Amyris (AMRSQ) 10-Q 9 Nov 15 2015 Q3 Quarterly report Financial data

Document And Entity Information

Document And Entity Information - shares	9 Months Ended
	Sep. 30, 2015	Oct. 31, 2015
Document and Entity Information [Abstract]
Entity Registrant Name	AMYRIS, INC.
Trading Symbol	amrs
Document Type	10-Q
Current Fiscal Year End Date	--12-31
Entity Common Stock, Shares Outstanding		192,174,168
Amendment Flag	false
Entity Central Index Key	1,365,916
Entity Current Reporting Status	Yes
Entity Voluntary Filers	No
Entity Filer Category	Accelerated Filer
Entity Well-known Seasoned Issuer	No
Document Period End Date	Sep. 30, 2015
Document Fiscal Year Focus	2,015
Document Fiscal Period Focus	Q3

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Current assets:
Cash and cash equivalents	$ 10,903	$ 42,047
Restricted cash	215
Short-term investments	995	1,375
Accounts receivable, net of allowance of $479 and $479, respectively	3,806	8,687
Related party accounts receivable	575	455
Inventories, net	11,102	14,506
Prepaid expenses and other current assets	7,034	6,534
Total current assets	34,630	73,604
Property, plant and equipment, net	81,941	118,980
Restricted cash	957	1,619
Equity and loans in affiliates	1,815	2,260
Other assets	9,591	13,635
Goodwill and intangible assets	6,085	6,085
Total assets	135,019	216,183
Current liabilities:
Accounts payable	11,275	3,489
Deferred revenue	9,204	5,303
Accrued and other current liabilities	16,832	13,565
Capital lease obligation, current portion	555	541
Debt, current portion	20,902	17,100
Total current liabilities	58,768	39,998
Capital lease obligation, net of current portion	280	275
Long-term debt, net of current portion	90,532	100,122
Related party debt	42,401	115,239
Deferred rent, net of current portion	9,845	10,250
Deferred revenue, net of current portion	4,462	6,539
Derivative liabilities	62,966	59,736
Other liabilities	7,230	9,087
Total liabilities	$ 276,484	$ 341,246
Commitments and contingencies (Note 6)
Stockholders’ deficit:
Preferred stock - $0.0001 par value, 5,000,000 shares authorized, none issued and outstanding	$ 0	$ 0
Common stock - $0.0001 par value, 400,000,000 and 300,000,000 shares authorized as of September 30, 2015 and December 31, 2014, respectively; 158,610,725 and 79,221,883 shares issued and outstanding as of September 30, 2015 and December 31, 2014, respectively	16	8
Additional paid-in capital	902,933	724,669
Accumulated other comprehensive loss	(48,932)	(29,977)
Accumulated deficit	(995,186)	(819,152)
Total Amyris, Inc. stockholders’ deficit	(141,169)	(124,452)
Noncontrolling interest	(296)	(611)
Total stockholders' deficit	(141,465)	(125,063)
Total liabilities and stockholders' deficit	$ 135,019	$ 216,183

Condensed Consolidated Balance3

Condensed Consolidated Balance Sheets (Unaudited) (Parentheticals) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Allowance for doubtful accounts (in Dollars)	$ 479	$ 479
Preferred stock par value (in Dollars per share)	$ 0.0001	$ 0.0001
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 (in Dollars per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized	400,000,000	300,000,000
Common stock, shares issued	158,610,725	79,221,883
Common stock, shares outstanding	158,610,725	79,221,883

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations (Unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Revenues
Renewable product sales	$ 4,226	$ 11,112	$ 9,661	$ 18,333
Related party renewable product sales	2	368	2	402
Total product sales	4,228	11,480	9,663	18,735
Grants and collaborations revenue	4,363	4,861	14,643	12,954
Total grants and collaborations revenue	4,363	4,861	14,643	12,954
Total revenues	8,591	16,341	24,306	31,689
Cost and operating expenses
Cost of products sold	8,455	10,146	26,057	23,893
Loss on purchase commitments and impairment of property, plant and equipment	7,259	952	7,259	1,111
Research and development	10,343	12,181	33,521	37,342
Sales, general and administrative	14,103	14,356	42,859	41,726
Total cost and operating expenses	40,160	37,635	109,696	104,072
Loss from operations	(31,569)	(21,294)	(85,390)	(72,383)
Other income (expense):
Interest income	61	100	205	304
Interest expense	(16,559)	(8,620)	(71,027)	(20,172)
Gain (loss) from change in fair value of derivative instruments	(21,690)	(6,000)	(10,268)	48,148
Loss from extinguishment of debt	(5,984)		(5,984)	(10,512)
Other income (expense), net	(168)	54	(1,204)	147
Total other income (expense)	(44,340)	(14,466)	(88,278)	17,915
Loss before income taxes and loss from investments in affiliates	(75,909)	(35,760)	(173,668)	(54,468)
Provision for income taxes	(119)	(134)	(355)	(370)
Net loss before loss from investments in affiliates	(76,028)	(35,894)	(174,023)	(54,838)
Loss from investments in affiliates	(660)	(778)	(2,089)	(988)
Net loss	(76,688)	(36,672)	(176,112)	(55,826)
Net loss attributable to noncontrolling interest	24	31	78	91
Net loss attributable to Amyris, Inc. common stockholders	$ (76,664)	$ (36,641)	$ (176,034)	$ (55,735)
Net loss per share attributable to common stockholders:
Basic (in Dollars per share)	$ (0.55)	$ (0.46)	$ (1.76)	$ (0.71)
Diluted (in Dollars per share)	$ (0.55)	$ (0.46)	$ (1.76)	$ (0.94)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:
Basic (in Shares)	140,374,297	78,980,402	100,103,007	78,146,365
Diluted (in Shares)	140,374,297	78,980,402	100,103,007	111,114,801

Condensed Consolidated Stateme5

Condensed Consolidated Statements of Comprehensive Income (Loss) (Unaudited) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Comprehensive income (loss):
Net loss	$ (76,688)	$ (36,672)	$ (176,112)	$ (55,826)
Foreign currency translation adjustment, net of tax	(10,459)	(8,164)	(18,562)	(3,753)
Total comprehensive loss	(87,147)	(44,836)	(194,674)	(59,579)
Loss attributable to noncontrolling interest	24	31	78	91
Foreign currency translation adjustment attributable to noncontrolling interest	(145)	(79)	(393)	(37)
Comprehensive loss attributable to Amyris, Inc.	$ (87,268)	$ (44,884)	$ (194,989)	$ (59,525)

Condensed Consolidated Stateme6

Condensed Consolidated Statements of Stockholders' Deficit (Unaudited) - 9 months ended Sep. 30, 2015 - USD ($) $ in Thousands	Common Stock [Member]	Additional Paid-in Capital [Member]	Retained Earnings [Member]	AOCI Attributable to Parent [Member]	Noncontrolling Interest [Member]	Total
Balance at Dec. 31, 2014	$ 8	$ 724,669	$ (819,152)	$ (29,977)	$ (611)	$ (125,063)
Balance (in Shares) at Dec. 31, 2014	79,221,883					79,221,883
Issuance of common stock upon exercise of stock options, net of restricted stock		15				$ 15
Issuance of common stock upon exercise of stock options, net of restricted stock (in Shares)	10,750					10,750
Issuance of common stock upon conversion of debt	$ 6	94,831				$ 94,837
Issuance of common stock upon conversion of debt (in Shares)	61,295,416
Issuance of warrants on conversion of debt		51,705				51,705
Shares issued from restricted stock settlement		(313)				(313)
Shares issued from restricted stock settlement (in Shares)	801,167
Shares issued upon ESPP purchase		428				428
Shares issued upon ESPP purchase (in Shares)	255,867
Issuance of common stock in a private placement, net of issuance costs	$ 2	24,624				24,626
Issuance of common stock in a private placement, net of issuance costs (in Shares)	16,025,642
Stock-based compensation		6,964				6,964
Issuance of common stock upon exercise of warrants		10				10
Issuance of common stock upon exercise of warrants (in Shares)	1,000,000
Foreign currency translation adjustment				(18,955)	393	(18,562)
Net loss			(176,034)		(78)	(176,112)
Balance at Sep. 30, 2015	$ 16	$ 902,933	$ (995,186)	$ (48,932)	$ (296)	$ (141,465)
Balance (in Shares) at Sep. 30, 2015	158,610,725					158,610,725

Condensed Consolidated Stateme7

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014
Operating activities
Net loss	$ (176,112)	$ (55,826)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	9,931	11,334
Loss on disposal of property, plant and equipment	121	152
Stock-based compensation	6,964	10,769
Amortization of debt discount	54,633	6,794
Loss from extinguishment of debt	5,984	10,512
Loss on purchase commitments and impairment of property, plant and equipment	7,259	1,111
Change in fair value of derivative instruments	10,268	(48,148)
Loss from investments in affiliates	2,089	988
Other non-cash expenses	414	(113)
Changes in assets and liabilities:
Accounts receivable	5,161	(3,088)
Related party accounts receivable	(10)	(79)
Inventories, net	3,306	(6,148)
Prepaid expenses and other assets	(3,218)	(2,334)
Accounts payable	7,302	(903)
Accrued and other liabilities	11,430	4,748
Deferred revenue	2,666	6,078
Deferred rent	(405)	46
Net cash used in operating activities	(52,217)	(64,107)
Investing activities
Purchase of short-term investments	(1,989)	(946)
Maturities of short-term investments	2,023	979
Change in restricted cash	238
Investment in joint venture		(2,075)
Loans to affiliate	(1,231)	(1,214)
Purchases of property, plant and equipment, net of disposals	(2,345)	(3,616)
Net cash used in investing activities	(3,304)	(6,872)
Financing activities
Proceeds from issuance of common stock, net of repurchases	453	2,159
Employees’ taxes paid upon vesting of restricted stock units	(313)	(1,797)
Proceeds from issuance of common stock in private placements, net of issuance costs	25,000	4,000
Principal payments on capital leases	(594)	(827)
Proceeds from debt issued	1,607	83,171
Proceeds from debt issued to related party	10,850	49,862
Principal payments on debt	(11,249)	(4,627)
Net cash provided by financing activities	25,754	131,947
Effect of exchange rate changes on cash and cash equivalents	(1,377)	(619)
Net (decrease)/increase in cash and cash equivalents	(31,144)	60,349
Cash and cash equivalents at beginning of period	42,047	6,868
Cash and cash equivalents at end of period	10,903	67,217
Supplemental disclosures of cash flow information:
Cash paid for interest	5,859	3,504
Supplemental disclosures of non-cash investing and financing activities:
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	(692)	(95)
Financing of equipment	613
Financing of insurance premium under notes payable	(236)	(361)
Interest capitalized to debt	6,354	2,812
Purchase of property, plant and equipment via deposit	(392)
Receivable of proceeds for options exercised		(355)
Non-cash investment in joint venture		$ (237)
Private placement issuance costs	$ (374)

Note 1 - The Company

Note 1 - The Company	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block [Abstract]
Nature of Operations [Text Block]	1. The Company Amyris, Inc. (the “Company”) was incorporated in California on July 17, 2003 and reincorporated in Delaware on June 10, 2010 for the purpose of leveraging breakthroughs in industrial bioscience technology to develop and provide renewable compounds for a variety of markets. The Company is currently applying its industrial bioscience technology platform to provide alternatives to select petroleum-sourced products used in consumer care, specialty chemical and transportation fuel markets worldwide. The Company's first commercialization efforts have been focused on a renewable hydrocarbon molecule called farnesene (Biofene®), which forms the basis for a wide range of products including emollients, fragrance oils and diesel fuel. While the Company's platform is able to use a wide variety of feedstocks, the Company is initially focused on Brazilian sugarcane. In addition, the Company is a party to various contract manufacturing agreements to support its commercial production needs. The Company has established two principal operating subsidiaries, Amyris Brasil Ltda. (formerly Amyris Brasil S.A., or "Amyris Brasil") for production in Brazil, and Amyris Fuels, LLC (or "Amyris Fuels"). The Company's renewable products business strategy is to focus on direct commercialization of specialty products while moving established commodity products into joint venture arrangements with leading industry partners. To commercialize its products, the Company must be successful in using its technology to manufacture products at commercial scale and on an economically viable basis (i.e., low per unit production costs) and developing sufficient sales volume for those products to support its operations. The Company's prospects are subject to risks, expenses and uncertainties frequently encountered by companies in this stage of development. The Company expects to fund its operations for the foreseeable future with cash and investments currently on hand, with new debt and equity financings, and with cash inflows from collaborations and grants, and cash contributions from product sales. The Company's planned 2015 and 2016 working capital needs and its planned operating and capital expenditures are dependent on significant inflows of cash from new and existing collaboration partners and from cash generated from renewable product sales, and may also require additional funding from debt or equity financings. Liquidity The Company has incurred significant losses since its inception and believes that it will continue to incur losses and negative cash flow from operations through at least 2016. As of September 30, 2015, the Company had an accumulated deficit of $995.2 million and had cash, cash equivalents and short term investments of $11.9 million. In October 2015, the Company completed a convertible notes offering with net proceeds after offering expenses of $54.4 million. $27.1 million of the proceeds were used to repay existing convertible notes. Refer to Note 18, “Subsequent Events” for further details. The Company has significant outstanding debt and contractual obligations related to capital and operating leases, as well as purchase commitments. As of September 30, 2015, the Company's debt, net of discount of $17.3 million, totaled $153.8 million, of which $20.9 million matures within the next twelve months. In addition to upcoming debt maturities, the Company's debt service obligations over the next twelve months are significant, including $9.2 million of anticipated cash interest payments. The Company's debt agreements contain various covenants, including certain restrictions on the Company's business that could cause the Company to be at risk of defaults, such as the requirement to maintain unrestricted, unencumbered cash in U.S.bank accounts an amount equal to at least 50% of the principal amount outstanding under its loan facility with Hercules Technology Growth Capital, Inc (Hercules). Please refer to Note 5, “Debt” and Note 6, “Commitments and Contingencies” for further details regarding the Company's debt service obligations and commitments. In addition, refer to Note 18, “Subsequent Events” for further details regarding the Company’s compliance with covenants in its loan facility with Hercules. The Company’s operating plan for 2015 contemplates significant reduction in the Company’s net cash outflows, resulting from (i) revenue growth from sales of existing and new products with positive gross margins, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2014, (iii) increased cash inflows from collaborations compared to 2014 (iv) maintaining operating expenses at levels comparable to 2014, and (v) access to various financing commitments. If the Company is unable to raise additional financing, or if other expected sources of funding are delayed or not received, the Company would take the following actions as early as the fourth quarter of 2015 to support its liquidity needs through the remainder of 2015 and into 2016: • Effect significant headcount reductions, particularly with respect to employees not connected to critical or contracted activities across all functions of the Company, including employees involved in general and administrative, research and development, and production activities. • Shift focus to existing products and customers with significantly reduced investment in new product and commercial development efforts. • Reduce production activity at the Company’s Brotas manufacturing facility to levels only sufficient to satisfy volumes required for product revenues forecast from existing products and customers. • Reduce expenditures for third party contractors, including consultants, professional advisors and other vendors. • Reduce or delay uncommitted capital expenditures, including non-essential facility and lab equipment, and information technology projects. • Closely monitor the Company’s working capital position with customers and suppliers, as well as suspend operations at pilot plants and demonstration facilities. Implementing this plan could have a negative impact on the Company's ability to continue its business as currently contemplated, including, without limitation, delays or failures in its ability to: • Achieve planned production levels; • Develop and commercialize products within planned timelines or at planned scales; and • Continue other core activities. Furthermore, any inability to scale-back operations as necessary, and any unexpected liquidity needs, could create pressure to implement more severe measures. Such measures could have an adverse effect on the Company's ability to meet contractual requirements, including obligations to maintain manufacturing operations, and increase the severity of the consequences described above.

Note 2 - Summary of Significant

Note 2 - Summary of Significant Accounting Policies	9 Months Ended
	Sep. 30, 2015
Accounting Policies [Abstract]
Significant Accounting Policies [Text Block]	2. Summary of Significant Accounting Policies Basis of Presentation The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K for the fiscal year ended December 31, 2014 as filed with the Securities and Exchange Commission (“SEC”) on March 31, 2015. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation. The Company uses the equity method to account for investments in companies, if its investments provide it with the ability to exercise significant influence over operating and financial policies of the investee. Consolidated net income or loss includes the Company’s proportionate share of the net income or loss of these companies. Judgments made by the Company regarding the level of influence over each equity method investment include considering key factors such as the Company’s ownership interest, representation on the board of directors, participation in policy-making decisions and material intercompany transactions. Principles of Consolidation The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated variable interest entities (or “VIEs”), with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest." Variable Interest Entities The Company has interests in joint venture entities that are VIEs. Determining whether to consolidate a VIE requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment. Use of Estimates In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates. Unaudited Interim Financial Information The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period. Recent Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (or “FASB”) issued new guidance related to revenue recognition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition update guidance provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. On July 9, 2015, the FASB voted to defer the effective date by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016. Therefore, the new standard will be effective commencing with our quarter ending March 31, 2018. In August 2014, FASB issued new guidance related to the disclosure around going concern. The new standard provides guidance around management's responsibility to evaluate whether there is substantial doubt about an entity's ability to continue as a going concern and to provide related footnote disclosure if substantial doubt exists. The new standard is effective for annual periods ending after December 15, 2016 and for annual periods and interim periods thereafter. Early adoption is permitted. The adoption of this standard is not expected to have a material impact on our financial statements. In January 2015, the FASB issued an update related to the presentation of extraordinary and unusual items. The update eliminates the concept of extraordinary items found in Subtopic 225-20, which required that an entity separately classify, present and disclose extraordinary events and transactions when the event or activity met both criteria of being unusual in nature and infrequent in occurrence. Although the concept of extraordinary items will be eliminated, the presentation and disclosure guidance for items that are unusual in nature or occur infrequently will be retained and will be expanded to include items that are both unusual in nature and infrequently occurring. The standard is effective for annual and interim periods within those annual years beginning after December 15, 2015. The Company expects that the adoption of the update will not materially affect its financial statements. In February 2015, FASB issued an amendment to ASC 810 Consolidation In April 2015, the FASB issued Accounting Standards Update 2015-3, Simplifying the Presentation of Debt Issuance Costs In July 2015, the FASB issued Accounting Standards Update 2015-11, Simplifying the Measurement of Inventory

Note 3 - Fair Value of Financia

Note 3 - Fair Value of Financial Instruments	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Financial Instruments Disclosure [Text Block]	3. Fair Value of Financial Instruments The inputs to the valuation techniques used to measure fair value are classified into the following categories: Level 1: Quoted market prices in active markets for identical assets or liabilities. Level 2: Observable market-based inputs or unobservable inputs that are corroborated by market data. Level 3: Unobservable inputs that are not corroborated by market data. As of September 30, 2015, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands): Level 1 Level 2 Level 3 Balance as of September 30, 2015 Financial Assets Money market funds $ 136 $ — $ — $ 136 Certificates of deposit 995 — — 995 Loans to affiliate (1) — — 1,747 1,747 Total financial assets $ 1,131 $ — $ 1,747 $ 2,878 Financial Liabilities Loans payable (1) $ — $ 9,421 $ — $ 9,421 Credit facilities (1) — 32,029 — 32,029 Convertible notes (1) — — 99,393 99,393 Compound embedded derivative liabilities — — 32,699 32,699 Temasek Funding Warrant derivative liability — 25,342 — $ 25,342 Currency interest rate swap derivative liability — 4,925 — 4,925 Total financial liabilities $ — $ 71,717 $ 132,092 $ 203,809 ________ (1) These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis (noting that the Remaining Notes subject to the Maturity Treatment Agreement were revalued to fair value on July 29, 2015, see Note 5 “Debt” for details). The Company’s assessment of the significance of a particular input to the fair value measurement in its entirety requires management to make judgments and consider factors specific to the asset or liability. The fair values of money market funds and certificates of deposit are based on fair values of identical assets. The fair values of the loans payable, convertible notes, credit facilities and currency interest rate swaps are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company. The method of determining the fair value of the compound embedded derivative liabilities is described below. Market risk associated with the fixed and variable rate long-term loans payable, credit facilities and convertible notes relates to the potential reduction in fair value and negative impact to future earnings, from an increase in interest rates. The fair value of loans to affiliates is based on the present value of expected future cash flows and assumptions about interest rates and the creditworthiness of the affiliate. Market risk associated with the compound embedded derivative liabilities relates to the potential reduction in fair value and negative impact to future earnings from a decrease in interest rates. The carrying amounts of certain financial instruments, such as cash equivalents, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. As of December 31, 2014, the Company’s financial assets and financial liabilities are presented below at fair value and were classified within the fair value hierarchy as follows (in thousands): Level 1 Level 2 Level 3 Balance as of December 31, 2014 Financial Assets Money market funds $ 20,160 $ — $ — $ 20,160 Certificates of deposit 1,375 — — 1,375 Loans to affiliate (1) — — 1,745 1,745 Total financial assets $ 21,535 $ — $ 1,745 $ 23,280 Financial Liabilities Loans payable $ — $ 16,720 $ — $ 16,720 Credit facilities — 39,332 — 39,332 Convertible notes (1) — — 222,031 222,031 Compound embedded derivative liabilities — — 56,026 56,026 Currency interest rate swap derivative liability — 3,710 — 3,710 Total financial liabilities $ — $ 59,762 $ 278,057 $ 337,819 (1) The following table provides a reconciliation of the beginning and ending balances for the convertible notes measured at fair value using significant unobservable inputs (Level 3) (in thousands): September 30, 2015 Balance at January 1 $ 222,031 Derecognition on debt conversion (124,175 ) Change in fair value of convertible notes 1,537 Balance at September 30 $ 99,393 Derivative Instruments The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liabilities measured at fair value using significant unobservable inputs (Level 3) (in thousands): September 30, 2015 Balance at January 1 $ 56,026 Additions to Level 3 229 Derecognition on debt conversion (24,598 ) Loss from change in fair value of derivative liabilities 1,042 Balance at September 30 $ 32,699 The compound embedded derivative liabilities, represent the fair value of the equity conversion options and "make-whole" provisions or down round conversion price adjustments to provisions of outstanding convertible promissory notes issued to Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or “Total” and such convertible promissory notes, the “Total Notes”), as well as Tranche I Notes (as defined below), Tranche II Notes (as defined below) and notes issued under the Rule 144A convertible notes offering (or the “Rule 144A Notes”) (see Note 5, "Debt"). There is no current observable market for these types of derivatives and, as a result, the Company determined the fair value of the embedded derivatives using a Monte Carlo simulation valuation model for the Total Notes and the binomial lattice model for the Tranche I Notes, Tranche II Notes and the Rule 144A Notes (or together the “Convertible Notes”). A Monte Carlo simulation valuation model combines expected cash outflows with market-based assumptions regarding risk-adjusted yields, stock price volatility, probability of a change of control and the trading information of the Company's common stock into which the notes are or may be convertible. A binomial lattice model generates two probable outcomes - one up and another down - arising at each point in time, starting from the date of valuation until the maturity date. A lattice model was used to determine if the convertible notes would be converted, called or held at each decision point. Within the lattice model, the following assumptions are made: (i) the Convertible Notes will be converted early if the conversion value is greater than the holding value and (ii) the Convertible Notes will be called if the holding value is greater than both (a) redemption price and (b) the conversion value at the time. If the Convertible Notes are called, then the holder will maximize their value by finding the optimal decision between (1) redeeming at the redemption price and (2) converting the Convertible Notes. Using this lattice method, the Company valued the embedded derivatives using the "with-and-without method", where the fair value of the Convertible Notes including the embedded derivative is defined as the "with", and the fair value of the Convertible Notes excluding the embedded derivatives is defined as the "without". This method estimates the fair value of the embedded derivatives by looking at the difference in the values between the Convertible Notes with the embedded derivatives and the fair value of the Convertible Notes without the embedded derivatives. The lattice model uses the stock price, conversion price, maturity date, risk-free interest rate, estimated stock volatility and estimated credit spread. The Company marks the compound embedded derivatives to market due to the conversion price not being indexed to the Company's own stock. Except for the "make-whole interest" provision included in the conversion option, which is only required to be settled in cash upon a change of control at the noteholder's option, the compound embedded derivative will be settled in either cash or shares. As of September 30, 2015, the Company has sufficient common stock available to settle the conversion option in shares. On July 29, 2015, the Company closed the "Exchange" pursuant to that certain Exchange Agreement dated as of July 26, 2015 (the "Exchange Agreement"), among the Company, Temasek and Total, under which these stockholders exchanged an aggregate of $138 million of Convertible Notes for common stock of the Company at a price of $2.30 per share (representing a change from the originally agreed conversion price for the relevant Convertible Notes, see Note 5 "Debt" for further details), with an additional $37 million of outstanding Convertible Notes held by Total and Temasek being restructured to eliminate the Company's repayment obligation at maturity and provide for mandatory conversion to the Company's common stock at maturity. As of September 30, 2015 and December 31, 2014, included in "Derivative Liabilities" on the consolidated balance sheet are the Company's compound embedded derivative liabilities of $32.7 million and $56.0 million, respectively, which represents the fair value of the equity conversion options and a "make-whole" provision relating to the outstanding Total Notes, Tranche I Notes, Tranche II Notes and 144A. The market-based assumptions and estimates used in valuing the compound embedded derivative liabilities include amounts in the following ranges/amounts: September 30, 2015 September 30, 2014 Risk-free interest rate 0.93% - 1.07% 0.79% - 1.67% Risk-adjusted yields 24.40% - 39.90% 15.10% - 24.40% Stock-price volatility 45% 45% Probability of change in control 5% 5% Stock price $2.01 $3.79 Credit spread 28.81% - 38.83% 13.54% - 22.73% Estimated conversion dates 2015 - 2019 2017 - 2019 Changes in valuation assumptions can have a significant impact on the valuation of the embedded derivative liabilities. For example, all other things being equal, a decrease/increase in the Company’s stock price, probability of change of control, credit spread, term to maturity/conversion or stock price volatility decreases/increases the valuation of the liabilities, whereas a decrease/increase in risk adjusted yields or risk-free interest rates increases/decreases the valuation of the liabilities. The conversion price of certain of the convertible notes also include conversion price adjustment features and for, example, issuances of common stock by the Company at prices lower than the conversion price result in a reset of the conversion price of such notes, which increases the value of the embedded derivative liabilities. See Note 5, "Debt" for further details of conversion price adjustment features. In June 2012, the Company entered into a loan agreement with Banco Pine S.A. (or Banco Pine) under which Banco Pine provided the Company with a loan (or the Banco Pine Bridge Loan) (see Note 5, "Debt"). At the time of the Banco Pine Bridge Loan, the Company also entered into a currency interest rate swap arrangement with Banco Pine with respect to the repayment of R$22.0 million (approximately US$5.5 million based on the exchange rate as of September 30, 2015) of the Banco Pine Bridge Loan. The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan for alternative principal and interest payments that are subject to adjustment based on fluctuations in the foreign exchange rate between the U.S. dollar and Brazilian real. The swap has a fixed interest rate of 3.94%. Changes in the fair value of the swap are recognized in “Gain (loss) from change in fair value of derivative instruments" in the condensed consolidated statements of operations are as follows (in thousands): Income Three Months Ended September 30, Nine Months Ended September 30, Type of Derivative Contract 2015 2014 2015 2014 Loss Recognized Loss Recognized Currency interest rate swap Gain (loss) from change in fair value of derivative instruments $ (1,796 ) $ (1,139 ) $ (3,201 ) $ (83 ) The Company granted a warrant to Temasek to purchase the Company’s common stock, (the “Temasek Funding Warrant”), as part of the Exchange transaction completed on July 29, 2015. The terms of the Temasek Funding Warrant provide for an adjustment to the number of shares issuable in the future based on the number of any additional shares for which certain other outstanding convertible promissory notes may become exercisable as a result of a reduction to the conversion price of such notes, including down-round provisions. As a result of the future adjustment feature (for reduction to the conversion price of outstanding convertible notes), the Company determined the Temasek Funding Warrant would not meet the conditions in ASC 815-40-15 to be considered indexed to the Company’s own equity. Consequently the Temasek Funding Warrant is a derivative and will be marked to market each reporting period. The Temasek Funding Warrant is valued using a Black-Scholes valuation model with the following assumptions (in addition to the Company’s share price): Initial recognition (July 29, 2015) September 30, 2015 Expected dividend yield 0 0 Risk-free interest rate 2 % 2 % Expected term (in years) 10.00 10.00 Expected volatility 74 % 74 % The Company recognized a derivative liability for the Temasek Funding Warrant of $19.4 million on July 29, 2015 and revalued the derivative liability to $25.3 million at September 30, 2015. The increase in the liability was principally due to the decrease in the Company’s share price between July 29, 2015 and September 30, 2015. 12.7 million shares were potentially issuable (for an exercise price of $0.01 per share) under the Temasek Funding Warrant on September 30, 2015. Derivative instruments measured at fair value as of September 30, 2015 and December 31, 2014, and their classification on the condensed consolidated balance sheets are as follows (in thousands): September 30, 2015 December 31, 2014 Fair market value of swap obligation $ 4,925 $ 3,710 Fair value of compound embedded derivative liabilities 32,699 56,026 Temasek Funding Warrant derivative liability 25,342 — Total derivative liabilities $ 62,966 $ 59,736

Note 4 - Balance Sheet Componen

Note 4 - Balance Sheet Components	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Supplemental Balance Sheet Disclosures [Text Block]	4. Balance Sheet Components Inventories, net Inventories are stated at the lower of cost or market and consist of the following (in thousands): September 30, 2015 December 31, 2014 Raw materials $ 1,928 $ 2,665 Work-in-process 6,470 5,269 Finished goods 2,704 6,572 Inventories, net $ 11,102 $ 14,506 Prepaid Expenses and Other Current Assets Prepaid expenses and other current assets are comprised of the following (in thousands): September 30, 2015 December 31, 2014 Maintenance $ 200 $ 399 Prepaid insurance 167 701 Manufacturing catalysts 2,928 1,166 Recoverable VAT and other taxes 2,085 2,411 Debt issuance costs 441 — Other 1,213 1,857 Prepaid expenses and other current assets $ 7,034 $ 6,534 Property, Plant and Equipment, net Property, plant and equipment, net is comprised of the following (in thousands): September 30, 2015 December 31, 2014 Leasehold improvements $ 38,505 $ 39,132 Machinery and equipment 72,433 90,657 Computers and software 8,947 8,946 Furniture and office equipment 2,231 2,445 Buildings 3,855 6,321 Vehicles 196 353 Construction in progress 33,082 38,815 159,249 186,669 Less: accumulated depreciation, amortization and impairment (77,308 ) (67,689 ) Property, plant and equipment, net $ 81,941 $ 118,980 The Company's first, purpose-built, large-scale Biofene production plant in southeastern Brazil commenced operations in December 2012. This plant is located at Brotas in the state of São Paulo, Brazil and is adjacent to an existing sugar and ethanol mill, Tonon Bioenergia S.A. (or “Tonon”) (formerly Paraíso Bioenergia) with which the Company has an agreement to purchase a certain number of tons of sugarcane per year, along with specified water and vapor volumes. In July 2015, the Company announced that it was in discussions with SMSA regarding the continuation of the joint venture. Specifically, the Company and SMSA agreed to continue the joint venture pending discussions through August 31, 2015 in order to evaluate the best investment options available to optimize returns and provide balanced economics for both parties. In September 2015, the Company entered into negotiations with SMSA to agree to terms for the termination of the joint venture and the Company has determined that there is no realistic prospect of the joint venture continuing. Consequently, an impairment assessment of the assets was performed by management during the third quarter of 2015. The Company expects to be required to remove the existing assets of the joint venture, which are currently situated on land owned by SMSA (the “SMSA site”). The Company plans to construct the production facility at an alternative location. The Company recorded an impairment charge of $7.3 million (included in ‘Loss on purchase commitments and impairment of property, plant and equipment’) for the quarter ended September 30, 2015 for the immovable assets at the SMSA site, which are to be abandoned with no expected salvage value, including $0.6 million of irrecoverable Brazilian VAT related to the assets. Moveable assets are to be relocated to an alternative location and used in construction of a comparable facility to that planned with SMSA, utilizing the joint venture assets that will be transferred from the SMSA site. If our plans or estimate of the value of the remaining assets change, additional impairment charges may arise in future periods. Property, plant and equipment, net includes $1.3 million and $4.1 million of machinery and equipment under capital leases as of September 30, 2015 and December 31, 2014, respectively. Accumulated amortization of assets under capital leases totaled $0.3 million and $2.3 million as of September 30, 2015 and December 31, 2014, respectively. Depreciation and amortization expense, including amortization of assets under capital leases was $3.1 million and $3.8 million for the three months ended September 30, 2015 and 2014, respectively, and was $9.9 million and $11.3 million for the nine months ended September 30, 2015 and 2014, respectively. Other Assets (non-current) Other assets are comprised of the following (in thousands): September 30, 2015 December 31, 2014 Deposits on property and equipment, including taxes $ 827 $ 1,738 Recoverable taxes from Brazilian government entities 6,814 9,747 Debt issuance costs 697 851 Other 1,253 1,299 Total other assets $ 9,591 $ 13,635 Accrued and Other Current Liabilities Accrued and other current liabilities are comprised of the following (in thousands): September 30, 2015 December 31, 2014 Professional services $ 3,876 $ 2,015 Accrued vacation 1,920 2,213 Payroll and related expenses 3,785 5,393 Tax-related liabilities 1,282 277 Deferred rent, current portion 1,110 1,111 Accrued interest 2,606 1,308 Contractual obligations to contract manufacturers 541 310 Commitment loan fee 750 — Other 962 938 Total accrued and other current liabilities $ 16,832 $ 13,565

Note 5 - Debt

Note 5 - Debt	9 Months Ended
	Sep. 30, 2015
Debt Disclosure [Abstract]
Debt Disclosure [Text Block]	5. Debt Debt is comprised of the following (in thousands): September 30, 2015 December 31, 2014 FINEP credit facility $ 889 $ 1,614 BNDES credit facility 2,163 4,314 Hercules loan facility 23,503 29,779 Total credit facilities 26,555 35,707 Convertible notes 71,971 60,418 Related party convertible notes 42,401 115,239 Loans payable 12,908 21,097 Total debt 153,835 232,461 Less: current portion (20,902 ) (17,100 ) Long-term debt $ 132,933 $ 215,361 FINEP Credit Facility In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (or the “FINEP Credit Facility”). The FINEP Credit Facility was extended to partially fund expenses related to the Company’s research and development project on sugarcane-based biodiesel (or the “FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$1.6 million based on the exchange rate as of September 30, 2015), which is secured by a chattel mortgage on certain equipment of Amyris Brasil as well as by bank letters of guarantee. All available credit under this facility is fully drawn. Interest on loans drawn under the FINEP Credit Facility is fixed at 5% per annum. In case of default under or non-compliance with the terms of the agreement, the interest on loans will be dependent on the long-term interest rate as published by the Central Bank of Brazil (such rate, the “TJLP”). If the TJLP at the time of default is greater than 6%, then the interest will be 5% plus a TJLP adjustment factor, otherwise the interest will be 11% per annum. In addition, a fine of up to 10% shall apply to the amount of any obligation in default. Interest on late balances will be 1% per month, levied on the overdue amount. Payment of the outstanding loan balance is being made in 81 monthly installments, which commenced in July 2012 and extends through March 2019. Interest on loans drawn and other charges are paid on a monthly basis and commenced in March 2011. As of September 30, 2015 and December 31, 2014, the total outstanding loan balance under the FINEP Credit Facility was R$3.5 million (approximately US$0.9 million based on the exchange rate as of September 30, 2015) and R$4.3 million (approximately US$1.6 million based on exchange rate as of December 31, 2014), respectively. The FINEP Credit Facility contains the following significant terms and conditions: • The Company was required to share with FINEP the costs associated with the FINEP Project. At a minimum, the Company was required to contribute from its own funds approximately R$14.5 million (approximately US$3.6 million based on the exchange rate as of September 30, 2015) of which R$11.1 million was contributed prior to the release of the second disbursement. All four disbursements were completed and the Company has fulfilled all of its cost sharing obligations; • After the release of the first disbursement, prior to any subsequent drawdown from the FINEP Credit Facility, the Company was required to provide bank letters of guarantee of up to R$3.3 million in aggregate (approximately US$0.8 million based on the exchange rate as of September 30, 2015). On December 17, 2012 and prior to release of the second disbursement on December 26, 2012, the Company obtained the required bank letter of guarantees from Banco ABC Brasil S.A. (or "ABC"); and • Amounts disbursed under the FINEP Credit Facility were required to be used towards the FINEP Project within 30 months after the contract execution. BNDES Credit Facility In December 2011, the Company entered into a credit facility with the Brazilian Development Bank (or “BNDES” and such credit facility is the “BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$5.6 million based on the exchange rate as of September 30, 2015). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line was divided into an initial tranche of up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that would become available upon delivery of additional guarantees. The credit line was cancelled in 2013. The principal of the loans under the BNDES Credit Facility is required to be repaid in 60 monthly installments, with the first installment paid in January 2013 and the last due in December 2017. Interest was due initially on a quarterly basis with the first installment due in March 2012. From and after January 2013, interest payments are due on a monthly basis together with principal payments. The loaned amounts carry interest of 7% per annum. Additionally, there is a credit reserve charge of 0.1% on the unused balance from each credit installment from the day immediately after it is made available through its date of use, when it is paid. The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets totaling R$24.9 million (approximately $6.3 million based on the exchange rate as of September 30, 2015). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company was required to provide a bank guarantee equal to 10% of the total approved amount (R$22.4 million in total debt) available under the BNDES Credit Facility. For advances of the second tranche (above R$19.1 million), the Company is required to provide additional bank guarantees equal to 90% of each such advance, plus additional Company guarantees equal to at least 130% of such advance. The BNDES Credit Facility contains customary events of default, including payment failures, failure to satisfy other obligations under this credit facility or related documents, defaults in respect of other indebtedness, bankruptcy, insolvency and inability to pay debts when due, material judgments, and changes in control of Amyris Brasil. If any event of default occurs, BNDES may terminate its commitments and declare immediately due all borrowings under the facility. As of September 30, 2015 and December 31, 2014, the Company had R$8.6 million (approximately US$2.2 million based on the exchange rate as of September 30, 2015) and R$11.5 million (approximately US$4.3 million based on the exchange rate as of December 31, 2014), respectively, in outstanding advances under the BNDES Credit Facility. Hercules Loan Facility In March 2014, the Company entered into a Loan and Security Agreement with Hercules Technology Growth Capital, Inc. (or “Hercules”) to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (or the "Hercules Loan Facility"). The original Hercules Loan Facility accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 6.25% or 9.50%. The Company may repay the loaned amounts before the maturity date (generally February 1, 2017) if it pays an additional fee of 3% of the outstanding loans (1% if after the initial twelve-month period of the loan). The Company was also required to pay a 1% facility charge at the closing of the transaction, and is required to pay a 10% end of term charge. In connection with the original Hercules Loan Facility, Amyris agreed to certain customary representations and warranties and covenants, as well as certain covenants that were subsequently amended (as described below). The total available credit of $25.0 million under this facility was fully drawn down by the Company. In June 2014, the Company and Hercules entered into a first amendment (or the “First Hercules Amendment”) of Hercules Loan Facility. Pursuant to the First Hercules Amendment, the parties agreed to adjust the term loan maturity date from May 31, 2015 to February 1, 2017 and remove (i) a requirement for the Company to pay a forbearance fee of $10.0 million in the event certain covenants were not satisfied, (ii) a covenant that the Company maintain positive cash flow commencing with the fiscal quarter beginning October 1, 2014, (iii) a covenant that, beginning with the fiscal quarter beginning July 1, 2014, the Company and its subsidiaries achieve certain projected cash product revenues and projected cash product gross profits, and (iv) an obligation for the Company to file a registration statement on Form S-3 with the SEC by no later than June 30, 2014 and complete an equity financing of more than $50.0 million by no later than September 30, 2014. The Company further agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in U.S. bank accounts an amount equal to at least 50% of the principal amount then outstanding under the Hercules Loan Facility and borrow an additional $5.0 million. The additional $5.0 million borrowing was completed in June 2014, and accrues interest at a rate per annum equal to the greater of either the prime rate reported in the Wall Street Journal plus 5.25% or 8.5%. The Hercules Loan Facility is secured by liens on the Company's assets, including on certain Company intellectual property. The Hercules Loan Facility includes customary events of default, including failure to pay amounts due, breaches of covenants and warranties, material adverse effect events, certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due. In March 2015, the Company and Hercules entered into a second amendment (or the “Second Hercules Amendment”) of the Hercules Loan Facility. Pursuant to the Second Hercules Amendment, the parties agreed to, among other things, establish an additional credit facility in the principal amount of up to $15.0 million, which would be available to be drawn by the Company at its sole election (in increments of $5.0 million) through the earlier of March 31, 2016 or such time as the Company raises an aggregate of at least $20.0 million through the sale of new equity securities, subject to certain conditions, including the receipt of third party consents and a requirement to first make certain draw-downs under an equity line of credit that the Company previously secured (to the extent the Company is permitted to do so under the terms thereof). Commencing with the quarter in which the Company borrows any amounts under this additional facility, the Company becomes subject to a covenant to achieve certain amounts of product revenues. Under the terms of the Second Hercules Amendment, the Company agreed to pay Hercules a 3.0% facility availability fee on April 1, 2015. If the facility was not canceled, and any outstanding borrowings were not repaid, before June 30, 2015, an additional 5.0% facility fee became payable on June 30, 2015. The Company did not pay the additional facility fee and thereafter received a waiver from Hercules with respect thereto. The Company had the ability to cancel the additional facility at any time prior to June 30, 2015 at its own option, and the additional facility would terminate upon the Company securing a new equity financing of at least $20.0 million. The additional facility was cancelled undrawn upon the completion of the Company’s Private Offering in July 2015. As of September 30, 2015, $23.5 million was outstanding under the Hercules Loan Facility, net of discount of $0.2 million. The Company’s loan facility with Hercules requires the Company to maintain unrestricted, unencumbered cash in U.S. bank accounts in an amount equal to at least 50% of the principal amount outstanding under such facility. The Company received a waiver from Hercules with respect to non-compliance with such covenants. As of the date of issuance of this report, the Company is in compliance with all of its Hercules debt agreements. Convertible Notes Fidelity In February 2012, the Company completed the sale of senior unsecured convertible promissory notes in an aggregate principal amount of $25.0 million pursuant to a securities purchase agreement, between the Company and certain investment funds affiliated with FMR LLC (or the "Fidelity Securities Purchase Agreement"). The offering consisted of the sale of 3% senior unsecured convertible promissory notes with a March 1, 2017 maturity date and an initial conversion price equal to $7.0682 per share of the Company's common stock, subject to proportional adjustment for adjustments to outstanding common stock and anti-dilution provisions in case of dividends and distributions (or the "Fidelity Notes"). As of September 30, 2015, the Fidelity Notes were convertible into an aggregate of up to 3,536,968 shares of the Company's common stock. Such note holders have a right to require repayment of 101% of the principal amount of the Fidelity Notes in an acquisition of the Company, and the notes provide for payment of unpaid interest on conversion following such an acquisition if the note holders do not require such repayment. The Fidelity Securities Purchase Agreement and Fidelity Notes include covenants regarding payment of interest, maintaining the Company's listing status, limitations on debt, maintenance of corporate existence, and timely filing of SEC reports. The Fidelity Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, material adverse effect clauses and breaches of the covenants in the Fidelity Securities Purchase Agreement and Fidelity Notes, with default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Fidelity Notes include restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Fidelity Notes provide that the Company's total outstanding debt at any time cannot exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt cannot exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of a short-term bridge loan for $35.0 million in October 2013, holders of the Fidelity Notes waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan (or the “Temasek Bridge Note”) and the August 2013 Financing (defined below). In consideration for such waiver, the Company granted to holders of the Fidelity Notes or their affiliates, the right to purchase up to an aggregate of $7.6 million worth of convertible promissory notes in the first tranche of the August 2013 Financing. Pursuant to a Securities Purchase Agreement among the Company, Maxwell (Mauritius) Pte Ltd (or “Temasek”) and Total, dated as of August 8, 2013 (or the “August 2013 SPA”), as amended in October 2013 to include certain entities affiliated with FMR LLC (or the “Fidelity Entities”), the Company sold and issued certain senior convertible promissory notes (or the "Tranche I Notes") pursuant to a financing (or the “August 2013 Financing”) exempt from registration under the Securities Act of 1933, as amended, (the "Securities Act"), with an aggregate principal amount of $7.6 million of Tranche I Notes sold to the Fidelity Entities. See "Related Party Convertible Notes" in Note 5, "Debt." Rule 144A Convertible Note Offering In May 2014, the Company entered into a Purchase Agreement with Morgan Stanley & Co. LLC, as the initial purchaser (or the “Initial Purchaser”), relating to the sale of $75.0 million aggregate in principal amount of its 6.50% Convertible Senior Notes due 2019 (or the "144A Notes") to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers (or the "Rule 144A Convertible Note Offering"). In addition, the Company granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of 144A Notes, which option expired according to its terms. Under the terms of the purchase agreement for the 144A Notes, the Company agreed to customary indemnification of the Initial Purchaser against certain liabilities. The Notes were issued pursuant to an Indenture, dated as of May 29, 2014 (or the “Indenture”), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the 144A Notes were approximately $72.0 million after payment of the Initial Purchaser’s discounts and offering expenses. In addition, in connection with obtaining a waiver from Total of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by the Company for new notes issued in the offering, the Company used approximately $9.7 million of the net proceeds to repay previously issued notes (representing the amount of 144A Notes purchased by Total from the Initial Purchaser). Certain of the Company's affiliated entities purchased $24.7 million in aggregate principal amount of 144A Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). The 144A Notes bear interest at a rate of 6.50% per year, payable semiannually in arrears on May 15 and November 15 of each year, beginning November 15, 2014. The 144A Notes mature on May 15, 2019, unless earlier converted or repurchased. The 144A Notes are convertible into shares of the Company's common stock at any time prior to the close of business day on May 15, 2019. The 144A Notes have an initial conversion rate of 267.037 shares of Common Stock per $1,000 principal amount of 144A Notes (subject to adjustment in certain circumstances). This represents an initial effective conversion price of approximately $3.74 per share of common stock. For any conversion on or after May 15, 2015, in the event that the last reported sale price of the Company’s common stock for 20 or more trading days (whether or not consecutive) in a period of 30 consecutive trading days ending within five trading days immediately prior to the date the Company receives a notice of conversion exceeds the conversion price of $3.74 per share on each such trading day, the holders, in addition to the shares deliverable upon conversion, will be entitled to receive a cash payment equal to the present value of the remaining scheduled payments of interest that would have been made on the 144A Notes being converted from the conversion date to the earlier of the date that is three years after the date the Company receives such notice of conversion and maturity (May 15, 2019). In the event of a fundamental change, as defined in the Indenture, holders of the 144A Notes may require the Company to purchase all or a portion of the 144A Notes at a price equal to 100% of the principal amount of the 144A Notes, plus any accrued and unpaid interest to, but excluding, the fundamental change repurchase date. Holders of the 144A Notes who convert their 144A Notes in connection with a make-whole fundamental change will receive additional shares representing the present value of the remaining interest payments which will be computed using a discount rate of 0.75%. If a holder of 144A Notes elects to convert its 144A Notes prior to the effective date of any make-whole fundamental change, such holder will not be entitled to an increased conversion rate in connection with such conversion. Refer to the “Exchange” and “Maturity Treatment Agreement” sections of this Note 5, "Debt", for details of the impact of the Maturity Treatment and Exchange agreements on the 144A Notes. Related Party Convertible Notes Total R&D Convertible Notes In July 2012, the Company entered into an agreement with Total that expanded Total's investment in its Biofene collaboration with the Company, provided new structure for a joint venture (or the "Fuels JV") to commercialize the products encompassed by the diesel and jet fuel research and development program (or the "Program"), and established a convertible debt structure for the collaboration funding from Total (or the "July 2012 Agreements"). The purchase agreement for the notes related to the funding from Total (or the “Total Purchase Agreement”) provided for the sale of the Total Notes consisting of an aggregate of $105.0 million in 1.5% Senior Unsecured Convertible Note due March 2017 as follows: • As part of an initial closing under the Total Purchase Agreement (which was completed in two installments), (i) on July 30, 2012, the Company sold a Total Note with a principal amount of $38.3 million, including $15.0 million in new funds and $23.3 million in previously-provided diesel research and development funding by Total, and (ii) on September 14, 2012, the Company sold another Total Note for $15.0 million in new funds from Total. • At a second closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Total Notes for an aggregate of $30.0 million in new funds from Total ($10.0 million in June 2013 and $20.0 million in July 2013). • At a third closing under the Total Purchase Agreement (also completed in two installments) the Company sold additional Total Notes for an aggregate of $21.7 million in new funds from Total ($10.85 million in July 2014 and $10.85 million in January 2015) (or the “Third Closing Notes”). The Total Notes have a maturity date of March 1, 2017, an initial conversion price equal to $7.0682 per share for the Total Notes issued under the initial closing, an initial conversion price equal to $3.08 per share for the Total Notes issued under the second closing and an initial conversion price equal to $4.11 per share for the Third Closing Notes. The Total Notes bear interest of 1.5% per annum (with a default rate of 2.5%), accruing from the date of funding and payable at maturity or on conversion or a change of control where Total exercises the right to require the Company to repay the notes. Accrued interest is partially or fully cancelled if the Total Notes are cancelled based on a final decision by Total to go forward with the fuels collaboration (either partially with respect to jet fuel or fully with respect to jet fuel and diesel (a “Go” decision) (see Note 8, "Significant Agreements"). The agreements contemplate that the research and development efforts under the Program may extend through 2016, with a series of “Go/No Go” decisions (see Note 8, "Significant Agreements") by Total through such date tied to funding by Total. The Total Notes become convertible into the Company's common stock (i) within 10 trading days prior to maturity (if they are not cancelled as described above prior to their maturity date), (ii) on a change of control of the Company, (iii) if Total is no longer the largest stockholder of the Company following a “No-Go” decision (subject to a six-month lock-up with respect to any shares of common stock issued upon conversion), and (iv) on a default by the Company. If Total makes a final “Go” decision with respect to the full fuels collaboration, then the Total Notes will be exchanged by Total for equity interests in the Fuels JV, after which the Total Notes will not be convertible and any obligation to pay principal or interest on the Total Notes will be extinguished. In case of a “Go” decision only with respect to jet fuel, the parties would form an operational joint venture only for jet fuel (and the rights associated with diesel would terminate), 70% of the outstanding Total Notes would remain outstanding and become payable by the Company, and 30% of the outstanding Total Notes would be cancelled. If Total makes a “No-Go” decision, outstanding Total Notes will remain outstanding and become payable at maturity. In connection with the December 2012 private placement of the Company’s common stock involving certain existing stockholders of the Company (see Note 10, "Stockholders' Equity"), Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in Total Notes issued in the initial closing into 1,677,852 of the Company's common stock at a price of $2.98 per share. As such, $5.0 million of Total's outstanding $53.3 million in Total Notes issued in the initial closing was cancelled. The cancellation of the debt was treated as an extinguishment of debt in accordance with the guidance outlined in ASC 470-50. As a result of the exchange and cancellation of the $5.0 million debt, the Company recorded a loss from extinguishment of debt of $0.9 million in the year ended December 31, 2012. In March 2013, the Company entered into a letter agreement with Total (or the “March 2013 Letter Agreement”) under which Total agreed to waive its right to cease its participation in the parties' fuels collaboration at the July 2013 decision point and committed to proceed with the second closing under the Total Purchase Agreement (subject to the Company's satisfaction of the relevant closing conditions for such funding in the Total Purchase Agreement). As consideration for this waiver and commitment, the Company agreed to: • reduce the conversion price for the $30.0 million in principal amount of Total Notes to be issued in connection with the second closing of the Total Notes (as described above) from $7.0682 per share to a price per share equal to the greater of (i) the consolidated closing bid price of the Company's common stock on the date of the March 2013 Letter Agreement, plus $0.01, and (ii) $3.08 per share, provided that the conversion price would not be reduced by more than the maximum possible amount permitted under the rules of The NASDAQ Stock Market (or “NASDAQ”) such that the new conversion price would require the Company to obtain stockholder consent; and • grant Total a senior security interest in the Company's intellectual property, subject to certain exclusions and subject to release by Total when the Company and Total enter into final documentation regarding the establishment of the Fuels JV. In addition to the waiver by Total described above, Total also agreed that, at the Company's request and contingent upon the Company meeting its obligations described above, it would pay advance installments of the amounts otherwise payable at the second closing. In June 2013, the Company sold and issued $10.0 million in principal amount of Total Notes to Total pursuant to the second closing of the Total Notes as discussed above. In accordance with the March 2013 Letter Agreement, this Total Note has an initial conversion price equal to $3.08 per share of the Company's common stock. In July 2013, the Company sold and issued $20.0 million in principal amount of Total Notes to Total pursuant to the second closing of the Total Notes as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of the Total Notes in the second closing by July 2013. In accordance with the March 2013 Letter Agreement, this Total Note has an initial conversion price equal to $3.08 per share of the Company's common stock. The conversion prices of the Total Notes were subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total had a right to require repayment of 101% of the principal amount of the Total Notes in the event of a change of control of the Company and the Total Notes provided for payment of unpaid interest on conversion following such a change of control if Total did not require such repayment. The Total Purchase Agreement and Total Notes included covenants regarding payment of interest, maintenance of the Company's listing status, limitations on debt, maintenance of corporate existence, and filing of SEC reports. The Total Notes include standard events of default resulting in acceleration of indebtedness, including failure to pay, bankruptcy and insolvency, cross-defaults, and breaches of the covenants in the Total Purchase Agreement and Total Notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the Total Notes included restrictions on the amount of debt the Company is permitted to incur. With exceptions for certain existing debt, refinancing of such debt and certain other exclusions and waivers, the Total Notes provided that the Company's total outstanding debt at any time could not exceed the greater of $200.0 million or 50% of its consolidated total assets and its secured debt could not exceed the greater of $125.0 million or 30% of its consolidated total assets. In connection with the Company’s closing of the Temasek Bridge Note for $35.0 million and the August 2013 Financing and in connection with the Rule 144A Convertible Note Offering in May 2014, Total waived compliance with the debt limitations outlined above as to the Temasek Bridge Note, the August 2013 Financing and the Rule 144A Convertible Note Offering. In December 2013, in connection with the Company's entry into a Shareholders Agreement dated December 2, 2013 and License Agreement dated December 2, 2013 (or, collectively, the “JV Documents”) with Total and Total Amyris BioSolutions B.V. (or “JVCO”) relating to the establishment of JVCO (see Note 7, "Joint Ventures and Noncontrolling Interest"), the Company (i) exchanged the $69.0 million of the then-outstanding Total Notes issued pursuant to the Total Purchase Agreement for replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (or the “Replacement Notes”) or, when referencing Replacement Notes outstanding as of June 30, 2015 sometimes referred to the Total Notes), ii) granted to Total a security interest in and lien on all Amyris’ rights, title and interest in and to Company’s shares in the capital of JVCO and (iii) agreed that any securities to be purchased and sold at the third closing under the Total Purchase Agreement by Total would be Replacement Notes instead of Total Notes. As a consequence of executing the JV Documents and forming JVCO, the security interest in all of the Company's intellectual property, granted by the Company in favor of Total, Temasek, and certain Fidelity Entities pursuant to the Restated Intellectual Property Security Agreement dated as of October 16, 2013, were automatically terminated effective as of December 2, 2013 upon Total’s and the Company’s joint written notice to Temasek and the Fidelity Entities. In April 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (or the “March 2014 Total Letter Agreement”) to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents) and the Total Purchase Agreement. Under the March 2014 Total Letter Agreement, the Company agreed to, (i) amend the conversion price of the Replacement Notes to be issued in the third closing under the Total Purchase Agreement from $7.0682 per share to $4.11 per share subject to stockholder approval at the Company's 2014 annual meeting (which was obtained in May 2014), (ii) extend the period during which Total may exchange for other Company securities Replacement Notes issued under the July 2012 Agreements from June 30, 2014 to the later of December 31, 2014 and the date on which the Company shall have raised $75.0 million of equity and/or convertible debt financing (excluding any convertible promissory notes issued pursuant to the Total Purchase Agreement), (iii) eliminate the Company’s ability to qualify, in a disclosure letter to Total, certain of the representations and warranties that the Company must make at the closing of any third closing sale, and (iv) beginning on March 31, 2014, provide Total with monthly reporting on the Company’s cash, cash equivalents and short-term investments. In consideration of these agreements, Total agreed to waive its right not to consummate the closing of the issuance of the Third Closing Notes if it had decided not to proceed with the collaboration and had made a "No-Go" decision with respect thereto. In July 2014, the Company sold and issued a Replacement Note to Total with a principal amount of $10.85 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement. This purchase and sale constituted the initial installment of the $21.7 million third closing described above. In accordance with the March 2014 Total Letter Agreement, this convertible note has an initial conversion price equal to $4.11 per share of the Company's common stock. In January 2015, the Company sold and issued a Replacement Note to Total with a principal amount of $10.85 million with a Mar

Note 6 - Commitments and Contin

Note 6 - Commitments and Contingencies	3 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Commitments Contingencies and Guarantees [Text Block]	6. Commitments and Contingencies Lease Obligations The Company leases certain facilities and finances certain equipment under operating and capital leases, respectively. Operating leases include leased facilities and capital leases include leased equipment (see Note 4, "Balance Sheet Components"). The Company recognizes rent expense on a straight-line basis over the non-cancellable lease term and records the difference between rent payments and the recognition of rent expense as a deferred rent liability. Where leases contain escalation clauses, rent abatements, and/or concessions, such as rent holidays and landlord or tenant incentives or allowances, the Company applies them as a straight-line rent expense over the lease term. The Company has non-cancellable operating lease agreements for office, research and development, and manufacturing space that expire at various dates, with the latest expiration in February 2031. Rent expense under operating leases was $1.4 million and $1.3 million for the three months ended September 30, 2015 and 2014, respectively, and was $3.9 million and $4.0 million for the nine months ended September 30, 2015 and 2014, respectively. Future minimum payments under the Company's lease obligations as of September 30, 2015, are as follows (in thousands): Years ending December 31: Capital Operating Total Lease Obligations 2015 (remaining three months) $ 187 $ 1,696 $ 1,883 2016 530 6,755 7,285 2017 187 6,642 6,829 2018 — 6,700 6,700 2019 — 6,748 6,748 Thereafter — 25,026 25,026 Total future minimum lease payments 904 $ 53,567 $ 54,471 Less: amount representing interest (70 ) Present value of minimum lease payments 834 Less: current portion (555 ) Long-term portion $ 279 Guarantor Arrangements The Company has agreements whereby it indemnifies its officers and directors for certain events or occurrences while the officer or directors are serving in their official capacities. The indemnification period remains enforceable for the officer's or director’s lifetime. The maximum potential amount of future payments the Company could be required to make under these indemnification agreements is unlimited; however, the Company has a director and officer insurance policy that limits its exposure and enables the Company to recover a portion of any future payments. As a result of its insurance policy coverage, the Company believes the estimated fair value of these indemnification agreements is minimal. Accordingly, the Company had no liabilities recorded for these agreements as of September 30, 2015 and December 31, 2014. The Company entered into the FINEP Credit Facility to finance a research and development project on sugarcane-based biodiesel (see Note 5, "Debt"). The FINEP Credit Facility is guaranteed by a chattel mortgage on certain equipment of the Company. The Company's total acquisition cost for the equipment under this guarantee is approximately R$6.0 million (approximately US$1.5 million based on the exchange rate as of September 30, 2015). The Company entered into the BNDES Credit Facility to finance a production site in Brazil (see Note 5, "Debt").The BNDES Credit Facility is collateralized by a first priority security interest in certain of the Company's equipment and other tangible assets with a total acquisition cost of R$24.9 million (approximately US$6.3 million based on the exchange rate as of September 30, 2015). The Company is a parent guarantor for the payment of the outstanding balance under the BNDES Credit Facility. Additionally, the Company is required to provide certain bank guarantees under the BNDES Credit Facility. Accordingly, the Company has $0.2 million and $0.6 million as restricted cash as of September 30, 2015 and December 31, 2014, respectively. The Company entered into loan agreements and security agreements whereby the Company pledged certain farnesene production assets as collateral (the fiduciary conveyance of movable goods) with each of Nossa Caixa and Banco Pine (see Note 5, "Debt"). The Company's total acquisition cost for the farnesene production assets pledged as collateral under these agreements is approximately R$68.0 million (approximately US$17.1 million based on the exchange rate as of September 30, 2015). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. The Company had an export financing agreement with ABC for approximately $2.5 million for a one year term to fund exports through March 2014. As of September 30, 2015, the loan was fully repaid. On April 8, 2015, the Company entered into another export financing agreement with the same bank for approximately $1.6 million for a one year term to fund exports through March 2016. This loan is collateralized by future exports from Amyris Brasil. The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. In October 2013, the Company entered into a letter agreement with Total relating to the Temasek Bridge Note and to the closing of the August 2013 Financing (or the "Amendment Agreement") (see Note 5, "Debt"). In the August 2013 Financing, the Company was required to provide the purchasers under the August 2013 SPA with a security interest in the Company’s intellectual property if Total still held such security interest as of the initial closing of the August 2013 Financing. Under the terms of a previous Intellectual Property Security Agreement by and between the Company and Total (or the "Security Agreement"), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under the Total Notes issued and issuable to Total under the Total Purchase Agreement. The Security Agreement provided that such security interest would terminate if Total and the Company entered into certain agreements relating to the formation of the Fuels JV. In connection with Total’s agreement to (i) permit the Company to grant the security interest under the Temasek Bridge Note and the August 2013 Financing and (ii) waive a secured debt limitation contained in the outstanding Total Notes issued pursuant to the Total Purchase Agreement and held by Total, the Company entered into the Amendment Agreement. Under the Amendment Agreement, the Company agreed to reduce, effective December 2, 2013, the conversion price for the Total Notes issued in 2012 (approximately $48.3 million of which are outstanding as of the date hereof) from $7.0682 per share to $2.20, the market price per share of the Company’s common stock as of the signing of the Amendment Agreement, as determined in accordance with applicable NASDAQ rules, unless the Company and Total entered into the JV Documents on or prior to December 2, 2013. The Company and Total entered into the JV agreements on December 2, 2013 and the Amendment Agreement and all security interests thereunder were automatically terminated and the conversion price of such Total Notes remained at $7.0682 per share. In December 2013, in connection with the execution of JV Documents entered into by and among Amyris, Total and JVCO relating to the establishment of the JVCO (see Note 5, "Debt" and Note 7, "Joint Venture and Noncontrolling Interests"), the Company agreed to exchange the $69.0 million outstanding Total Notes issued pursuant to the Total Purchase Agreement and issue replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each Total Note and grant a security interest to Total in and lien on all the Company’s rights, title and interest in and to the Company’s shares in the capital of the JVCO. Following execution of the JV Documents, all Total Notes that have been issued became Replacement Notes. Further, the $10.85 million in principal amount of such notes issued in the initial tranche of the third closing under the Total Purchase Agreement in July 2014 and the $10.85 million in principal amount of such notes issued in the second tranche of the third closing are secured Replacement Notes instead of unsecured Total Notes. "See Note 5,"Debt" for the impact of the Exchange and Maturity Treatment Agreement on the Replacement Notes". The Hercules Loan Facility (see Note 5, "Debt") is collateralized by liens on the Company's assets, including certain Company intellectual property. Purchase Obligations As of September 30, 2015, the Company had $2.0 million in purchase obligations which included $1.1 million in non-cancellable contractual obligations and construction commitments, of which zero have been accrued as loss on purchase commitments. Other Matters Certain conditions may exist as of the date the financial statements are issued, which may result in a loss to the Company but will only be recorded when one or more future events occur or fail to occur. The Company's management assesses such contingent liabilities, and such assessment inherently involves an exercise of judgment. In assessing loss contingencies related to legal proceedings that are pending against and by the Company or unasserted claims that may result in such proceedings, the Company's management evaluates the perceived merits of any legal proceedings or unasserted claims as well as the perceived merits of the amount of relief sought or expected to be sought. If the assessment of a contingency indicates that it is probable that a material loss has been incurred and the amount of the liability can be estimated, then the estimated liability would be accrued in the Company's financial statements. If the assessment indicates that a potential material loss contingency is not probable but is reasonably possible, or is probable but cannot be estimated, then the nature of the contingent liability, together with an estimate of the range of possible loss if determinable and material would be disclosed. Loss contingencies considered to be remote by management are generally not disclosed unless they involve guarantees, in which case the guarantee would be disclosed. The Company is subject to disputes and claims that arise or have arisen in the ordinary course of business and that have not resulted in legal proceedings or have not been fully adjudicated. Such matters that may arise in the ordinary course of business are subject to many uncertainties and outcomes are not predictable with assurance. Therefore, if one or more of these legal disputes or claims resulted in settlements or legal proceedings that were resolved against the Company for amounts in excess of management’s expectations, the Company’s consolidated financial statements for the relevant reporting period could be materially adversely affected.

Note 7 - Joint Ventures and Non

Note 7 - Joint Ventures and Noncontrolling Interest	9 Months Ended
	Sep. 30, 2015
Equity Method Investments and Joint Ventures [Abstract]
Equity Method Investments and Joint Ventures Disclosure [Text Block]	7. Joint Ventures and Noncontrolling Interests Novvi LLC In September 2011, the Company and Cosan US, Inc. (or “Cosan U.S.”) formed Novvi LLC (or “Novvi”), a U.S. entity that is jointly owned by the Company and Cosan U.S.. In March 2013, the Company and Cosan U.S. entered into agreements to (i) expand their base oils joint venture to also include additives and lubricants and (ii) operate their joint venture exclusively through Novvi. Specifically, the parties entered into an Amended and Restated Operating Agreement for Novvi (or the “Operating Agreement”), which sets forth the governance procedures for Novvi and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (or the "IP License Agreement") under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royaty-free license to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in automotive and industrial lubricants markets, and (ii) a non-exclusive, royalty free license, subject to certain conditions, to manufacture Biofene solely for its own products. In addition, both the Company and Cosan U.S. granted Novvi certain rights of first refusal with respect to alternative base oil and additive technologies that may be acquired by the Company or Cosan U.S. during the term of the IP License Agreement. Under these agreements, the Company and Cosan U.S. each own 50% of Novvi and each party shares equally in any costs and any profits ultimately realized by the joint venture. Novvi is governed by a six member Board of Managers (or the “Board of Managers”), with three managers represented by each investor. The Board of Managers appoints the officers of Novvi, who are responsible for carrying out the daily operating activities of Novvi as directed by the Board of Managers. The IP License Agreement has an initial term of 20 years from the date of the agreement, subject to standard early termination provisions such as uncured material breach or a party's insolvency. Under the terms of the Operating Agreement, Cosan U.S. was obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company was obligated to fund its 50% ownership share of Novvi through the granting of an IP License to develop, produce and commercialize base oils, additives, and lubricants derived from Biofene for use in the automotive, commercial and industrial lubricants markets, which Cosan U.S. and Amyris agreed was valued at $10.0 million. In March 2013, the Company measured its initial contribution of intellectual property to Novvi at the Company's carrying value of the licenses granted under the IP License Agreement, which was zero. Additional funding requirements to finance the ongoing operations of Novvi are expected to happen through revolving credit or other loan facilities provided by unrelated parties (i.e., such as financial institutions); cash advances or other credit or loan facilities provided by the Company and Cosan U.S. or their affiliates; or additional capital contributions by the Company and Cosan U.S. In April 2014, the Company purchased additional membership units of Novvi for an aggregate purchase price of $0.2 million. Also in April 2014, the Company contributed $2.1 million in cash in exchange for receiving additional membership units in Novvi. Each member owns 50% of Novvi's issued and outstanding membership units. In September 2014, the Company and Cosan U.S. entered into a member senior loan agreement to grant Novvi a loan amounting to approximately $3.7 million. The loan is due on September 1, 2017 and bears interest at a rate of 0.36% per annum. Interest accrues daily and is due and payable in arrears on September 1, 2017. The Company and Cosan U.S. each agreed to provide 50% of the loan. The Company's share of approximately $1.8 million was disbursed in two installments. The first installment of $1.2 million was made in September 2014 and the second installment of $0.6 million was made in October 2014. In November 2014, the Company and Cosan U.S. entered into a second member senior loan agreement to grant Novvi a loan of approximately $1.9 million on the same terms as the loan issued in September 2014. The Company and Cosan U.S. each agreed to provide 50% of the loan. The Company disbursed its share of approximately $1.0 million in November 2014. In May 2015, the Company and Cosan U.S. entered into a third member senior loan agreement to grant Novvi a loan of approximately $1.1 million on the same terms as the loan issued in September 2014, except that the due date is May 14, 2018. As of September 30, 2015 and December 31, 2014, total loans to Novvi were $2.5 million and $1.7 million, net of imputation of interest of $1.5 million and $1.0 million as result of the below market interest rate on the loan to affiliate, respectively. In August, 2015, the Company and Cosan U.S. entered into a fourth member senior loan agreement to grant Novvi a loan of approximately $0.2 million on the same terms as the loan issued in September 2014, except that the due date is August 19, 2018. The following table is a reconciliation of our equity and loans in Novvi: September 30, (In thousands) 2015 2014 Balance at January 1 $ 2,192 $ — Loans to affiliate 770 — Imputation of interest 461 — Capital contribution (cash) — 2,075 Capital contribution (non – cash) — 237 Share in net loss offset to equity investment (908 ) (988 ) Share in net loss offset to loans to affiliate (1,181 ) — Accretion of imputed interest 413 — Balance at September 30 $ 1,747 $ 1,324 The Company has identified Novvi as a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture (i.e., continuing research and development, marketing, sales, distribution and manufacturing of Novvi products), is equally shared between the Company and Cosan U.S. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi under the equity method of accounting. The Company will continue to reassess its primary beneficiary analysis of Novvi if there are changes in events and circumstances impacting the power to direct activities that most significantly affect Novvi's economic success. Under the equity method, the Company's share of profits and losses are included in “Loss from investments in affiliates” in the condensed consolidated statements of operations. The Company recorded $0.7 million and $0.8 million for its share of Novvi's net loss for the three months ended September 30, 2015 and 2014, respectively, and $2.1 million and $1.0 million for the nine months ended September 30, 2015 and 2014, respectively. The carrying amount of the Company's equity investment in Novvi was $1.7 million and $1.3 million as of September 30, 2015 and 2014, respectively. Total Amyris BioSolutions B.V. In November 2013, the Company and Total formed JVCO. The common equity of JVCO is jointly owned (50%/50%) by the Company and Total, and the preferred equity of JVCO is 100% owned by the Company. The Parties have agreed that JVCO’s purpose is limited to executing the License Agreement and maintaining such licenses under it, unless and until either (i) Total elects to go forward with either the full (diesel and jet fuel) JVCO commercialization program or the jet fuel component of the JVCO commercialization program (or a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (or a “No-Go Decision”), or (iii) Total exercises any of its rights to buy out the Company’s interest in JVCO. Following a Go Decision, the articles and shareholders’ agreement of JVCO would be amended and restated to be consistent with the shareholders’ agreement contemplated by the July 2012 Agreements (see Note 5, "Debt" and Note 8, "Significant Agreements"). The JVCO has an initial capitalization of €0.1 million (approximately US$0.1 million based on the exchange rate as of September 30, 2015). The Company has identified JVCO as a VIE and determined that the Company is not the primary beneficiary and therefore accounts for its investment in JVCO under the equity method of accounting. Following a "Go" decision, no later than six months prior to July 31, 2016, the Company and Total are required to amend the July 2012 Agreements to reflect the corporate structure of JVCO, amend and restate the articles of association of JVCO, finalize and agree on a five-year plan and an initial budget, maximize economic viability and value of JVCO and enter into the Total license agreement. The Company will reevaluate its assessment in 2016 based on the specific terms of the final shareholders' agreement. On July 26, 2015, the Company entered into a Letter Agreement with Total (the “JVCO Letter Agreement”) regarding the restructuring of ownership and rights of Total Amyris BioSolutions B.V., the jointly-owned entity incorporated in November 2013 to house the JV (“TAB"), pursuant to which the parties agreed to enter into an Amended and Restated Shareholders' Agreement among the Company, Total and TAB, a Deed of Amendment of Articles of Association of TAB, an Amended & Restated Jet Fuel License Agreement among the Company and TAB, and a License Agreement regarding Diesel Fuel in the EU between the Company and Total, all in order to reflect certain changes to the structure of TAB and license grants and related rights pertaining to TAB (together, with the Pilot Plant Agreement Amendment described below, collectively, the "Commercial Agreements"). The Pilot Plant Agreement Amendment was entered into on July 26, 2015. The parties continue to finalize the terms of the Commercial Agreements related to TAB and expect to complete the transactions before the end of 2015. Under the Commercial Agreements relating to TAB, the Company will grant exclusive (excluding its Brazil jet fuels business), world-wide, royalty-free rights to TAB for commercialization of farnesene- or farnesane-based jet fuel, and the parties agreed that, if TAB wishes to purchase farnesene- or farnesane for such business, they would negotiate a supply agreement on a "most-favored" pricing basis. TAB would also have an option until March 1, 2018 to purchase the assets of the jet portion of the Company's Brazil fuel business at a price based on the fair value of the commercial assets and the Company's investment in other related assets. If it exercises that option, TAB would no longer have any licenses or rights with regards to farnesene- or farnesane-based diesel fuel. In addition, the Company will grant Total an exclusive, royalty-free license for the rights to offer for sale and sell in the European Union (" EU Further, in accordance with the Commercial Agreements and pursuant to the JVCO Letter Agreement, Total will cancel R&D Notes in an aggregate principal amount of $5 million, plus all PIK and accrued interest under all outstanding R&D Notes and a note in the principal amount of Euro 50,000, plus accrued interest, issued by Amyris to Total in connection with the existing TAB capitalization, in exchange for an additional 25% of TAB (giving Total an aggregate ownership stake of 75% of TAB and giving the Company an aggregate ownership stake of 25% of TAB). Additionally, in connection with the restructuring of the terms of TAB and the other Commercial Agreements, Total and the Company entered into Amendment #1 (the "Pilot Plant Agreement Amendment") to that certain Pilot Plant Services Agreement dated as of April 4, 2014 (as amended, the " Pilot Plant Agreement SMA Indústria Química S.A. In April 2010, the Company established SMA Indústria Química (or "SMA"), a joint venture with São Martinho S.A. (or "São Martinho"), to build a production facility in Brazil. SMA is located at the São Martinho mill in Pradópolis, São Paulo state. The joint venture agreements establishing SMA have a 20 year initial term. SMA is managed by a three member executive committee, of which the Company appoints two members, one of whom is the plant manager who is the most senior executive responsible for managing the construction and operation of the facility. SMA is governed by a four member board of directors, of which the Company and São Martinho each appoint two members. The board of directors has certain protective rights which include final approval of the engineering designs and project work plan developed and recommended by the executive committee. The joint venture agreements require the Company to fund the construction costs of the new facility and São Martinho would reimburse the Company up to R$61.8 million (approximately US$15.6 million based on the exchange rate as of September 30, 2015) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and São Martinho would sell feedstock and provide certain other services to SMA. The cost of the feedstock to SMA would be a price that is based on the average return that São Martinho could receive from the production of its current products, sugar and ethanol. The Company would be required to purchase the output of SMA for the first four years at a price that guarantees the return of São Martinho’s investment plus a fixed interest rate. After this four year period, the price would be set to guarantee a break-even price to SMA plus an agreed upon return. Under the terms of the joint venture agreements, if the Company becomes controlled, directly or indirectly, by a competitor of São Martinho, then São Martinho has the right to acquire the Company’s interest in SMA. If São Martinho becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to São Martinho. In either case, the purchase price shall be determined in accordance with the joint venture agreements, and the Company would continue to have the obligation to acquire products produced by SMA for the remainder of the term of the supply agreement then in effect even though the Company would no longer be involved in SMA’s management. The Company has a 50% ownership interest in SMA. The Company has identified SMA as a VIE pursuant to the accounting guidance for consolidating VIEs because the amount of total equity investment at risk is not sufficient to permit SMA to finance its activities without additional subordinated financial support, as well as because the related commercialization agreement provides a substantive minimum price guarantee. Under the terms of the joint venture agreement, the Company directs the design and construction activities, as well as production and distribution. In addition, the Company has the obligation to fund the design and construction activities until commercialization is achieved. Subsequent to the construction phase, both parties equally fund SMA for the term of the joint venture. Based on those factors, the Company was determined to have the power to direct the activities that most significantly impact SMA’s economic performance and the obligation to absorb losses and the right to receive benefits. Accordingly, the financial results of SMA are included in the Company’s consolidated financial statements and amounts pertaining to São Martinho’s interest in SMA are reported as noncontrolling interests in subsidiaries. The Company completed a significant portion of the construction of the new facility in 2012. The Company suspended construction of the facility in 2013 in order to focus on completing and operating the Company's smaller production facility in Brotas, Brazil. In February 2014, the Company entered into an amendment to the joint venture agreement with São Martinho which updated and documented certain preexisting business plan requirements related to the recommencement of construction at the joint venture operated plant and sets forth, among other things, (i) the extension of the deadline for the commencement of operations at the joint venture operated plant to no later than 18 months following the construction of the plant no later than March 31, 2017, and (ii) the extension of an option held by São Martinho to build a second large-scale farnesene production facility to no later than December 31, 2018 with the commencement of operations at such second facility to occur no later than April 1, 2019. On July 1, 2015 SMSA filed a material fact document with CVM (Securities Exchange Commission of Brazil) that announced that certain contractual targets undertaken by the Company have not been achieved, which affects the feasibility of the project. Therefore, SMSA decided not to approve continuing construction of the plant for the joint venture with Amyris Inc and its Brazilian subsidiary Amyris Brasil Ltda. In July 2015, the Company announced that it was in discussions with SMSA regarding the continuation of the joint venture. Specifically, the Company and SMSA agreed to continue the joint venture pending discussions through August 31, 2015 in order to evaluate the best investment options available to optimize returns and provide balanced economics for both parties. The Company now expects to enter into agreements in 2015 documenting a planned termination of the joint venture. Refer to Note 4 “Balance Sheet Components” for details of the impact of these developments on the quarter ended September 30, 2015. Glycotech In January 2011, the Company entered into a production service agreement (or the "Glycotech Agreement") with Glycotech, Inc. (or "Glycotech"), under which Glycotech provides process development and production services for the manufacturing of various Company products at its leased facility in Leland, North Carolina. The Company products manufactured by Glycotech are owned and distributed by the Company. Pursuant to the terms of the Glycotech Agreement, the Company is required to pay the manufacturing and operating costs of the Glycotech facility, which is dedicated solely to the manufacture of Amyris products. The initial term of the Glycotech Agreement was for a two year period commencing on February 1, 2011 and the Glycotech Agreement renews automatically for successive one-year terms, unless terminated by the Company. Concurrent with the Glycotech Agreement, the Company also entered into a Right of First Refusal Agreement with the lessor of the facility and site leased by Glycotech (or the "ROFR Agreement"). Per conditions of the ROFR Agreement, the lessor agreed not to sell the facility and site leased by Glycotech during the term of the Glycotech Agreement. In the event that the lessor is presented with an offer to sell or decides to sell an adjacent parcel, the Company has the right of first refusal to acquire it. The Company has determined that the arrangement with Glycotech qualifies as a VIE. The Company determined that it is the primary beneficiary of this arrangement since it has the power through the management committee over which it has majority control to direct the activities that most significantly impact Glycotech's economic performance. In addition, the Company is required to fund 100% of Glycotech's actual operating costs for providing services each month while the facility is in operation under the Glycotech Agreement. Accordingly, the Company consolidates the financial results of Glycotech. As of September 30, 2015, the carrying amounts of Glycotech's assets and liabilities were not material to the Company's condensed consolidated financial statements. The table below reflects the carrying amount of the assets and liabilities of the two consolidated VIEs for which the Company is the primary beneficiary. As of September 30, 2015, the assets include $6.4 million in property, plant and equipment, $1.5 million in other assets and $0.4 million in current assets. The liabilities include $0.3 million in accounts payable and accrued current liabilities and $0.1 million in loan obligations by Glycotech to its shareholders that are non-recourse to the Company. The creditors of each consolidated VIE have recourse only to the assets of that VIE. (In thousands) September 30, 2015 December 31, 2014 Assets* $ 8,291 $ 22,812 Liabilities $ 444 $ 290 *Net of impairment at September 30, 2015 of $7.3 million related to SMA assets (see Note 4 “Balance Sheet Components” for details). The change in noncontrolling interest for the nine months ended September 30, 2015 and 2014, is summarized below (in thousands): September 30, 2015 September 30, 2014 Balance at January 1 $ 611 $ 584 Foreign currency translation adjustment (393 ) (37 ) Income attributable to noncontrolling interest 78 91 Balance at September 30 $ 296 $ 638

Note 8 - Significant Agreements

Note 8 - Significant Agreements	9 Months Ended
	Sep. 30, 2015
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Collaborative Arrangement Disclosure [Text Block]	8. Significant Agreements Research and Development Activities Total Collaboration Arrangement In June 2010, the Company entered into a technology license, development, research and collaboration agreement (or the “Collaboration Agreement”) with Total Gas & Power USA Biotech, Inc., an affiliate of Total. This agreement provided for joint collaboration on the development of products through the use of the Company’s synthetic biology platform. In November 2011, the Company entered into an amendment of the Collaboration Agreement with respect to development and commercialization of Biofene for fuels. This represented an expansion of the initial collaboration with Total, and established a global, exclusive collaboration for the development of Biofene for fuels and a framework for the creation of a joint venture to manufacture and commercialize Biofene for diesel. In addition, a limited number of other potential products were subject to development by the joint venture on a non-exclusive basis. In November 2011, the Company and Total entered into an amendment of the Collaboration Agreement (or the “Amendment”). The Amendment provided for an exclusive strategic collaboration for the development of renewable diesel products and contemplated that the parties would establish a joint venture (or the “JV”) for the production and commercialization of such renewable diesel products on an exclusive, worldwide basis. In addition, the Amendment contemplated providing the JV with the right to produce and commercialize certain other chemical products on a non-exclusive basis. The amendment further provided that definitive agreements to form the JV had to be in place by March 31, 2012 or such other date as agreed to by the parties or the renewable diesel program, including any further collaboration payments by Total related to the renewable diesel program, would terminate. In the second quarter of 2012, the parties extended the deadline to June 30, 2012, and, through June 30, 2012, the parties were engaged in discussions regarding the structure of future payments related to the program, until the amendment was superseded by a further amendment in July 2012 (as further described below). Pursuant to the Amendment, Total agreed to fund the following amounts: (i) the first $30.0 million in research and development costs related to the renewable diesel program incurred since August 1, 2011, which amount would be in addition to the $50.0 million in research and development funding contemplated by the Collaboration Agreement, and (ii) for any research and development costs incurred following the JV formation date that were not covered by the initial $30.0 million, an additional $10.0 million in 2012 and up to an additional $10.0 million in 2013, which amounts would be considered part of the $50.0 million contemplated by the Collaboration Agreement. In addition to these payments, Total further agreed to fund 50% of all remaining research and development costs for the renewable diesel program under the Amendment. In July 2012, the Company entered into a further amendment of the Collaboration Agreement that expanded Total’s investment in the Biofene collaboration, incorporated the development of certain JV products for use in diesel and jet fuel into the scope of the collaboration, and changed the structure of the funding from Total for the collaboration by establishing a convertible debt structure for the collaboration funding (see Note 5, “Debt”). In connection with such additional amendment Total and the Company also executed certain other related agreements. Under these agreements, (collectively referred to as the “July 2012 Agreements”), the parties would grant exclusive manufacturing and commercial licenses to the JV for the JV products (diesel and jet fuel from Biofene) when the JV was formed. The licenses to the JV were to be consistent with the principle that development, production and commercialization of the JV products in Brazil would remain with Amyris unless Total elected, after formation of the operational JV, to have such business contributed to the joint venture (see below for additional detail). Further, as part of the July 2012 Agreements, Total's royalty option contingency related to diesel was removed and the jet fuel collaboration was combined with the expanded Biofene collaboration. As a result, $46.5 million of payments previously received from Total that had been recorded as an advance from Total were no longer contingently repayable. Of this amount, $23.3 million was treated as a repayment by the Company and included as part of the senior unsecured convertible promissory note issued to Total in July 2012 and the remaining $23.2 million was recorded as a contract to perform research and development services, which was offset by the reduction of the capitalized deferred charge asset of $14.4 million resulting in the Company recording revenue from a related party of $8.9 million in 2012. See Note 5, "Debt" for details of the Exchange and Maturity Treament Agreements and Note 7," Joint Ventures and Noncontrolling Interest" for further details of the relationship with Total. F&F Collaboration Partner Joint Development and License Agreement In April 2013, the Company entered into a joint development and license agreement with a collaboration partner. Under the terms of the multi-year agreement, the collaboration partner and the Company will jointly develop certain fragrance ingredients. The collaboration partner will have exclusive rights to these fragrance ingredients for applications in the flavors and fragrances field, and the Company will have exclusive rights in other fields. The collaboration partner and the Company will share in the economic value derived from these ingredients. The joint development and license agreement provided for up to $6.0 million in funding based upon the achievement of certain technical milestones, which are considered substantive by the Company, during the first phase of the collaboration. In February 2014, the Company entered into an amendment to the joint development and license agreement with the collaboration partner noted in the preceding paragraph to proceed with the second phase of the collaboration and the development of a certain fragrance ingredient. The Company recognized collaboration revenue for the three and nine months ended September 30, 2015, of $0.8 million and $2.3 million, respectively, under this agreement. As of September 30, 2015 and 2014, zero was recorded in deferred revenue. F&F Collaboration Partner Master Collaboration and Joint Development Agreement In November 2010, the Company entered into a Master Collaboration and Joint Development Agreement with a collaboration partner. Under the agreement, the collaboration partner was to fund technical development at the Company to produce an ingredient for the flavors and fragrances market. The Company agreed to manufacture the ingredient and the collaboration partner would market it, and the parties would share in any resulting economic value. The agreement also grants exclusive worldwide flavors and fragrances commercialization rights to the collaboration partner for the ingredient. Under further agreements, the collaboration partner has an option to collaborate with the Company to develop additional ingredients. These agreements continue in effect until the later of the expiration or termination of the development agreements or the supply agreements. The Company is also eligible to receive potential total payments of $6.0 million upon the achievement of certain performance milestones towards which the Company will be required to make a contributory performance. The Company concluded that these milestone payments are substantive. All performance milestones under this agreement were achieved in 2013. In March 2013, the Company entered into a Master Collaboration Agreement (or the “March 2013 Agreement”) with the collaboration partner to establish a collaboration arrangement for the development and commercialization of multiple renewable flavors and fragrances compounds. Under this agreement, except for rights granted under preexisting collaboration relationships, the Company granted the collaboration partner exclusive access for such compounds to specified Company intellectual property for the development and commercialization of flavors and fragrances products in exchange for research and development funding and a profit sharing arrangement. The agreement superseded and expanded the prior collaboration agreement between the Company and the collaboration partner. The agreement provided for annual, up-front funding to the Company by the collaboration partner of $10.0 million for each of the first three years of the collaboration. Payments of $10.0 million were received by the Company in each of March 2015, 2014 and 2013. The Company recognized collaboration revenues under the March 2013 Agreement with the collaboration partner of $2.5 million for each of the three months ended September 30, 2015 and 2014 and of $7.5 million and $7.5 million for the nine months ended September 30, 2015 and 2014, respectively. The agreement contemplated additional funding by the collaboration partner of up to $5.0 million under three potential milestone payments, as well as additional funding by the collaboration partner on a discretionary basis. Through September 2015, the Company achieved the second performance milestone under the Master Collaboration Agreement and recognized collaboration revenues of $1.0 million for the nine months ended September 30, 2015. In addition, the March 2013 Agreement contemplated that the parties will mutually agree on a supply price for each compound and share product margins from sales of each compound on a 70/30 basis (70% for the collaboration partner) until the collaboration partner receives $15.0 million more than the Company in the aggregate, after which the parties will share 50/50 in the product margins on all compounds. The Company also agreed to pay a one-time success bonus of up to $2.5 million to the collaboration partner's for outperforming certain commercialization targets. The collaboration partner eligibility to receive the one-time success bonus commences upon the first sale of the collaboration partner's product. The March 2013 Agreement does not impose any specific research and development commitments on either party after year six, but if the parties mutually agree to perform development after year six, the agreement provides that the parties will fund it equally. Under the March 2013 Agreement, the parties agreed to jointly select target compounds, subject to final approval of compound specifications by the collaboration partner. During the development phase, the Company would be required to provide labor, intellectual property and technology infrastructure and the collaboration partner would be required to contribute downstream polishing expertise and market access. The March 2013 Agreement provided that the Company would own research and development and strain engineering intellectual property, and the collaboration partner would own blending and, if applicable, chemical conversion intellectual property. Under certain circumstances such as the Company's insolvency, the collaboration partner would gain expanded access to the Company's intellectual property. Following development of flavors and fragrances compounds under the March 2013 Agreement, the March 2013 Agreement contemplated that the Company would manufacture the initial target molecules for the compounds and the collaboration partner will perform any required downstream polishing and distribution, sales and marketing. In September 2014, the Company entered into a supply agreement with the collaboration partner to provide target compounds to make a certain finished ingredient and market and sell such finished ingredient and/or products to the flavors and fragrances market. The Company recognized $1.3 million revenues from product sales under this agreement for the three and nine months ended September 30, 2015. Michelin and Braskem Collaboration Agreements In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise de Pnematiques Michelin (or “Michelin”). Under the terms of the September 2011 collaboration agreement, the Company and Michelin agreed to collaborate on the development, production and worldwide commercialization of isoprene or isoprenol, generally for tire applications, using the Company's technology. Under the agreement, Michelin made an upfront payment to the Company of $5.0 million. In June 2014, the Company entered into a collaboration agreement with Braskem S.A. (or “Braskem”) and Michelin to collaborate to develop the technology to produce and possibly commercialize renewable isoprene. The term of the collaboration agreement commenced on June 30, 2014 and will continue, unless earlier terminated in accordance with the agreement, until the first to occur of (i) the date that is three years following the actual date on which a work plan is completed, which date is estimated to occur on or about December 30, 2020, or (ii) the date of the commencement of commissioning of a production plant for the production of renewable isoprene. The June 2014 collaboration agreement terminated and supersedes the September 2011 collaboration agreement with Michelin, and, as a result of the signing of the June 2014 collaboration agreement, the upfront payment by Michelin of $5.0 million is being rolled into the new collaboration agreement between Michelin, Braskem and the Company as Michelin's collaboration funding towards the research and development activities to be performed. As of December 31, 2014, the Company accrued a total contribution from Braskem to the collaboration of $4.0 million, of which $2.0 million was received in July 2014 and $2.0 million was received in January 2015. The Company recognized collaboration revenues of zero for the three months ended September 30, 2015 and $1.9 million for the nine months ended September 30, 2015 under this agreement. As of September 30, 2015, $6.3 million of deferred revenues was recorded in the condensed consolidated balance sheet related to these agreements. Kuraray Collaboration Agreement and Securities Purchase Agreement In March 2014, the Company entered into the Second Amended and Restated Collaboration Agreement with Kuraray Co., Ltd (or “Kuraray”) in order to extend the term of the original agreement dated July 21, 2011 for an additional two years and add additional fields and products to the scope of development. In consideration for the Company’s agreement to extend the term of the original collaboration agreement and add additional fields and products, Kuraray agreed to pay the Company $4.0 million in two equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment was due on April 30, 2015. In connection with the collaboration agreement, Kuraray signed a Securities Purchase Agreement in March 2014 to purchase 943,396 shares of the Company's common stock at a price per share of $4.24 per share. The Company issued 943,396 shares of its common stock at a price per share of $4.24 in April 2014 for aggregate cash proceeds of $4.0 million. In March 2015, the Company entered into the First Amendment to the Second Amended and Restated Collaboration Agreement with Kuraray Co., Ltd (or Kuraray) to extend the term of the original agreement until December 31, 2016 and accelerated payment to the Company of the second installment of $2.0 million to March 31, 2015. The Company recognized collaboration revenues of $0.3 million for the three months ended September 30, 2015 and $1.2 million for the nine months ended September 30, 2015 under this agreement. DARPA In September 2015, the Company entered into a Technology Investment Agreement (the “Agreement”) with The Defense Advanced Research Projects Agency (“DARPA”), under which the Company, with the assistance of five specialized subcontractors, will work to create new research and development tools and technologies for strain engineering and scale-up activities. The program that is the subject of the Agreement is scheduled to commence on November 1, 2015 and will be performed and funded on a milestone basis, where DARPA, upon the Company’s successful completion of each milestone event in the Agreement, pays the Company the amount in the Agreement corresponding to such milestone event. Under the Agreement, the Company and its subcontractors could collectively receive DARPA funding of up to $35.0 million over the program’s four year term if all of the program’s milestones are achieved. In conjunction with DARPA’s funding, the Company and its subcontractors are obligated to collectively contribute approximately $15.5 million toward the program over its four year term (primarily by providing specified labor and/or purchasing certain equipment). The Company can elect to retain title to the patentable inventions it produces in the program, but DARPA receives certain data rights as well as a government purposes license to certain of such inventions. Either party may, upon written notice and subject to certain consultation obligations, terminate the Agreement upon a reasonable determination that the program will not produce beneficial results commensurate with the expenditure of resources. Financing Agreements Nomis Bay Ltd. Common Stock Purchase Agreement In February 2015, the Company entered into a Common Stock Purchase Agreement (or the “Common Stock Purchase Agreement”) and a Registration Rights Agreement (or the “Registration Rights Agreement”) with Nomis Bay Ltd. (or “Nomis Bay”) under which the Company may from time to time sell up to $50.0 million of its common stock to Nomis Bay over a 24-month period. In connection with such Common Stock Purchase Agreement and Registration Rights Agreement, the Company also entered into a Placement Agent Letter Agreement (or the “Placement Agent Agreement”) with Financial West Group (or “FWG”, the Common Stock Purchase Agreement, the Registration Rights Agreement and the Placement Agent Agreement are collectively referred to as the “Committed Equity Facility Agreements”). The equity commitment arrangement entered into under the Committed Equity Facility Agreements is sometimes referred to as a committed equity line financing facility. Subject to customary covenants and conditions, from time to time over the 24-month term, and in the Company’s sole discretion, the Company may present Nomis Bay with up to 24 draw down notices requiring Nomis Bay to purchase a specified dollar amount of shares of the Company’s common stock, based on the volume weighted average price of our common stock over 10 consecutive trading days prior to the date the Company delivers a draw down notice (or the “10-Day VWAP”). The per share purchase price for these shares equals the daily volume weighted average price of the Company’s common stock on each date during the 10 consecutive trading days following delivery of the draw down notice (or a “Draw Down Period”) on which shares are purchased, less a discount ranging from 3.0% to 6.25%, which discount is based on the 10-Day VWAP. The maximum amount of shares that may be sold in any Draw Down Period ranges from shares having aggregate purchase prices of $325,000 to $3,250,000, based on the 10-Day VWAP. Alternatively, in the Company’s sole discretion, but subject to certain limitations, the Company may require Nomis Bay to purchase a percentage of the daily trading volume of the Company’s common stock for each trading day during the Draw Down Period. The Company will not sell under the Common Stock Purchase Agreement a number of shares of voting common stock which, when aggregated with all other shares of voting common stock then beneficially owned by Nomis Bay and its affiliates, would result in the beneficial ownership by Nomis Bay or any of its affiliates of more than 9.9% of the then issued and outstanding shares of common stock. Under the Committed Equity Facility Agreements, the Company agreed to pay up to $35,000 of Nomis Bay’s legal fees and expenses. The Company also agreed to pay Nomis Bay a commitment fee of $0.1 million which was paid at the signing of the Purchase Agreement, and $0.3 million paid in May 2015. The issuance of the shares of common stock to Nomis Bay would be exempt from registration under the Securities Act pursuant to the exemption for transactions by an issuer not involving a public offering. The Company agreed to indemnify Nomis Bay and its affiliates for losses related to a breach of the representations and warranties by the Company under the Committed Equity Facility Agreements and the other transaction documents, or any action instituted against Nomis Bay or its affiliates due to the transactions contemplated by the Committed Equity Facility Agreements or other transaction documents, subject to certain limitations. Under the Registration Rights Agreement, the Company granted to Nomis Bay certain registration rights related to the shares issuable in accordance with the Common Stock Purchase Agreement and agreed to use its commercially reasonable efforts to prepare and file with the SEC one or more registration statements for the purpose of registering the resale of the maximum shares of common stock issuable pursuant to the Common Stock Purchase Agreement. Under the Placement Agent Agreement, the Company agreed to pay Financial West Group ("FWG") a fee not to exceed $15,000 in the aggregate for FWG’s reasonable attorney’s fees and expenses incurred in connection with the transaction . Naxyris Securities Purchase Agreement In March, 2015, the Company entered into a Securities Purchase Agreement (or the “Naxyris SPA”) for the sale of up to $10.0 million in principal amount of an unsecured convertible note of the Company (or the “Naxyris Note”) to Naxyris, S.A. (or “Naxyris”), an existing holder of more than 5% of the Company’s outstanding common stock as of September 30, 2015. Naxyris is an affiliate of Carole Piwnica, a member of the Company’s Board of Directors (or the “Board”) who was designated by Naxyris to serve on the Board under a February 2012 letter agreement among the Company, Naxyris and certain other investors in the Company. The Naxyris SPA contemplated that the Naxyris Note may be issued in one closing to occur at the option of the Company at any time prior to the earlier of March 31, 2016 or the Company completing a new financing (or series of financings) of equity, debt or similar instruments in the amount of at least $10.0 million in the aggregate (excluding amounts that may be raised under existing commitments and agreements in existence as of March 30, 2015), following the satisfaction of certain closing conditions, including the receipt of certain third party consents, and required that the Company pay a commitment availability fee of $0.2 million to Naxyris on April 1, 2015. The agreement expired in July 2015 following the Company’s private placement of shares of its common stock, as described below. Private Offering In July 2015, the Company sold and issued 16,025,642 shares of the Company’s Common Stock, $0.0001 par value per share (the “ Common Stock ”), at a price per share of $1.56, under a Securities Purchase Agreement, dated as of July 24, 2015 (the “SPA”), by and among the Company, Foris Ventures, LLC, Wolverine Flagship Fund Trading Limited, Nomis Bay Ltd., Total, Connective Capital I Master Fund, LTD, Connective Capital Emerging Energy QP, LP and Naxyris SA (collectively, the “ Purchasers ”). Pursuant to the SPA, the Company agreed to grant to each of the Purchasers a Private Offering Warrant with a term of five years exercisable at an exercise price of $0.01 per share for the purchase of a number of shares of the Company’s common stock equal to 10% of the shares purchased by such investor. The exercisability of the Private Offering Warrants was subject to stockholder approval, which was obtained on September 17, 2015. Second Hercules Amendment In March 2015, the Company and Hercules entered into the Second Hercules Amendment. Pursuant to the Second Hercules Amendment, the parties agreed to, among other things, establish an additional credit facility in the principal amount of up to $15.0 million, which would be available to be drawn by the Company at its sole election (in increments of $5.0 million) through the earlier of March 31, 2016 or such time as the Company raises an aggregate of at least $20.0 million through the sale of new equity securities, subject to certain conditions, including the receipt of third party consents and a requirement to first make certain draw-downs under an equity line of credit that the Company previously secured (to the extent the Company is permitted to do so under the terms thereof) The additional credit facility expired in July 2015 following the Company’s private placement of shares of its common stock, as described above.

Note 9 - Goodwill and Intangibl

Note 9 - Goodwill and Intangible Assets	9 Months Ended
	Sep. 30, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Goodwill and Intangible Assets Disclosure [Text Block]	9. Goodwill and Intangible Assets The following table presents the components of the Company's intangible assets (in thousands): September 30, 2015 December 31, 2014 Useful Life in Years Gross Carrying Amount Accumulated Amortization Net Carrying Value Gross Carrying Amount Accumulated Net Carrying Value In-process research and development Indefinite $ 8,560 $ 3,035 $ 5,525 $ 8,560 $ (3,035 ) $ 5,525 Acquired licenses and permits 2 772 (772 ) — 772 (772 ) — Goodwill Indefinite 560 — 560 560 — 560 $ 9,892 $ (3,807 ) $ 6,085 $ 9,892 $ (3,807 ) $ 6,085 The intangible assets acquired through the acquisition of Draths Corporation in October 2011 of in-process research and development (or “IPR&D”) of $8.6 million are treated as indefinite lived intangible assets until completion or abandonment of the projects, at which time the assets will be amortized over the remaining useful life or written-off, as appropriate. If the carrying amount of the assets is greater than the measures of fair value, impairment is considered to have occurred and a write-down of the asset is recorded. Any finding that the value of its intangible assets has been impaired would require the Company to write-down the impaired portion, which could reduce the value of its assets and reduce (increase) its net income (loss) for the period in which the related impairment charges occur. During the fourth quarter of 2014, the Company updated its ongoing analysis of the technical and commercial viability of the IPR&D. The complex scientific and significant funding requirements of certain potential products, caused the Company to re-focus its research and development efforts on a narrower range of potential products. As a result of the change in strategy, the forecast discounted future cash flows of the IPR&D were updated, resulting in an impairment to the value of the IP&D assets for the year ended December 31, 2014 of $3.0 million. Acquired licenses and permits are amortized using a straight-line method over their estimated useful life. Amortization expense for these intangibles was zero for the nine months ended September 30, 2015 and 2014. As of September 30, 2015, acquired licenses and permits were fully amortized. The Company has a single reportable segment (see Note 15, “Reporting Segments” for further details). Consequently, all of the Company's goodwill is attributable to the single reportable segment.

Note 10 - Stockholders' Deficit

Note 10 - Stockholders' Deficit	9 Months Ended
	Sep. 30, 2015
Stockholders' Equity Note [Abstract]
Stockholders' Equity Note Disclosure [Text Block]	10. Stockholders’ Deficit Common Stock Warrants In December 2011, in connection with a capital lease agreement, the Company issued warrants to purchase 21,087 shares of the Company's common stock at an exercise price of $10.67 per share. The Company estimated the fair value of these warrants as of the issuance date to be $0.2 million and recorded these warrants as other assets, amortizing them subsequently over the term of the lease. The fair value was based on the contractual term of the warrants of 10 years, risk free interest rate of 2%, expected volatility of 86% and zero expected dividend yield. These warrants remain unexercised and outstanding as of September 30, 2015. In October 2013, in connection with the issuance of the Tranche I Notes (see Note 5, "Debt"), the Company issued to Temasek contingently exercisable warrants to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share. The Company estimated the fair value of these warrants as of the issuance date at $1.3 million and recorded these warrants as debt issuance cost to be amortized over the term of the note. The fair-value was calculated using a Monte Carlo simulation valuation model based on the contractual term of the warrants of 3.4 years, risk free interest rate of 0.77%, expected volatility of 45% and zero expected dividend yield. These warrants have been exercised as of September 30, 2015 and $2.6 million for the quarter ended September 30, 2015. The Temasek Exchange Warrant and Total Funding Warrant issued under the Exchange Agreement were recognized in equity at fair value on July 29, 2015. The fair value was calculated using a Black-Scholes valuation model based on the contractual term of the warrants, risk free interest rate of 2%, expected volatility of 74% and zero expected dividend yield. See Note 5, "Debt," for further details. Each of these warrants includes a cashless exercise provision which permits the holder of the warrant to elect to exercise the warrant without paying the cash exercise price, and receive a number of shares determined by multiplying (i) the number of shares for which the warrant is being exercised by (ii) the difference between the fair market value of the stock on the date of exercise and the warrant exercise price, and dividing such by (iii) the fair market value of the stock on the date of exercise. During the nine months ended September 30, 2015 and 2014, no warrants were exercised through the cashless exercise provision. As of September 30, 2015 and 2014, the Company had 50,699,368 and 1,021,087, respectively, of unexercised common stock warrants.

Note 11 - Stock-Based Compensat

Note 11 - Stock-Based Compensation	9 Months Ended
	Sep. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Disclosure of Compensation Related Costs, Share-based Payments [Text Block]	11. Stock-Based Compensation The Company’s stock option activity and related information for the nine months ended September 30, 2015 was as follows: Number Weighted- Weighted-Average Aggregate (in thousands) Outstanding - December 31, 2014 10,539,978 $ 6.10 7.22 $ 50 Options granted 2,582,353 $ 1.98 — — Options exercised (10,750 ) $ 1.41 — — Options cancelled (1,803,902 ) $ 5.06 — — Outstanding - September 30, 2015 11,307,679 $ 5.33 7.16 $ 283 Vested and expected to vest after September 30, 2015 10,603,529 $ 5.52 7.04 $ 245 Exercisable at September 30, 2015 6,075,541 $ 7.53 5.77 $ 40 The aggregate intrinsic value of options exercised under all option plans was $0.0 million and $0.1 million for the three months ended September 30, 2015 and 2014, respectively, and was $0.0 million and $0.6 million for the nine months ended September 30, 2015 and 2014, respectively, determined as of the date of option exercise. The Company’s restricted stock units (or "RSUs") and restricted stock activity and related information for the nine months ended September 30, 2015 was as follows: RSUs Weighted-Average Grant-Date Fair Value Weighted Average Remaining Contractual Life (Years) Outstanding - December 31, 2014 1,975,503 $ 3.59 0.93 Awarded 2,767,355 $ 1.92 — Vested (929,322 ) $ 3.19 — Forfeited (255,293 ) $ 2.95 — Outstanding - September 30, 2015 3,558,243 $ 2.63 1.54 Expected to vest after September 30, 2015 3,029,826 $ 2.63 1.42 The following table summarizes information about stock options outstanding as of September 30, 2015: Options Outstanding Options Exercisable Exercise Price Number of Options Weighted- Weighted-Average Exercise Price Number of Options Weighted-Average Exercise Price $0.10—$1.80 687,093 8.74 $ 1.70 68,093 $ 1.43 $1.96—$1.96 1,412,533 9.62 $ 1.96 — $ — $1.98—$2.73 1,200,797 7.72 $ 2.53 478,181 $ 2.66 $2.75—$2.87 1,299,025 7.55 $ 2.83 800,584 $ 2.83 $2.89—$3.44 1,031,420 7.45 $ 3.11 613,405 $ 3.10 $3.51—$3.51 2,027,865 8.28 $ 3.51 738,773 $ 3.51 $3.55—$3.93 1,515,548 5.16 $ 3.87 1,302,162 $ 3.88 $4.06—$16.00 1,164,094 4.34 $ 9.17 1,131,706 $ 9.27 $16.50—$26.84 909,304 5.13 $ 23.04 882,637 $ 22.93 $30.17—$30.17 60,000 5.45 $ 30.17 60,000 $ 30.17 $0.10—$30.17 11,307,679 7.16 $ 5.33 6,075,541 $ 7.53 Stock-Based Compensation Expense Stock-based compensation expense related to options and restricted stock units granted to employees and nonemployees was allocated to research and development expense and sales, general and administrative expense as follows (in thousands): Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Research and development $ 530 $ 915 $ 1,776 $ 2,622 Sales, general and administrative 1,726 2,657 5,188 8,147 Total stock-based compensation expense $ 2,256 $ 3,572 $ 6,964 $ 10,769 As of September 30, 2015, there was unrecognized compensation expense of $7.8 million related to stock options, and the Company expects to recognize this expense over a weighted average period of 2.78 years. As of September 30, 2015, there was unrecognized compensation expense of $5.6 million related to RSUs, and the Company expects to recognize this expense over a weighted average period of 2.60 years. Stock-based compensation expense for RSUs is measured based on the closing fair market value of the Company's common stock on the date of grant. Stock-based compensation expense for stock options and employee stock purchase plan rights is estimated at the grant date and offering date, respectively, based on the fair-value using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards. The fair value of employee stock options was estimated using the following weighted-average assumptions: Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Expected dividend yield — % — % — % — % Risk-free interest rate 2 % 2 % 2 % 2 % Expected term (in years) 6.03 6.06 6.00 6.09 Expected volatility 74 % 74 % 74 % 75 % Expected Dividend Yield Risk-Free Interest Rate Expected Term Expected Volatility Forfeiture Rate Each of the inputs discussed above is subjective and generally requires significant management and director judgment.

Note 12 - Employee Benefit Plan

Note 12 - Employee Benefit Plan	9 Months Ended
	Sep. 30, 2015
Compensation and Retirement Disclosure [Abstract]
Pension and Other Postretirement Benefits Disclosure [Text Block]	12. Employee Benefit Plan The Company established a 401(k) Plan to provide tax deferred salary deductions for all eligible employees. Participants may make voluntary contributions to the 401(k) Plan up to 90% of their eligible compensation, limited by certain Internal Revenue Service (or the "IRS") restrictions. Effective January 2014, the Company implemented a discretionary employer match plan whereby the Company will match employee contributions up to the IRS limit or 90% of compensation, with a minimum one year of service required for vesting. The total matching amount for the three and nine months ended September 30, 2015 was $0.1 million and $0.4 million, respectively.

Note 13 - Related Party Transac

Note 13 - Related Party Transactions	9 Months Ended
	Sep. 30, 2015
Related Party Transactions [Abstract]
Related Party Transactions Disclosure [Text Block]	13. Related Party Transactions Related Party Financings See the Naxyris Securities Purchase Agreement Significant Agreements As of September 30, 2015 and December 31, 2014, convertible notes with related parties were outstanding in aggregate principal amount of $42.4 million and $115.2 million, respectively, net of debt discount of $1.7 million and $53.8 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes of $5.9 million and zero for each of three months ended September 30, 2015 and 2014, and, $5.9 million and $10.5 million for the nine months ended September 30, 2015 and 2014, respectively. The fair value of the derivative liability related to the related party convertible notes as of September 30, 2015 and December 31, 2014 was $35.6 million and $39.8 million, respectively. The Company recognized a loss from change in fair value of the derivative instruments of $12.4 million and $3.1 million for the three months ended September 30, 2015 and 2014, respectively, and a loss from change in fair value of the derivative instruments of $0.7 million for the nine months ended September 30, 2015 and a gain from change in fair value of the derivative instruments of $68.2 million for the nine months ended September 30, 2014, respectively, related to these derivative liabilities (see Note 3, "Fair Value of Financial Instruments"). In July, 2015, the Company sold and issued 16,025,642 shares of the Company’s Common Stock, $0.0001 par value per share (the “ Common Stock ”), at a price per share of $1.56, under a Securities Purchase Agreement, dated as of July 24, 2015 (the “SPA”) for a total of $25.0 million. Pursuant to the SPA, the Company agreed to grant to each of the Purchasers a Private Offering Warrant with a term of five years exercisable at an exercise price of $0.01 per share for the purchase of a number of shares of the Company’s common stock equal to 10% of the shares purchased by such investor. Among the investors of the SPA were Total Energies Nouvelles Activites, Foris Ventures, LLC, and Naxyris SA, all related parties to the Company. The related parties purchased 13,141,029 shares or $20.5 million of the SPA. Refer to Note 5, "Debt", for details of the related party transactions under the Exchange and Maturity Treatment agreements. See Note 18, “Subsequent Events,” for information regarding changes since September 30, 2015 to certain related party convertible notes. Related Party Revenues The Company recognized related party revenues from product sales to Total of $2,000 and $0.2 million for the three months ended September 30, 2015 and 2014, respectively, and $2,000 and $0.3 million for the nine months ended September 30, 2015 and 2014, respectively. Related party accounts receivable from Total as of September 30, 2015 and December 31, 2014, were both $0.3 million, which is related to a sale of jet fuel. Transactions with affiliate, Novvi See Note 7, "Joint Ventures and Noncontrolling Interest" for details of the Company's loans to its affiliate, Novvi LLC. Related party accounts receivable from Novvi as of September 30, 2015 and December 31, 2014 was $0.3 million and $0.1 million, respectively, which was related to operating expenses and rent. Joint Venture with Total In November 2013, the Company and Total formed JVCO and, in July 2015, the Company entered into a letter agreement with Total regarding the restructuring of ownership and rights of Total Amyris BioSolutions B.V., the jointly owned entity formed in November 2013 to house the joint venture, both as discussed above under Note 7, "Joint Venture and Noncontrolling Interests." Pilot Plant Agreements In May 2014, the Company received the final consents necessary for the Pilot Plant Services Agreement (or "Pilot Plant Services Agreement") and a Sublease Agreement (or the "Sublease Agreement"), each dated as of April 4, 2014 (collectively the “Pilot Plant Agreements”), between the Company and Total. The Pilot Plant Agreements generally have a term of five years. Under the terms of the Pilot Plant Services Agreement, the Company will provide certain fermentation and downstream separations scale-up services and training to Total and will receive an aggregate annual fee payable by Total for all services in the amount of up to approximately $0.9 million. Under the Sublease Agreement, the Company will receive an annual base rent payable by Total of approximately $0.1 million. In July 2015, the Company and Total entered into an amendment to the Pilot Plan Agreement (the “Pilot Plant Amendment”) whereby the parties agreed to restructure Total’s payment obligations under the Pilot Plant Agreement. Under the Pilot Plant Amendment, in connection with the restructuring of TAB discussed above, the Company agreed to waive a portion of the annual fees up to approximately $2.0 million over the term of the Pilot Plant Agreement. The Company expects to complete the Pilot Plant Amendment before the end of 2015. As of September 30, 2015, the Company had received $1.7 million in cash under the Pilot Plant Agreements from Total. In connection with these arrangements, sublease payments and service fees of $0.3 million and $0.8 million were offset against cost and operating expenses for the three and nine months ended September 30, 2015, respectively. As of September 30, 2015, $0.2 million of cash received under the Pilot Plant Agreements from Total was recorded as "Accrued and other current liabilities" on the condensed consolidated balance sheet.

Note 14 - Income Taxes

Note 14 - Income Taxes	9 Months Ended
	Sep. 30, 2015
Income Tax Disclosure [Abstract]
Income Tax Disclosure [Text Block]	14. Income Taxes The Company recorded a provision for income taxes for the three months ended September 30, 2015 and 2014 of $0.1 million and $0.1 million, respectively and for the nine months ended September 30, 2015 and 2014 of $0.4 million and $0.4 million, respectively. The provision for income taxes for the nine months ended September 30, 2015 and 2014 consisted of an accrual of Brazilian withholding tax on intercompany interest liability. Other than the above mentioned provision for income tax, no additional provision for income taxes has been made, net of the valuation allowance, due to cumulative losses since the commencement of operations. On December 15, 2011, the IRS completed its audit of the Company for tax year 2008 which concluded that there were no adjustments resulting from the audit. While the statutes are closed for tax year 2008, the US federal tax carryforwards (net operating losses and tax credits) may be adjusted by the IRS in the year in which the carryforward is utilized.

Note 15 - Reporting Segments

Note 15 - Reporting Segments	9 Months Ended
	Sep. 30, 2015
Segment Reporting [Abstract]
Segment Reporting Disclosure [Text Block]	15. Reporting Segments The chief operating decision maker for the Company is the chief executive officer. The chief executive officer reviews financial information presented on a consolidated basis, accompanied by information about revenue by geographic region, for purposes of allocating resources and evaluating financial performance. The Company has one business activity comprised of research and development and sales of fuels and farnesene-derived products and there are no segment managers who are held accountable for operations, operating results or plans for levels or components below the consolidated unit level. Accordingly, the Company has determined that it has a single reportable segment and operating segment structure. Revenues by geography are based on the location of the customer. The following tables set forth revenue and long-lived assets by geographic area (in thousands): Revenues Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 United States $ 6,177 $ 10,189 $ 15,550 $ 14,977 Brazil 964 1,933 3,850 3,983 Europe 459 2,836 2,138 9,174 Asia 991 1,383 2,769 3,555 Total $ 8,591 $ 16,341 $ 24,307 $ 31,689 Long-Lived Assets (Property, Plant and Equipment) September 30, 2015 December 31, 2014 United States $ 39,417 $ 44,418 Brazil 42,206 74,197 Europe 318 365 Total $ 81,941 $ 118,980

Note 16 - Comprehensive Income

Note 16 - Comprehensive Income (Loss)	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block [Abstract]
Comprehensive Income (Loss) Note [Text Block]	16. Comprehensive Income (Loss) Comprehensive income (loss) represents all changes in stockholders’ deficit except those resulting from investments or contributions by stockholders. The Company’s foreign currency translation adjustments represent the components of comprehensive income (loss) excluded from the Company’s net loss and have been disclosed in the condensed consolidated statements of comprehensive loss for all periods presented. The components of accumulated other comprehensive loss are as follows (in thousands): September 30, 2015 December 31, 2014 Foreign currency translation adjustment, net of tax $ (48,932 ) $ (29,977 ) Total accumulated other comprehensive loss $ (48,932 ) $ (29,977 )

Note 17 - Net Loss Attributable

Note 17 - Net Loss Attributable to Common Stockholders and Net Loss per Share	9 Months Ended
	Sep. 30, 2015
Earnings Per Share [Abstract]
Earnings Per Share [Text Block]	17. Net Loss Attributable to Common Stockholders and Net Loss per Share The Company computes net loss per share in accordance with ASC 260, “Earnings per Share.” Basic net loss per share of common stock is computed by dividing the Company’s net loss attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net loss per share of common stock is computed by giving effect to all potentially dilutive securities, including stock options, restricted stock units, common stock warrants, convertible promissory notes using the treasury stock method or the as converted method, as applicable. For the three and nine months ended September 30, 2015, basic net loss per share was the same as diluted net loss per share because the inclusion of all potentially dilutive securities outstanding was anti-dilutive. As such, the numerator and the denominator used in computing both basic and diluted net loss was the same for those periods. The following table presents the calculation of basic and diluted net loss per share of common stock attributable to Amyris, Inc. common stockholders (in thousands, except share and per share amounts): Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Numerator: Net loss attributable to Amyris, Inc. common stockholders $ (76,664 ) $ (36,641 ) $ (176,034 ) $ (55,735 ) Interest on convertible debt — — — 4,835 Accretion of debt discount — — — 3,856 Gain from change in fair value of derivative instruments — — — (57,580 ) Net loss attributable to Amyris, Inc. common stockholders after assumed conversion $ (76,664 ) $ (36,641 ) $ (176,034 ) $ (104,624 ) Denominator: Weighted average shares of common stock outstanding for basic EPS 140,374,297 78,980,402 100,103,007 78,146,365 Basic loss per share $ (0.55 ) $ (0.46 ) $ (1.76 ) $ (0.71 ) Weighted average shares of common stock outstanding 140,374,297 78,980,402 100,103,007 78,146,365 Effect of dilutive securities: Convertible promissory notes 0 — — 32,968,436 Weighted common stock equivalents 0 — — 32,968,436 Diluted weighted-average common shares 140,374,297 78,980,402 100,103,007 111,114,801 Diluted loss per share $ (0.55 ) $ (0.46 ) $ (1.76 ) $ (0.94 ) The following outstanding shares of potentially dilutive securities were excluded from the computation of diluted net loss per share of common stock because including them would have been anti-dilutive: Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Period-end stock options to purchase common stock 11,307,679 10,340,375 11,307,679 10,340,375 Convertible promissory notes 43,451,433 72,367,114 43,451,433 39,283,005 Period-end common stock subject to repurchase — — — — Period-end common stock warrants 2,901,926 1,021,087 2,901,926 1,021,087 Period-end restricted stock units 3,558,243 2,090,252 3,558,243 2,090,252 Total 61,219,281 85,818,828 61,219,281 52,734,719

Note 18 - Subsequent Events

Note 18 - Subsequent Events	9 Months Ended
	Sep. 30, 2015
Subsequent Events [Abstract]
Subsequent Events [Text Block]	18. Subsequent Events Convertible Senior Notes On October 20, 2015, the Company sold and issued $57.6 million aggregate principal amount of the Company's 9.50% Convertible Senior Notes due 2019 in a private placement. The notes pay interest semi-annually at a rate of 9.50% per annum and mature on April 15, 2019, unless earlier converted or repurchased. Interest is payable, at the Company's election, entirely in cash or entirely in shares of common stock. The notes have an initial conversion rate, subject to adjustment, of 443.6557 shares of the Company's common stock per $1,000 principal amount of the notes, representing a conversion price of approximately $2.25 per share of the Company's common stock. The notes are convertible at any time until the close of business on the scheduled trading day immediately preceding the maturity date. Upon conversion, the notes will be settled in shares of the Company's common stock. With respect to any conversion on or after the earlier of (i) the date that a registration statement covering the resale of common stock issuable upon conversion of the notes, in connection with an early conversion payment or as interest payments on the notes, is effective or (ii) April 15, 2016, in addition to the shares deliverable upon conversion, holders will be entitled to receive a payment equal to the present value of the remaining scheduled payments of interest that would have been made on the notes being converted from the date of conversion (or, in the case of conversion between a record date and the following interest payment date, from such interest payment date) until the earlier of the date that is three years after the date the Company receives such notice of conversion or maturity. The net proceeds from the offering after offering expenses were $54.4 million. The Company expects to use the net proceeds from the offering of the notes for general corporate purposes, which may include the development of the Company's sales and marketing infrastructure, as well as other strategic transactions and acquisitions. In addition, the Company used approximately $18.3 million of the proceeds of the offering to repurchase $22.9 million aggregate principal amount of the Company's outstanding 6.50% Convertible Senior Notes due 2019 and approximately $8.8 million to repurchase $9.7 million aggregate principal amount of the Company's outstanding 3% Convertible Senior Notes due 2017, in each case held by purchasers of notes participating in the offering. Hercules Loan Facility The Company’s loan facility with Hercules requires the Company to maintain unrestricted, unencumbered cash in U.S. bank accounts an amount equal to at least 50% of the principal amount outstanding under such facility. The Company received a waiver from Hercules with respect to non-compliance with such covenants. As of the date of issuance of this report, the Company is in compliance with all its Hercules debt agreements.

Accounting Policies, by Policy

Accounting Policies, by Policy (Policies)	9 Months Ended
	Sep. 30, 2015
Accounting Policies [Abstract]
Basis of Accounting, Policy [Policy Text Block]	Basis of Presentation The accompanying interim condensed consolidated financial statements have been prepared in accordance with the accounting principles generally accepted in the United States of America (“GAAP”) and with the instructions for Form 10-Q and Regulation S-X. Accordingly, they do not include all of the information and notes required for complete financial statements. These interim condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in the Company’s Form 10-K for the fiscal year ended December 31, 2014 as filed with the Securities and Exchange Commission (“SEC”) on March 31, 2015. The unaudited condensed consolidated financial statements include the accounts of the Company and its consolidated subsidiaries. All intercompany accounts and transactions have been eliminated in consolidation. The Company uses the equity method to account for investments in companies, if its investments provide it with the ability to exercise significant influence over operating and financial policies of the investee. Consolidated net income or loss includes the Company’s proportionate share of the net income or loss of these companies. Judgments made by the Company regarding the level of influence over each equity method investment include considering key factors such as the Company’s ownership interest, representation on the board of directors, participation in policy-making decisions and material intercompany transactions.
Consolidation, Policy [Policy Text Block]	Principles of Consolidation The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated variable interest entities (or “VIEs”), with respect to which the Company is considered the primary beneficiary, after elimination of intercompany accounts and transactions. Disclosure regarding the Company’s participation in the VIEs is included in Note 7, "Joint Ventures and Noncontrolling Interest.
Consolidation, Variable Interest Entity, Policy [Policy Text Block]	Variable Interest Entities The Company has interests in joint venture entities that are VIEs. Determining whether to consolidate a VIE requires judgment in assessing (i) whether an entity is a VIE and (ii) if the Company is the entity’s primary beneficiary and thus required to consolidate the entity. To determine if the Company is the primary beneficiary of a VIE, the Company evaluates whether it has (i) the power to direct the activities that most significantly impact the VIE’s economic performance and (ii) the obligation to absorb losses or the right to receive benefits of the VIE that could potentially be significant to the VIE. The Company’s evaluation includes identification of significant activities and an assessment of its ability to direct those activities based on governance provisions and arrangements to provide or receive product and process technology, product supply, operations services, equity funding and financing and other applicable agreements and circumstances. The Company’s assessment of whether it is the primary beneficiary of its VIEs requires significant assumptions and judgment.
Use of Estimates, Policy [Policy Text Block]	Use of Estimates In preparing the unaudited condensed consolidated financial statements, management must make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities as of the date of the unaudited condensed consolidated financial statements and the reported amounts of revenues and expenses during the reporting period. Actual results could differ from those estimates.
Unaudited Interim Financial Information, Policy [Policy Text Block]	Unaudited Interim Financial Information The accompanying interim condensed consolidated financial statements and related disclosures are unaudited, have been prepared on the same basis as the annual consolidated financial statements and, in the opinion of management, reflect all adjustments, which include only normal recurring adjustments, necessary for a fair statement of the results of operations for the periods presented. The year-end condensed consolidated balance sheet data was derived from audited financial statements, but does not include all disclosures required by GAAP. The condensed consolidated results of operations for any interim period are not necessarily indicative of the results to be expected for the full year or for any other future year or interim period.
New Accounting Pronouncements, Policy [Policy Text Block]	Recent Accounting Pronouncements In May 2014, the Financial Accounting Standards Board (or “FASB”) issued new guidance related to revenue recognition. This new standard will replace all current GAAP guidance on this topic and eliminate all industry-specific guidance. The new revenue recognition update guidance provides a unified model to determine how revenue is recognized. The core principle of the guidance is that an entity should recognize revenue to depict the transfer of promised goods or services to customers in an amount that reflects the consideration to which the entity expects to be entitled in exchange for those goods or services. On July 9, 2015, the FASB voted to defer the effective date by one year to December 15, 2017 for interim and annual reporting periods beginning after that date and permitted early adoption of the standard, but not before the original effective date of December 15, 2016. Therefore, the new standard will be effective commencing with our quarter ending March 31, 2018. In August 2014, FASB issued new guidance related to the disclosure around going concern. The new standard provides guidance around management's responsibility to evaluate whether there is substantial doubt about an entity's ability to continue as a going concern and to provide related footnote disclosure if substantial doubt exists. The new standard is effective for annual periods ending after December 15, 2016 and for annual periods and interim periods thereafter. Early adoption is permitted. The adoption of this standard is not expected to have a material impact on our financial statements. In January 2015, the FASB issued an update related to the presentation of extraordinary and unusual items. The update eliminates the concept of extraordinary items found in Subtopic 225-20, which required that an entity separately classify, present and disclose extraordinary events and transactions when the event or activity met both criteria of being unusual in nature and infrequent in occurrence. Although the concept of extraordinary items will be eliminated, the presentation and disclosure guidance for items that are unusual in nature or occur infrequently will be retained and will be expanded to include items that are both unusual in nature and infrequently occurring. The standard is effective for annual and interim periods within those annual years beginning after December 15, 2015. The Company expects that the adoption of the update will not materially affect its financial statements. In February 2015, FASB issued an amendment to ASC 810 Consolidation In April 2015, the FASB issued Accounting Standards Update 2015-3, Simplifying the Presentation of Debt Issuance Costs In July 2015, the FASB issued Accounting Standards Update 2015-11, Simplifying the Measurement of Inventory

Note 3 - Fair Value of Financ27

Note 3 - Fair Value of Financial Instruments (Tables)	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis [Table Text Block]	Level 1 Level 2 Level 3 Balance as of September 30, 2015 Financial Assets Money market funds $ 136 $ — $ — $ 136 Certificates of deposit 995 — — 995 Loans to affiliate (1) — — 1,747 1,747 Total financial assets $ 1,131 $ — $ 1,747 $ 2,878 Financial Liabilities Loans payable (1) $ — $ 9,421 $ — $ 9,421 Credit facilities (1) — 32,029 — 32,029 Convertible notes (1) — — 99,393 99,393 Compound embedded derivative liabilities — — 32,699 32,699 Temasek Funding Warrant derivative liability — 25,342 — $ 25,342 Currency interest rate swap derivative liability — 4,925 — 4,925 Total financial liabilities $ — $ 71,717 $ 132,092 $ 203,809 Level 1 Level 2 Level 3 Balance as of December 31, 2014 Financial Assets Money market funds $ 20,160 $ — $ — $ 20,160 Certificates of deposit 1,375 — — 1,375 Loans to affiliate (1) — — 1,745 1,745 Total financial assets $ 21,535 $ — $ 1,745 $ 23,280 Financial Liabilities Loans payable $ — $ 16,720 $ — $ 16,720 Credit facilities — 39,332 — 39,332 Convertible notes (1) — — 222,031 222,031 Compound embedded derivative liabilities — — 56,026 56,026 Currency interest rate swap derivative liability — 3,710 — 3,710 Total financial liabilities $ — $ 59,762 $ 278,057 $ 337,819
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]	September 30, 2015 Balance at January 1 $ 222,031 Derecognition on debt conversion (124,175 ) Change in fair value of convertible notes 1,537 Balance at September 30 $ 99,393
Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation [Table Text Block]	September 30, 2015 Balance at January 1 $ 56,026 Additions to Level 3 229 Derecognition on debt conversion (24,598 ) Loss from change in fair value of derivative liabilities 1,042 Balance at September 30 $ 32,699
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Table Text Block]	September 30, 2015 September 30, 2014 Risk-free interest rate 0.93% - 1.07% 0.79% - 1.67% Risk-adjusted yields 24.40% - 39.90% 15.10% - 24.40% Stock-price volatility 45% 45% Probability of change in control 5% 5% Stock price $2.01 $3.79 Credit spread 28.81% - 38.83% 13.54% - 22.73% Estimated conversion dates 2015 - 2019 2017 - 2019 Initial recognition (July 29, 2015) September 30, 2015 Expected dividend yield 0 0 Risk-free interest rate 2 % 2 % Expected term (in years) 10.00 10.00 Expected volatility 74 % 74 %
Derivative Instruments, Gain (Loss) [Table Text Block]	Income Three Months Ended September 30, Nine Months Ended September 30, Type of Derivative Contract 2015 2014 2015 2014 Loss Recognized Loss Recognized Currency interest rate swap Gain (loss) from change in fair value of derivative instruments $ (1,796 ) $ (1,139 ) $ (3,201 ) $ (83 )
Schedule of Derivative Liabilities at Fair Value [Table Text Block]	September 30, 2015 December 31, 2014 Fair market value of swap obligation $ 4,925 $ 3,710 Fair value of compound embedded derivative liabilities 32,699 56,026 Temasek Funding Warrant derivative liability 25,342 — Total derivative liabilities $ 62,966 $ 59,736

Note 4 - Balance Sheet Compon28

Note 4 - Balance Sheet Components (Tables)	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Schedule of Inventory, Current [Table Text Block]	September 30, 2015 December 31, 2014 Raw materials $ 1,928 $ 2,665 Work-in-process 6,470 5,269 Finished goods 2,704 6,572 Inventories, net $ 11,102 $ 14,506
Schedule of Prepaid and Other Current Assets [Table Text Block]	September 30, 2015 December 31, 2014 Maintenance $ 200 $ 399 Prepaid insurance 167 701 Manufacturing catalysts 2,928 1,166 Recoverable VAT and other taxes 2,085 2,411 Debt issuance costs 441 — Other 1,213 1,857 Prepaid expenses and other current assets $ 7,034 $ 6,534
Property, Plant and Equipment [Table Text Block]	September 30, 2015 December 31, 2014 Leasehold improvements $ 38,505 $ 39,132 Machinery and equipment 72,433 90,657 Computers and software 8,947 8,946 Furniture and office equipment 2,231 2,445 Buildings 3,855 6,321 Vehicles 196 353 Construction in progress 33,082 38,815 159,249 186,669 Less: accumulated depreciation, amortization and impairment (77,308 ) (67,689 ) Property, plant and equipment, net $ 81,941 $ 118,980
Schedule of Other Assets, Noncurrent [Table Text Block]	September 30, 2015 December 31, 2014 Deposits on property and equipment, including taxes $ 827 $ 1,738 Recoverable taxes from Brazilian government entities 6,814 9,747 Debt issuance costs 697 851 Other 1,253 1,299 Total other assets $ 9,591 $ 13,635
Schedule of Accrued and Other Current Liabilities [Table Text Block]	September 30, 2015 December 31, 2014 Professional services $ 3,876 $ 2,015 Accrued vacation 1,920 2,213 Payroll and related expenses 3,785 5,393 Tax-related liabilities 1,282 277 Deferred rent, current portion 1,110 1,111 Accrued interest 2,606 1,308 Contractual obligations to contract manufacturers 541 310 Commitment loan fee 750 — Other 962 938 Total accrued and other current liabilities $ 16,832 $ 13,565

Note 5 - Debt (Tables)

Note 5 - Debt (Tables)	9 Months Ended
	Sep. 30, 2015
Debt Disclosure [Abstract]
Schedule of Debt [Table Text Block]	September 30, 2015 December 31, 2014 FINEP credit facility $ 889 $ 1,614 BNDES credit facility 2,163 4,314 Hercules loan facility 23,503 29,779 Total credit facilities 26,555 35,707 Convertible notes 71,971 60,418 Related party convertible notes 42,401 115,239 Loans payable 12,908 21,097 Total debt 153,835 232,461 Less: current portion (20,902 ) (17,100 ) Long-term debt $ 132,933 $ 215,361
Schedule of Long-term Debt Instruments [Table Text Block]	Years ending December 31: Related Party Convertible Debt Convertible Debt Loans Credit Facility Total 2015 (remaining three months) $ 807 $ 2,019 $ 704 $ 4,816 $ 8,346 2016 1,606 4,020 3,813 19,216 28,655 2017 6,798 29,090 2,091 6,821 44,800 2018 16,780 15,685 2,002 262 34,729 2019 35,298 56,798 1,914 70 94,080 Thereafter — — 4,533 — 4,533 Total future minimum payments 61,289 107,612 15,057 31,185 215,143 Less: amount representing interest (1) (24,414 ) (35,640 ) (2,149 ) (4,631 ) (66,834 ) Present value of minimum debt payments 36,875 71,972 12,908 26,554 148,309 Less: current portion — — (3,364 ) (17,538 ) (20,902 ) Add: FV change due to conversion on 7/29/2015 5,526 $ — — — 5,526 Noncurrent portion of debt $ 42,401 $ 71,972 $ 9,544 $ 9,016 $ 132,933

Note 6 - Commitments and Cont30

Note 6 - Commitments and Contingencies (Tables)	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block Supplement [Abstract]
Schedule of Future Minimum Payments for Lease Obligations [Table Text Block]	Years ending December 31: Capital Operating Total Lease Obligations 2015 (remaining three months) $ 187 $ 1,696 $ 1,883 2016 530 6,755 7,285 2017 187 6,642 6,829 2018 — 6,700 6,700 2019 — 6,748 6,748 Thereafter — 25,026 25,026 Total future minimum lease payments 904 $ 53,567 $ 54,471 Less: amount representing interest (70 ) Present value of minimum lease payments 834 Less: current portion (555 ) Long-term portion $ 279

Note 7 - Joint Ventures and N31

Note 7 - Joint Ventures and Noncontrolling Interest (Tables)	9 Months Ended
	Sep. 30, 2015
Equity Method Investments and Joint Ventures [Abstract]
Equity Method Investments [Table Text Block]	September 30, (In thousands) 2015 2014 Balance at January 1 $ 2,192 $ — Loans to affiliate 770 — Imputation of interest 461 — Capital contribution (cash) — 2,075 Capital contribution (non – cash) — 237 Share in net loss offset to equity investment (908 ) (988 ) Share in net loss offset to loans to affiliate (1,181 ) — Accretion of imputed interest 413 — Balance at September 30 $ 1,747 $ 1,324
Schedule of Variable Interest Entities [Table Text Block]	(In thousands) September 30, 2015 December 31, 2014 Assets* $ 8,291 $ 22,812 Liabilities $ 444 $ 290
Noncontrolling Interest [Table Text Block]	September 30, 2015 September 30, 2014 Balance at January 1 $ 611 $ 584 Foreign currency translation adjustment (393 ) (37 ) Income attributable to noncontrolling interest 78 91 Balance at September 30 $ 296 $ 638

Note 9 - Goodwill and Intangi32

Note 9 - Goodwill and Intangible Assets (Tables)	9 Months Ended
	Sep. 30, 2015
Goodwill and Intangible Assets Disclosure [Abstract]
Schedule of Intangible Assets and Goodwill [Table Text Block]	September 30, 2015 December 31, 2014 Useful Life in Years Gross Carrying Amount Accumulated Amortization Net Carrying Value Gross Carrying Amount Accumulated Net Carrying Value In-process research and development Indefinite $ 8,560 $ 3,035 $ 5,525 $ 8,560 $ (3,035 ) $ 5,525 Acquired licenses and permits 2 772 (772 ) — 772 (772 ) — Goodwill Indefinite 560 — 560 560 — 560 $ 9,892 $ (3,807 ) $ 6,085 $ 9,892 $ (3,807 ) $ 6,085

Note 11 - Stock-Based Compens33

Note 11 - Stock-Based Compensation (Tables)	9 Months Ended
	Sep. 30, 2015
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Table Text Block]	Number Weighted- Weighted-Average Aggregate (in thousands) Outstanding - December 31, 2014 10,539,978 $ 6.10 7.22 $ 50 Options granted 2,582,353 $ 1.98 — — Options exercised (10,750 ) $ 1.41 — — Options cancelled (1,803,902 ) $ 5.06 — — Outstanding - September 30, 2015 11,307,679 $ 5.33 7.16 $ 283 Vested and expected to vest after September 30, 2015 10,603,529 $ 5.52 7.04 $ 245 Exercisable at September 30, 2015 6,075,541 $ 7.53 5.77 $ 40
Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Table Text Block]	RSUs Weighted-Average Grant-Date Fair Value Weighted Average Remaining Contractual Life (Years) Outstanding - December 31, 2014 1,975,503 $ 3.59 0.93 Awarded 2,767,355 $ 1.92 — Vested (929,322 ) $ 3.19 — Forfeited (255,293 ) $ 2.95 — Outstanding - September 30, 2015 3,558,243 $ 2.63 1.54 Expected to vest after September 30, 2015 3,029,826 $ 2.63 1.42
Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range [Table Text Block]	Options Outstanding Options Exercisable Exercise Price Number of Options Weighted- Weighted-Average Exercise Price Number of Options Weighted-Average Exercise Price $0.10—$1.80 687,093 8.74 $ 1.70 68,093 $ 1.43 $1.96—$1.96 1,412,533 9.62 $ 1.96 — $ — $1.98—$2.73 1,200,797 7.72 $ 2.53 478,181 $ 2.66 $2.75—$2.87 1,299,025 7.55 $ 2.83 800,584 $ 2.83 $2.89—$3.44 1,031,420 7.45 $ 3.11 613,405 $ 3.10 $3.51—$3.51 2,027,865 8.28 $ 3.51 738,773 $ 3.51 $3.55—$3.93 1,515,548 5.16 $ 3.87 1,302,162 $ 3.88 $4.06—$16.00 1,164,094 4.34 $ 9.17 1,131,706 $ 9.27 $16.50—$26.84 909,304 5.13 $ 23.04 882,637 $ 22.93 $30.17—$30.17 60,000 5.45 $ 30.17 60,000 $ 30.17 $0.10—$30.17 11,307,679 7.16 $ 5.33 6,075,541 $ 7.53
Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Table Text Block]	Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Research and development $ 530 $ 915 $ 1,776 $ 2,622 Sales, general and administrative 1,726 2,657 5,188 8,147 Total stock-based compensation expense $ 2,256 $ 3,572 $ 6,964 $ 10,769
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions [Table Text Block]	Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Expected dividend yield — % — % — % — % Risk-free interest rate 2 % 2 % 2 % 2 % Expected term (in years) 6.03 6.06 6.00 6.09 Expected volatility 74 % 74 % 74 % 75 %

Note 15 - Reporting Segments (T

Note 15 - Reporting Segments (Tables)	9 Months Ended
	Sep. 30, 2015
Segment Reporting [Abstract]
Schedule of Revenue from External Customers Attributed to Foreign Countries by Geographic Area [Table Text Block]	Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 United States $ 6,177 $ 10,189 $ 15,550 $ 14,977 Brazil 964 1,933 3,850 3,983 Europe 459 2,836 2,138 9,174 Asia 991 1,383 2,769 3,555 Total $ 8,591 $ 16,341 $ 24,307 $ 31,689
Schedule of Disclosure on Geographic Areas, Long-Lived Assets in Individual Foreign Countries by Country [Table Text Block]	September 30, 2015 December 31, 2014 United States $ 39,417 $ 44,418 Brazil 42,206 74,197 Europe 318 365 Total $ 81,941 $ 118,980

Note 16 - Comprehensive Incom35

Note 16 - Comprehensive Income (Loss) (Tables)	9 Months Ended
	Sep. 30, 2015
Disclosure Text Block [Abstract]
Schedule of Accumulated Other Comprehensive Income (Loss) [Table Text Block]	September 30, 2015 December 31, 2014 Foreign currency translation adjustment, net of tax $ (48,932 ) $ (29,977 ) Total accumulated other comprehensive loss $ (48,932 ) $ (29,977 )

Note 17 - Net Loss Attributab36

Note 17 - Net Loss Attributable to Common Stockholders and Net Loss per Share (Tables)	9 Months Ended
	Sep. 30, 2015
Earnings Per Share [Abstract]
Schedule of Earnings Per Share, Basic and Diluted [Table Text Block]	Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Numerator: Net loss attributable to Amyris, Inc. common stockholders $ (76,664 ) $ (36,641 ) $ (176,034 ) $ (55,735 ) Interest on convertible debt — — — 4,835 Accretion of debt discount — — — 3,856 Gain from change in fair value of derivative instruments — — — (57,580 ) Net loss attributable to Amyris, Inc. common stockholders after assumed conversion $ (76,664 ) $ (36,641 ) $ (176,034 ) $ (104,624 ) Denominator: Weighted average shares of common stock outstanding for basic EPS 140,374,297 78,980,402 100,103,007 78,146,365 Basic loss per share $ (0.55 ) $ (0.46 ) $ (1.76 ) $ (0.71 ) Weighted average shares of common stock outstanding 140,374,297 78,980,402 100,103,007 78,146,365 Effect of dilutive securities: Convertible promissory notes 0 — — 32,968,436 Weighted common stock equivalents 0 — — 32,968,436 Diluted weighted-average common shares 140,374,297 78,980,402 100,103,007 111,114,801 Diluted loss per share $ (0.55 ) $ (0.46 ) $ (1.76 ) $ (0.94 )
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share [Table Text Block]	Three Months Ended September 30, Nine Months Ended September 30, 2015 2014 2015 2014 Period-end stock options to purchase common stock 11,307,679 10,340,375 11,307,679 10,340,375 Convertible promissory notes 43,451,433 72,367,114 43,451,433 39,283,005 Period-end common stock subject to repurchase — — — — Period-end common stock warrants 2,901,926 1,021,087 2,901,926 1,021,087 Period-end restricted stock units 3,558,243 2,090,252 3,558,243 2,090,252 Total 61,219,281 85,818,828 61,219,281 52,734,719

Note 1 - The Company (Details)

Note 1 - The Company (Details) $ in Thousands	1 Months Ended	9 Months Ended
	Oct. 31, 2015USD ($)	Sep. 30, 2015USD ($)	Dec. 31, 2014USD ($)
Note 1 - The Company (Details) [Line Items]
Number of Operating Segments		2
Retained Earnings (Accumulated Deficit)		$ (995,186)	$ (819,152)
Cash, Cash Equivalents, and Short-term Investments		11,900
Debt Instrument, Unamortized Discount		17,300
Long-term Debt		153,835	232,461
Long-term Debt, Current Maturities		20,902	$ 17,100
Interest Payable		$ 9,200
Percentage of Outstanding Principle to be Maintained in Unencumbered Cash		50.00%
Subsequent Event [Member]
Note 1 - The Company (Details) [Line Items]
Proceeds from Convertible Debt	$ 54,400
Repayments of Convertible Debt	$ 27,100

Note 2 - Summary of Significa38

Note 2 - Summary of Significant Accounting Policies (Details)	9 Months Ended
	Sep. 30, 2015
Accounting Policies [Abstract]
Variable Interest Entity Number of Entities	2

Note 3 - Fair Value of Financ39

Note 3 - Fair Value of Financial Instruments (Details) $ / shares in Units, $ in Thousands, shares in Millions, BRL in Millions	Jul. 29, 2015USD ($)$ / shares	Sep. 30, 2015USD ($)$ / sharesshares	Dec. 31, 2014USD ($)	Jun. 30, 2012USD ($)	Jun. 30, 2012BRL
Temasek Funding Warrant [Member]
Note 3 - Fair Value of Financial Instruments (Details) [Line Items]
Derivative Liability	$ 19,400	$ 25,300
Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares		12.7
Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares		$ 0.01
Convertible Debt Securities [Member] | Total and Temasek [Member]
Note 3 - Fair Value of Financial Instruments (Details) [Line Items]
Debt Conversion, Original Debt, Amount	$ 138,000
Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares	$ 2.30
Convertible Notes, Restructuring	$ 37,000
Banco Pine July 2012 Loan Agreement [Member] | Interest Rate Swap [Member]
Note 3 - Fair Value of Financial Instruments (Details) [Line Items]
Derivative, Notional Amount				$ 5,500	BRL 22
Derivative, Fixed Interest Rate				3.94%	3.94%
Fair Value, Inputs, Level 3 [Member] | Derivative Liability, Compound Embedded Derivatives [Member]
Note 3 - Fair Value of Financial Instruments (Details) [Line Items]
Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value		$ 32,699	$ 56,026

Note 3 - Fair Value of Financ40

Note 3 - Fair Value of Financial Instruments (Details) - Fair Value, Assets, and Liabilities Measured on Recurring Basis - USD ($) $ in Thousands		Sep. 30, 2015	Dec. 31, 2014
Financial Liabilities
Temasek Funding Warrant derivative liability		$ 25,342
Fair Value, Measurements, Recurring [Member]
Financial Assets
Money market funds		136	$ 20,160
Certificates of deposit		995	1,375
Loans to affiliate	[1]	1,747	1,745
Total financial assets		2,878	23,280
Financial Liabilities
Loans payable	[1]	9,421	16,720
Credit facilities	[1]	32,029	39,332
Convertible notes	[1]	99,393	222,031
Compound embedded derivative liability		32,699	56,026
Temasek Funding Warrant derivative liability		25,342
Currency interest rate swap derivative liability		4,925	3,710
Total financial liabilities		203,809	337,819
Fair Value, Inputs, Level 1 [Member] | Fair Value, Measurements, Recurring [Member]
Financial Assets
Money market funds		136	20,160
Certificates of deposit		$ 995	$ 1,375
Loans to affiliate	[1]
Total financial assets		$ 1,131	$ 21,535
Financial Liabilities
Loans payable	[1]
Credit facilities	[1]
Convertible notes	[1]
Fair Value, Inputs, Level 2 [Member] | Fair Value, Measurements, Recurring [Member]
Financial Assets
Loans to affiliate	[1]
Financial Liabilities
Loans payable	[1]	$ 9,421	$ 16,720
Credit facilities	[1]	$ 32,029	$ 39,332
Convertible notes	[1]
Temasek Funding Warrant derivative liability		$ 25,342
Currency interest rate swap derivative liability		4,925	$ 3,710
Total financial liabilities		71,717	59,762
Fair Value, Inputs, Level 3 [Member] | Fair Value, Measurements, Recurring [Member]
Financial Assets
Loans to affiliate	[1]	1,747	1,745
Total financial assets		$ 1,747	$ 1,745
Financial Liabilities
Loans payable	[1]
Credit facilities	[1]
Convertible notes	[1]	$ 99,393	$ 222,031
Compound embedded derivative liability		32,699	56,026
Total financial liabilities		$ 132,092	$ 278,057
[1]	These liabilities are carried on the condensed consolidated balance sheet on a historical cost basis.

Note 3 - Fair Value of Financ41

Note 3 - Fair Value of Financial Instruments (Details) - Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation - Fair Value, Inputs, Level 3 [Member] - Convertible Debt [Member] $ in Thousands	9 Months Ended
	Sep. 30, 2015USD ($)
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Balance	$ 222,031
Derecognition on debt conversion	(124,175)
Change in fair value of convertible notes	1,537
Balance	$ 99,393

Note 3 - Fair Value of Financ42

Note 3 - Fair Value of Financial Instruments (Details) - Reconciliation for Compound Embedded Derivative Liability - Fair Value, Inputs, Level 3 [Member] - Derivative Liability, Compound Embedded Derivatives [Member] $ in Thousands	9 Months Ended
	Sep. 30, 2015USD ($)
Fair Value, Net Derivative Asset (Liability) Measured on Recurring Basis, Unobservable Input Reconciliation [Line Items]
Balance	$ 56,026
Additions to Level 3	229
Derecognition on debt conversion	(24,598)
Loss from change in fair value of derivative liabilities	1,042
Balance	$ 32,699

Note 3 - Fair Value of Financ43

Note 3 - Fair Value of Financial Instruments (Details) - Market-based Assumption and Estimates - $ / shares	Jul. 29, 2015	Sep. 30, 2015	Sep. 30, 2015	Sep. 30, 2014
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Expected volatility			45.00%	45.00%
Probability of change in control			5.00%	5.00%
Stock price (in Dollars per share)		$ 2.01	$ 2.01	$ 3.79
Temasek Funding Warrant [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Risk-free interest rate	2.00%	2.00%
Expected term (in years)	10 years	10 years
Risk-adjusted yields	0.00%	0.00%
Expected volatility	74.00%	74.00%
Minimum [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Risk-free interest rate			0.93%	0.79%
Risk-adjusted yields			24.40%	15.10%
Credit spread			28.81%	13.54%
Estimated conversion dates			2,015	2,017
Maximum [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Risk-free interest rate			1.07%	1.67%
Risk-adjusted yields			39.90%	24.40%
Credit spread			38.83%	22.73%
Estimated conversion dates			2,019	2,019

Note 3 - Fair Value of Financ44

Note 3 - Fair Value of Financial Instruments (Details) - Derivative Instruments Classification - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Currency Interest Rate Swap [Member] | Not Designated as Hedging Instrument [Member] | Gain (Loss) from Change in Fair Value of Derivative Instruments [Member]
Derivative Instruments, Gain (Loss) [Line Items]
Currency interest rate swap	$ (1,796)	$ (1,139)	$ (3,201)	$ (83)

Note 3 - Fair Value of Financ45

Note 3 - Fair Value of Financial Instruments (Details) - Derivative Liabilities - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Derivative Liability [Abstract]
Fair market value of swap obligation	$ 4,925	$ 3,710
Fair value of compound embedded derivative liabilities	32,699	56,026
Temasek Funding Warrant derivative liability	25,342
Total derivative liabilities	$ 62,966	$ 59,736

Note 4 - Balance Sheet Compon46

Note 4 - Balance Sheet Components (Details) - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014	Dec. 31, 2014
Note 4 - Balance Sheet Components (Details) [Line Items]
Property, Plant and Equipment, Gross	$ 159,249		$ 159,249		$ 186,669
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment	77,308		77,308		67,689
Depreciation, Depletion and Amortization			9,931	$ 11,334
Capital Lease Obligations [Member]
Note 4 - Balance Sheet Components (Details) [Line Items]
Accumulated Depreciation, Depletion and Amortization, Property, Plant, and Equipment	300		300		2,300
Loss on Purchase Commitments and Impairment of Property, Plant and Equipment [Member] | SMA Industria Quimica S.A. [Member]
Note 4 - Balance Sheet Components (Details) [Line Items]
Impaired Assets to be Disposed of by Method Other than Sale, Amount of Impairment Loss			7,300	7,300
Loss on Purchase Commitments and Impairment of Property, Plant and Equipment [Member] | SMA Industria Quimica S.A. [Member] | Brazilian VAT [Member]
Note 4 - Balance Sheet Components (Details) [Line Items]
Impaired Assets to be Disposed of by Method Other than Sale, Carrying Value of Asset		$ 600		600
Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member] | Capital Lease Obligations [Member]
Note 4 - Balance Sheet Components (Details) [Line Items]
Property, Plant and Equipment, Gross	1,300		1,300		$ 4,100
Property Plant and Equipment Including Capital Leases [Member]
Note 4 - Balance Sheet Components (Details) [Line Items]
Depreciation, Depletion and Amortization	$ 3,100	$ 3,800	$ 9,900	$ 11,300

Note 4 - Balance Sheet Compon47

Note 4 - Balance Sheet Components (Details) - Inventory, Current - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Inventory, Current [Abstract]
Raw materials	$ 1,928	$ 2,665
Work-in-process	6,470	5,269
Finished goods	2,704	6,572
Inventories, net	$ 11,102	$ 14,506

Note 4 - Balance Sheet Compon48

Note 4 - Balance Sheet Components (Details) - Prepaid and Other Current Assets - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Prepaid and Other Current Assets [Abstract]
Maintenance	$ 200	$ 399
Prepaid insurance	167	701
Manufacturing catalysts	2,928	1,166
Recoverable VAT and other taxes	2,085	2,411
Debt issuance costs	441
Other	1,213	1,857
Prepaid expenses and other current assets	$ 7,034	$ 6,534

Note 4 - Balance Sheet Compon49

Note 4 - Balance Sheet Components (Details) - Property, Plant and Equipment - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	$ 159,249	$ 186,669
Less: accumulated depreciation, amortization and impairment	(77,308)	(67,689)
Property, plant and equipment, net	81,941	118,980
Leasehold Improvements [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	38,505	39,132
Machinery and Equipment [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	72,433	90,657
Computer Equipment and Software [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	8,947	8,946
Furniture and Fixtures [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	2,231	2,445
Building [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	3,855	6,321
Vehicles [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	196	353
Construction in Progress [Member]
Property, Plant and Equipment [Line Items]
Property, Plant, and Equipment	$ 33,082	$ 38,815

Note 4 - Balance Sheet Compon50

Note 4 - Balance Sheet Components (Details) - Other Assets, Noncurrent - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Other Assets, Noncurrent [Abstract]
Deposits on property and equipment, including taxes	$ 827	$ 1,738
Recoverable taxes from Brazilian government entities	6,814	9,747
Debt issuance costs	697	851
Other	1,253	1,299
Total other assets	$ 9,591	$ 13,635

Note 4 - Balance Sheet Compon51

Note 4 - Balance Sheet Components (Details) - Accrued and Other Current Liabilities - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Accrued and Other Current Liabilities [Abstract]
Professional services	$ 3,876	$ 2,015
Accrued vacation	1,920	2,213
Payroll and related expenses	3,785	5,393
Tax-related liabilities	1,282	277
Deferred rent, current portion	1,110	1,111
Accrued interest	2,606	1,308
Contractual obligations to contract manufacturers	541	310
Commitment loan fee	750
Other	962	938
Total accrued and other current liabilities	$ 16,832	$ 13,565

Note 5 - Debt (Details)

Note 5 - Debt (Details) $ / shares in Units, $ in Thousands, l in Millions, BRL in Millions

Jul. 29, 2015USD ($)$ / sharesshares

Apr. 02, 2015

Aug. 31, 2013USD ($)$ / sharesshares

Jun. 30, 2015

Jun. 30, 2014USD ($)

May. 31, 2014USD ($)$ / shares

Mar. 31, 2014USD ($)

Jan. 31, 2014USD ($)$ / shares

Oct. 31, 2013USD ($)$ / sharesl

Aug. 31, 2013USD ($)$ / sharesshares

Jun. 30, 2013USD ($)$ / shares

Jul. 31, 2012USD ($)

Jul. 31, 2012BRL

Jul. 30, 2012USD ($)$ / shares

Dec. 31, 2011USD ($)

Dec. 31, 2011BRL

Nov. 30, 2010USD ($)

Sep. 30, 2015USD ($)$ / shares

Jun. 30, 2015USD ($)

Sep. 30, 2014USD ($)

Sep. 30, 2015USD ($)$ / sharesshares

Sep. 30, 2014USD ($)

Dec. 31, 2014USD ($)

Dec. 31, 2013USD ($)

Dec. 31, 2012USD ($)$ / sharesshares

Sep. 30, 2015BRL

Apr. 30, 2015USD ($)

Mar. 31, 2015USD ($)

Jan. 31, 2015USD ($)$ / shares

Dec. 31, 2014BRL

Oct. 31, 2014USD ($)

Jul. 31, 2014USD ($)$ / shares

May. 29, 2014USD ($)

Apr. 30, 2014USD ($)$ / shares

Sep. 30, 2013USD ($)shares

Jul. 31, 2013USD ($)$ / shares

Mar. 31, 2013USD ($)$ / shares

Dec. 26, 2012USD ($)

Dec. 26, 2012BRL

Sep. 14, 2012USD ($)

Jul. 31, 2012BRL

Jun. 30, 2012USD ($)

Feb. 28, 2012USD ($)$ / shares

Dec. 31, 2011BRL

Nov. 30, 2010BRL

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Unamortized Discount

$ 17,300

$ 17,300

Convertible Notes Payable

$ 130,900

Gains (Losses) on Extinguishment of Debt

(5,984)

(5,984)

$ (10,512)

Long-term Debt

153,835

153,835

$ 232,461

Letters of Credit Outstanding, Amount

$ 1,000

Restricted Cash and Cash Equivalents, Noncurrent

957

$ 957

1,619

Private Placement [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares

$ 0.01

Class of Warrant or Right, Term

5 years

Common Stock [Member]

Note 5 - Debt (Details) [Line Items]

Stock Issued During Period, Shares, New Issues (in Shares) | shares

16,025,642

Common Stock [Member] | Private Placement [Member]

Note 5 - Debt (Details) [Line Items]

Stock Issued During Period, Shares, New Issues (in Shares) | shares

16,025,642

TJLP Adjustment Factor [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate of the Central Bank of Brazil Used as a Threshold

6.00%

6.00%

Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Debt

42,400

$ 42,400

115,200

Gains (Losses) on Extinguishment of Debt

$ (9,400)

$ (5,900)

$ (10,500)

Long-term Debt

42,401

42,401

115,239

Future Cancellation of Debt, Amount

$ 14,600

Debt Instrument, Debt Discount, Related Party

1,700

1,700

53,800

Rule 14A Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Unamortized Discount

1,700

1,700

Convertible Debt

14,600

14,600

Convertible Promissory Notes 1 [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 25,000

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 7.0682

Loans Payable [Member]

Note 5 - Debt (Details) [Line Items]

Long-term Debt

12,908

12,908

21,097

Convertible Promissory Notes 2 [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 5,000

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.08

Future Cancellation of Debt, Amount

$ 5,000

Tranche Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 25,900

Exchange Warrants [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares

$ 0.01

Minimum [Member] | Tranche Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

2.44

Maximum [Member] | Tranche Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

2.87

Loans Payable [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

3.24%

Debt Instrument, Term

9 months

Loans Payable to Bank, Current

$ 600

Loans Payable to Bank

0

0

300

$ 600

FINEP Credit Facility [Member]

Note 5 - Debt (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity

$ 1,600

BRL 6.4

Debt Instrument, Interest Rate, Stated Percentage

5.00%

5.00%

Debt Default, Penalty and Fine on Obligation in Default, Percentage

10.00%

10.00%

Debt Instrument Interest On Late Balance Percentage Per Month

1.00%

1.00%

Debt Instrument, Number of Monthly Installments

81

81

Long-term Line of Credit

900

900

1,600

BRL 3.5

BRL 4.3

Research and Development Project Amount to be Contributed from Company Funds

3,600

3,600

14.5

Period of Time Amounts Released Must be Used

30 months

FINEP Credit Facility [Member] | Threshold Met [Member] | TJLP Adjustment Factor [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Basis Spread on Variable Rate

5.00%

FINEP Credit Facility [Member] | Threshold not Met [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

11.00%

11.00%

FINEP Credit Facility [Member] | Prior to the Release of the Second Disbursement [Member]

Note 5 - Debt (Details) [Line Items]

Research and Development Project Amount to be Contributed from Company Funds | BRL

11.1

BNDES Credit Facility [Member]

Note 5 - Debt (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity

$ 5,600

BRL 22.4

Debt Instrument, Interest Rate, Stated Percentage

7.00%

7.00%

Debt Instrument, Number of Monthly Installments

60

60

Long-term Line of Credit

2,200

2,200

4,300

BRL 8.6

BRL 11.5

Line of Credit Facility, Unused Capacity, Commitment Fee Percentage

0.10%

0.10%

Collateral Provided by Company Certain Equipment and Other Tangible Assets Amount

$ 6,300

BRL 24.9

Line of Credit Facility Bank Guarantee Percentage

10.00%

10.00%

Guarantor Obligations, Liquidation Proceeds, Percentage

130.00%

130.00%

BNDES Credit Facility [Member] | The First Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity | BRL

BRL 19.1

BNDES Credit Facility [Member] | The Second Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity | BRL

3.3

Line of Credit Facility Bank Guarantee Percentage

90.00%

90.00%

Line of Credit Facility, Borrowings Above Which is New Tranche (in Brazil Real) | BRL

BRL 19.1

Letter of Credit [Member]

Note 5 - Debt (Details) [Line Items]

Restricted Cash and Cash Equivalents, Noncurrent

1,000

1,000

1,000

Temasek [Member] | August 2013 Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Bridge Loan

35,000

Temasek [Member] | Rule 14A Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Debt

$ 10,000

Total and Temasek [Member] | Convertible Debt Securities [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.30

Debt Conversion, Original Debt, Amount

$ 138,000

Foris Ventures, LLC [Member] | Rule 14A Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Debt

$ 5,000

Banco ABC Brasil S.A. (ABC) [Member] | FINEP Credit Facility [Member] | Prior to the Release of the Second Disbursement [Member]

Note 5 - Debt (Details) [Line Items]

Guaranty Liabilities

$ 800

BRL 3.3

Hercules Technology Growth Capital, Inc. (Hercules) [Member]

Note 5 - Debt (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity

$ 15,000

Long-term Line of Credit

$ 25,000

Loans Payable

$ 25,000

23,500

23,500

Debt Instrument, Prepayment Penalty, Percentage

3.00%

Debt Instrument, Facility Charge, Percentage

1.00%

Debt Instrument, End of Term Fee, Percentage

10.00%

Debt Instrument, Forbearance Fee, Forgiven

$ 10,000

Debt Instrument, Required Equity Financing, Amount

$ 50,000

Debt Instrument, Unencumbered, Unrestricted, Cash Required, Percentage

50.00%

50.00%

Line of Credit Facility, Incremental Draw Down Amount

5,000

Line of Credit Facility, Amount to be Raised Through Equity Triggering Withdrawal of the Credit Facility

$ 20,000

Line of Credit Facility, Commitment Fee Percentage

3.00%

5.00%

Debt Instrument, Unamortized Discount

200

200

Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Minimum [Member] | Prime Rate [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Basis Spread on Variable Rate

6.25%

Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Maximum [Member] | Prime Rate [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Basis Spread on Variable Rate

9.50%

Hercules Technology Growth Capital, Inc. (Hercules) [Member] | After the Initial Twelve-month Period [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Prepayment Penalty, Percentage

1.00%

Total [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 25,000

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.30

Debt Conversion, Original Debt, Amount

$ 70,000

Debt Conversion, Converted Instrument, Shares Issued (in Shares) | shares

30,434,782

Total [Member] | Convertible Promissory Notes 1 [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 5,000

$ 5,000

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.74

$ 3.74

Total [Member] | Total Funding Warrant [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

18,860,992

Class of Warrant or Right, Term

5 years

Total [Member] | Total R&D Warrant [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

2,000,000

Class of Warrant or Right, Term

5 years

Nossa Caixa and Banco Pine Agreements [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

5.50%

5.50%

Collateral Provided by Company Certain Equipment and Other Tangible Assets Amount

$ 17,100

BRL 68

Debt Instrument, Face Amount

13,100

BRL 52

Certain Farnesene Production Assets Pledged as Collateral for Loans (in Brazil Real) | BRL

52

Debt Instrument, Period of Interest Only QuarterlyPayments

2 years

Nossa Caixa and Banco Pine Agreements [Member] | Loans Payable [Member]

Note 5 - Debt (Details) [Line Items]

Long-term Debt

$ 11,200

$ 11,200

18,600

Banco Pine [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount | BRL

22

Nossa Caixa [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount | BRL

BRL 30

Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.30

Debt Conversion, Original Debt, Amount

$ 71,000

Debt Conversion, Converted Instrument, Shares Issued (in Shares) | shares

30,860,633

Temasek [Member] | Temasek Warrant 1 [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

14,677,861

Class of Warrant or Right, Term

10 years

Temasek [Member] | Temasek Warrant 2 [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Term

10 years

Class of Warrant or Right, Threshold Number of Securities (in Shares) | shares

2,000,000

Class of Warrant or Right, Numerator One

30.60%

Class of Warrant or Right, Denominator One

69.40%

Class of Warrant or Right, Numerator Two

13.30%

Class of Warrant or Right, Denominator Two

86.70%

Temasek [Member] | Temasek Warrant Three [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Term

10 years

Class of Warrant or Right, Threshold Number of Securities (in Shares) | shares

2,000,000

Class of Warrant or Right, Common Stock Shares Used In Calculation (in Shares) | shares

880,339

Temasek [Member] | The 2013 Warrant [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

1,000,000

Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares

$ 0.01

Temasek [Member] | If Total R&D Warrant is Exercised in Full [Member] | Temasek Warrant Three [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

880,339

Total and Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Interest Expense, Debt

2,600

$ 36,600

Hercules Credit Additional Amount [Member] | Hercules Technology Growth Capital, Inc. (Hercules) [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Additional Amount Required

$ 5,000

Hercules Credit Additional Amount [Member] | Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Minimum [Member] | Prime Rate [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Basis Spread on Variable Rate

5.25%

Hercules Credit Additional Amount [Member] | Hercules Technology Growth Capital, Inc. (Hercules) [Member] | Maximum [Member] | Prime Rate [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Basis Spread on Variable Rate

8.50%

Fidelity Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 7.0682

Debt Instrument, Convertible, Number of Equity Instruments

3,536,968

Convertible Promissory Note, Acquisition Right Amount Redeemable, Percentage

101.00%

Convertible Promissory Note, Maximum Allowable Debt

$ 200,000

Convertible Promissory Notes, Debt Percentage of Total Assets

50.00%

Convertible Promissory Note, Maximum Amount of Secured Debt

$ 125,000

Convertible Promissory Note, Secured Debt as a Percentage of consolidated Total Assets

30.00%

Convertible Promissory Note, Bridge Loan Amount, Convertible Promissory Note Covenants Waived

35,000

Additional Consideration for Covenant Waiving, Convertible Promissory Notes

7,600

Fidelity Convertible Notes [Member] | Convertible Subordinated Debt [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 25,000

Debt Instrument, Interest Rate, Effective Percentage

3.00%

Rule 144A Convertible Note Offering [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.74

Convertible Note Offering

$ 75,000

Additional Convertible Note Offering

15,000

Proceeds from Convertible Debt

72,000

Proceeds from Convertible Debt Used to Repay Previously Issued Convertible Debt

$ 9,700

Debt Instrument, Convertible, Threshold Trading Days

20

Debt Instrument, Convertible, Threshold Consecutive Trading Days

30 days

Debt Instrument, Convertible, Threshold Days for Conversion Notification

5 days

Convertible Note Substantial Change, Percentage of Principal Repurchase Price

100.00%

Convertible Note Substantial Change, Discount Rate Used in Calculate Value of Remaining Interest Payments

0.75%

Rule 144A Convertible Note Offering [Member] | Convertible Debt Securities [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Effective Percentage

6.50%

Rule 144A Convertible Note Offering [Member] | Numerator [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Ratio

267.037

Rule 144A Convertible Note Offering [Member] | Denominator [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Ratio

1,000

Rule 144A Convertible Note Offering [Member] | Affiliated Entity [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

6.50%

Amount of Convertible Debt Purchased by Affiliated Entities

$ 24,700

Total Purchase Agreement [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Promissory Note, Acquisition Right Amount Redeemable, Percentage

101.00%

Debt Instrument, Face Amount

$ 105,000

Debt Restrictions, Maximum Outstanding Debt

$ 200,000

Debt Restrictions, Maximum Outstanding Debt, Percentage of Consolidated Total Assets

50.00%

Total Purchase Agreement [Member] | Total [Member] | Secured Debt [Member]

Note 5 - Debt (Details) [Line Items]

Debt Restrictions, Maximum Outstanding Debt

$ 125,000

Debt Restrictions, Maximum Outstanding Debt, Percentage of Consolidated Total Assets

30.00%

Unsecured Senior Convertible Promissory Notes [Member] | Related Party Convertible Notes [Member] | Second Closing [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 20,000

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

1.50%

Debt Instrument, Face Amount

$ 69,000

Debt Instrument Default Rate

2.50%

Number of Trading Days Notes Become Convertible

10 years

Debt Instrument Percentage Outstanding and Payable

70.00%

Percentage of Outstanding Notes To Be Cancelled

30.00%

Convertible Debt

$ 53,300

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Private Placement [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.98

Debt Conversion, Original Debt, Amount

$ 5,000

Stock Issued During Period, Shares, New Issues (in Shares) | shares

1,677,852

Debt Instrument Cancelled

$ 5,000

Gains (Losses) on Extinguishment of Debt

$ (900)

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Initial Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

1.50%

1.50%

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 7.0682

Debt Instrument, Face Amount

$ 38,300

$ 15,000

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Second Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.08

Number of Installments

2

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Third Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 4.11

Debt Instrument, Face Amount

$ 10,850

$ 10,850

Convertible Debt, Number of Installments

2

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Two Installments In Third Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 21,700

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | New Funding [Member] | Initial Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

15,000

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Diesel Research and Development Funding [Member] | Initial Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 23,300

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 10,000

20,000

Debt Instrument, Notes Related Party Committed to Purchase, Completed

$ 30,000

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Related Party Convertible Notes [Member] | Second Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

10,000

Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Related Party Convertible Notes [Member] | Two Installments in Second Closing [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 30,000

March 2013 Letter Agreement [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.08

$ 3.08

$ 7.0682

Debt Instrument Closing Price Plus Incremental Rate (in Dollars per share) | $ / shares

0.01

March 2013 Letter Agreement [Member] | Total [Member] | Minimum [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 3.08

August 2013 Convertible Notes [Member] | Private Placement [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 110,000

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

1,000,000

August 2013 Convertible Notes [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Cancellation of Convertible Debt

$ 13,000

August 2013 Convertible Notes [Member] | Total [Member] | First Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Cancellation of Convertible Debt

7,600

August 2013 Convertible Notes [Member] | Total [Member] | Second Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Cancellation of Convertible Debt

5,400

August 2013 Convertible Notes [Member] | Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Proceeds from Convertible Debt

$ 60,000

Bridge Loan

$ 35,000

August 2013 Convertible Notes [Member] | Temasek [Member] | Common Stock [Member]

Note 5 - Debt (Details) [Line Items]

Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares) | shares

1,000,000

1,000,000

Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares

$ 0.01

$ 0.01

August 2013 Convertible Notes [Member] | Temasek [Member] | First Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Proceeds from Convertible Debt

$ 35,000

August 2013 Convertible Notes [Member] | Temasek [Member] | Second Closing [Member]

Note 5 - Debt (Details) [Line Items]

Proceeds from Convertible Debt

25,000

August 2013 Convertible Notes [Member] | Total and Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 73,000

$ 73,000

Private Placement Convertible Notes, Period

24 months

Debt Instrument, Number of Tranches

2

August 2013 Convertible Notes [Member] | Total and Temasek [Member] | First Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 42,600

$ 42,600

August 2013 Convertible Notes [Member] | Total and Temasek [Member] | Second Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 30,400

30,400

Senior Secured Convertible Note [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

1.50%

Debt Instrument, Face Amount

10,850

Senior Secured Convertible Note [Member] | Total [Member] | Initial Tranche [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 21,700

July 2012 Agreements [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 7.0682

Debt Instrument, Face Amount

$ 10,850

March 2014 Letter Agreement [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 4.11

$ 4.11

$ 4.11

Convertible Debt

$ 75,000

Replacement Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Unamortized Discount

0

$ 0

13,100

Long-term Debt

5,000

5,000

51,000

Temasek Bridge Loan [Member] | Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

5.50%

First Tranche [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.44

Proceeds from Convertible Debt

$ 7,600

Debt Instrument, Face Amount

51,800

Gains (Losses) on Extinguishment of Debt

(19,900)

Cancellation of Convertible Debt

44,200

Debt Instrument, Amended Additional Investor Amount

$ 7,600

Future Cancellation of Debt, Amount

$ 9,200

Convertible Promissory Notes, Period After Which Notes Will Be Due

60 months

Convertible Notes, Discount Percentage to Determine Conversion Price

15.00%

Convertible Note Discount, Number of Days for Trailing Weighted-average Closing Price

60 years

Convertible Notes, Period After Which Convertible at the Option of Holder

18 months

Debt Instrument, Convertible, Conversion Price, Event Date Price (in Dollars per share) | $ / shares

$ 2.15

Plant Manufacturing Production, Product Sales, Percentage

5.00%

Plant Manufacturing Production, Volume (in Liters) | l

1

Plant Manufacturing Production, Period

45 days

Plant Manufacturing Gross Margin

8.00%

Debt Instrument, Interest Rate, Stated Percentage, per Six Months

5.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued, Rate Applicable to the First 180 Days

6.50%

Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter

8.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults

6.50%

Convertible Notes, Period Over Which Interest is Payable in Kind

30 months

Convertible Notes, Initial Prepayment Term

30 months

Convertible Notes, Recurring Term of Option to Prepay After Initial Payment Period

6 months

First Tranche [Member] | Total [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Extinguishment of Debt, Amount

$ 9,200

First Tranche [Member] | Temasek [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Extinguishment of Debt, Amount

35,000

The Second Tranche [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.87

Debt Instrument, Face Amount

$ 34,000

Future Cancellation of Debt, Amount

$ 5,400

Convertible Promissory Notes, Period After Which Notes Will Be Due

60 months

Debt Instrument, Convertible, Conversion Price, Interest Accrued, Rate Applicable to the First 180 Days

13.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter

16.00%

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Defaults

12.00%

Convertible Notes Exchanged and Cancelled

$ 6,000

Debt Instrument, Term

12 months

Debt Instrument, Convertible, Conversion Price, Interest Accrued

10.00%

Debt Instrument, Convertible, Conversion Price, Interest Period

36 months

The Second Tranche [Member] | Temasek [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Purchased

$ 25,000

The Second Tranche [Member] | Wolverine [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Purchased

3,000

The Second Tranche [Member] | Total [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Purchased

$ 6,000

Tranche I and Tranche II Notes [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Unamortized Discount

0

0

30,700

Convertible Debt

22,700

22,700

49,200

Percentage of Principal Amount of Notes, Required to Be Repaid in Change of Control

101.00%

Tranche I and Tranche II Notes [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

$ 15,300

Rule 14A Related Party Convertible Notes [Member] | Total [Member] | Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Proceeds from Convertible Debt

9,700

Convertible Debt

$ 75,000

Gains (Losses) on Extinguishment of Debt

$ (1,100)

Extinguishment of Debt, Amount

$ 9,700

Related Party Convertible Notes [Member]

Note 5 - Debt (Details) [Line Items]

Gains (Losses) on Extinguishment of Debt

0

(5,900)

Related Party Convertible Notes [Member] | Secured Debt [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Face Amount

$ 10,850

ABC Brasil Agreement [Member] | Banco ABC Brasil S.A. (ABC) [Member]

Note 5 - Debt (Details) [Line Items]

Long-term Debt

1,600

1,600

Export Financing Agreement

$ 2,500

Additional Export Financing Agreement

$ 2,200

$ 1,600

Rule 144A Convertible Notes [Member] | Total [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

9,700

Rule 144A Convertible Notes [Member] | Temasek [Member]

Note 5 - Debt (Details) [Line Items]

Convertible Notes Payable

10,000

Related Party and Non-Related Party Convertible Debt [Member]

Note 5 - Debt (Details) [Line Items]

Debt Instrument, Unamortized Discount

$ 17,100

$ 17,100

Exchange and Maturity Treatment Agreements [Member]

Note 5 - Debt (Details) [Line Items]

Gains (Losses) on Extinguishment of Debt

(6,000)

Extinguishment of Debt, Amount

$ 178,100

Note 5 - Debt (Details) - Debt

Note 5 - Debt (Details) - Debt - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	$ 153,835	$ 232,461
Less: current portion	(20,902)	(17,100)
Long-term debt	132,933	215,361
FINEP Credit Facility [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	889	1,614
BNDES Credit Facility [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	2,163	4,314
Hercules Loan Facility [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	23,503	29,779
Credit Facility [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	26,555	35,707
Convertible Debt [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	71,971	60,418
Related Party Convertible Notes [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	42,401	115,239
Loans Payable [Member]
Note 5 - Debt (Details) - Debt [Line Items]
Long-term Debt	$ 12,908	$ 21,097

Note 5 - Debt (Details) - Long-

Note 5 - Debt (Details) - Long-term Debt Instruments $ in Thousands	Sep. 30, 2015USD ($)
Debt Instrument [Line Items]
2015 (remaining three months)	$ 8,346
2,016	28,655
2,017	44,800
2,018	34,729
2,019	94,080
Thereafter	4,533
Total future minimum payments	215,143
Less: amount representing interest(1)	(66,834)	[1]
Present value of minimum debt payments	148,309
Less: current portion	(20,902)
Add: FV change due to conversion on 7/29/2015	5,526
Noncurrent portion of debt	132,933
Related Party Convertible Notes [Member]
Debt Instrument [Line Items]
2015 (remaining three months)	807
2,016	1,606
2,017	6,798
2,018	16,780
2,019	35,298
Total future minimum payments	61,289
Less: amount representing interest(1)	(24,414)	[1]
Present value of minimum debt payments	36,875
Add: FV change due to conversion on 7/29/2015	5,526
Noncurrent portion of debt	42,401
Convertible Debt [Member]
Debt Instrument [Line Items]
2015 (remaining three months)	2,019
2,016	4,020
2,017	29,090
2,018	15,685
2,019	56,798
Total future minimum payments	107,612
Less: amount representing interest(1)	(35,640)	[1]
Present value of minimum debt payments	71,972
Noncurrent portion of debt	71,972
Loans Payable [Member]
Debt Instrument [Line Items]
2015 (remaining three months)	704
2,016	3,813
2,017	2,091
2,018	2,002
2,019	1,914
Thereafter	4,533
Total future minimum payments	15,057
Less: amount representing interest(1)	(2,149)	[1]
Present value of minimum debt payments	12,908
Less: current portion	(3,364)
Noncurrent portion of debt	9,544
Credit Facility [Member]
Debt Instrument [Line Items]
2015 (remaining three months)	4,816
2,016	19,216
2,017	6,821
2,018	262
2,019	70
Total future minimum payments	31,185
Less: amount representing interest(1)	(4,631)	[1]
Present value of minimum debt payments	26,554
Less: current portion	(17,538)
Noncurrent portion of debt	$ 9,016
[1]	Including debt discount of $17.1 million related to the embedded derivatives associated with the related party and non-related party convertible debt which will be accreted to interest expense under the effective interest method over the term of the convertible debt.

Note 6 - Commitments and Cont55

Note 6 - Commitments and Contingencies (Details) $ / shares in Units, BRL in Millions

Apr. 08, 2015USD ($)

Dec. 02, 2013USD ($)$ / shares

Mar. 31, 2013USD ($)

Dec. 31, 2011USD ($)

Dec. 31, 2011BRL

Sep. 30, 2015USD ($)

Sep. 30, 2015BRL

Sep. 30, 2014USD ($)

Sep. 30, 2015USD ($)

Sep. 30, 2015BRL

Sep. 30, 2014USD ($)

Dec. 31, 2014USD ($)

Dec. 31, 2013USD ($)

Dec. 01, 2013$ / shares

Nov. 30, 2010

Note 6 - Commitments and Contingencies (Details) [Line Items]

Operating Leases, Rent Expense

$ 1,400,000

$ 1,300,000

$ 3,900,000

$ 4,000,000

Purchase Obligation

2,000,000

2,000,000

Contractual Obligation

1,100,000

1,100,000

Accrued Loss on Purchase Commitments

0

0

Performance Guarantee [Member] | Payment Guarantee [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Restricted Cash and Cash Equivalents

200,000

200,000

$ 600,000

FINEP Credit Facility [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Debt Instrument, Interest Rate, Stated Percentage

5.00%

FINEP Credit Facility [Member] | Chattel Mortgage [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Research and Development Asset Acquired Other than Through Business Combination, Fair Value Acquired

1,500,000

BRL 6

BNDES Credit Facility [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Collateral Provided by Company Certain Equipment and Other Tangible Assets Amount

$ 6,300,000

BRL 24.9

Debt Instrument, Interest Rate, Stated Percentage

7.00%

7.00%

Unsecured Senior Convertible Promissory Notes [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Debt Instrument, Convertible Promissory Note, Held by Third Party

$ 48,300,000

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 2.20

$ 7.0682

Unsecured Senior Convertible Promissory Notes [Member] | JV Agreements [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Debt Instrument, Convertible, Conversion Price (in Dollars per share) | $ / shares

$ 7.0682

BNDES [Member] | BNDES Credit Facility [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Collateral Provided by Company Certain Equipment and Other Tangible Assets Amount

$ 6,300,000

BRL 24.9

Banco ABC Brasil S.A. (ABC) [Member] | ABC Brasil Agreement [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Export Financing Agreement

$ 1,600,000

$ 2,500,000

Export Funding Agreement, Term

1 year

1 year

Nossa Caixa and Banco Pine Agreements [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Collateral Provided by Company Certain Equipment and Other Tangible Assets Amount

$ 17,100,000

BRL 68

Related Party Convertible Notes [Member] | Unsecured Debt [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Debt Instrument, Face Amount

$ 69,000,000

Debt Instrument, Interest Rate, Stated Percentage

1.50%

Related Party Convertible Notes [Member] | Secured Debt [Member]

Note 6 - Commitments and Contingencies (Details) [Line Items]

Debt Instrument, Face Amount

$ 10,850,000

Purchase Obligation, Due in Second Year

$ 10,850,000

Note 6 - Commitments and Cont56

Note 6 - Commitments and Contingencies (Details) - Future Minimum Payments for Lease Obligations - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Future Minimum Payments for Lease Obligations [Abstract]
2015 (remaining three months)	$ 187
2015 (remaining three months)	1,696
2015 (remaining three months)	1,883
2,016	530
2,016	6,755
2,016	7,285
2,017	187
2,017	6,642
2,017	6,829
2,018	6,700
2,018	6,700
2,019	0
2,019	6,748
2,019	6,748
Thereafter	0
Thereafter	25,026
Thereafter	25,026
Total future minimum lease payments	904
Total future minimum lease payments	53,567
Total future minimum lease payments	54,471
Less: amount representing interest	(70)
Present value of minimum lease payments	834
Less: current portion	(555)	$ (541)
Long-term portion	$ 280	$ 275

Note 7 - Joint Ventures and N57

Note 7 - Joint Ventures and Noncontrolling Interest (Details) BRL in Millions	Sep. 18, 2015USD ($)	Sep. 18, 2015EUR (€)	Jul. 26, 2015USD ($)	May. 31, 2015USD ($)	Nov. 30, 2014USD ($)	Oct. 31, 2014USD ($)	Sep. 30, 2014USD ($)	May. 31, 2014USD ($)	Apr. 30, 2014USD ($)	Feb. 28, 2014	Mar. 31, 2013USD ($)	Jan. 31, 2011	Apr. 30, 2010	Oct. 31, 2014USD ($)	Sep. 30, 2015USD ($)	Sep. 30, 2014USD ($)	Sep. 30, 2015USD ($)	Sep. 30, 2014USD ($)	Dec. 31, 2014USD ($)	Sep. 30, 2015BRL	Sep. 30, 2015EUR (€)	Aug. 31, 2015USD ($)	Jun. 30, 2015	May. 01, 2015USD ($)
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Income (Loss) from Equity Method Investments															$ (660,000)	$ (778,000)	$ (2,089,000)	$ (988,000)
Equity Method Investment, Number of Members of Board of Directors Appointed by Each Venture															2		2			2	2
Variable Interest Entity Number of Entities																	2
Glycotech Agreement [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Period of Initial Term of Collaboration Agreement												2 years
Variable Interest Entity, Financial or Other Support, Percentage												100.00%
Variable Interest Entity Number of Entities																	2
Variable Interest Entity, Consolidated, Carrying Amount, Property and Equipment															$ 6,400,000		$ 6,400,000
Variable Interest Entity, Consolidated, Carrying Amount, Other Assets															1,500,000		1,500,000
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets															400,000		400,000
Variable Interest Entity, Consolidated, Carrying Amount, Accounts Payable and Accrued Liabilities															300,000		300,000
Variable Interest Entity, Consolidated, Carrying Amount, Loan Obligations																	100,000
Novvi LLC [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage									50.00%		50.00%
Equity Method Investment, Number of MembersOfBoard of Directors											6
Joint Venture, Number of Managers Representing Each Investor											3
Initial Term of Joint Venture											20 years
IP License, Value											$ 10,000,000
Carrying Value of the Licenses Granted Under the IP License Agreement											$ 0
Investments in and Advance to Affiliates, Subsidiaries, Associates, and Joint Ventures									$ 2,100,000
Loan Granted to Joint Venture					$ 1,900,000		$ 3,700,000									$ 3,700,000		$ 3,700,000				$ 200,000		$ 1,100,000
Loan Granted to Joint Venture, Stated Annual Interest Rate							0.36%									0.36%		0.36%
Loan to Joint Venture, Percentage Provided by Each the Company and the Partner					50.00%		50.00%									50.00%		50.00%
Loan Granted to Joint Venture, Amount Disbursed by Company					$ 1,000,000									$ 1,800,000
Loan Granted to Joint Venture, Number of Installments Paid by the Company														2
Loan Granted to Joint Venture, Amount of First Installment Paid by Company							$ 1,200,000
Loan Granted to Joint Venture, Amount of Second Installment Paid by Company						$ 600,000
Loan Granted to Joint Venture Outstanding, Amount Net of Imputed Interest																	2,500,000		$ 1,700,000
Imputed Interest on Loan to Joint Venture																	1,500,000		1,000,000
Income (Loss) from Equity Method Investments																$ 800,000	2,100,000	$ 1,000,000
Equity Method Investments							$ 1,324,000								1,747,000	$ 1,324,000	1,747,000	1,324,000	$ 2,192,000
Novvi S.A. [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Joint Venture, Additional Membership Units Purchased, Aggregate Purchase Price									$ 200,000
JVCO Joint Venture [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage					50.00%
Equity Method Investment, Preferred Stock Ownership Percentage					100.00%
Capitalization, Long-term Debt and Equity															$ 100,000		$ 100,000				€ 100,000
JVCO Joint Venture [Member] | Scenario, Forecast [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage	25.00%	25.00%
SMA Industria Quimica S.A. [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage																							50.00%
Equity Method Investment, Number of MembersOfBoard of Directors															4		4			4	4
Initial Term of Joint Venture																	20 years
Equity Method Investment, Number of Members of Executive Committee															3		3			3	3
Equity Method Investment, Number of Company-appointed Members of Executive Committee															2		2			2	2
Equity Method Investment, Period Company is Required to Purchase Output of Joint Venture													4 years
Operation Commencement Timeline Requirement, Extension										18 months
SMA Industria Quimica S.A. [Member] | Loss on Purchase Commitments and Impairment of Property, Plant and Equipment [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Impaired Assets to be Disposed of by Method Other than Sale, Amount of Impairment Loss																	$ 7,300,000	$ 7,300,000
SMA Industria Quimica S.A. [Member] | SMSA [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Due from Joint Ventures															$ 15,600,000		$ 15,600,000			BRL 61.8
Novvi LLC [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Income (Loss) from Equity Method Investments															$ 700,000
Total [Member] | JVCO Joint Venture [Member] | Scenario, Forecast [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage Exchanged for Cancellation of Debt	25.00%	25.00%
Equity Method Investment, Ownership Percentage by Counterparty	75.00%	75.00%
Total [Member] | Pilot Plant Agreements [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Related Party Agreement, Term				5 years				5 years
Related Party Transaction, Fees Waived			$ 2,000,000
Total [Member] | Pilot Plant Agreements [Member] | Scale-up Services and Training [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Related Party Transaction, Amounts of Transaction				$ 900,000				$ 900,000
Total [Member] | Pilot Plant Agreement Amendment [Member] | Subsequent Event [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Related Party Transaction, Fees Waived			$ 2,000,000
Cosan [Member] | Novvi LLC [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage											50.00%
Obligation to Fund Agreement, Cash Portion											$ 10,000,000
Total Amyris Biosolutions B.V. [Member] | JVCO Joint Venture [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Equity Method Investment, Ownership Percentage					50.00%
Total [Member] | Scenario, Forecast [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Extinguishment of Debt, Amount | €		€ 50,000
Unsecured Senior Convertible Promissory Notes [Member] | Total [Member] | Scenario, Forecast [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) [Line Items]
Extinguishment of Debt, Amount	$ 5,000,000

Note 7 - Joint Ventures and N58

Note 7 - Joint Ventures and Noncontrolling Interest (Details) - Reconciliation of Equity and Loans in Novvi - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Schedule of Equity Method Investments [Line Items]
Loans to affiliate			$ 1,231	$ 1,214
Capital contribution (non – cash)				237
Share in net loss offset	$ (660)	$ (778)	(2,089)	(988)
Novvi LLC [Member]
Schedule of Equity Method Investments [Line Items]
Balance			2,192
Loans to affiliate			770
Imputation of interest			461
Capital contribution (cash)				2,075
Capital contribution (non – cash)				237
Share in net loss offset		800	2,100	1,000
Accretion of imputed interest			413
Balance	$ 1,747	$ 1,324	1,747	1,324
Offset to Equity Investment [Member] | Novvi LLC [Member]
Schedule of Equity Method Investments [Line Items]
Share in net loss offset			(908)	$ (988)
Offset to Loans to Affiliate [Member] | Novvi LLC [Member]
Schedule of Equity Method Investments [Line Items]
Share in net loss offset			$ (1,181)

Note 7 - Joint Ventures and N59

Note 7 - Joint Ventures and Noncontrolling Interest (Details) - Variable Interest Entities - Variable Interest Entity, Primary Beneficiary [Member] - USD ($) $ in Thousands		Sep. 30, 2015	Dec. 31, 2014
Variable Interest Entity [Line Items]
Assets*	[1]	$ 8,291	$ 22,812
Liabilities		$ 444	$ 290
[1]	Net of impairment at September 30, 2015 of $7.3 million related to SMA assets (see Note 4 "Balance Sheet Components" for details).

Note 7 - Joint Ventures and N60

Note 7 - Joint Ventures and Noncontrolling Interest (Details) - Noncontrolling Interest - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Note 7 - Joint Ventures and Noncontrolling Interest (Details) - Noncontrolling Interest [Line Items]
Balance at January 1			$ (611)
Foreign currency translation adjustment	$ 10,459	$ 8,164	18,562	$ 3,753
Income attributable to noncontrolling interest	24	31	78	91
Balance at September 30	(296)		(296)
Noncontrolling Interest [Member]
Note 7 - Joint Ventures and Noncontrolling Interest (Details) - Noncontrolling Interest [Line Items]
Balance at January 1			611	584
Foreign currency translation adjustment			(393)	(37)
Income attributable to noncontrolling interest			78	91
Balance at September 30	$ 296	$ 638	$ 296	$ 638

Note 8 - Significant Agreemen61

Note 8 - Significant Agreements (Details)

Jul. 29, 2015$ / sharesshares

Apr. 30, 2015USD ($)

Sep. 30, 2015USD ($)$ / shares

Mar. 31, 2015USD ($)

Feb. 28, 2015USD ($)

Jan. 31, 2015USD ($)

Jul. 31, 2014USD ($)

Jun. 30, 2014USD ($)

Apr. 30, 2014USD ($)$ / sharesshares

Mar. 31, 2014USD ($)$ / sharesshares

Apr. 30, 2013USD ($)

Mar. 31, 2013USD ($)

Jul. 30, 2012USD ($)

Sep. 30, 2015USD ($)$ / shares

Sep. 30, 2014USD ($)$ / shares

Jan. 31, 2015USD ($)

Sep. 30, 2015USD ($)$ / sharesshares

Sep. 30, 2014USD ($)$ / shares

Dec. 31, 2013USD ($)

Mar. 30, 2015USD ($)

Dec. 31, 2014$ / shares

Dec. 31, 2012USD ($)

Nov. 30, 2011USD ($)

Sep. 30, 2011USD ($)

Jun. 30, 2010USD ($)

Note 8 - Significant Agreements (Details) [Line Items]

Grants and Collaborations Revenue

$ 4,363,000

$ 4,861,000

$ 14,643,000

$ 12,954,000

Sales Revenue Product Net

$ 4,226,000

$ 11,112,000

$ 9,661,000

$ 18,333,000

Share Price (in Dollars per share) | $ / shares

$ 2.01

$ 2.01

$ 3.79

$ 2.01

$ 3.79

Proceeds from Issuance of Common Stock

$ 453,000

$ 2,159,000

Common Stock, Par or Stated Value Per Share (in Dollars per share) | $ / shares

$ 0.0001

$ 0.0001

$ 0.0001

$ 0.0001

Private Placement [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock, Par or Stated Value Per Share (in Dollars per share) | $ / shares

$ 0.0001

Class of Warrant or Right, Term

5 years

Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share) | $ / shares

$ 0.01

Class of Warrant or Right, Securities Called by Warrants As Percentage of Shares Purchased By Investor

10.00%

Flavors and Fragrances Compounds [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Sales Revenue Product Net

$ 1,300,000

$ 1,300,000

Research and Development Collaboration with Total [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Additional Amount to the Initial Amount Research and Development Collaborative Agreement Contribution Amount

$ 30,000,000

Initial Amount Research and Development Collaborative Agreement Contributed by Collaborator

$ 50,000,000

Research and Development Collaboration Agreement Amount to be Considered as Part of Initial Amount Pledged

$ 10,000,000

$ 10,000,000

Remaining Percentage of Research and Development Collaboration Funding

50.00%

Advanced Payments Recognized and no Longer Contigently Repayable

$ 46,500,000

Amount from Advanced Payment Rolled into Unsecured Convertible Promissory Note

23,300,000

Research and Development Arrangement, Contract to Perform for Others, Compensation Earned

23,200,000

Reduction in Capitalized Deferred Charge Asset

14,400,000

Technology Investment Agreement with DARPA [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Collaboration Agreement Period

4 years

Maximum DARPA Funding to be Received if all Milestones are Achieved

$ 35,000,000

35,000,000

35,000,000

Collective Obligation Due

15,500,000

15,500,000

15,500,000

Nomis Bay Common Stock Purchase Agreement [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock Purchase Agreement Amount

$ 50,000,000

Common Stock Purchase Agreement Term

24 months

Common Stock Purchase Agreement, Number of Draw Down Notices

24

Common Stock Purchase Agreement Number Consecutive Trading Days in Draw Down Share Price Determination

10 days

Common Stock Purchase Agreement Share Purchase Amount Per Draw Down Period

$ 0.099

Common Stock Purchase Agreement Commitment Fee

100,000

Common Stock Purchase Agreement Additional Commitment Fee

300,000

Nomis Bay Common Stock Purchase Agreement [Member] | Nomis Bay's Legal Fees and Expense [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock Purchase Agreement Legal Fees Paid by Company

35,000

Nomis Bay Common Stock Purchase Agreement [Member] | Financial West Group (FWG) [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock Purchase Agreement Legal Fees Paid by Company

$ 15,000

Securities Purchase Agreement With Naxyris S.A. [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Securities Purchase Agreement Amount

$ 10,000,000

Security Purchase Agreement Amount of New Financing Cancelling Agreement

10,000,000

Security Purchase Agreement Commitment Fee

$ 200,000

Total [Member] | Research and Development Collaboration with Total [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Revenue from Related Parties

$ 8,900,000

Collaboration Partner [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Collaboration Agreement Range of Funding First Phase of Collaberation

$ 6,000,000

Revenue Recognition, Milestone Method, Revenue Recognized

800,000

2,300,000

Deferred Revenue

0

0

$ 0

0

0

Additional Grants and Collaboration Funding

5,000,000

Collaboration Partner [Member] | Flavors and Fragrances Compounds [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Revenue Recognition, Milestone Method, Revenue Recognized

$ 6,000,000

Collaboration Agreement Annual Funding Year One

$ 10,000,000

Collaboration Agreement Annual Funding Year Three

10,000,000

Collaboration Agreement Annual Funding Year Two

10,000,000

Proceeds from Collaborators

$ 10,000,000

Grants and Collaborations Revenue

2,500,000

$ 2,500,000

7,500,000

$ 7,500,000

Collaboration Partner [Member] | Flavors and Fragrances Compounds [Member] | First Payment [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Proceeds from Collaborators

$ 10,000,000

Collaboration Partner [Member] | Flavors and Fragrances Compounds [Member] | Second Payment [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Proceeds from Collaborators

$ 10,000,000

Collaboration Partner [Member] | Master Collaboration Agreement [Member] | Flavors and Fragrances Compounds [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Revenue Recognition, Milestone Method, Revenue Recognized

1,000,000

Sales Margin Collaborator Percentage Split

70.00%

Sales Margin Company Percentage Split

30.00%

Return Required for Collaboration Partner Before Adjusting Split on Sales Margin

$ 15,000,000

Sales Margin Collaborator Percentage Split Following Return Requirements

50.00%

Sales Margin Company Percentage Split Following Return Requirements

50.00%

Success Bonus

$ 2,500,000

Research and Development Collaboration Term

6 years

Michelin [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Proceeds from Collaborators

$ 5,000,000

Advances on Collaboration Services

$ 5,000,000

Braskem and Michelin [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Collaboration Agreement Period

3 years

Braskem [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Revenue Recognition, Milestone Method, Revenue Recognized

0

1,900,000

Deferred Revenue

$ 6,300,000

6,300,000

6,300,000

Proceeds from Collaborators

$ 2,000,000

$ 2,000,000

$ 4,000,000

Kuraray [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Proceeds from Collaborators

$ 2,000,000

2,000,000

$ 4,000,000

Collaboration Agreement Period

2 years

Collaborative Agreement Number of Installments

2

Collaboration Arrangement, Shares To Be Sold (in Shares) | shares

943,396

Collaboration Arrangement, Price Per Share (in Dollars per share) | $ / shares

$ 4.24

Stock Issued During Period, Shares, New Issues (in Shares) | shares

943,396

Share Price (in Dollars per share) | $ / shares

$ 4.24

Deferred Revenue, Revenue Recognized

$ 300,000

$ 1,200,000

Kuraray [Member] | Subsequent Event [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Proceeds from Issuance of Common Stock

$ 4,000,000

Naxyris S.A. [Member] | Securities Purchase Agreement With Naxyris S.A. [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Noncontrolling Interest, Ownership Percentage by Noncontrolling Owners

5.00%

Common Stock [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Stock Issued During Period, Shares, New Issues (in Shares) | shares

16,025,642

Common Stock [Member] | Private Placement [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Stock Issued During Period, Shares, New Issues (in Shares) | shares

16,025,642

Share Price (in Dollars per share) | $ / shares

$ 1.56

Second Hercules Amendment [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Line of Credit Facility, Maximum Borrowing Capacity

15,000,000

Line of Credit Facility, Draw Down Increments

5,000,000

Line of Credit Facility, Early Draw Down Equity Raise Requirement

$ 20,000,000

Minimum [Member] | Nomis Bay Common Stock Purchase Agreement [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock Purchase Agreement Share Price Discount Percentage

3.00%

Common Stock Purchase Agreement Share Purchase Amount Per Draw Down Period

$ 325,000

Maximum [Member] | Nomis Bay Common Stock Purchase Agreement [Member]

Note 8 - Significant Agreements (Details) [Line Items]

Common Stock Purchase Agreement Share Price Discount Percentage

6.25%

Common Stock Purchase Agreement Share Purchase Amount Per Draw Down Period

$ 3,250,000

Note 9 - Goodwill and Intangi62

Note 9 - Goodwill and Intangible Assets (Details) - USD ($)	1 Months Ended	9 Months Ended		12 Months Ended
	Oct. 31, 2011	Sep. 30, 2015	Sep. 30, 2014	Dec. 31, 2014
Draths Corporation [Member] | In Process Research and Development, Indefinite [Member]
Note 9 - Goodwill and Intangible Assets (Details) [Line Items]
Indefinite-lived Intangible Assets Acquired	$ 8,600,000
Impairment of Intangible Assets (Excluding Goodwill)				$ 3,000,000
Acquired Licenses and Permits [Member]
Note 9 - Goodwill and Intangible Assets (Details) [Line Items]
Amortization of Intangible Assets		$ 0	$ 9

Note 9 - Goodwill and Intangi63

Note 9 - Goodwill and Intangible Assets (Details) - Intangible Assets and Goodwill - USD ($) $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2015	Dec. 31, 2014
Note 9 - Goodwill and Intangible Assets (Details) - Intangible Assets and Goodwill [Line Items]
In-process research and development
Acquired licenses and permits
Goodwill
Goodwill	$ 560	$ 560
Goodwill	560	560
	9,892	9,892
	(3,807)	(3,807)
	$ 6,085	6,085
In Process Research and Development, Indefinite [Member]
Note 9 - Goodwill and Intangible Assets (Details) - Intangible Assets and Goodwill [Line Items]
In-process research and development
In-process research and development	$ 8,560	8,560
In-process research and development	3,035	(3,035)
In-process research and development	$ 5,525	5,525
Acquired licenses and permits
Acquired licenses and permits	$ 8,560	8,560
Goodwill
Acquired Licenses and Permits [Member]
Note 9 - Goodwill and Intangible Assets (Details) - Intangible Assets and Goodwill [Line Items]
In-process research and development	2 years
In-process research and development	$ 772	772
Acquired licenses and permits	2 years
Acquired licenses and permits	$ 772	772
Acquired licenses and permits	$ (772)	$ (772)
Goodwill	2 years

Note 10 - Stockholders' Defic64

Note 10 - Stockholders' Deficit (Details) - USD ($) $ / shares in Units, $ in Millions	Jul. 29, 2015	Oct. 31, 2013	Dec. 31, 2011	Sep. 30, 2015	Sep. 30, 2015	Sep. 30, 2014
Note 10 - Stockholders' Deficit (Details) [Line Items]
Class of Warrant or Right, Outstanding (in Shares)				50,699,368	50,699,368	1,021,087
Warrants in Connection With Capital Lease Arrangement [Member]
Note 10 - Stockholders' Deficit (Details) [Line Items]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares)			21,087
Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share)			$ 10.67
Warrants and Rights Outstanding (in Dollars)			$ 0.2
Class of Warrant or Right, Fair Value Assumptions, Expected Term			10 years
Class of Warrant or Right, Fair Value Assumptions, Risk Free Interest Rate			2.00%
Class of Warrant or Right, Fair Value Assumptions, Expected Volatility Rate			86.00%
Class of Warrant or Right, Fair Value Assumptions, Expected Dividend Rate			0.00%
Warrants in Connection with Issuance of Tranche I Convertible Promissory Notes [Member]
Note 10 - Stockholders' Deficit (Details) [Line Items]
Class of Warrant or Right, Number of Securities Called by Warrants or Rights (in Shares)		1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share)		$ 0.01
Warrants and Rights Outstanding (in Dollars)		$ 1.3
Class of Warrant or Right, Fair Value Assumptions, Expected Term		3 years 146 days
Class of Warrant or Right, Fair Value Assumptions, Risk Free Interest Rate		0.77%
Class of Warrant or Right, Fair Value Assumptions, Expected Volatility Rate		45.00%
Class of Warrant or Right, Fair Value Assumptions, Expected Dividend Rate		0.00%
Proceeds from Warrant Exercises (in Dollars)				$ 2.6
Class of Warrant or Right, Cashless Exercise Provision, Number Exercised (in Shares)					0	0
Temasek Warrant 2 [Member] | Temasek [Member]
Note 10 - Stockholders' Deficit (Details) [Line Items]
Class of Warrant or Right, Fair Value Assumptions, Risk Free Interest Rate	2.00%
Class of Warrant or Right, Fair Value Assumptions, Expected Volatility Rate	74.00%
Class of Warrant or Right, Fair Value Assumptions, Expected Dividend Rate	0.00%

Note 11 - Stock-Based Compens65

Note 11 - Stock-Based Compensation (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Note 11 - Stock-Based Compensation (Details) [Line Items]
Share-based Compensation Arrangement by Share-based Payment Award, Options, Exercises in Period, Intrinsic Value	$ 0	$ 100,000	$ 0	$ 600,000
Employee Stock Option [Member]
Note 11 - Stock-Based Compensation (Details) [Line Items]
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized	7,800,000		$ 7,800,000
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition			2 years 284 days
Share-based Compensation Arrangement by Share-based Payment Award, Fair Value Assumptions, Expected Dividend Payments			$ 0
Restricted Stock Units (RSUs) [Member]
Note 11 - Stock-Based Compensation (Details) [Line Items]
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized	$ 5,600,000		$ 5,600,000
Employee Service Share-based Compensation, Nonvested Awards, Compensation Cost Not yet Recognized, Period for Recognition			2 years 219 days

Note 11 - Stock-Based Compens66

Note 11 - Stock-Based Compensation (Details) - Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity - USD ($) $ / shares in Units, $ in Thousands	9 Months Ended	12 Months Ended
	Sep. 30, 2015	Dec. 31, 2014
Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity [Abstract]
Number outstanding	11,307,679	10,539,978
Weighted-average exercise price	$ 5.33	$ 6.10
Weighted-average remaining contractual term	7 years 58 days	7 years 80 days
Aggregate intrinsic value	$ 283	$ 50
Vested and expected to vest after September 30, 2015	10,603,529
Vested and expected to vest after September 30, 2015	$ 5.52
Vested and expected to vest after September 30, 2015	7 years 14 days
Vested and expected to vest after September 30, 2015	$ 245
Exercisable at September 30, 2015	6,075,541
Exercisable at September 30, 2015	$ 7.53
Exercisable at September 30, 2015	5 years 281 days
Exercisable at September 30, 2015	$ 40
Options granted	2,582,353
Options granted	$ 1.98
Options exercised	(10,750)
Options exercised	$ 1.41
Options cancelled	(1,803,902)
Options cancelled	$ 5.06

Note 11 - Stock-Based Compens67

Note 11 - Stock-Based Compensation (Details) - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity - Restricted Stock Units (RSUs) [Member] - $ / shares	9 Months Ended	12 Months Ended
	Sep. 30, 2015	Dec. 31, 2014
Note 11 - Stock-Based Compensation (Details) - Temporal Display of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity [Line Items]
Number outstanding	3,558,243	1,975,503
Weighted-average grant-date fair value	$ 2.63	$ 3.59
Weighted average remaining contractual life	1 year 197 days	339 days
Expected to vest after September 30, 2015	3,029,826
Expected to vest after September 30, 2015	$ 2.63
Expected to vest after September 30, 2015	1 year 153 days
Awarded	2,767,355
Awarded	$ 1.92
Vested	(929,322)
Vested	$ 3.19
Forfeited	(255,293)
Forfeited	$ 2.95

Note 11 - Stock-Based Compens68

Note 11 - Stock-Based Compensation (Details) - Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range	9 Months Ended
	Sep. 30, 2015$ / sharesshares
Exercise Price Range 1 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	$ 0.10
Exercise Price - upper range limit	$ 1.80
Options Outstanding - Number of Options (in Shares) | shares	687,093
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	8 years 270 days
Options Outstanding - Weighted-Average Exercise Price	$ 1.70
Options Exercisable - Number of Options (in Shares) | shares	68,093
Options Exercisable - Weighted-Average Exercise Price	$ 1.43
Exercise Price Range 2 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	1.96
Exercise Price - upper range limit	$ 1.96
Options Outstanding - Number of Options (in Shares) | shares	1,412,533
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	9 years 226 days
Options Outstanding - Weighted-Average Exercise Price	$ 1.96
Exercise Price Range 3 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	1.98
Exercise Price - upper range limit	$ 2.73
Options Outstanding - Number of Options (in Shares) | shares	1,200,797
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	7 years 262 days
Options Outstanding - Weighted-Average Exercise Price	$ 2.53
Options Exercisable - Number of Options (in Shares) | shares	478,181
Options Exercisable - Weighted-Average Exercise Price	$ 2.66
Exercise Price Range 4 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	2.75
Exercise Price - upper range limit	$ 2.87
Options Outstanding - Number of Options (in Shares) | shares	1,299,025
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	7 years 200 days
Options Outstanding - Weighted-Average Exercise Price	$ 2.83
Options Exercisable - Number of Options (in Shares) | shares	800,584
Options Exercisable - Weighted-Average Exercise Price	$ 2.83
Exercise Price Range 5 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	2.89
Exercise Price - upper range limit	$ 3.44
Options Outstanding - Number of Options (in Shares) | shares	1,031,420
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	7 years 164 days
Options Outstanding - Weighted-Average Exercise Price	$ 3.11
Options Exercisable - Number of Options (in Shares) | shares	613,405
Options Exercisable - Weighted-Average Exercise Price	$ 3.10
Exercise Price Range 6 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	3.51
Exercise Price - upper range limit	$ 3.51
Options Outstanding - Number of Options (in Shares) | shares	2,027,865
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	8 years 102 days
Options Outstanding - Weighted-Average Exercise Price	$ 3.51
Options Exercisable - Number of Options (in Shares) | shares	738,773
Options Exercisable - Weighted-Average Exercise Price	$ 3.51
Exercise Price Range 7 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	3.55
Exercise Price - upper range limit	$ 3.93
Options Outstanding - Number of Options (in Shares) | shares	1,515,548
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	5 years 58 days
Options Outstanding - Weighted-Average Exercise Price	$ 3.87
Options Exercisable - Number of Options (in Shares) | shares	1,302,162
Options Exercisable - Weighted-Average Exercise Price	$ 3.88
Exercise Price Range 8 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	4.06
Exercise Price - upper range limit	$ 16
Options Outstanding - Number of Options (in Shares) | shares	1,164,094
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	4 years 124 days
Options Outstanding - Weighted-Average Exercise Price	$ 9.17
Options Exercisable - Number of Options (in Shares) | shares	1,131,706
Options Exercisable - Weighted-Average Exercise Price	$ 9.27
Exercise Price Range 9 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	16.50
Exercise Price - upper range limit	$ 26.84
Options Outstanding - Number of Options (in Shares) | shares	909,304
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	5 years 47 days
Options Outstanding - Weighted-Average Exercise Price	$ 23.04
Options Exercisable - Number of Options (in Shares) | shares	882,637
Options Exercisable - Weighted-Average Exercise Price	$ 22.93
Exercise Price Range 10 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	30.17
Exercise Price - upper range limit	$ 30.17
Options Outstanding - Number of Options (in Shares) | shares	60,000
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	5 years 164 days
Options Outstanding - Weighted-Average Exercise Price	$ 30.17
Options Exercisable - Number of Options (in Shares) | shares	60,000
Options Exercisable - Weighted-Average Exercise Price	$ 30.17
Exercise Price Range 11 [Member]
Share-based Compensation, Shares Authorized under Stock Option Plans, Exercise Price Range [Line Items]
Exercise Price - lower range limit	0.10
Exercise Price - upper range limit	$ 30.17
Options Outstanding - Number of Options (in Shares) | shares	11,307,679
Options Outstanding - Weighted-Average Remaining Contractual Life (Years)	7 years 58 days
Options Outstanding - Weighted-Average Exercise Price	$ 5.33
Options Exercisable - Number of Options (in Shares) | shares	6,075,541
Options Exercisable - Weighted-Average Exercise Price	$ 7.53

Note 11 - Stock-Based Compens69

Note 11 - Stock-Based Compensation (Details) - Employee Service Share-based Compensation, Allocation of Recognized Period Costs - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Allocated share-based compensation expense	$ 2,256	$ 3,572	$ 6,964	$ 10,769
Research and Development Expense [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Allocated share-based compensation expense	530	915	1,776	2,622
Selling, General and Administrative Expenses [Member]
Share-based Compensation Arrangement by Share-based Payment Award, Compensation Cost [Line Items]
Allocated share-based compensation expense	$ 1,726	$ 2,657	$ 5,188	$ 8,147

Note 11 - Stock-Based Compens70

Note 11 - Stock-Based Compensation (Details) - Share-based Payment Award, Stock Options, Valuation Assumptions - Employee Stock Option [Member]	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Note 11 - Stock-Based Compensation (Details) - Share-based Payment Award, Stock Options, Valuation Assumptions [Line Items]
Risk-free interest rate	2.00%	2.00%	2.00%	2.00%
Expected term (in years)	6 years 10 days	6 years 21 days	6 years	6 years 32 days
Expected volatility	74.00%	74.00%	74.00%	75.00%

Note 12 - Employee Benefit Pl71

Note 12 - Employee Benefit Plan (Details) - USD ($) $ in Millions	3 Months Ended	9 Months Ended
	Sep. 30, 2015	Sep. 30, 2015
Compensation and Retirement Disclosure [Abstract]
Defined Contribution Plan, Maximum Annual Contributions Per Employee, Percent		90.00%
Defined Contribution Plan, Employer Matching Contribution, Percent of Employees' Gross Pay		90.00%
Defined Contribution Plan, Minimum Service Vesting Period		1 year
Defined Contribution Plan, Employer Discretionary Contribution Amount	$ 0.1	$ 0.4

Note 13 - Related Party Trans72

Note 13 - Related Party Transactions (Details) - USD ($)	Jul. 29, 2015	Jul. 26, 2015	May. 31, 2015	May. 31, 2014	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014	Dec. 31, 2014
Note 13 - Related Party Transactions (Details) [Line Items]
Debt Instrument, Unamortized Discount					$ 17,300,000		$ 17,300,000
Gains (Losses) on Extinguishment of Debt					$ (5,984,000)		$ (5,984,000)	$ (10,512,000)
Common Stock, Par or Stated Value Per Share (in Dollars per share)					$ 0.0001		$ 0.0001		$ 0.0001
Share Price (in Dollars per share)					$ 2.01	$ 3.79	$ 2.01	$ 3.79
Stock Issued During Period, Value, New Issues							$ 24,626,000
Accounts Receivable, Related Parties					$ 575,000		575,000		$ 455,000
Private Placement [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Common Stock, Par or Stated Value Per Share (in Dollars per share)	$ 0.0001
Class of Warrant or Right, Term	5 years
Class of Warrant or Right, Exercise Price of Warrants or Rights (in Dollars per share)	$ 0.01
Class of Warrant or Right, Securities Called by Warrants As Percentage of Shares Purchased By Investor	10.00%
Related Party Convertible Notes [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Convertible Debt					42,400,000		42,400,000		115,200,000
Debt Instrument, Unamortized Discount					1,700,000		1,700,000		53,800,000
Gains (Losses) on Extinguishment of Debt					5,900,000	$ 0	5,900,000	$ (10,500,000)
Derivative Liability					35,600,000		35,600,000		39,800,000
Derivative, Gain (Loss) on Derivative, Net					(12,400,000)	(3,100,000)	(700,000)	68,200,000
Total Entergies Nouvelles Activites, Foris Ventures, and Naxyris SA [Member] | Private Placement [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Stock Issued During Period, Shares, New Issues (in Shares)	13,141,029
Stock Issued During Period, Value, New Issues	$ 20,500,000
Novvi LLC [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Revenue from Related Parties					2,000	$ 200,000	2,000	$ 300,000
Accounts Receivable, Related Parties					300,000		300,000		100,000
Product Sales [Member] | Total [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Accounts Receivable, Related Parties					300,000		300,000		$ 300,000
Total [Member] | Pilot Plant Agreements [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Related Party Agreement, Term			5 years	5 years
Related Party Transaction, Fees Waived		$ 2,000,000
Total [Member] | Pilot Plant Agreements [Member] | Scale-up Services and Training [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Related Party Transaction, Amounts of Transaction			$ 900,000	$ 900,000
Total [Member] | Pilot Plant Agreements [Member] | Annual Fee [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Due from Related Parties				$ 100,000
Total [Member] | Pilot Plant Agreements [Member] | Sublease Payments and Service Fees [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Related Party Transaction, Amounts of Transaction							800,000
Accrued and Other Current Liabilities [Member] | Total [Member] | Pilot Plant Agreements [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Proceeds Received from Related Parties							$ 200,000
Common Stock [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Stock Issued During Period, Shares, New Issues (in Shares)							16,025,642
Stock Issued During Period, Value, New Issues							$ 2,000
Common Stock [Member] | Private Placement [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Stock Issued During Period, Shares, New Issues (in Shares)	16,025,642
Share Price (in Dollars per share)	$ 1.56
Stock Issued During Period, Value, New Issues	$ 25,000,000
Sublease Agreement [Member] | Total [Member] | Pilot Plant Agreements [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Proceeds from Fees Received							$ 1,700,000
Sublease Payments and Service Fees [Member] | Total [Member] | Pilot Plant Agreements [Member]
Note 13 - Related Party Transactions (Details) [Line Items]
Related Party Transaction, Amounts of Transaction					$ 300,000

Note 14 - Income Taxes (Details

Note 14 - Income Taxes (Details) - USD ($)	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Note 14 - Income Taxes (Details) [Line Items]
Income Tax Expense (Benefit)	$ 119,000	$ 134,000	$ 355,000	$ 370,000
Additional Provision [Member]
Note 14 - Income Taxes (Details) [Line Items]
Income Tax Expense (Benefit)			$ 0

Note 15 - Reporting Segments (D

Note 15 - Reporting Segments (Details)	Sep. 30, 2015
Segment Reporting [Abstract]
Segment Reporting Number of Business Activities	1

Note 15 - Reporting Segments 75

Note 15 - Reporting Segments (Details) - Revenues by Geography - USD ($) $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Note 15 - Reporting Segments (Details) - Revenues by Geography [Line Items]
Revenues	$ 8,591	$ 16,341	$ 24,306	$ 31,689
UNITED STATES
Note 15 - Reporting Segments (Details) - Revenues by Geography [Line Items]
Revenues	6,177	10,189	15,550	14,977
BRAZIL
Note 15 - Reporting Segments (Details) - Revenues by Geography [Line Items]
Revenues	964	1,933	3,850	3,983
Europe [Member]
Note 15 - Reporting Segments (Details) - Revenues by Geography [Line Items]
Revenues	459	2,836	2,138	9,174
Asia [Member]
Note 15 - Reporting Segments (Details) - Revenues by Geography [Line Items]
Revenues	$ 991	$ 1,383	$ 2,769	$ 3,555

Note 15 - Reporting Segments 76

Note 15 - Reporting Segments (Details) - Long-Lived Assets by Geography - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Note 15 - Reporting Segments (Details) - Long-Lived Assets by Geography [Line Items]
Long-Lived Assets	$ 81,941	$ 118,980
UNITED STATES
Note 15 - Reporting Segments (Details) - Long-Lived Assets by Geography [Line Items]
Long-Lived Assets	39,417	44,418
BRAZIL
Note 15 - Reporting Segments (Details) - Long-Lived Assets by Geography [Line Items]
Long-Lived Assets	42,206	74,197
Europe [Member]
Note 15 - Reporting Segments (Details) - Long-Lived Assets by Geography [Line Items]
Long-Lived Assets	$ 318	$ 365

Note 16 - Comprehensive Incom77

Note 16 - Comprehensive Income (Loss) (Details) - Accumulated Other Comprehensive Income (Loss) - USD ($) $ in Thousands	Sep. 30, 2015	Dec. 31, 2014
Accumulated Other Comprehensive Income (Loss) [Abstract]
Foreign currency translation adjustment, net of tax	$ (48,932)	$ (29,977)
Total accumulated other comprehensive loss	$ (48,932)	$ (29,977)

Note 17 - Net Loss Attributab78

Note 17 - Net Loss Attributable to Common Stockholders and Net Loss per Share (Details) - Calculation of Basic and Diluted Net Loss Per Share of Common Stock Attributable to Amyris, Inc. Common Stockholders - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Numerator:
Net loss attributable to Amyris, Inc. common stockholders (in Dollars)	$ (76,664)	$ (36,641)	$ (176,034)	$ (55,735)
Interest on convertible debt (in Dollars)				4,835
Accretion of debt discount (in Dollars)				3,856
Gain from change in fair value of derivative instruments (in Dollars)				(57,580)
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion (in Dollars)	$ (76,664)	$ (36,641)	$ (176,034)	$ (104,624)
Denominator:
Weighted average shares of common stock outstanding for basic EPS	140,374,297	78,980,402	100,103,007	78,146,365
Basic loss per share (in Dollars per share)	$ (0.55)	$ (0.46)	$ (1.76)	$ (0.71)
Weighted average shares of common stock outstanding	140,374,297	78,980,402	100,103,007	78,146,365
Effect of dilutive securities:
Convertible promissory notes	0			32,968,436
Weighted common stock equivalents	0			32,968,436
Diluted weighted-average common shares	140,374,297	78,980,402	100,103,007	111,114,801
Diluted loss per share (in Dollars per share)	$ (0.55)	$ (0.46)	$ (1.76)	$ (0.94)

Note 17 - Net Loss Attributab79

Note 17 - Net Loss Attributable to Common Stockholders and Net Loss per Share (Details) - Antidilutive Securities Excluded from Computation of Earnings Per Share - shares	3 Months Ended		9 Months Ended
	Sep. 30, 2015	Sep. 30, 2014	Sep. 30, 2015	Sep. 30, 2014
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	61,219,281	85,818,828	61,219,281	52,734,719
Stock Options to Purchase Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	11,307,679	10,340,375	11,307,679	10,340,375
Convertible Promissory Notes [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	43,451,433	72,367,114	43,451,433	39,283,005
Warrant [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	2,901,926	1,021,087	2,901,926	1,021,087
Restricted Stock Units (RSUs) [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount	3,558,243	2,090,252	3,558,243	2,090,252

Note 18 - Subsequent Events (De

Note 18 - Subsequent Events (Details) - USD ($) $ / shares in Units, $ in Millions	Oct. 20, 2015	Sep. 30, 2015	Jul. 29, 2015
Note 18 - Subsequent Events (Details) [Line Items]
Percentage of Outstanding Principle to be Maintained in Unencumbered Cash		50.00%
Hercules Technology Growth Capital, Inc. (Hercules) [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Percentage of Outstanding Principle to be Maintained in Unencumbered Cash		50.00%
Convertible Promissory Notes 1 [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Convertible, Conversion Price (in Dollars per share)			$ 7.0682
Convertible Senior Notes, 9.5% [Member] | Subsequent Event [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Face Amount	$ 57.6
Debt Instrument, Interest Rate, Stated Percentage	9.50%
Debt Instrument, Convertible, Conversion Rate, Shares (in Shares)	443.6557
Debt Instrument, Convertible, Conversion Rate, Principle Amount (in Dollars per share)	$ 1,000
Debt Instrument, Convertible, Conversion Price (in Dollars per share)	$ 2.25
Debt Instrument, Post Conversion Interest Payment Period, Maximum	3 years
Proceeds from Issuance of Senior Long-term Debt	$ 54.4
Convertible Senior Notes, 6.5% [Member] | Subsequent Event [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Repurchase Amount	18.3
Debt Instrument, Repurchased Face Amount	$ 22.9
Convertible Senior Notes, 6.5% [Member] | Convertible Promissory Notes 1 [Member] | Subsequent Event [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	6.50%
Convertible Senior Notes, 3% [Member] | Subsequent Event [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Repurchase Amount	$ 8.8
Debt Instrument, Repurchased Face Amount	$ 9.7
Convertible Senior Notes, 3% [Member] | Convertible Promissory Notes 3 [Member] | Subsequent Event [Member]
Note 18 - Subsequent Events (Details) [Line Items]
Debt Instrument, Interest Rate, Stated Percentage	3.00%