the adoption of the Shareholder Rights Plan, the Board of Directors of the Company declared a dividend distribution of one preferred stock purchase right (a "Right") for each outstanding share of common stock to shareholders of record as of the close of business on July 8, 2009. The Rights currently are not exercisable and are attached to and trade with the outstanding shares of common stock. Under the Shareholder Rights Plan, the Rights become exercisable if a person becomes an "acquiring person" by acquiring 15% or more of the outstanding shares of common stock or if a person commences a tender offer that would result in that person owning 15% or more of the common stock. If a person becomes an "acquiring person," each holder of a Right (other than the acquiring person) would be entitled to purchase, at the then-current exercise price, such number of shares of the Company's preferred stock which are equivalent to shares of common stock having twice the exercise price of the Right. If the Company is acquired in a merger or other business combination transaction after any such event, each holder of a Right would then be entitled to purchase, at the then-current exercise price, shares of the acquiring company's common stock having a value of twice the exercise price of the Right. On February 6, 2012, the Company entered into a letter agreement (the "Schuler Agreement") with Jack W. Schuler, Renate Schuler and the Schuler Family Foundation, a tax-exempt private operating foundation of which Jack W. Schuler and Renate Schuler serve as two of the three directors (collectively, the "Schuler Stockholders"). The Schuler Stockholders may be deemed to have aggregate beneficial ownership of up to 5,091,295 shares, or approximately 14.7%, of the Company's outstanding common stock, par value $0.01 per share (the "common stock"). Pursuant to the Schuler Agreement, the Schuler Stockholders have made certain representations and covenants regarding ownership, voting support arrangements, standstill arrangements and rights of first refusal. In exchange for these representations and covenants, the Company agreed to amend the Shareholder Rights Plan to allow the Schuler Stockholders, under certain circumstances, to increase their beneficial ownership up to 19.99% of the outstanding common stock without becoming Acquiring Persons (as defined in the Rights Agreement). On February 6, 2012, contemporaneously with the execution of the Schuler Agreement, the Company amended the Shareholder Rights Plan to provide that, generally, so long as the Schuler Stockholders and their respective affiliates and associates do not at any time have Control Intent (as defined in the Shareholder Rights Plan), they may acquire additional shares of common stock without becoming acquiring persons under the Rights Plan, provided that their collective beneficial ownership does not at any time equal or exceed 20% of the then outstanding shares of common stock.

Stock-Based Compensation

12 Months Ended

Dec. 31, 2013

Stock-Based Compensation

Stock-Based Compensation

14. Stock-Based Compensation

The Company adopted a stock plan in 1995 (the "1995 Plan"), which provided for the granting of incentive stock options, nonqualified stock options, stock awards, and opportunities to make direct purchases of stock, to employees, officers, directors and consultants of the Company. In June 2005, the 1995 Plan was terminated and the Company adopted a new plan (the "2005 Plan"). No further grants or awards were subsequently made under the 1995 Plan. A total of 907,679 options were awarded from the 1995 Plan, and as of December 31, 2013, 29,192 of these options remain outstanding and eligible for future exercise and continue to be governed by the terms of the 1995 Plan.

The 2005 Plan provided for the granting of incentive stock options, nonqualified stock options, stock awards, and opportunities to make direct purchases of stock, to employees, officers, directors and consultants of the Company. In November 2006, the 2005 Plan was terminated and the Company adopted a new plan (the "2006 Plan"). No further grants or awards were subsequently made under the 2005 Plan. A total of 1,619,134 options were awarded from the 2005 Plan, and as of December 31, 2013, 231,229 of these options remain outstanding and eligible for future exercise and continue to be governed by the terms of the 2005 Plan.

The 2006 Plan provides for the granting of incentive stock options, nonqualified stock options, stock appreciation rights, deferred stock awards, restricted stock awards, unrestricted stock awards, cash-based awards and dividend equivalent rights. The 2006 Plan states that not more than 10,000,000 shares shall be issued under the plan. A total of 8,677,227 options have been awarded from the 2006 Plan and as of December 31, 2013, 5,941,008 of these options remain outstanding and eligible for future exercise.

Options granted under the 1995 Plan, the 2005 Plan and the 2006 Plan (the "Plans") generally vest ratably over periods of two to four years from the date of hire for new employees, or date of award for existing employees, or date of commencement of services with the Company for nonemployees, and generally expire ten years from the date of issuance. The Company's policy is to issue new shares upon the exercise of stock options.

The Company's Board of Directors granted on December 19, 2013, a stock option for the purchase of 1,150,000 shares of common stock to Joseph Shaulson in connection with his agreement to serve as a member of the Company's Board on that date and as an inducement for him to accept employment with the Company as its President and Chief Executive Officer starting in January 2014. This option was not granted under any of the Plans. The option has an exercise price equal to the fair market value of the Company's common stock at the date of grant, and it has a four-year vesting schedule in which 25%, 25% and 50% of the option vests on the 2^nd, 3^rd and 4^th anniversary dates, respectively, of Mr. Shaulson commencing employment. The Company assessed the terms of this award and determined there was no possibility that it would have to settle this award in cash and, therefore, equity accounting was applied.

A summary of the activity related to the shares of common stock covered by outstanding options under the Plans follows:

			Weighted Average Exercise Price			Aggregate Intrinsic value

Balance at December 31, 2012	5,579,042		$	6.68
Granted	1,654,315			1.64
Exercised	(7,550	)		1.82
Forfeited	(670,291	)		2.11
Expired	(354,087	)		9.26


Balance at December 31, 2013	6,201,429			5.68	6.09	$	—




Vested and expected to vest at December 31, 2013	6,009,973			5.79	6.04		—
Exercisable at December 31, 2013	3,913,834			7.49	5.18		—

The weighted average grant date fair value per share of options granted during fiscal years 2013, 2012, and 2011 was $1.14, $1.46 and $5.02, respectively. The total intrinsic value of options exercised was $2, $15 and $81 for the years ended December 31, 2013, 2012 and 2011, respectively.

A summary of information about the shares of common stock covered by outstanding and exercisable options under the Plans at December 31, 2013 follows:

	Stock Options Outstanding						Stock Options Exercisable

Range of exercise prices	Number of shares		Weighted average remaining contractual life (in years)		Weighted average exercise price per share		Number of shares		Weighted average exercise price per share
$1.27 - 1.48		240,400		9.65	$	1.41		15,610	$	1.40
1.55 - 1.55		1,045,000		7.56		1.55		600,000		1.55
1.56 - 1.69		1,038,479		6.69		1.68		358,018		1.66
1.74 - 2.46		360,014		7.41		2.09		190,189		2.11
2.66 - 2.66		866,949		6.60		2.66		380,256		2.66
2.72 - 7.25		737,997		5.15		5.98		561,599		6.12
7.31 - 9.77		668,092		5.26		8.95		602,927		8.93
10.08 - 14.49		872,086		4.07		12.49		832,823		12.42
14.53 - 23.99		342,412		3.72		18.86		342,412		18.86
24.97 - 24.97		30,000		3.39		24.97		30,000		24.97


		6,201,429		6.09		5.68		3,913,834		7.49

Expense Information for Employee Stock Option Awards

The Company recognized stock-based compensation expense, related to employee stock option awards, including awards to members of the Board of Directors, of $3,193, $3,825 and $4,621 for the years ended December 31, 2013, 2012 and 2011, respectively. At December 31, 2013, there was approximately $3,544 of pre-tax stock-based compensation expense; net of estimated forfeitures, related to unvested awards not yet recognized which is expected to be recognized over a weighted average period of 2.02 years.

For the years ended December 31, 2013, 2012 and 2011, the Company determined the fair value of stock options using the Black-Scholes option pricing model with the following assumptions for option grants, respectively:

	Year Ended December 31,

	2013	2012	2011
Expected dividend yield	—	—	—
Risk-free rate	0.71% - 2.05%	0.67% - 1.15%	0.88% - 2.38%
Expected option term (in years)	6.0 - 6.1	5.3 - 5.5	5.5 - 5.6
Volatility	84% - 85%	84% - 87%	77% - 80%

For the years ended December 31, 2013 and 2012, the Company determined its volatility assumption based on actual market price fluctuations experienced during its trading history. For the year ended December 31, 2011 expected volatility was estimated based on the Company's historical volatility benchmarked against the historical volatilities of a peer group of similar public companies. Due to the Company's limited trading history prior to 2012, the Company believed that this approach provided additional information about future stock price movements when compared to analyzing the historical volatility of the Company on its own.

The risk-free interest rate used for each grant is equal to the U.S. Treasury yield curve in effect at the time of grant for instruments with a term similar to the expected life of the related option.

For the years ended December 31, 2013, 2012 and 2011, the expected term of the options is based upon evaluation of historical and expected future exercise behavior.

The stock price volatility and expected terms utilized in the calculation involve management's best estimates at that time, both of which impact the fair value of the option calculated under the Black-Scholes methodology and, ultimately, the expense that will be recognized over the life of the option. The accounting standard for stock-based compensation requires that the Company recognize compensation expense for only the portion of options that are expected to vest. Therefore, the Company has estimated expected forfeitures of stock options for the grants valued. In developing a forfeiture rate estimate, the Company considered its historical experience and actual forfeitures for the year. The Company will continue to evaluate its forfeiture rate as compared to the actual number of forfeitures in future periods to determine if adjustments to compensation expense may be required.

Expense Information for Non-employee Stock Option Awards

During the years ended December 31, 2011, the Company granted stock options to purchase 34,500 shares of common stock to non-employee consultants. No stock options were awarded to non-employees during the years ended December 31, 2013 and 2012, and all remaining non-employee awards were cancelled in early 2012 in connection with the Company's restructuring. Compensation expense related to non-employee options previously awarded were recognized over a period of four years and vested quarterly, contingent upon future services being provided by the consultants to the Company. The amount of non-employee stock compensation expense recorded by the Company for each of the two years ended December 31, 2012 was insignificant.

- Definition

The entire disclosure for compensation-related costs for equity-based compensation, which may include disclosure of policies, compensation plan details, allocation of equity compensation, incentive distributions, equity-based arrangements to obtain goods and services, deferred compensation arrangements, employee stock ownership plan details and employee stock purchase plan details.

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-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5070-113901

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-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5047-113901

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-Paragraph 4
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 123R
-Paragraph 64, 65, A240
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Statement of Position (SOP)
-Number 93-6
-Paragraph 53
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Income Taxes

12 Months Ended

Dec. 31, 2013

Income Taxes

Income Taxes

15. Income Taxes

The components of profit (loss) before provision for income taxes consist of the following:

	Year Ended December 31,

	2013			2012		2011
Domestic	$	(28,200	)	$	3,502	$	(38,872	)
Foreign		(2,295	)		72		30


Profit (loss) before taxes	$	(30,495	)	$	3,574	$	(38,842	)

The reported amount of income tax expense for the years differs from the amount that would result from applying domestic federal statutory tax rates to pretax losses primarily because of changes in valuation allowance. Significant components of the Company's net deferred tax assets are as follows:

	Year Ended December 31,

	2013			2012
Deferred Tax Assets:
Net operating loss carryforward	$	81,699		$	72,016
Capitalization of research and development expense		1,945			2,763
Credit carryforwards		8,118			7,024
Depreciation		2,403			2,603
Non-Qualified Stock Options		4,437			4,213
Other temporary differences		1,813			1,958


Total deferred tax assets.		100,415			90,577
Valuation allowance		(100,405	)		(90,558	)
Net deferred tax assets		10			19
Deferred Tax Liabilities:
Other temporary differences		(10	)		(19	)


Net deferred tax loss	$	—		$	—

The items accounting for the difference between the income tax benefit computed at the federal statutory rate of 34% and the provision for income taxes were as follows:

	Year Ended December 31,

	2013			2012			2011
Federal income tax at statutory federal rate		34.0	%		34.0	%		34.0	%
State taxes		3.5	%		7.8	%		5.0	%
Permanent differences		(1.9	)%		19.6	%		(2.4	)%
Tax credits		2.7	%		(10.5	)%		2.4	%
State rate change on deferred balances		(0.4	)%		3.1	%		1.4	%
Expiration of net operating losses and credits		(5.8	)%		49.2	%		(1.6	)%
Other		0.2	%		9.8	%		1.0	%
Change in valuation allowance		(32.3	)%		(113.0	)%		(39.8	)%


Total		0.00	%		0.00	%		0.00	%

The Company follows the accounting guidance for income taxes including guidance, which addresses accounting for uncertainty in income taxes. This guidance prescribes a threshold for the financial statement recognition and measurement of a tax position taken or expected to be taken in a tax return. It also provides guidance on de-recognition, classification, interest and penalties, accounting in interim periods, disclosures and transitions. The Company had no amounts recorded for any unrecognized tax benefits as of December 31, 2013, 2012 and 2011.

The tax years 2010 through 2013 remain open to examination by major taxing jurisdictions to which the Company is subject, which are primarily in the U.S. Additionally, the Company can be audited for any loss year up to three years after the year in which the loss is utilized to offset taxable income. This would include loss years prior to 2010.

The Company's policy is to record estimated interest and penalties related to uncertain tax positions as income tax expense. As of December 31, 2013, 2012 and 2011, the Company had no accrued interest or penalties recorded related to uncertain tax positions.

At December 31, 2013, the Company had net operating loss carryforwards (NOLs) for federal and state income tax purposes of approximately $236,705 and $148,783, respectively. Included in the federal and state net operating loss carryforwards is approximately $19,213 of deductions related to the exercise of stock options subsequent to the adoption of amended accounting guidance related to stock-based compensation. This amount represents an excess tax benefit as defined under the amended accounting guidance related to stock-based compensation and has not been recorded as a deferred tax asset. The Company's existing federal and state net operating loss carryforwards begin to expire in 2019 and 2014, respectively. The Company also had available research and development credits for federal and state income tax purposes of approximately $5,281 and $3,920, respectively. These federal and state research and development credits will begin to expire in 2019 and 2016, respectively. As of December 31, 2013, the Company also had available investment tax credits for state income tax purposes of $86, which begin to expire in 2014. Management of the Company has evaluated the positive and negative evidence bearing upon the realizability of its deferred tax assets, which are comprised principally of net operating loss carryforwards and research and development credits. Under the applicable accounting standards, management has considered the Company's history of losses and concluded that it is more likely than not that the Company will not recognize the benefits of federal and state deferred tax assets. Accordingly, a full valuation allowance has been established against the deferred tax assets.

Utilization of the net operating loss and research and development credit carryforwards may be subject to a substantial annual limitation under Section 382 of the Internal Revenue Code of 1986 due to ownership change limitations that have occurred previously or that could occur in the future. These ownership changes may limit the amount of net operating loss and research and development credit carryforwards that can be utilized annually to offset future taxable income and tax, respectively. The Company completed an evaluation of its ownership changes through December 31, 2012 and has determined that its NOL and R&D credit carryforwards as of that date were not subject to an annual limitation under Section 382. The Company has not currently completed an evaluation of ownership changes through December 31, 2013. To the extent an ownership change occurs in the future, the net operating loss and credit carryforwards may be subject to limitation.

No additional provision has been made for U.S. income taxes related to the undistributed earnings of the wholly-owned subsidiaries of Metabolix, Inc. or for unrecognized deferred tax liabilities for temporary differences related to investments in subsidiaries. As such, earnings are expected to be permanently reinvested, the investments are essentially permanent in duration, or the Company has concluded that no additional tax liability will arise as a result of the distribution of such earnings. A liability could arise if amounts are distributed by such subsidiaries or if such subsidiaries are ultimately disposed. It is not practical to estimate the additional income taxes related to permanently reinvested earnings or the basis differences related to investment in subsidiaries. Unremitted earnings at December 31, 2013 and December 31, 2012 approximated $273 and $252, respectively.

- Definition

The entire disclosure for income taxes. Disclosures may include net deferred tax liability or asset recognized in an enterprise's statement of financial position, net change during the year in the total valuation allowance, approximate tax effect of each type of temporary difference and carryforward that gives rise to a significant portion of deferred tax liabilities and deferred tax assets, utilization of a tax carryback, and tax uncertainties information.

+ References

+ Details

Employee Benefits	12 Months Ended
Employee Benefits	Dec. 31, 2013
Employee Benefits
Employee Benefits	16. Employee Benefits The Company maintains a 401(k) savings plan in which substantially all of its regular U.S. employees are eligible to participate. Participants may contribute up to 60% of their annual compensation to the plan, subject to eligibility requirements and annual IRS limitations. The Company's plan provides for a matching contribution in common stock of up to 4.5% of a participant's total compensation dependent upon the level of participant contributions made during the plan year. Pursuant to this plan, the Company issued 267,329, 179,336 and 68,558 shares of common stock during the twelve months ended December 31, 2013, 2012 and 2011, respectively, and recorded $397, $408 and $529, respectively, of related expense. Company contributions are fully vested upon issuance.

- Definition

The entire disclosure for pension and other postretirement benefits.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 715
-URI http://asc.fasb.org/topic&trid=2235017

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-Publisher FASB
-Name Implementation Guide (Q and A)
-Number FAS88
-Paragraph 63
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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-Name Statement of Financial Accounting Standard (FAS)
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
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Reference 9: http://www.xbrl.org/2003/role/presentationRef
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Reference 10: http://www.xbrl.org/2003/role/presentationRef
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Reference 11: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 12: http://www.xbrl.org/2003/role/presentationRef
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-Name Statement of Financial Accounting Standard (FAS)
-Number 158
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
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Reference 14: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Principles Board Opinion (APB)
-Number 30
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

U.S. Department of Energy Grant	12 Months Ended
U.S. Department of Energy Grant	Dec. 31, 2013
U.S. Department of Energy Grant
U.S. Department of Energy Grant	17. U.S. Department of Energy Grant In 2011, the Company entered into a multi-year $6.0 million grant agreement entitled, Renewable Enhanced Feedstocks for Advanced Biofuels and Bioproducts, with the U.S. Department of Energy for the development of switchgrass. The Company will use the funds to perform research to enhance the yield of bio-based products, biopower, or fuels made from switchgrass to produce denser biomass and other products that can be further processed to make fuels such as butanol, chemicals such as propylene, and other materials to improve the economic competitiveness of future biorefineries. Continued receipt of grant proceeds is contingent upon the availability of government appropriated funds and the Company's ability to make substantial progress towards meeting the objectives of the award. The Company will recognize revenue from the grant over the term of the agreement as it incurs related research and development costs and provided it meets its prorated cost-sharing obligation of approximately $3.9 million. The Company may elect to retain rights to inventions it conceives or reduces to practice in the performance of work under the award, subject to certain rights of the U.S. Government. During the years ended December 31, 2013, 2012 and 2011, the Company recognized $1,640, $1,578 and $515 in revenue related to this grant, respectively.

Restructuring	12 Months Ended
Restructuring	Dec. 31, 2013
Restructuring
Restructuring	18. Restructuring In connection with the termination of the Telles joint venture with ADM, in 2012, the Company restructured its biopolymers business and downsized its operations. The Company recognized $920 of restructuring charges during its fiscal year ended December 31, 2012 and there were no remaining balances accrued for restructuring charges at either December 31, 2012 or December 31, 2013.

- Definition

The entire disclosure for restructuring and related activities. Description of restructuring activities such as exit and disposal activities, include facts and circumstances leading to the plan, the expected plan completion date, the major types of costs associated with the plan activities, total expected costs, the accrual balance at the end of the period, and the periods over which the remaining accrual will be settled.

+ References + Details

Geographic Information

12 Months Ended

Dec. 31, 2013

Geographic Information

Geographic Information

19. Geographic Information

The geographic distribution of the Company's revenues and long-lived assets from continuing operations is summarized as follows:

	U.S.		Canada		Germany		Eliminations			Total

Year Ended December 31, 2013
Net revenues to unaffiliated customers	$	4,222	$	273	$	899	$	—		$	5,394
Inter-geographic revenues		928		794		—		(1,722	)		—


Net revenues	$	5,150	$	1,067	$	899	$	(1,722	)	$	5,394




Identifiable long-lived assets	$	752	$	41	$	—	$	—		$	793
Year Ended December 31, 2012
Net revenues to unaffiliated customers	$	42,136	$	180	$	—	$	—		$	42,316
Inter-geographic revenues		—		737		—		(737	)		—


Net revenues	$	42,136	$	917	$	—	$	(737	)	$	42,316




Identifiable long-lived assets	$	1,309	$	49			$	—		$	1,358
Year Ended December 31, 2011
Net revenues to unaffiliated customers	$	1,300	$	125	$	—	$	—		$	1,425
Inter-geographic revenues		—		859		—		(859	)		—


Net revenues	$	1,300	$	984	$	—	$	(859	)	$	1,425




Identifiable long-lived assets	$	2,185	$	91	$	—	$	—		$	2,276

Foreign revenue is based on the country in which the Company's legal subsidiary is domiciled. During 2013, revenue earned from the Company's REFABB grant with U.S. Department of Energy totaled $1,640 and represented 30% of total revenue for the year. Revenue earned from three additional customers represented 13%, 12% and 11%, respectively.

- Definition

The entire disclosure for reporting segments including data and tables. Reportable segments include those that meet any of the following quantitative thresholds a) it's reported revenue, including sales to external customers and intersegment sales or transfers is 10 percent or more of the combined revenue, internal and external, of all operating segments b) the absolute amount of its reported profit or loss is 10 percent or more of the greater, in absolute amount of 1) the combined reported profit of all operating segments that did not report a loss or 2) the combined reported loss of all operating segments that did report a loss c) its assets are 10 percent or more of the combined assets of all operating segments.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 34
-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8981-108599

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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Summary of Quarterly Financial Data (unaudited)

12 Months Ended

Dec. 31, 2013

Summary of Quarterly Financial Data (unaudited)

Summary of Quarterly Financial Data (unaudited)

20. Summary of Quarterly Financial Data (unaudited)

The following tables summarize the unaudited quarterly financial data for the last two fiscal years.

	Quarter ended

	March 31,			June 30,			September 30,			December 31,
*2013*
Total revenues	$	1,943		$	1,706		$	855		$	890
Loss from operations		(6,785	)		(7,857	)		(7,242	)		(8,618	)
Net loss		(6,763	)		(7,866	)		(7,251	)		(8,626	)
Basic net loss per share		(0.20	)		(0.23	)		(0.21	)		(0.24	)
Diluted net loss per share		(0.20	)		(0.23	)		(0.21	)		(0.24	)
*2012*
Total revenues	$	39,322	(1)	$	923		$	674		$	1,397
Income (loss) from operations		28,823			(7,957	)		(7,743	)		(9,520	)
Net income (loss)		28,840			(7,948	)		(7,745	)		(9,517	)
Basic net income (loss) per share		0.84			(0.23	)		(0.23	)		(0.28	)
Diluted net income (loss) per share		0.84			(0.23	)		(0.23	)		(0.28	)

: Full year amounts may not sum due to rounding.

(1): In 2012, the Company recognized $38,885 of deferred revenue associated with the termination of its commercial alliance with Archer Daniels Midland Company. See Note 3 to these financial statements for a more detailed explanation for the Company's recognition of this deferred revenue.

- Definition

The entire disclosure for the quarterly financial data in the annual financial statements. The disclosure may include a tabular presentation of financial information for each fiscal quarter for the current and previous year, including revenues, gross profit, income or loss before extraordinary items and earnings per share data. It also includes an indication if the information in the note is unaudited, comments on the aggregate effect of year-end adjustments, and an explanation of matters or transactions that affect comparability or are pertinent to an understanding of the information furnished.

+ References + Details

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2013

Summary of Significant Accounting Policies

Principles of Consolidation

Principles of Consolidation

Use of Estimates

Use of Estimates

Cash and Cash Equivalents

Cash and Cash Equivalents

The Company considers all highly liquid investments purchased with an original maturity date of ninety days or less at the date of purchase to be cash equivalents.

Investments

Investments

Restricted Cash

Restricted Cash

Foreign Currency Translation

Foreign Currency Translation

Comprehensive Income (Loss)

Comprehensive Income (Loss)

Concentration of Credit Risk

Concentration of Credit Risk

Fair Value Measurements

Fair Value Measurements

Segment Information

Segment Information

Inventory

Inventory

Property and Equipment

Property and Equipment

Asset Description		Estimated Useful Life

Equipment		2.5 - 3 years
Furniture and Fixtures		5
Software		3
Leasehold improvements		Shorter of useful life or term of lease

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

Revenue Recognition

Revenue Recognition

	Year ended December 31,

	2013		2012
Deferred product revenue	$	537	$	786
Deferred cost of product revenue	$	476	$	219

Research and Development Expenses

Research and Development Expenses

Selling, General, and Administrative Expenses

Selling, General, and Administrative Expenses

Intellectual Property Costs

Intellectual Property Costs

The Company includes all costs associated with the prosecution and maintenance of patents within selling, general and administrative expenses in the consolidated statement of operations.

Stock-Based Compensation

Stock-Based Compensation

Basic and Diluted Net Loss per Share

Basic and Diluted Net Loss per Share

Shares used to calculate diluted earnings per share for the three years ended December 31, 2013, 2012 and 2011, respectively, are shown below:

	Year Ended December 31,

	2013			2012		2011
Numerator:
Net income (loss)	$	(30,506	)	$	3,630	$	(38,785	)
Denominator:
Weighted average number of common shares outstanding		34,471,301			34,217,298		31,257,376
Effect of dilutive securities:
Stock options		—			62,481		—


Dilutive potential common shares		—			62,481		—


Shares used in calculating diluted earnings per share		34,471,301			34,279,779		31,257,376

	Year ended December 31,

	2013		2012		2011
Options		6,201,429		5,579,042		3,858,685
Warrants		4,086		4,086		4,086


Total		6,205,515		5,583,128		3,862,771

Income Taxes

Income Taxes

Recent Accounting Standards Changes

Recent Accounting Standards Changes

Reclassifications

Reclassifications

Certain amounts reported in the prior year financial statements have been reclassified for comparative purposes to conform with the presentation in the current year consolidated financial statements.

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2013

Summary of Significant Accounting Policies

Schedule of estimated useful life of assets used to compute depreciation using the straight-line method

Asset Description		Estimated Useful Life

Equipment		2.5 - 3 years
Furniture and Fixtures		5
Software		3
Leasehold improvements		Shorter of useful life or term of lease

Schedule of deferred product revenue and associated cost of product revenue

	Year ended December 31,
	2013		2012
Deferred product revenue	$	537	$	786
Deferred cost of product revenue	$	476	$	219

Schedule of shares used to calculate diluted earnings per share

	Year Ended December 31,
	2013			2012		2011
Numerator:
Net income (loss)	$	(30,506	)	$	3,630	$	(38,785	)
Denominator:
Weighted average number of common shares outstanding		34,471,301			34,217,298		31,257,376
Effect of dilutive securities:
Stock options		—			62,481		—


Dilutive potential common shares		—			62,481		—


Shares used in calculating diluted earnings per share		34,471,301			34,279,779		31,257,376

Schedule of number of shares of potentially dilutive common stock related to options and warrants that were excluded from the calculation of dilutive shares

	Year ended December 31,

	2013		2012		2011
Options		6,201,429		5,579,042		3,858,685
Warrants		4,086		4,086		4,086


Total		6,205,515		5,583,128		3,862,771

Significant Collaborations (Tables)

12 Months Ended

Dec. 31, 2013

Significant Collaborations

Schedule of payments received that were recorded as deferred revenue under the Technology Alliance and Option Agreement and Commercial Alliance Agreement


Upfront payment	$	3,000
Milestone payments		2,000
Support payments		22,050
Cost sharing payments for pre-commercial manufacturing plant construction and operations		11,835


Total	$	38,885

Inventory (Tables)

12 Months Ended

Dec. 31, 2013

Inventory

Schedule of the components of the Company's biopolymer inventories

	Year ended December 31

	2013		2012
Raw materials	$	537	$	640
Work-in-process		—		2
Finished goods		3,537		2,562


Total inventory	$	4,074	$	3,204

Investments (Tables)

12 Months Ended

Dec. 31, 2013

Investments

Schedule of investments

			Unrealized
	Amortized Cost		Unrealized				Market Value
	Amortized Cost		Gain		(Loss)		Market Value
December 31, 2013
Short-term investments
Government-sponsored enterprises	$	11,510	$	1	$	—	$	11,511


Total	$	11,510	$	1	$	—	$	11,511




December 31, 2012
Short-term investments
Government sponsored enterprises	$	29,189	$	12	$	—	$	29,201
Long-term investments
Government-sponsored enterprises		2,507		1		—		2,508


Total	$	31,696	$	13	$	—	$	31,709

Fair Value Measurements (Tables)

12 Months Ended

Dec. 31, 2013

Fair Value Measurements

Schedule of information about assets that are measured at fair value on a recurring basis

	Fair value measurements at reporting date using

Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2013
Cash equivalents:
Money market funds	$	6,332	$	—	$	—	$	6,332
Short-term investments:
Government securities		—		11,511		—		11,511


Total	$	6,332	$	11,511	$	—	$	17,843

	Fair value measurements at reporting date using

Description	Quoted prices in active markets for identical assets (Level 1)		Significant other observable inputs (Level 2)		Significant unobservable inputs (Level 3)		Balance as of December 31, 2012
Cash equivalents:
Money market funds	$	11,157	$	—	$	—	$	11,157
Government securities		—		2,015		—		2,015
Short-term investments:
Government securities		—		29,201		—		29,201
Long-term investments:
Government securities		—		2,508		—		2,508


	$	11,157	$	33,724	$	—	$	44,881

- Definition

Tabular disclosure of assets, including [financial] instruments measured at fair value that are classified in stockholders' equity, if any, by class that are measured at fair value on a recurring basis. The disclosures contemplated herein include the fair value measurements at the reporting date by the level within the fair value hierarchy in which the fair value measurements in their entirety fall, segregating fair value measurements using quoted prices in active markets for identical assets (Level 1), significant other observable inputs (Level 2), and significant unobservable inputs (Level 3).

+ References + Details

Property and Equipment, Net (Tables)

12 Months Ended

Dec. 31, 2013

Property and Equipment, Net

Schedule of components of property and equipment

	Year ended December 31,

	2013			2012
Equipment	$	4,868		$	5,151
Furniture and fixtures		227			227
Leasehold improvements		2,652			2,641
Software		381			381


Total property and equipment, at cost		8,128			8,400
Less: Accumulated depreciation		(7,335	)		(7,042	)


Property and equipment, net	$	793		$	1,358

Accrued Expenses (Tables)

12 Months Ended

Dec. 31, 2013

Accrued Expenses

Schedule of accrued expenses

	Year ended December 31,

	2013		2012
Employee compensation and benefits	$	2,595	$	2,379
Commercial manufacturing		815		229
Professional services		578		301
Other		904		610


Total accrued expenses	$	4,892	$	3,519

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2013

Commitments and Contingencies

Schedule of the Company's future minimum payments required under operating leases

At December 31, 2013, the Company's future minimum payments required under operating leases are as follows:

Year ended December 31,	Minimum lease payment

2014	$	1,449
2015		1,383
2016		1,419
2017		1,454
2018 and thereafter		3,576


Total	$	9,281

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2013

Stock-Based Compensation

Summary of the activity related to the shares of common stock covered by outstanding options under the plans

			Weighted Average Exercise Price			Aggregate Intrinsic value

Balance at December 31, 2012	5,579,042		$	6.68
Granted	1,654,315			1.64
Exercised	(7,550	)		1.82
Forfeited	(670,291	)		2.11
Expired	(354,087	)		9.26


Balance at December 31, 2013	6,201,429			5.68	6.09	$	—




Vested and expected to vest at December 31, 2013	6,009,973			5.79	6.04		—
Exercisable at December 31, 2013	3,913,834			7.49	5.18		—

Summary of information about the shares of common stock covered by outstanding and exercisable options under the plans

A summary of information about the shares of common stock covered by outstanding and exercisable options under the Plans at December 31, 2013 follows:

	Stock Options Outstanding						Stock Options Exercisable

Range of exercise prices	Number of shares		Weighted average remaining contractual life (in years)		Weighted average exercise price per share		Number of shares		Weighted average exercise price per share
$1.27 - 1.48		240,400		9.65	$	1.41		15,610	$	1.40
1.55 - 1.55		1,045,000		7.56		1.55		600,000		1.55
1.56 - 1.69		1,038,479		6.69		1.68		358,018		1.66
1.74 - 2.46		360,014		7.41		2.09		190,189		2.11
2.66 - 2.66		866,949		6.60		2.66		380,256		2.66
2.72 - 7.25		737,997		5.15		5.98		561,599		6.12
7.31 - 9.77		668,092		5.26		8.95		602,927		8.93
10.08 - 14.49		872,086		4.07		12.49		832,823		12.42
14.53 - 23.99		342,412		3.72		18.86		342,412		18.86
24.97 - 24.97		30,000		3.39		24.97		30,000		24.97


		6,201,429		6.09		5.68		3,913,834		7.49

Schedule of assumptions used in determining fair value of stock options granted using the Black-Scholes option pricing model

	Year Ended December 31,

	2013	2012	2011
Expected dividend yield	—	—	—
Risk-free rate	0.71% - 2.05%	0.67% - 1.15%	0.88% - 2.38%
Expected option term (in years)	6.0 - 6.1	5.3 - 5.5	5.5 - 5.6
Volatility	84% - 85%	84% - 87%	77% - 80%

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2013

Income Taxes

Schedule of components of profit (loss) before provision for income taxes

	Year Ended December 31,

	2013			2012		2011
Domestic	$	(28,200	)	$	3,502	$	(38,872	)
Foreign		(2,295	)		72		30


Profit (loss) before taxes	$	(30,495	)	$	3,574	$	(38,842	)

Schedule of significant components of the Company's net deferred tax asset

	Year Ended December 31,

	2013			2012
Deferred Tax Assets:
Net operating loss carryforward	$	81,699		$	72,016
Capitalization of research and development expense		1,945			2,763
Credit carryforwards		8,118			7,024
Depreciation		2,403			2,603
Non-Qualified Stock Options		4,437			4,213
Other temporary differences		1,813			1,958


Total deferred tax assets.		100,415			90,577
Valuation allowance		(100,405	)		(90,558	)
Net deferred tax assets		10			19
Deferred Tax Liabilities:
Other temporary differences		(10	)		(19	)


Net deferred tax loss	$	—		$	—

Schedule of items accounting for the difference between the income tax benefit computed at the federal statutory rate and the provision for income taxes

	Year Ended December 31,

	2013			2012			2011
Federal income tax at statutory federal rate		34.0	%		34.0	%		34.0	%
State taxes		3.5	%		7.8	%		5.0	%
Permanent differences		(1.9	)%		19.6	%		(2.4	)%
Tax credits		2.7	%		(10.5	)%		2.4	%
State rate change on deferred balances		(0.4	)%		3.1	%		1.4	%
Expiration of net operating losses and credits		(5.8	)%		49.2	%		(1.6	)%
Other		0.2	%		9.8	%		1.0	%
Change in valuation allowance		(32.3	)%		(113.0	)%		(39.8	)%


Total		0.00	%		0.00	%		0.00	%

Geographic Information (Tables)

12 Months Ended

Dec. 31, 2013

Geographic Information

Schedule of the geographic distribution of revenues and long-lived assets from continuing operations

	U.S.		Canada		Germany		Eliminations			Total
Year Ended December 31, 2013
Net revenues to unaffiliated customers	$	4,222	$	273	$	899	$	—		$	5,394
Inter-geographic revenues		928		794		—		(1,722	)		—


Net revenues	$	5,150	$	1,067	$	899	$	(1,722	)	$	5,394




Identifiable long-lived assets	$	752	$	41	$	—	$	—		$	793
Year Ended December 31, 2012
Net revenues to unaffiliated customers	$	42,136	$	180	$	—	$	—		$	42,316
Inter-geographic revenues		—		737		—		(737	)		—


Net revenues	$	42,136	$	917	$	—	$	(737	)	$	42,316




Identifiable long-lived assets	$	1,309	$	49			$	—		$	1,358
Year Ended December 31, 2011
Net revenues to unaffiliated customers	$	1,300	$	125	$	—	$	—		$	1,425
Inter-geographic revenues		—		859		—		(859	)		—


Net revenues	$	1,300	$	984	$	—	$	(859	)	$	1,425




Identifiable long-lived assets	$	2,185	$	91	$	—	$	—		$	2,276

Summary of Quarterly Financial Data (unaudited) (Tables)

12 Months Ended

Dec. 31, 2013

Summary of Quarterly Financial Data (unaudited)

Summary of unaudited quarterly financial data

	Quarter ended

	March 31,			June 30,			September 30,			December 31,
*2013*
Total revenues	$	1,943		$	1,706		$	855		$	890
Loss from operations		(6,785	)		(7,857	)		(7,242	)		(8,618	)
Net loss		(6,763	)		(7,866	)		(7,251	)		(8,626	)
Basic net loss per share		(0.20	)		(0.23	)		(0.21	)		(0.24	)
Diluted net loss per share		(0.20	)		(0.23	)		(0.21	)		(0.24	)
*2012*
Total revenues	$	39,322	(1)	$	923		$	674		$	1,397
Income (loss) from operations		28,823			(7,957	)		(7,743	)		(9,520	)
Net income (loss)		28,840			(7,948	)		(7,745	)		(9,517	)
Basic net income (loss) per share		0.84			(0.23	)		(0.23	)		(0.28	)
Diluted net income (loss) per share		0.84			(0.23	)		(0.23	)		(0.28	)

: Full year amounts may not sum due to rounding.

(1): In 2012, the Company recognized $38,885 of deferred revenue associated with the termination of its commercial alliance with Archer Daniels Midland Company. See Note 3 to these financial statements for a more detailed explanation for the Company's recognition of this deferred revenue.

Nature of Business (Details) - USD ($) $ in Thousands	12 Months Ended
Nature of Business (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Nature of Business
Deferred revenue recognized from the terminated Telles joint venture		$ 38,885
Unrestricted cash, cash equivalents and investments	$ 19,209
Period over which company's present capital resources are not sufficient to fund its planned operations	12 months
Minimum
Significant additional funding
Expected fund to be raised for additional financing to continue operations	$ 50,000
Period over which expected fund to be raised	12 months
Maximum
Significant additional funding
Expected fund to be raised for additional financing to continue operations	$ 60,000
Period over which expected fund to be raised	15 months

Summary of Significant Accounting Policies (Details) $ in Thousands	12 Months Ended
	Dec. 31, 2013 USD ($) item	Dec. 31, 2012 USD ($) item
Restricted Cash
Restricted cash	$ 619	$ 594
Restricted cash held in connection with the company's corporate credit card program	494	494
Restricted cash held in connection with the lease agreement for the company's Cambridge, Massachusetts facility	$ 125	$ 100
Receivables \| Credit risk concentration
Concentration of credit risk
Receivables/Sales (as a percent)	23.00%	41.00%
Number of customers \| item	0	1
Receivables \| Credit risk concentration \| Customer product receivables
Concentration of credit risk
Accounts receivable	$ 528	$ 535
Receivables/Sales (as a percent)	44.00%	44.00%
Receivables \| Credit risk concentration \| Government grants
Concentration of credit risk
Accounts receivable	$ 552	$ 561
Receivables/Sales (as a percent)	46.00%	46.00%
Receivables \| Credit risk concentration \| REFABB grant with the Department of Energy
Concentration of credit risk
Receivables/Sales (as a percent)	56.00%

Summary of Significant Accounting Policies (Details 2)	12 Months Ended
Summary of Significant Accounting Policies (Details 2)	Dec. 31, 2013 item
Segment Information
Number of operating segments	1
Equipment \| Minimum
Property and Equipment
Estimated Useful Life	2 years 6 months
Equipment \| Maximum
Property and Equipment
Estimated Useful Life	3 years
Furniture and fixtures
Property and Equipment
Estimated Useful Life	5 years
Software
Property and Equipment
Estimated Useful Life	3 years

Summary of Significant Accounting Policies (Details 3) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Revenue Recognition
Period for which company is having option of accepting returns from customers									60 days
Deferred product revenue	$ 537				$ 786				$ 537	$ 786
Deferred cost of product revenue	476				219				$ 476	219
Basic and Diluted Net Loss per Share
Difference in basic and dilutive loss per share (in dollars per share)									$ 0.00
Numerator:
Net income (loss)	$ (8,626)	$ (7,251)	$ (7,866)	$ (6,763)	$ (9,517)	$ (7,745)	$ (7,948)	$ 28,840	$ (30,506)	$ 3,630	$ (38,785)
Denominator:
Weighted average number of common shares outstanding									34,471,301	34,217,298	31,257,376
Effect of dilutive securities:
Stock options (in shares)										62,481
Dilutive potential common shares										62,481
Shares used in calculating diluted earnings per share									34,471,301	34,279,779	31,257,376
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares									6,205,515	5,583,128	3,862,771
Options
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares									6,201,429	5,579,042	3,858,685
Warrants
Antidilutive securities
Antidilutive common stock excluded from the calculation of dilutive shares									4,086	4,086	4,086

Significant Collaborations (Details) $ in Thousands, lb in Millions			3 Months Ended	12 Months Ended		36 Months Ended
	Feb. 28, 2013 USD ($)	Feb. 08, 2012 USD ($)	Mar. 31, 2012 USD ($)	Dec. 31, 2013 USD ($) lb	Dec. 31, 2012 USD ($)	Dec. 31, 2013 USD ($) item	Dec. 31, 2011 USD ($)	Dec. 31, 2010 USD ($)
Significant collaboration
Total deferred revenue				$ 537	$ 786	$ 537
Deferred revenue recognized					38,885
Aggregate cash balances of joint venture				$ 7,698	$ 14,572	$ 7,698	$ 21,277	$ 12,526
Commercial Alliance Agreement
Significant collaboration
Number of significant collaboration arrangements with Archer Daniels Midland Company \| item						1
Period over which payments recorded as deferred revenue is expected to be recognized				10 years
Commercial Alliance Agreement \| Telles
Significant collaboration
Purchase price to acquire assets of joint venture		$ 2,982
Aggregate cash balances of joint venture		3,778
Amount retained by joint venture to settle any remaining trade obligations		100
Commercial Alliance Agreement \| Telles \| Maximum
Significant collaboration
Remaining trade obligations of joint venture		100
Commercial Alliance Agreement \| ADM Polymer
Significant collaboration
Annual production capability of manufacturing facility that will be constructed under the agreement (in pounds) \| lb				110
Total deferred revenue		38,885
Performance obligations in connection with the termination of the commercial alliance			$ 0
Deferred revenue recognized			$ 38,885
Purchase price to acquire assets of joint venture		3,678
Amount reimbursed by ADM		$ 3,678
Percentage of costs incurred by the entity, agreed to be reimbursed by ADM		50.00%
Commercial Alliance Agreement \| ADM Polymer \| Upfront payment
Significant collaboration
Total deferred revenue		$ 3,000
Commercial Alliance Agreement \| ADM Polymer \| Milestone payments
Significant collaboration
Total deferred revenue		2,000
Commercial Alliance Agreement \| ADM Polymer \| Support payments
Significant collaboration
Total deferred revenue		22,050
Commercial Alliance Agreement \| ADM Polymer \| Cost sharing payments for pre-commercial manufacturing plant construction and operations
Significant collaboration
Total deferred revenue		$ 11,835
Commercial Alliance Agreement \| ADM Polymer \| Telles
Significant collaboration
Ownership and voting interest in Telles (as a percent)				50.00%		50.00%
Third party creditor trade obligations paid	$ 0

Inventory (Details) - USD ($) $ in Thousands	12 Months Ended
Inventory (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Inventory
Raw materials	$ 537	$ 640
Work-in-process		2
Finished goods	3,537	2,562
Total inventory	4,074	3,204
Inventory on which revenue not recognized	537	786
Cost of obsolete raw material and finished goods	$ 818	$ 138

- Definition

Charge to cost of goods sold that represents the reduction of the carrying amount of inventory, generally attributable to obsolescence or market conditions.

+ References + Details

Investments (Details) - USD ($) $ in Thousands	12 Months Ended
Investments (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Investments
Amortized Cost	$ 11,510	$ 31,696
Unrealized Gain	1	13
Market Value	$ 11,511	$ 31,709
Average maturity of marketable securities available-for-sale	2 months	4 months
Short-term investments \| Government sponsored enterprises
Investments
Amortized Cost	$ 11,510	$ 29,189
Unrealized Gain	1	12
Market Value	$ 11,511	29,201
Long-term investments \| Government sponsored enterprises
Investments
Amortized Cost		2,507
Unrealized Gain		1
Market Value		$ 2,508

- Definition

This element represents the portion of the balance sheet assertion valued at fair value by the entity whether such amount is presented as a separate caption or as a parenthetical disclosure. Additionally, this element may be used in connection with the fair value disclosures required in the footnote disclosures to the financial statements. The element may be used in both the balance sheet and disclosure in the same submission. This item represents Available-for-sale Securities which consist of all investments in certain debt and equity securities neither classified as trading or held-to-maturity securities. A debt security represents a creditor relationship with an enterprise. Debt securities include, among other items, US Treasury securities, US government securities, municipal securities, corporate bonds, convertible debt, commercial paper, and all securitized debt instruments. An equity security represents an ownership interest in an enterprise or the right to acquire or dispose of an ownership interest in an enterprise at fixed or determinable prices. Equity securities include, among other things, common stock, certain preferred stock, warrant rights, call options, and put options, but do not include convertible debt. An entity may opt to provide the reader with additional narrative text to better understand the nature of investments in debt and equity securities which are categorized as Available-for-sale.

+ References + Details

Fair Value Measurements (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Fair value measurements
Short-term investments	$ 11,511	$ 29,201
Long-term investments		2,508
Recurring \| Quoted prices in active markets for identical assets (Level 1)
Fair value measurements
Total	6,332	11,157
Recurring \| Quoted prices in active markets for identical assets (Level 1) \| Money market funds
Fair value measurements
Cash equivalents:	6,332	11,157
Recurring \| Significant other observable inputs (Level 2)
Fair value measurements
Total	11,511	33,724
Recurring \| Significant other observable inputs (Level 2) \| Government securities
Fair value measurements
Cash equivalents:		2,015
Short-term investments	11,511	29,201
Long-term investments		2,508
Recurring \| Balance as of the end of the period
Fair value measurements
Total	17,843	44,881
Recurring \| Balance as of the end of the period \| Money market funds
Fair value measurements
Cash equivalents:	6,332	11,157
Recurring \| Balance as of the end of the period \| Government securities
Fair value measurements
Cash equivalents:		2,015
Short-term investments	$ 11,511	29,201
Long-term investments		$ 2,508

Property and Equipment, Net (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Property and equipment, net
Total property and equipment, at cost	$ 8,128	$ 8,400
Less: Accumulated depreciation	(7,335)	(7,042)
Property and equipment, net	793	1,358	$ 2,276
Depreciation expense	928	1,298	$ 1,507
Equipment
Property and equipment, net
Total property and equipment, at cost	4,868	5,151
Furniture and fixtures
Property and equipment, net
Total property and equipment, at cost	227	227
Leasehold improvements
Property and equipment, net
Total property and equipment, at cost	2,652	2,641
Software
Property and equipment, net
Total property and equipment, at cost	381	381
Capitalized leased equipment
Property and equipment, net
Total property and equipment, at cost	$ 0	$ 0

Accrued Expenses (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Accrued Expenses
Employee compensation and benefits	$ 2,595	$ 2,379
Commercial manufacturing	815	229
Professional services	578	301
Other	904	610
Total accrued expenses	$ 4,892	$ 3,519

- Definition

Carrying value as of the balance sheet date of obligations incurred through that date and payable for professional fees, such as for legal and accounting services received. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer).

+ References + Details

- Definition

Carrying value as of the balance sheet date of obligations incurred through that date and payable arising from transactions not otherwise specified in the taxonomy. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer).

+ References + Details

Commitments and Contingencies (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Commitments and Contingencies
Rental payments under operating leases	$ 1,662	$ 1,814	$ 1,808
Future minimum lease payments
2014	1,449
2015	1,383
2016	1,419
2017	1,454
2018 and thereafter	3,576
Total	$ 9,281

Related Party Transactions (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Related party transactions
Outstanding receivable	$ 51	$ 75
Tepha, Inc.
Related party transactions
License and royalty revenue	149	149	$ 444
Outstanding receivable	$ 51	$ 75

- Definition

The aggregate amount of receivables to be collected from related parties where one party can exercise control or significant influence over another party; including affiliates, owners or officers and their immediate families, pension trusts, and so forth, at the financial statement date. which are usually due within one year (or one business cycle).

+ References + Details

- Definition

Amount of revenue, fees and commissions earned from transactions between (a) a parent company and its subsidiaries; (b) subsidiaries of a common parent; (c) an entity and trusts for the benefit of employees, for example, but not limited to, pension and profit-sharing trusts that are managed by or under the trusteeship of the entity's management; (d) an entity and its principal, owners, management, or members of their immediate families; and (e) affiliates.

+ References + Details

Preferred Stock (Details) - $ / shares	Dec. 31, 2013	Dec. 31, 2012
Preferred Stock
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, par value per share (in dollars per share)	$ 0.01	$ 0.01
Preferred stock issued (in shares)	0	0
Preferred stock outstanding (in shares)	0	0

Common Stock (Details) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
Common Stock (Details) $ / shares in Units, $ in Thousands	May 31, 2011 USD ($) $ / shares shares	Dec. 31, 2013 $ / shares shares	Dec. 31, 2011 USD ($)
Common Stock Issuances
Number of shares of common stock issued in public offering \| shares	7,130,000
Issuance price per share (in dollars per share) \| $ / shares	$ 7.25
Net proceeds from public offering \| $	$ 49,333		$ 49,333
Underwriting discounts, commissions and offering costs \| $	$ 2,360
Warrants
Number of shares that can be purchased by warrants issued \| shares		4,086
Exercise price of warrants issued to purchase shares of common stock (in dollars per share) \| $ / shares		3.30
Period of expiration of warrants from the lease term commencement date		10 years

Shareholder Rights Plan (Details) - $ / shares	Feb. 06, 2012	Jul. 08, 2009	Dec. 31, 2013	Dec. 31, 2012
Shareholder Rights Plan
Number of preferred stock purchase rights distributed as dividend per common stock share (in shares)		1
Minimum percentage of outstanding common stock to be acquired for rights to be exercisable		15.00%
Minimum percentage of common stock to be acquired in a tender or exchange offer for rights to be exercisable		15.00%
Shareholder rights plan
Maximum number of shares beneficially owned by Schuler Stockholders			34,581,449	34,306,570
Common stock, par value per share (in dollars per share)			$ 0.01	$ 0.01
Schuler stockholders
Shareholder rights plan
Common stock, par value per share (in dollars per share)	$ 0.01
Percentage of outstanding common stock up to which Schuler Stockholders are allowed to increase their beneficial ownership without becoming Acquiring Persons	19.99%
Aggregate percentage of outstanding shares of common stock which beneficial owner, affiliates, and associates of beneficial owner can own less than without triggering exercise of rights	20.00%
Schuler stockholders \| Maximum
Shareholder rights plan
Maximum number of shares beneficially owned by Schuler Stockholders	5,091,295
Percentage of the company's outstanding common stock deemed to be owned by Schuler Stockholders	14.70%

Stock-Based Compensation (Details) - Stock options - USD ($) $ / shares in Units, $ in Thousands		12 Months Ended
	Dec. 19, 2013	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stock-based compensation
Expiration period		10 years
Number of Shares
Balance at the beginning of the period (in shares)		5,579,042
Granted (in shares)		1,654,315
Exercised (in shares)		(7,550)
Forfeited (in shares)		(670,291)
Expired (in shares)		(354,087)
Balance at the end of the period (in shares)		6,201,429	5,579,042
Vested and expected to vest at the end of the period (in shares)		6,009,973
Options exercisable at the end of the period (in shares)		3,913,834
Weighted Average Exercise Price
Balance at the beginning of the period (in dollars per share)		$ 6.68
Granted (in dollars per share)		1.64
Exercised (in dollars per share)		1.82
Forfeited (in dollars per share)		2.11
Expired (in dollars per share)		9.26
Balance at the end of the period (in dollars per share)		5.68	$ 6.68
Vested and expected to vest at the end of the period (in dollars per share)		5.79
Options exercisable at the end of the period (in dollars per share)		$ 7.49
Remaining Contractual Term
Balance at the end of the period		6 years 1 month 2 days
Vested and expected to vest at the end of the period		6 years 14 days
Options exercisable at the end of the period		5 years 2 months 5 days
Additional disclosures
Weighted average grant date fair value of options granted (in dollars per share)		$ 1.14	$ 1.46	$ 5.02
Total intrinsic value of options exercised		$ 2	$ 15	$ 81
Joseph Shaulson
Stock-based compensation
Expiration period		4 years
Number of Shares
Granted (in shares)	1,150,000
Joseph Shaulson \| Option vesting on 2nd anniversary date
Stock-based compensation
Vesting percentage		25.00%
Joseph Shaulson \| Option vesting on 3rd anniversary date
Stock-based compensation
Vesting percentage		25.00%
Joseph Shaulson \| Option vesting on 4th anniversary date
Stock-based compensation
Vesting percentage		50.00%
Minimum
Stock-based compensation
Vesting period for options granted		2 years
Maximum
Stock-based compensation
Vesting period for options granted		4 years
1995 Plan
Stock-based compensation
Further grants or awards after termination of plan (in shares)		0
Options awarded		907,679
Number of Shares
Balance at the end of the period (in shares)		29,192
2005 Plan
Stock-based compensation
Further grants or awards after termination of plan (in shares)		0
Options awarded		1,619,134
Number of Shares
Balance at the end of the period (in shares)		231,229
2006 Plan
Stock-based compensation
Options awarded		8,677,227
Maximum number of shares issuable under the plan		10,000,000
Number of Shares
Balance at the end of the period (in shares)		5,941,008

Stock-Based Compensation (Details 2)	12 Months Ended
Stock-Based Compensation (Details 2)	Dec. 31, 2013 $ / shares shares
Stock Options Outstanding
Number of shares \| shares	6,201,429
Weighted average remaining contractual life	6 years 1 month 2 days
Weighted average exercise price per share (in dollars per share)	$ 5.68
Stock Options Exercisable
Number of shares \| shares	3,913,834
Weighted average exercise price per share (in dollars per share)	$ 7.49
$1.27 - 1.48
Stock-based compensation
Exercise price, minimum (in dollars per share)	1.27
Exercise price, maximum (in dollars per share)	$ 1.48
Stock Options Outstanding
Number of shares \| shares	240,400
Weighted average remaining contractual life	9 years 7 months 24 days
Weighted average exercise price per share (in dollars per share)	$ 1.41
Stock Options Exercisable
Number of shares \| shares	15,610
Weighted average exercise price per share (in dollars per share)	$ 1.40
1.55 - 1.55
Stock-based compensation
Exercise price, minimum (in dollars per share)	1.55
Exercise price, maximum (in dollars per share)	$ 1.55
Stock Options Outstanding
Number of shares \| shares	1,045,000
Weighted average remaining contractual life	7 years 6 months 22 days
Weighted average exercise price per share (in dollars per share)	$ 1.55
Stock Options Exercisable
Number of shares \| shares	600,000
Weighted average exercise price per share (in dollars per share)	$ 1.55
1.56 - 1.69
Stock-based compensation
Exercise price, minimum (in dollars per share)	1.56
Exercise price, maximum (in dollars per share)	$ 1.69
Stock Options Outstanding
Number of shares \| shares	1,038,479
Weighted average remaining contractual life	6 years 8 months 8 days
Weighted average exercise price per share (in dollars per share)	$ 1.68
Stock Options Exercisable
Number of shares \| shares	358,018
Weighted average exercise price per share (in dollars per share)	$ 1.66
1.74 - 2.46
Stock-based compensation
Exercise price, minimum (in dollars per share)	1.74
Exercise price, maximum (in dollars per share)	$ 2.46
Stock Options Outstanding
Number of shares \| shares	360,014
Weighted average remaining contractual life	7 years 4 months 28 days
Weighted average exercise price per share (in dollars per share)	$ 2.09
Stock Options Exercisable
Number of shares \| shares	190,189
Weighted average exercise price per share (in dollars per share)	$ 2.11
2.66 - 2.66
Stock-based compensation
Exercise price, minimum (in dollars per share)	2.66
Exercise price, maximum (in dollars per share)	$ 2.66
Stock Options Outstanding
Number of shares \| shares	866,949
Weighted average remaining contractual life	6 years 7 months 6 days
Weighted average exercise price per share (in dollars per share)	$ 2.66
Stock Options Exercisable
Number of shares \| shares	380,256
Weighted average exercise price per share (in dollars per share)	$ 2.66
2.72 - 7.25
Stock-based compensation
Exercise price, minimum (in dollars per share)	2.72
Exercise price, maximum (in dollars per share)	$ 7.25
Stock Options Outstanding
Number of shares \| shares	737,997
Weighted average remaining contractual life	5 years 1 month 24 days
Weighted average exercise price per share (in dollars per share)	$ 5.98
Stock Options Exercisable
Number of shares \| shares	561,599
Weighted average exercise price per share (in dollars per share)	$ 6.21
7.31 - 9.77
Stock-based compensation
Exercise price, minimum (in dollars per share)	7.31
Exercise price, maximum (in dollars per share)	$ 9.77
Stock Options Outstanding
Number of shares \| shares	668,092
Weighted average remaining contractual life	5 years 3 months 4 days
Weighted average exercise price per share (in dollars per share)	$ 8.95
Stock Options Exercisable
Number of shares \| shares	602,927
Weighted average exercise price per share (in dollars per share)	$ 8.93
10.08 - 14.49
Stock-based compensation
Exercise price, minimum (in dollars per share)	10.08
Exercise price, maximum (in dollars per share)	$ 14.49
Stock Options Outstanding
Number of shares \| shares	872,086
Weighted average remaining contractual life	4 years 25 days
Weighted average exercise price per share (in dollars per share)	$ 12.49
Stock Options Exercisable
Number of shares \| shares	832,823
Weighted average exercise price per share (in dollars per share)	$ 12.42
14.53 - 23.99
Stock-based compensation
Exercise price, minimum (in dollars per share)	14.53
Exercise price, maximum (in dollars per share)	$ 23.99
Stock Options Outstanding
Number of shares \| shares	342,412
Weighted average remaining contractual life	3 years 8 months 19 days
Weighted average exercise price per share (in dollars per share)	$ 18.86
Stock Options Exercisable
Number of shares \| shares	342,412
Weighted average exercise price per share (in dollars per share)	$ 18.86
24.97 - 24.97
Stock-based compensation
Exercise price, minimum (in dollars per share)	24.97
Exercise price, maximum (in dollars per share)	$ 24.97
Stock Options Outstanding
Number of shares \| shares	30,000
Weighted average remaining contractual life	3 years 4 months 20 days
Weighted average exercise price per share (in dollars per share)	$ 24.97
Stock Options Exercisable
Number of shares \| shares	300,000
Weighted average exercise price per share (in dollars per share)	$ 24.97

Stock-Based Compensation (Details 3) - Stock options - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Stock-based compensation
Stock options granted (in shares)	1,654,315
Non-employee
Stock-based compensation
Weighted average period over which unrecognized compensation expense is expected to be recognized		4 years
Stock options granted (in shares)	0	0	34,500
Employee including members of the Board of Directors
Stock-based compensation
Stock-based compensation expense	$ 3,193	$ 3,825	$ 4,621
Stock-based compensation expense, net of estimated forfeitures, related to unvested awards not yet recognized	$ 3,544
Weighted average period over which unrecognized compensation expense is expected to be recognized	2 years 7 days
Assumptions used to determine fair value of stock options
Risk-free rate, minimum (as a percent)	0.71%	0.67%	0.88%
Risk-free rate, maximum (as a percent)	2.05%	1.15%	2.38%
Volatility, minimum (as a percent)	84.00%	84.00%	77.00%
Volatility, maximum (as a percent)	85.00%	87.00%	80.00%
Minimum \| Employee including members of the Board of Directors
Assumptions used to determine fair value of stock options
Expected option term	6 years	5 years 3 months 18 days	5 years 6 months
Maximum \| Employee including members of the Board of Directors
Assumptions used to determine fair value of stock options
Expected option term	6 years 1 month 6 days	5 years 6 months	5 years 7 months 6 days

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Components of profit (loss) before provision for income taxes
Domestic	$ (28,200)	$ 3,502	$ (38,872)
Foreign	(2,295)	72	30
Profit (loss) before taxes	(30,495)	3,574	$ (38,842)
Deferred Tax Assets:
Net operating loss carryforward	81,699	72,016
Capitalization of research and development expense	1,945	2,763
Credit carryforwards	8,118	7,024
Depreciation	2,403	2,603
Non-Qualified Stock Options	4,437	4,213
Other temporary differences	1,813	1,958
Total deferred tax assets	100,415	90,577
Valuation allowance	(100,405)	(90,558)
Net deferred tax asset	10	19
Deferred Tax Liabilities:
Other temporary differences	$ (10)	$ (19)
Difference between income tax benefit computed at the federal statutory rate and the provision for income taxes
Federal income tax at statutory federal rate (as a percent)	34.00%	34.00%	34.00%
State taxes (as a percent)	3.50%	7.80%	5.00%
Permanent differences (as a percent)	(1.90%)	19.60%	(2.40%)
Tax credits (as a percent)	2.70%	(10.50%)	2.40%
State rate change on deferred balances (as a percent)	(0.40%)	3.10%	1.40%
Expiration of net operating losses and credits (as a percent)	(5.80%)	49.20%	(1.60%)
Other (as a percent)	0.20%	9.80%	1.00%
Change in valuation allowance (as a percent)	(32.30%)	(113.00%)	(39.80%)
Total (as a percent)	0.00%	0.00%	0.00%
Unrecognized tax benefits	$ 0	$ 0	$ 0
Accrued interest or penalties related to uncertain tax positions	$ 0	$ 0	$ 0

Income Taxes (Details 2) $ in Thousands	12 Months Ended
Income Taxes (Details 2) $ in Thousands	Dec. 31, 2013 USD ($)
Net operating loss carryforwards
Deduction related to the exercise of stock options	$ 19,213
Maximum period to audit for loss	3 years
Federal
Net operating loss carryforwards
NOL carryforwards	$ 236,705
State
Net operating loss carryforwards
NOL carryforwards	$ 148,783

Income Taxes (Details 3) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details 3) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012
Tax credits
Additional provision for income taxes related to the undistributed earnings	$ 0
Additional tax liability as a result of the distribution of earnings which are expected to be permanently reinvested	0
Unremitted earnings	273	$ 252
Federal \| Research and development
Tax credits
Available tax credits	5,281
State \| Research and development
Tax credits
Available tax credits	3,920
State \| Investment
Tax credits
Available tax credits	$ 86

- Definition

Amount of deferred tax liability attributable to taxable temporary differences from undistributed earnings of subsidiaries and other recognized entities not within the country of domicile of the entity.

+ References + Details

Employee Benefits (Details) - USD ($) $ in Thousands	12 Months Ended
Employee Benefits (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Employee Benefits
Maximum contribution by participants under the 401(k) savings plan (as a percent)	60.00%
Employer's matching contribution in common stock as a percentage of a participant's total compensation	4.50%
Common stock issued under the 401(k) savings plan (in shares)	267,329	179,336	68,558
Related expense for common stock issued under the 401(k) savings plan	$ 397	$ 408	$ 529

U.S. Department of Energy Grant (Details) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
U.S. Department of Energy Grant
Multi-year grant agreement amount			$ 6,000
Prorated cost-sharing obligation amount			3,900
Revenue recognized related to the multi-year grant agreement	$ 1,640	$ 1,578	$ 515

Restructuring (Details) - USD ($) $ in Thousands	12 Months Ended
Restructuring (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2013
Restructuring
Restructuring charges recognized	$ 920
Restructuring charges accrued	$ 0	$ 0

Geographic Information (Details) - USD ($) $ in Thousands	3 Months Ended								12 Months Ended
Geographic Information (Details) - USD ($) $ in Thousands	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Geographic Information
Net revenues to unaffiliated customers	$ 890	$ 855	$ 1,706	$ 1,943	$ 1,397	$ 674	$ 923	$ 39,322	$ 5,394	$ 42,316	$ 1,425
Net revenues									5,394	42,316	1,425
Identifiable long-lived assets	793				1,358				793	1,358	2,276
U.S.
Geographic Information
Net revenues to unaffiliated customers									4,222	42,136	1,300
Inter-geographic revenues									928
Net revenues									5,150	42,136	1,300
Identifiable long-lived assets	752				1,309				752	1,309	2,185
Canada
Geographic Information
Net revenues to unaffiliated customers									273	180	125
Inter-geographic revenues									794	737	859
Net revenues									1,067	917	984
Identifiable long-lived assets	$ 41				$ 49				41	49	91
Germany
Geographic Information
Net revenues to unaffiliated customers									899
Net revenues									899
Eliminations
Geographic Information
Inter-geographic revenues									(1,722)	(737)	(859)
Net revenues									$ (1,722)	$ (737)	$ (859)

Geographic Information (Details 2) $ in Thousands	12 Months Ended
Geographic Information (Details 2) $ in Thousands	Dec. 31, 2013 USD ($) item	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)
Revenue earned
Revenue earned from the REFABB grant	$ 2,490	$ 1,971	$ 918
Number of additional customers \| item	3
U.S. Department of Energy
Revenue earned
Revenue earned from the REFABB grant	$ 1,640
Percentage of total revenue	30.00%
Customer one
Revenue earned
Percentage of total revenue	13.00%
Customer two
Revenue earned
Percentage of total revenue	12.00%
Customer three
Revenue earned
Percentage of total revenue	11.00%

Summary of Quarterly Financial Data (unaudited) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2013	Sep. 30, 2013	Jun. 30, 2013	Mar. 31, 2013	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2013	Dec. 31, 2012	Dec. 31, 2011
Summary of Quarterly Financial Data (unaudited)
Total revenues	$ 890	$ 855	$ 1,706	$ 1,943	$ 1,397	$ 674	$ 923	$ 39,322	$ 5,394	$ 42,316	$ 1,425
Income (loss) from operations	(8,618)	(7,242)	(7,857)	(6,785)	(9,520)	(7,743)	(7,957)	28,823	(30,502)	3,603	(38,861)
Net income (loss)	$ (8,626)	$ (7,251)	$ (7,866)	$ (6,763)	$ (9,517)	$ (7,745)	$ (7,948)	$ 28,840	$ (30,506)	$ 3,630	$ (38,785)
Basic net income (loss) per share (in dollars per share)	$ (0.24)	$ (0.21)	$ (0.23)	$ (0.20)	$ (0.28)	$ (0.23)	$ (0.23)	$ 0.84	$ (0.88)	$ 0.11	$ (1.24)
Diluted net income (loss) per share (in dollars per share)	$ (0.24)	$ (0.21)	$ (0.23)	$ (0.20)	$ (0.28)	$ (0.23)	$ (0.23)	$ 0.84	$ (0.88)	$ 0.11	$ (1.24)
Summary of quarterly financial data
Deferred revenue recognized associated with termination of agreement										$ 38,885
Commercial Alliance Agreement \| Archer Daniels Midland
Summary of quarterly financial data
Deferred revenue recognized associated with termination of agreement								$ 38,885