Amyris (AMRSQ) 10-Q 8 Aug 14 2014 Q2 Quarterly report Financial data

Document_and_Entity_Informatio

Document and Entity Information	6 Months Ended
	Jun. 30, 2014	Jul. 31, 2014
Document and Entity Information [Abstract]	'	'
Entity Registrant Name	'AMYRIS, INC.	'
Entity Central Index Key	'0001365916	'
Current Fiscal Year End Date	'--12-31	'
Entity Filer Category	'Accelerated Filer	'
Document Type	'10-Q	'
Document Period End Date	30-Jun-14	'
Document Fiscal Year Focus	'2014	'
Document Fiscal Period Focus	'Q2	'
Amendment Flag	'false	'
Entity Common Stock, Shares Outstanding	'	78,914,505

Condensed_Consolidated_Balance

Condensed Consolidated Balance Sheets (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Current assets:	'	'
Cash and cash equivalents	$88,828	$6,868
Short-term investments	1,379	1,428
Accounts receivable, net of allowance of $479 and $479, respectively	4,675	7,734
Related party accounts receivable	51	484
Inventories, net	14,753	10,888
Prepaid expenses and other current assets	7,138	9,518
Total current assets	116,824	36,920
Property, plant and equipment, net	140,656	140,591
Restricted cash	1,721	1,648
Other assets	15,826	10,585
Goodwill and intangible assets	9,120	9,120
Total assets	284,147	198,864
Current liabilities:	'	'
Accounts payable	8,503	6,512
Deferred revenue	10,372	2,222
Accrued and other current liabilities	12,761	21,221
Capital lease obligation, current portion	882	956
Debt, current portion	9,923	6,391
Total current liabilities	42,441	37,302
Capital lease obligation, net of current portion	228	287
Long-term debt, net of current portion	111,952	56,172
Related party debt	100,480	89,499
Deferred rent, net of current portion	10,223	10,191
Deferred revenue, net of current portion	4,100	5,000
Derivative liability	147,840	134,717
Other liabilities	6,560	1,544
Total liabilities	423,824	334,712
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, 300,000,000 and 200,000,000 shares authorized as of June 30, 2014 and December 31, 2013; 78,914,451 and 76,662,812 shares issued and outstanding as of June 30, 2014 and December 31, 2013, respectively	8	8
Additional paid-in capital	717,167	706,253
Accumulated other comprehensive loss	-15,634	-20,087
Accumulated deficit	-840,532	-821,438
Total Amyris, Inc. stockholders’ deficit	-138,991	-135,264
Noncontrolling interest	-686	-584
Total stockholders' deficit	-139,677	-135,848
Total liabilities and stockholders' deficit	$284,147	$198,864

Consolidated_Balance_Sheets_Pa

Consolidated Balance Sheets (Parentheticals) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, except Share data, unless otherwise specified
Allowance for Doubtful Accounts	$479	$479
Stockholders' Equity:	'	'
Preferred stock, par value	$0.00	$0.00
Preferred stock, shares authorized	5,000,000	5,000,000
Preferred stock, shares issued	0	0
Preferred stock, shares outstanding	0	0
Common stock, par value	$0.00	$0.00
Common stock, shares authorized	300,000,000	200,000,000
Common stock, shares issued	78,914,451	76,662,812
Common Stock, Shares, Outstanding	78,914,451	76,662,812

Condensed_Consolidated_Stateme

Condensed Consolidated Statements of Operations (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Revenues	'	'	'	'
Renewable product sales	$4,379	$4,011	$7,221	$6,991
Related party renewable product sales	31	174	34	177
Total product sales	4,410	4,185	7,255	7,168
Grants and collaborations revenue	4,897	6,555	8,093	8,903
Related party grants and collaborations revenue	0	109	0	2,647
Total grants and collaborations revenue	4,897	6,664	8,093	11,550
Total revenues	9,307	10,849	15,348	18,718
Cost and operating expenses	'	'	'	'
Cost of products sold	7,511	8,853	13,747	17,813
Loss on purchase commitments and write-off of production assets	52	8,423	159	8,423
Research and development	12,175	13,992	25,161	29,746
Sales, general and administrative	13,971	14,718	27,370	29,545
Total cost and operating expenses	33,709	45,986	66,437	85,527
Loss from operations	-24,402	-35,137	-51,089	-66,809
Other income (expense):	'	'	'	'
Interest income	148	57	204	93
Interest expense	-6,802	-1,558	-11,552	-3,120
Gain (loss) from change in fair value of derivative instruments	-3,252	-254	54,148	785
Loss from extinguishment of debt	-1,100	0	-10,512	0
Other income (expense), net	5	-1,776	-117	-1,696
Total other income (expense)	-10,983	-3,531	32,171	-3,938
Loss before income taxes	-35,385	-38,668	-18,918	-70,747
Provision for income taxes	-125	-246	-236	-482
Net loss	-35,510	-38,914	-19,154	-71,229
Net income (loss) attributable to noncontrolling interest	31	38	60	-261
Net loss attributable to Amyris, Inc. common stockholders	($35,479)	($38,876)	($19,094)	($71,490)
Net income (loss) per share attributable to common stockholders:	'	'	'	'
Basic (in dollars per share)	($0.45)	($0.51)	($0.25)	($0.96)
Diluted (in dollars per share)	($0.45)	($0.51)	($0.66)	($0.96)
Weighted-average shares of common stock outstanding used in computing net loss per share of common stock:	'	'	'	'
Basic (in shares)	78,604,692	75,959,228	77,722,437	74,640,314
Diluted (in shares)	78,604,692	75,959,228	110,632,078	74,640,314

Condensed_Consolidated_Stateme1

Condensed Consolidated Statements of Comprehensive Loss (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Comprehensive income (loss):	'	'	'	'
Net loss	$35,510	$38,914	$19,154	$71,229
Foreign currency translation adjustment, net of tax	1,578	-4,742	4,411	-4,031
Total comprehensive loss	-33,932	-43,656	-14,743	-75,260
Income (loss) attributable to noncontrolling interest	31	38	60	-261
Foreign currency translation adjustment attributable to noncontrolling interest	19	-62	42	-54
Comprehensive loss attributable to Amyris, Inc.	($33,882)	($43,680)	($14,641)	($75,575)

Condensed_Consolidated_Stateme2

Condensed Consolidated Statements of Stockholders' Deficit (USD $)	Total	Common Stock [Member]	Additional Paid-in Capital [Member]	Accumulated Deficit [Member]	Accumulated Other Comprehensive Income (Loss) [Member]	Noncontrolling Interest [Member]
In Thousands, except Share data, unless otherwise specified
Beginning Balance at Dec. 31, 2013	'	'	'	'	'	($584)
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Foreign currency translation adjustment, net of tax	'	'	'	'	'	-42
Ending Balance at Mar. 31, 2014	'	'	'	'	'	'
Beginning Balance at Dec. 31, 2013	-135,848	8	706,253	-821,438	-20,087	-584
Beginning Balance, shares at Dec. 31, 2013	76,662,812	76,662,812	'	'	'	'
Increase (Decrease) in Stockholders' Equity [Roll Forward]	'	'	'	'	'	'
Stock Issued During Period, Shares, Employee Stock Purchase Plans	'	551,707	'	'	'	'
Issuance of common stock upon exercise of stock options	1,507	'	1,507	'	'	'
Shares issued under restricted stock unit settlement, shares	'	756,536	'	'	'	'
Shares issued under restricted stock unit settlement	-1,790	'	-1,790	'	'	'
Issuance of common stock in a private placement, shares	'	943,396	'	'	'	'
Issuance of common stock in a private placement	4,000	4,000	4,000	'	'	'
Stock-based compensation	7,197	'	7,197	'	'	'
Foreign currency translation adjustment, net of tax	4,411	'	'	'	4,453	-42
Net loss attributable to Amyris, Inc. common stockholders	-19,094	'	'	-19,094	'	'
Net loss	-19,154	'	'	'	'	-60
Ending Balance at Jun. 30, 2014	($139,677)	$8	$717,167	($840,532)	($15,634)	($686)
Ending Balance, shares at Jun. 30, 2014	78,914,451	78,914,451	'	'	'	'

Condensed_Consolidated_Stateme3

Condensed Consolidated Statements of Cash Flows (USD $)	6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013
Operating activities	'	'
Net loss	($19,154,000)	($71,229,000)
Adjustments to reconcile net loss to net cash used in operating activities:	'	'
Depreciation and amortization	7,539,000	8,491,000
Loss (gain) on disposal of property, plant and equipment	57,000	-38,000
Stock-based compensation	7,197,000	9,178,000
Amortization of debt discount	3,763,000	1,061,000
Loss on extinguishment of debt	10,512,000	0
Loss on purchase commitments and write-off of production assets	159,000	8,423,000
Change in fair value of derivative instruments	-54,148,000	-719,000
Other non-cash expenses	-113,000	213,000
Changes in assets and liabilities:	'	'
Accounts receivable	3,423,000	-3,812,000
Related party accounts receivable	147,000	345,000
Inventories, net	-3,570,000	1,150,000
Prepaid expenses and other assets	-323,000	1,098,000
Accounts payable	1,879,000	-1,912,000
Accrued and other liabilities	-608,000	-5,619,000
Deferred revenue	7,380,000	8,549,000
Deferred rent	33,000	-447,000
Net cash used in operating activities	-35,827,000	-45,268,000
Investing activities	'	'
Purchase of investments	-883,000	-1,763,000
Maturities of investments	1,032,000	334,000
Change in restricted cash	0	-1,000
Investment in joint venture	-2,075,000	0
Purchases of property and equipment, net of disposals	-2,064,000	-3,711,000
Net cash used in investing activities	-3,990,000	-5,141,000
Financing activities	'	'
Proceeds from issuance of common stock, net of repurchases	71,000	167,000
Proceeds from issuance of common stock in private placements, net of issuance costs	4,000,000	19,980,000
Principal payments on capital leases	-515,000	-867,000
Proceeds from debt issued, net of issuance costs	83,171,000	2,645,000
Proceeds from debt issued to related party	39,012,000	10,000,000
Principal payments on debt	-3,596,000	-1,902,000
Net cash provided by financing activities	122,143,000	30,023,000
Effect of exchange rate changes on cash and cash equivalents	-366,000	1,297,000
Net increase (decrease) in cash and cash equivalents	81,960,000	-19,089,000
Cash and cash equivalents at beginning of period	6,868,000	30,592,000
Cash and cash equivalents at end of period	88,828,000	11,503,000
Supplemental disclosures of cash flow information:	'	'
Cash paid for interest	1,847,000	1,004,000
Income Taxes Paid, Net	0	0
Supplemental disclosures of non-cash investing and financing activities:	'	'
Acquisitions of property, plant and equipment under accounts payable, accrued liabilities and notes payable	-226,000	307,000
Financing of insurance premium under notes payable	-318,000	147,000
Receivable of proceeds for options exercised	-355,000	0
Accrued offering cost of common stock in private placement	0	-19,000
Capitalized interest	2,812,000	0
Non-cash investment in joint venture	($237,000)	$0

The_Company

The Company	6 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
The Company	'
	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 has entered into various contract manufacturing agreements to support commercial production. 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 its products at commercial scale and on an economically viable basis (i.e., low per unit production costs). The Company is building its experience producing renewable products at commercial scale. 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 cash equivalents and investments currently on hand, with cash inflows from collaboration and grant funding, cash contributions from product sales, and with new debt and equity financings. The Company's planned 2014 and 2015 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 contributions from growth in renewable product sales, as well as additional funding from new joint ventures or other collaborations, and may also require additional funding from debt or equity financings. The Company will continue to need to fund its research and development and related activities and to provide working capital to fund production, storage, distribution and other aspects of its business. The Company's operating plan contemplates capital expenditures of approximately $9.0 million in 2014 and the Company expects to continue to incur costs in connection with its existing contract manufacturing arrangements.
	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 2014. As of June 30, 2014, the Company had an accumulated deficit of $840.5 million and had cash, cash equivalents and short term investments of $90.2 million. The Company has significant outstanding debt and contractual obligations related to purchase commitments, as well as capital and operating leases. As of June 30, 2014, the Company's debt, net of discount of $83.9 million, totaled $222.4 million, of which $9.9 million matures within the next twelve months. In addition, the Company's debt agreements contain various covenants, including restrictions on the Company's business that could cause the Company to be at risk of defaults. Please refer to Note 5, “Debt” and Note 6, “Commitments and Contingencies” for further details regarding the Company's debt obligations and commitments.
	The Company’s operating plan for 2014 contemplates significant reduction in the Company’s net cash outflows, resulting from (i) revenue growth from sales of existing and new products, (ii) reduced production costs compared to prior periods as a result of manufacturing and technical developments in 2013, (iii) cash inflows from collaborations consistent with levels achieved in 2013 and (iv) operating expenses maintained at reduced levels. Achieving a reduction in net cash outflows from these factors is subject to risks and uncertainties, including those set forth in Part II, Item 1A of this Quarterly Report on Form 10-Q, “Risk Factors.”
	In addition to cash contributions from product sales and debt and equity financings, the Company also depends on collaboration funding to support its operating expenses. While part of this funding is committed based on existing collaboration agreements, the Company will need to identify and obtain funding under additional collaborations that are not yet subject to any definitive agreement or are not yet identified. In addition, some of the Company’s existing collaboration funding is subject to achievement by the Company of milestones or other funding conditions.
	If the Company is unable to increase positive gross margin product sales or generate sufficient additional payments from existing and new collaboration partners, it may need to obtain additional funding from equity financings, credit facilities, loans or issue additional preferred and/or discounted equity, agree to burdensome covenants, grant further security interest in its assets, enter into collaboration and licensing arrangements that require it to relinquish commercial rights, or grant licenses on terms that are not favorable. If the Company fails to generate positive gross margins product sales or secure such funding, the Company could be forced to curtail its operations, which would have a material adverse effect on the Company's ability to continue with its business plans.

Summary_of_Significant_Account

Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Summary of Significant Accounting Policies	'
	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 filed with the Securities and Exchange Commission (“SEC”) on April 2, 2014. 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.
	Principles of Consolidation
	The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity 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.
	The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated 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."
	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 revenue 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 July 2013, the Financial Accounting Standards Board ("FASB") issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance became effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there was no significant impact to the Company resulting from the guidance.
	In May 2014, the FASB issued a 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 standard 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. This guidance will be effective for the Company beginning January 1, 2017 and can be applied either retrospectively to each period presented or as a cumulative-effect adjustment as of the date of adoption. The Company is currently assessing the impact of adopting this new accounting standard on its financial statements.

Fair_Value_of_Financial_Instru

Fair Value of Financial Instruments	6 Months Ended
	Jun. 30, 2014
Fair Value Disclosures [Abstract]	'
Fair Value of Financial Instruments	'
	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 June 30, 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 June 30, 2014
	Financial Assets
	Money market funds	$	74,765			$	—			$	—			$	74,765
	Certificates of deposit	1,453				—				—				1,453
	Total financial assets	$	76,218			$	—			$	—			$	76,218
	Financial Liabilities
	Loans payable (1)	$	—			$	20,360			$	—			$	20,360
	Credit facilities  (1)	—				39,864				—				39,864
	Convertible notes (1)	—				—				227,638				227,638
	Compound embedded derivative liability	—				—				145,032				145,032
	Currency interest rate swap derivative liability	—				2,808				—				2,808
	Total financial liabilities	$	—			$	63,032			$	372,670			$	435,702
	________
	(1) These liabilities are carried on the condensed consolidated balance sheet on a historical basis.
	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 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. Market risk associated with the fixed and variable rate long-term debt relates to the potential reduction in fair value and negative impact to future earnings, respectively, from an increase in interest rates.
	The carrying amounts of certain financial instruments, such as cash equivalents, short term investments, accounts receivable, accounts payable and accrued liabilities, approximate fair value due to their relatively short maturities and low market interest rates, if applicable. The fair values of the loans payable, convertible notes and credit facilities are based on the present value of expected future cash flows and assumptions about current interest rates and the creditworthiness of the Company.
	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):
		2014
	Balance at January 1	$	131,952
	Additions to convertible notes	93,295
	Change in fair value of convertible notes	2,391
	Balance at June 30	$	227,638
	The Company’s financial assets and financial liabilities as of December 31, 2013 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, 2013
	Financial Assets
	Money market funds	$	398			$	—			$	—			$	398
	Certificates of deposit	1,428				—				—				1,428
	Total financial assets	$	1,826			$	—			$	—			$	1,826
	Financial Liabilities
	Loans payable	$	—			$	18,491			$	—			$	18,491
	Credit facilities	—				7,571				—				7,571
	Convertible notes	—				—				131,952				131,952
	Compound embedded derivative liability	—				—				131,117				131,117
	Currency interest rate swap derivative liability	—				3,600				—				3,600
	Total financial liabilities	$	—			$	29,662			$	263,069			$	292,731
	Derivative Instruments
	The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):
		2014
	Balance at January 1	$	131,117
	Transfers in to Level 3 net of cancellation (1)	86,551
	Total (income) loss from change in fair value of derivative liability	(72,636		)
	Balance at June 30	$	145,032
	________
	(1) Includes $1.1 million removal of derivative liability related to debt extinguishment.
	The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions of outstanding convertible promissory notes issued to Total Energies Nouvelles Activités USA (formerly known as Total Gas & Power USA, SAS, or “Total”), as well as Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering (see Note 5, "Debt"). There is no current observable market for this type of derivative and, as such, the Company determined the fair value of the embedded derivative 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 Convertible Note Offering. 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 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 initially 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 or (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 derivative 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 derivative is defined as the "without". This method estimates the fair value of the embedded derivative by looking at the difference in the values between the convertible notes with the embedded derivative and the fair value of the convertible notes without the embedded derivative. 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 derivative 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 June 30, 2014, the Company has sufficient common stock available to settle the conversion option in shares. As of June 30, 2014 and December 31, 2013, included in "Derivative Liability" on the condensed consolidated balance sheet is the Company's compound embedded derivative liability of $145.0 million and $131.1 million, respectively, which represents the fair value of the equity conversion option or a "make-whole" provision relating to the outstanding senior secured convertible promissory notes issued to Total, Tranche I Notes, Tranche II Notes and notes issued under the Rule 144A Convertible Note Offering as described above.
	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 short term loan (referred to as 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$10.0 million based on the exchange rate as of June 30, 2014). The swap arrangement exchanges the principal and interest payments under the Banco Pine Bridge Loan of R$22.0 million entered into in July 2012 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.
	Derivative instruments measured at fair value as of June 30, 2014 and December 31, 2013, and their classification on the condensed consolidated balance sheets and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):
			Liability as of
			30-Jun-14							31-Dec-13
	Type of Derivative Contract		Quantity of			Fair Value				Quantity of			Fair Value
			Short							Short
			Contracts							Contracts
	Currency interest rate swap, included as net liability in derivative liability		1			$	2,808			1			$	3,600
			Income	Three Months Ended June 30,								Six Months Ended June 30,
	Type of Derivative Contract		Statement Classification	2014				2013				2014		2013
				Gain (Loss) Recognized								Gain (Loss) Recognized
	Currency interest rate swap (1)		Gain (loss) from change in fair value of derivative instruments	$	722			$	(1,639	)		$1,056		$	(1,651	)
___________
(1)	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Balance_Sheet_Components

Balance Sheet Components	6 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Balance Sheet Components	'
	Balance Sheet Components
	Inventories, net
	Inventories are stated at the lower of cost or market and consist of the following (in thousands):
		June 30,			December 31,
		2014			2013
	Raw materials	$	2,468		$	1,796
	Work-in-process	6,536			7,292
	Finished goods	5,749			1,800
	Inventories, net	$	14,753		$	10,888
	Prepaid Expenses and Other Current Assets
	Prepaid expenses and other current assets is comprised of the following (in thousands):
		June 30,			December 31,
		2014			2013
	Maintenance (1)	$	393		$	258
	Prepaid insurance(1)	603			894
	Manufacturing catalysts	1,715			1,536
	Recoverable VAT and other taxes	2,776			5,125
	Other (1)	1,651			1,705
	Prepaid expenses and other current assets	$	7,138		$	9,518
	______________
	(1)	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.
	Property, Plant and Equipment, net
	Property, plant and equipment, net is comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Leasehold improvements	$	39,208		$	39,034
	Machinery and equipment	101,383			96,585
	Computers and software	8,946			8,509
	Furniture and office equipment	2,584			2,535
	Buildings	7,606			7,148
	Vehicles	436			488
	Construction in progress	44,635			41,387
		204,798			195,686
	Less: accumulated depreciation and amortization	(64,142		)	(55,095		)
	Property, plant and equipment, net	$	140,656		$	140,591
	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, Paraíso Bioenergia. The Company's construction in progress consists primarily of the upfront plant design and the initial construction of a second large-scale production plant in Brazil, located at the Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.) sugar and ethanol mill (also in the state of São Paulo, Brazil).
	Property, plant and equipment, net includes $3.8 million and $3.4 million of machinery and equipment under capital leases as of June 30, 2014 and December 31, 2013, respectively. Accumulated amortization of assets under capital leases totaled $1.8 million and $1.5 million as of June 30, 2014 and December 31, 2013, respectively.
	Depreciation and amortization expense, including amortization of assets under capital leases was $3.7 million and $4.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $7.5 million and $8.5 million for the six months ended June 30, 2014 and 2013, respectively.
	The Company capitalizes interest costs incurred to construct plant and equipment. The capitalized interest is recorded as part of the depreciable cost of the asset to which it relates to and is amortized over the asset's estimated useful life. Interest cost capitalized as of June 30, 2014 and December 31, 2013 was $0.5 million and $0.5 million, respectively.
	Other Assets
	Other assets are comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Deposits on property and equipment, including taxes	$	2,095		$	1,970
	Recoverable taxes from Brazilian government entities	9,064			6,599
	Debt issuance cost (2)	978			454
	Investments in joint venture (1)	2,170			68
	Other (2)	1,519			1,494
	Total other assets	$	15,826		$	10,585
	______________
	(1)	The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.
	(2)	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.
	Accrued and Other Current Liabilities
	Accrued and other current liabilities are comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Professional services	$	2,093		$	2,279
	Accrued vacation	2,516			2,274
	Payroll and related expenses	3,939			5,066
	Tax-related liabilities	157			825
	Deferred rent, current portion	1,111			1,111
	Accrued interest	1,246			3,176
	Contractual obligations to contract manufacturers	853			4,241
	Other	846			2,249
	Total accrued and other current liabilities	$	12,761		$	21,221
	Derivative Liability
Derivative liability is comprised of the following (in thousands):
	June 30, 2014			December 31, 2013
Fair market value of swap obligation	$	2,808		$	3,600
Fair value of compound embedded derivative liability(1)	145,032			131,117
Total derivative liability	$	147,840		$	134,717
______________
(1)	The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

Debt

Debt	6 Months Ended
	Jun. 30, 2014
Debt Disclosure [Abstract]	'
Debt	'
	Debt
	Debt is comprised of the following (in thousands):
		June 30, 2014			December 31, 2013
	Credit facilities	$	37,972		$	8,767
	Convertible notes	57,904			28,537
	Related party convertible notes	100,480			89,499
	Loans payable	25,999			25,259
	Total debt	222,355			152,062
	Less: current portion	(9,923		)	(6,391		)
	Long-term debt	$	212,432		$	145,671
	FINEP Credit Facility
	In November 2010, the Company entered into a credit facility with Financiadora de Estudos e Projetos (referred to as 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 (“FINEP Project”) and provided for loans of up to an aggregate principal amount of R$6.4 million (approximately US$2.9 million based on the exchange rate as of June 30, 2014), which is secured by a chattel mortgage on certain equipment of the Company 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 at 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% interest 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 June 30, 2014 and December 31, 2013, the total outstanding loan balance under this credit facility was R$4.8 million (approximately US$2.2 million based on the exchange rate as of June 30, 2014) and R$5.2 million (approximately US$2.2 million based on exchange rate as of December 31, 2013), 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$6.6 million based on the exchange rate as of June 30, 2014) 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$1.5 million based on the exchange rate as of June 30, 2014). 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 (the bank is referred to as “BNDES” and the credit facility referred to as the “BNDES Credit Facility”) in the amount of R$22.4 million (approximately US$10.2 million based on the exchange rate as of June 30, 2014). This BNDES Credit Facility was extended as project financing for a production site in Brazil. The credit line is divided into an initial tranche of up to approximately R$19.1 million and an additional tranche of approximately R$3.3 million that becomes available upon delivery of additional guarantees. The credit line is available for 12 months from the date of the BNDES Credit Facility, subject to extension by the lender. 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 $11.3 million based on the exchange rate as of June 30, 2014). 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 this 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, the Lender may terminate its commitments and declare immediately due all borrowings under the facility. As of June 30, 2014 and December 31, 2013, the Company had R$13.4 million (approximately US$6.1 million based on the exchange rate as of June 30, 2014) and R$15.3 million (approximately US$6.5 million based on the exchange rate as of December 31, 2013), 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. (referred to as “Hercules”) to make available to Amyris a loan in the aggregate principal amount of up to $25.0 million (referred to as 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 (referred to as the “Hercules Amendment”) of the Loan and Security Agreement entered into in March 2014. Pursuant to the 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 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, certain cross defaults and judgments, and insolvency. If an event of default occurs, Hercules may require immediate repayment of all amounts due.
	As of June 30, 2014, $29.7 million was outstanding under the Hercules Loan Facility, net of discount of $0.3 million, and the Company maintains cash in excess of the approximately $15.0 million current minimum cash covenant described above.
	Notes Payable
	During the period between May 2008 and October 2008, the Company entered into notes payable agreements with the lessor of its headquarters under which it borrowed a total of $3.3 million for the purchase of tenant improvements, bearing an interest rate of 9.5% per annum and to be repaid over a period of 55 to 120 months. As of June 30, 2014 and December 31, 2013, no principal amount was outstanding under these notes payable. In June 2013, as part of the April 30, 2013 Amendment to the Company's operating lease for its headquarters, the Company recorded the elimination of these notes payable as a lease incentive and recorded approximately $1.4 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.
	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 (referred to as 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 (referred to as the "Fidelity Notes"). As of June 30, 2014, 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 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 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.
	In August 2013, the Company entered into that certain Securities Purchase Agreement, dated as of August 8, 2013 (referred to as the “August 2013 SPA”), for the sale of senior convertible promissory notes (referred to as the “August 2013 Notes”) to Maxwell (Mauritius) Pte Ltd (or “Temasek”) and Total, each of whom are existing stockholders of the Company. The August 2013 SPA contemplated the sale of up to an aggregate of $73.0 million in principal amount of the August 2013 Notes in a private placement (referred to as the “August 2013 Financing”) exempt from registration under the Securities Act of 1933, as amended, (the "Securities Act") in an initial tranche of $42.6 million in aggregate principal amount and a second tranche of $30.4 million in aggregate principal amount.
	In October 2013, the Company amended the August 2013 SPA to include certain entities affiliated with FMR LLC (referred to as the “Fidelity Entities”) in the first tranche of the August 2013 Financing. Pursuant to the amended agreement the Company sold senior convertible notes with an aggregate principal amount of $7.6 million to the Fidelity Entities (referred to as the "Tranche I Notes"). The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on The NASDAQ Stock Market (or “NASDAQ”) through August 7, 2013, subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes will be reduced to $2.15 if either (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1,000,000 liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to not occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes would be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment date; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.
	As of June 30, 2014 and December 31, 2013, principal amount of $29.3 million and $28.5 million, respectively, were outstanding under these convertible notes, net of debt discount of $3.7 million and $4.0 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding 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 (the “Initial Purchaser”), relating to the sale of $75.0 million aggregate principal amount of its 6.50% Convertible Senior Notes due 2019 (the "144A Notes") to the Initial Purchaser in a private placement, and for initial resale by the Initial Purchaser to certain qualified institutional buyers. In addition, the Company granted the Initial Purchaser an option to purchase up to an additional $15.0 million aggregate principal amount of notes, which option expired according to its terms. Under the terms of the Purchase Agreement, 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 (the “Indenture”), between the Company and Wells Fargo Bank, National Association, as trustee. The net proceeds from the offering of the 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 one of its existing investors, Total Energies Nouvelles Activités USA (“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 has 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 Rule 144A Notes from the Initial Purchaser (described further below under "Related Party Convertible Notes"). The 144A Notes will 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 will 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 Notes will have an initial conversion rate of 267.0370 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 receive 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 their 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.
	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 the Biofene collaboration with the Company, provided new structure for a joint venture (referred to as 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 (referred to as the "July 2012 Agreements").
	The purchase agreement for the notes related to the funding from Total (referred to as the "Total Purchase Agreement") provides for the sale of an aggregate of $105.0 million in notes as follows:
	•	As part of an initial closing under the purchase agreement (which initial closing was completed in two installments), (i) on July 30, 2012, the Company sold a 1.5% Senior Unsecured Convertible Note due March 2017 to Total in the face 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 note (in the same form) 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 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).
	•	The Total Purchase Agreement provides that additional notes may be sold in subsequent closings in July 2014 (for cash proceeds to the Company of $21.7 million, which would be settled in an initial installment of $10.85 million payable at such closing and a second installment of $10.85 million payable in January 2015).
	The notes issued to Total pursuant to the Total Purchase Agreement have a maturity date of March 1, 2017, an initial conversion price equal to $7.0682 per share for the notes issued under the initial closing, an initial conversion price equal $3.08 per share for the notes issued under the second closing and an initial conversion price equal to $4.11 per share for the notes issued (and that remain to be issued) under the third closing. The 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 cancelled if the notes are cancelled based on 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 by Total through such date tied to funding by Total. The notes issuable under the third closing will be senior secured promissory notes, pursuant to the exchange agreed to by Total and the Company in December 2013.
	The 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, then the notes will be exchanged by Total for equity interests in the Fuels JV, after which the notes will not be convertible and any obligation to pay principal or interest on the 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 notes would remain outstanding and become payable by the Company, and 30% of the outstanding notes would be cancelled. If Total makes a “No-Go” decision, outstanding notes will remain outstanding and become payable at maturity.
	In connection with a December 2012 private placement of the Company’s common stock involving certain existing stockholders of the Company, Total elected to participate in the private placement by exchanging approximately $5.0 million of its $53.3 million in senior unsecured convertible promissory notes into 1,677,852 shares 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 senior unsecured convertible promissory notes 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 March 2013, the Company entered into a letter agreement with Total (referred to as 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 July 2013 funding tranche of $30.0 million (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 senior unsecured convertible promissory notes to be issued in connection with such funding 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 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 July 2013 closing. Specifically, if the Company requested such advance installments, subject to certain closing conditions and delivery of certifications regarding the Company's cash levels, Total was obligated to fund $10.0 million no later than May 15, 2013, and an additional $10.0 million no later than June 15, 2013, with the remainder to be funded on the original July 2013 closing date.
	In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock. The Company did not request the May advance of $10.0 million, but did request the June advance (as described above), under which this convertible note was issued.
	In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above. This purchase and sale completed Total's commitment to purchase $30.0 million of such notes by July 2013. In accordance with the March 2013 Letter Agreement, this convertible note has an initial conversion price equal to $3.08 per share of the Company's common stock.
	The conversion prices of the notes issued under the Total Purchase Agreement are subject to adjustment for proportional adjustments to outstanding common stock and under anti-dilution provisions in case of certain dividends and distributions. Total has a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if Total does not require such repayment. The Total Purchase Agreement and notes include 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 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 purchase agreement and notes, with added default interest rates and associated cure periods applicable to the covenant regarding SEC reporting. Furthermore, the 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 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 provided by Temasek in October 2013, Total waived compliance with the debt limitations outlined above as to the $35.0 million bridge loan and the August 2013 Financing.
	In April 2014, the Company and Total entered into a letter agreement dated as of March 29, 2014 (referred to as the "March 2014 Letter Agreement") to amend the Amended and Restated Master Framework Agreement entered into as of December 2, 2013 (included as part of JV Documents, as defined below) and the Total Purchase Agreement. Under the March 2014 Letter Agreement, the Company agreed to, (i) amend the conversion price of the convertible notes to be issued in the third closing under the Total Purchase Agreement from $7.0682 to $4.11 subject to stockholder approval at the Company's 2014 annual meeting (which was attained in May 2014), (ii) extend the period during which Total may exchange for other Company securities certain outstanding convertible promissory 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 decides not to proceed with the collaboration and makes a "No-Go" decision with respect thereto.
	JVCO Convertible Notes
	In December 2013, in connection with the Company's entry into a Shareholders Agreement and License Agreement and related documents (collectively, referred to as the "JV Documents") with Total and Total Amyris BioSolutions B.V. (or "JVCO") relating to the establishment of JVCO (see Note 7, "Joint Venture and Noncontrolling Interest"), Amyris (i) exchanged the $69.0 million of the outstanding Total unsecured convertible notes issued pursuant to the Total Purchase Agreement and issued replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (the “Replacement Notes”), (ii) granted to Total a security interest in and lien on all Amyris’s rights, title and interest in and to Amyris’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 will be 1.5%, senior secured convertible notes instead of senior unsecured convertible notes. As a consequence of executing the JV Documents and forming JVCO, the security interests in all of the Company’s intellectual property, granted by Amyris in favor of Total, Temasek, and certain Fidelity Entities pursuant 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.
	As of June 30, 2014 and December 31, 2013, $40.3 million and $51.5 million, respectively, of Replacement Notes were outstanding, net of debt discount of $13.1 million and $17.6 million, respectively.
	August 2013 Financing Convertible Notes and 2013 Bridge Loans
	In connection with the August 2013 Financing, the Company entered into the August 2013 SPA with Total and Temasek to sell up to $73.0 million in convertible promissory notes in private placements, with such notes to be sold and issued over a period of up to 24 months from the date of signing. The August 2013 SPA provided for the August 2013 Financing to be divided into two tranches (the first tranche for $42.6 million and the second tranche for $30.4 million), each with differing closing conditions. Of the total possible purchase price in the financing, $60.0 million to be paid in the form of cash by Temasek ($35.0 million in the first tranche and up to $25.0 million in the second tranche) and $13.0 million to be paid by the exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights ($7.6 million in the first tranche and $5.4 million in the second tranche). The August 2013 SPA included requirements that the Company meet certain production milestones before the second tranche would become available, obtain stockholder approval prior to completing any closing of the transaction, and issue a warrant to Temasek to purchase 1,000,000 shares of the Company's common stock at an exercise price of $0.01 per share, exercisable only if Total converts notes previously issued to Total in the second closing under the Total Purchase Agreement. In September 2013, prior to the initial closing of the August 2013 Financing, the Company's stockholders approved the issuance in the private placement of up to $110.0 million aggregate principal amount of senior convertible promissory notes, the issuance of a warrant to purchase 1,000,000 shares of the Company's common stock and the issuance of the common stock issuable upon conversion or exercise of such notes and warrant, which approval included the transactions contemplated by the August 2013 Financing.
	In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million. As of June 30, 2014, the Company had not drawn any funds from the agreement and the facility expired in October 2013 in accordance with its terms.
	In October 2013, the Company sold and issued a bridge note to Temasek (referred to as the “Temasek Bridge Note”) in exchange for a bridge loan of $35.0 million. The Temasek Bridge Note was due on February 2, 2014 and accrued interest at a rate of 5.5% quarterly from the October 4, 2013 date of issuance. The Temasek Bridge Note was cancelled on October 16, 2013 as payment for Temasek’s purchase of Tranche I Notes in the first tranche of the August 2013 Financing as further described below.
	In October 2013, the Company amended the August 2013 SPA to include the Fidelity Entities in the first tranche of the August 2013 Financing with an investment amount of $7.6 million, and to proportionally increase the amount acquired by exchange and cancellation of outstanding convertible promissory notes held by Total in connection with its exercise of pro rata rights to $14.6 million ($9.2 million in the first tranche and up to $5.4 million in the second tranche). Also in October 2013, the Company completed the closing of the first tranche of the August 2013 Financing, issuing a total of $51.8 million in Tranche I Notes for cash proceeds of $7.6 million and cancellation of outstanding convertible promissory notes of $44.2 million, of which $35.0 million resulted from cancellation of the Temasek Bridge Note and the remaining $9.2 million from the exchange and cancellation of an outstanding convertible note held by Total. As a result of the exchange and cancellation of the $35.0 million Temasek Bridge Note and the $9.2 million Total convertible note for the Tranche I Notes, the Company recorded a loss from extinguishment of debt of $19.9 million. The Tranche I Notes are due sixty months from the date of issuance and will be convertible into the Company’s common stock at a conversion price equal to $2.44, which represents a 15% discount to a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. The Tranche I Notes are convertible at the option of the holder: (i) at any time after 18 months from the date of the August 2013 SPA, (ii) on a change of control of the Company and (iii) upon the occurrence of an event of default. The conversion price of the Tranche I Notes would be reduced to $2.15 if (a)(i) a specified Company manufacturing plant had failed to achieve a total production of 1.0 million liters within a run period of 45 days prior to June 30, 2014, or (ii) the Company fails to achieve gross margins from product sales of at least 5% prior to June 30, 2014, or (b) the Company reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes. In 2013, the Company achieved a total production of 1.0 million liters within a run period of 45 days in satisfaction of clause (a)(i) of the preceding sentence and the Company is currently evaluating the achievement of clause (a)(ii) of the preceding sentence. If either of the production and margin milestones in clause (a) above were to occur, and the Company also reduces the conversion price of certain existing promissory notes held by Total prior to the repayment or conversion of the Tranche I Notes as set forth in clause (b) above, the conversion price of the Tranche I Notes will be reduced to $1.87. Each Tranche I Note accrues interest from the date of issuance until the earlier of the date that such Tranche I Note is converted into the Company’s common stock or is repaid in full. Interest accrues at a rate of 5% per six months, compounded semiannually (with graduated interest rates of 6.5% applicable to the first 180 days and 8% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 6.5% for all other defaults). Interest for the first 30 months is payable in kind and added to the principal every six-months and thereafter, the Company may continue to pay interest in kind by adding to the principal every six-months or may elect to pay interest in cash. The Tranche I Notes may be prepaid by the Company after 30 months from the issuance date and initial interest payment; thereafter the Company has the option to prepay the Tranche I Notes every six months at the date of payment of the semi-annual coupon.
	In January 2014, the Company sold and issued, for face value, approximately $34.0 million of convertible promissory notes in the second tranche of the August 2013 Financing (referred to as the “Tranche II Notes”). At the closing, Temasek purchased $25.0 million of the Tranche II Notes and Wolverine Asset Management, LLC (referred to as “Wolverine”) purchased $3.0 million of the Tranche II Notes, each for cash. Total purchased approximately $6.0 million of the Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total. As a result of the exchange and cancellation of the $6.0 million Total convertible note for the Tranche II Notes, the Company recorded a loss from extinguishment of debt of $9.4 million. The Tranche II Notes will be due sixty months from the date of issuance and will be convertible into shares of common stock at a conversion price equal to $2.87, which represents a trailing 60-day weighted-average closing price of the common stock on NASDAQ through August 7, 2013, subject to adjustment as described below. Specifically, the Tranche II Notes are convertible at the option of the holder (i) at any time 12 months after issuance, (ii) on a change of control of the Company, and (iii) upon the occurrence of an event of default. Each Tranche II Note will accrue interest from the date of issuance until the earlier of the date that such Tranche II Note is converted into common stock or repaid in full. Interest will accrue at a rate per annum equal to 10%, compounded annually (with graduated interest rates of 13% applicable to the first 180 days and 16% applicable thereafter as the sole remedy should the Company fail to maintain NASDAQ listing status or at 12% for all other defaults). Interest for the first 36 months shall be payable in kind and added to principal every year following the issue date and thereafter, the Company may continue to pay interest in kind by adding to principal on every year anniversary of the issue date or may elect to pay interest in cash.
	In addition to the conversion price adjustments set forth above, the conversion prices of the Tranche I Notes and Tranche II Notes are subject to further adjustment (i) according to proportional adjustments to outstanding common stock of the Company in case of certain dividends and distributions, (ii) according to anti-dilution provisions, and (iii) with respect to notes held by any purchaser other than Total, in the event that Total exchanges existing convertible notes for new securities of the Company in connection with future financing transactions in excess of its pro rata amount. Notwithstanding the foregoing, holders of a majority of the principal amount of the notes outstanding at the time of conversion may waive any anti-dilution adjustments to the conversion price. The purchasers have a right to require repayment of 101% of the principal amount of the notes in the event of a change of control of the Company and the notes provide for payment of unpaid interest on conversion following such a change of control if the purchasers do not require such repayment. The August 2013 SPA, Tranche I Notes and Tranche II Notes include covenants regarding payment of interest, maintenance of the Company’s listing status, limitations on debt and on certain liens, maintenance of corporate existence, and filing of SEC reports. The 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 August 2013 SPA, Tranche I Notes and Tranche II Notes, with default interest rates and associated cure periods applicable to the covenant.
As of June 30, 2014 and December 31, 2013, the related party convertible notes outstanding under the Tranche I and Tranche II Notes were $46.2 million and $37.9 million, respectively, net of debt discount of $31.6 million and $6.3 million, respectively. The debt discount is the result of the bifurcation of the conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions associated with the outstanding debt.
Rule 144A Convertible Notes Sold to Related Parties
As discussed above under “Rule 144A Convertible Note Offering”, the Company sold and issued $75.0 million aggregate principal amount of 144A Notes pursuant to Rule 144A of the Securities Act. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris pursuant to the Total Purchase Agreement for 144A Notes issued in the transaction, Amyris used approximately $9.7 million of the net proceeds to repay such amount of previously issued notes held by Total, which represented the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering. As a result of the settlement of the $9.7 million Total convertible notes, the Company recorded a loss from extinguishment of debt of $1.1 million.
Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder.
As of June 30, 2014 the related party convertible notes outstanding under the 144A Notes were $14.0 million, net of discount of $10.7 million.
As of June 30, 2014 and December 31, 2013 the total related party convertible notes outstanding were $100.5 million and $89.5 million, respectively, net of discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively.
Loans Payable
In December 2009, the Company entered into a loans payable agreement with the lessor of its Emeryville, California pilot plant under which it borrowed a total of $0.3 million, bearing an interest rate of 10.0% per annum and to be repaid over a period of 96 months. As of June 30, 2014 and December 31, 2013, there was no amount outstanding under the loan. In June 2013, as part of the April 30, 2013 amendment entered into regarding the Company's operating lease for its headquarters, the Company recorded the elimination of this loan payable as a lease incentive and recorded approximately $0.2 million to deferred rent liability in the condensed consolidated balance sheet. The deferred rent liability is being amortized to expense over the remaining lease term.
In July 2012, the Company entered into a Note of Bank Credit and a Fiduciary Conveyance of Movable Goods Agreement (together, referred to as the "July 2012 Bank Agreements") with each of Nossa Caixa Desenvolvimento (or “Nossa Caixa”) and Banco Pine S.A. (or “Banco Pine”). Under the July 2012 Bank Agreements, the Company pledged certain farnesene production assets as collateral for the loans of R$52.0 million. The Company's total acquisition cost for such pledged assets was approximately R$68.0 million (approximately US$30.9 million based on the exchange rate as of June 30, 2014). The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements. Under the July 2012 Bank Agreements, the Company could borrow an aggregate of R$52.0 million (approximately US$23.6 million based on the exchange rate as of June 30, 2014) as financing for capital expenditures relating to the Company's manufacturing facility located in Brotas, Brazil. Specifically, Banco Pine, agreed to lend R$22.0 million and Nossa Caixa agreed to lend R$30.0 million. The funds for the loans are provided by BNDES, but are guaranteed by the lenders. The loans have a final maturity date of July 15, 2022 and bear a fixed interest rate of 5.5% per year. The loans are also subject to early maturity and delinquency charges upon occurrence of certain events including interruption of manufacturing activities at the Company's manufacturing facility in Brotas, Brazil for more than 30 days, except during sugarcane off-season. For the first two years that the loans are outstanding, the Company is required to pay interest only on a quarterly basis. After August 15, 2014, the Company is required to pay equal monthly installments of both principal and interest for the remainder of the term of the loans. As of June 30, 2014 and December 31, 2013, a principal amount of $23.6 million and $22.2 million, respectively, was outstanding under these loan agreements.
In October 2013, the Company borrowed $0.6 million from a third party lender to pay for the Company's current insurance premiums. The loan is payable in nine monthly installments of principal and interest. Interest accrues at a rate of 3.24% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was zero and $0.4 million, respectively.
In February 2014, the Company borrowed $0.2 million from a third party lender to pay for the Company's consolidated VIE's current insurance premiums. The loan is payable in ten monthly installments of principal and interest. Interest accrues at a rate of 5.95% per annum. As of June 30, 2014 and December 31, 2013, the outstanding unpaid loan balance was $0.1 million and zero, respectively.
In March 2013, the Company entered into a one-year-term export financing agreement with ABC for approximately $2.5 million to fund exports through March 2014. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the loan was fully paid.
In March 2014, the Company entered into an additional one-year-term export financing agreement with ABC for approximately $2.2 million to fund exports through March 2015. This loan is collateralized by future exports from the Company's subsidiary in Brazil. As of June 30, 2014, the principal amount outstanding under this agreement was $2.2 million.The Company is also a parent guarantor for the payment of the outstanding balance under these loan agreements.
Letters of Credit
In June 2012, the Company entered into a letter of credit agreement for $1.0 million under which it provided a letter of credit to the landlord of its headquarters in Emeryville, California, in order to cover the security deposit on the lease. This letter of credit is secured by a certificate of deposit. Accordingly, the Company has $1.7 million and $0.9 million as restricted cash as of June 30, 2014 and December 31, 2013.
Future minimum payments under the debt agreements as of June 30, 2014 are as follows (in thousands):
Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
2014 (remaining six months)	$	744		$	1,891		$	4,080		$	2,539
2015	1,606			4,020			4,114			15,426
2016	1,606			4,020			3,935			20,301
2017	58,849			28,715			3,772			7,822
2018	74,485			15,685			3,612			472
Thereafter	75,825			56,798			11,751			131
Total future minimum payments	213,115			111,129			31,264			46,691
Less: amount representing interest(1)	(112,635		)	(53,225		)	(5,265		)	(8,719		)
Present value of minimum debt payments	100,480			57,904			25,999			37,972
Less: current portion	—			—			(5,218		)	(4,705		)
Noncurrent portion of debt	$	100,480		$	57,904		$	20,781		$	33,267
______________
(1) Including debt discount of $83.9 million related to the embedded derivative 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.

Commitments_and_Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Commitments and Contingencies	'
	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 $1.3 million and $1.4 million for the three months ended June 30, 2014 and 2013, respectively, and was $2.7 million and $2.1 million for the six months ended June 30, 2014 and 2013, respectively.
	Future minimum payments under the Company's lease obligations as of June 30, 2014, are as follows (in thousands):
	Years ending December 31:	Capital			Operating		Total Lease Obligations
		Leases			Leases
	2014 (remaining six months)	$	557		$	3,182	$	3,739
	2015	462			6,606		7,068
	2016	159			6,614		6,773
	2017	—			6,588		6,588
	2018	—			6,675		6,675
	Thereafter	—			32,320		32,320
	Total future minimum lease payments	1,178			$	61,985	$	63,163
	Less: amount representing interest	(68		)
	Present value of minimum lease payments	1,110
	Less: current portion	(882		)
	Long-term portion	$	228
	Guarantor Arrangements
	The Company has agreements to indemnify its officers and directors for certain events or occurrences while the officers 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 June 30, 2014 and December 31, 2013.
	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$2.7 million based on the exchange rate as of June 30, 2014).
	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$11.3 million based on the exchange rate as of June 30, 2014). 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 a $0.8 million and $0.7 million as restricted cash as of June 30, 2014 and December 31, 2013, respectively.
	The Company entered into loan agreements and security agreement where 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$30.9 million based on the exchange rate as of June 30, 2014). 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 June 30, 2014, the loan was fully paid. The Company has entered into another export financing agreement with the same bank for approximately $2.2 million for a one year term to fund exports through March 2015. 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.
	Under an operating lease agreement for its office facilities in Brazil, which commenced on November 15, 2011, the Company is required to maintain restricted cash or letters of credit equal to 3 months of rent of approximately R$0.2 million (approximately US$0.1 million based on the exchange rate as of June 30, 2014) in the aggregate as a guarantee that the Company will meet its performance obligations under such operating lease agreement.
	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 (referred to as 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 (referred to as the "Security Agreement"), the Company had previously granted a security interest in favor of Total to secure the obligations of the Company under certain convertible promissory 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 convertible promissory notes issued pursuant to the Total Purchase Agreement and held by Total (referred to as the “Total Securities”), 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 Securities 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 the Total Securities 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 Interest"), Amyris agreed to exchange the $69.0 million outstanding Total unsecured convertible 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 Replacement Notes and grant a security interest to Total in and lien on all Amyris’s rights, title and interest in and to Amyris’s shares in the capital of the JVCO. Following execution of the JV Documents, all notes that have been issued and that remain to be issued in connection with the third closing under the Total Purchase Agreement (up to $21.7 million in the aggregate; with $10.85 million in principal amount of such remaining notes issued on July 31, 2014, and an additional $10.85 million in principal amount of such remaining notes to be issued by January 31, 2015) are senior secured convertible notes instead of senior unsecured convertible notes.
	In March 2014, the Company and Hercules Technology Growth Capital, Inc. entered into a loan and security agreement to make available to the Company a loan in the aggregate principal amount of up to $25.0 million (see Note5 "Debt"). Loans under the facility are secured by various liens, including a lien on certain Company intellectual property. In connection with the Hercules loan, the Company agreed to certain customary representations and warranties and covenants, as well as certain covenants with respect to obtaining additional financing as described above and performance covenants related to revenues and cash flows starting with the third quarter of 2014. If the Company had not satisfied the equity financing covenant, a forbearance fee of $10.0 million would have become due and payable at the end of the initial term of the loan. The Company borrowed the full amount available under the facility and received the funds on March 31, 2014. In June 2014, the Company and Hercules entered into the Hercules Amendment of the Loan and Security Agreement entered into on March 29, 2014. Pursuant to the Hercules Amendment, the parties agreed to 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. Under the Hercules Amendment, in connection with the amendments and modification or removal of the covenants described above, the Company agreed to include a new covenant requiring the Company to maintain unrestricted, unencumbered cash in an amount equal to at least 50% of the remaining principal amount then outstanding under the Hercules Loan Facility and borrow an additional tranche of $5.0 million, subject to obtaining specified third party consents under outstanding convertible promissory notes. The Hercules Loan Facility is collateralized by liens on the Company's assets, including on certain Company intellectual property.
	Purchase Obligations
	As of June 30, 2014, the Company had $6.8 million in purchase obligations which included $5.9 million in non-cancellable contractual obligations and construction commitments, of which $2.4 million 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.
	In May 2013, a securities class action complaint was filed against the Company and its CEO, John G. Melo, in the U.S. District Court for the Northern District of California. In October 2013, the lead plaintiffs filed a consolidated amended complaint. The complaint, as amended, sought unspecified damages on behalf of a purported class that would comprise all individuals who acquired the Company's common stock between April 29, 2011 and February 8, 2012. The complaint alleged securities law violations based on the Company's commercial projections during that period. In December 2013, the Company filed a motion to dismiss the complaint. In March 2014, the court issued an order granting the Company's motion to dismiss with leave to amend the complaint. The plaintiffs declined to amend their complaint further and, on June 12, 2014, the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.
	In August 2013, a complaint entitled Steve Shannon, derivatively on behalf of Amyris, Inc. v. John G. Melo et al and Amyris, Inc., was filed against the Company as nominal defendant in the United States District Court for the Northern District of California. The lawsuit sought unspecified damages on behalf of the Company from certain of its current and former officers, directors and employees and alleges these defendants breached their fiduciary duties to the Company and unjustly enriched themselves by making allegedly false and misleading statements and omitting certain material facts in the Company's securities filings. Because this purported stockholder derivative action is based on substantially the same facts as the securities class action described above, the two actions were related and were heard by the same judge. On June 23, 2014, following the dismissal of the related class action (discussed above), the court issued an order (based on stipulation of the parties) dismissing the action with prejudice.
	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.

Joint_Ventures_and_Noncontroll

Joint Ventures and Noncontrolling Interest	6 Months Ended
	Jun. 30, 2014
Joint Ventures and Noncontrolling Interest [Abstract]	'
Joint Ventures and Noncontrolling Interest	'
	Joint Ventures and Noncontrolling Interest
	Novvi S.A.
	In June 2011, the Company entered into joint venture agreements with Cosan Combustíveis e Lubrificantes S.A. and Cosan S.A. Industria e Comércio (such Cosan entities, collectively or individually, “Cosan”), related to the formation of a joint venture to focus on the worldwide development, production and commercialization of base oils made from Biofene for the automotive, commercial and industrial lubricants markets (referred to as the "Original JV Agreement"). The parties originally envisioned operating their joint venture through Novvi S.A., a Brazilian entity jointly owned by Cosan and Amyris Brasil.
	Under the Original JV Agreement and related agreements, the Company and Cosan each owned 50% of the Novvi S.A. and each party would share equally in any costs and any profits ultimately realized by Novvi S.A. The joint venture agreement had an initial term of 20 years from the date of the Original JV Agreement, subject to earlier termination by mutual written consent or by a non-defaulting party in the event of specified defaults by the other party. The shareholders' agreement had an initial term of 10 years from the date of the agreement, subject to earlier termination if either the Company or Cosan ceases to own at least 10% of the voting stock of Novvi S.A. Since its formation, Novvi S.A. had minimal operating activities while the Company and Cosan continued to determine and finalize the strategy and operating activities for the joint venture. Upon determination by the Company and Cosan that the joint venture should be operated out of a U.S. entity, the operating activities of Novvi S.A. ceased. The Company has identified that Novvi S.A. is a VIE and determined that the power to direct activities, which most significantly impact the economic success of the joint venture, is equally shared between the Company and Cosan. Accordingly, the Company is not the primary beneficiary and therefore accounts for its investment in Novvi S.A. under the equity method of accounting.
	In March 2013, the Company, Amyris Brasil and Cosan entered into a termination agreement to terminate the Original JV Agreement. In addition, Amyris Brasil agreed to sell, its 50% ownership in Novvi S.A. to Cosan for approximately R$22,000 (approximately US$9,989 based on the exchange rate as of June 30, 2014), which represented the current value of its 50% equity ownership in Novvi S.A., a now-dormant company. Upon the consummation of the transaction with the shares transferring from Amyris Brasil to Cosan, the Novvi S.A. shareholders agreement automatically terminated.
	Novvi LLC
	In September 2011, the Company and Cosan US, Inc. (or "Cosan U.S.") formed Novvi LLC, a U.S. entity that is jointly owned by the Company and Cosan U.S. (or "Novvi"). 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 (referred to as the "Operating Agreement"), which sets forth the governance procedures for Novvi and the joint venture and the parties' initial contribution. The Company also entered into an IP License Agreement with Novvi (referred to as the "IP License Agreement") under which the Company granted Novvi (i) an exclusive (subject to certain limited exceptions for the Company), worldwide, royalty-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. will each own 50% of Novvi and each party will share 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 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. is obligated to fund its 50% ownership share of Novvi in cash in the amount of $10.0 million and the Company is 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 has been agreed upon by Cosan U.S. and Amyris 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 subscribed and purchased 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 of receiving additional Membership Units in Novvi. Each member owns 50% of Novvi's issued and outstanding Membership Units. The Company recorded its investment in Novvi of $2.1 million under "Other Assets" in the condensed consolidated balance sheet.
	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 “Other income (expense), net” in the condensed consolidated statements of operations. For the three and six months ended June 30, 2014, the Company recorded $0.2 million of its share of Novvi's net loss. The Company recorded collaboration revenue of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi.
	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 (referred to as a “Go Decision”), (ii) Total elects to not continue its participation in the R&D Program and JVCO (referred to as 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 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 June 30, 2014). 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. Under the equity method, the Company's share of profits and losses are included in "Other income (expense), net" in the condensed consolidated statements of operations. No later than six months prior to July 31, 2016, the Company and Total shall 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.
	SMA Indústria Química S.A.
	In April 2010, the Company established SMA Indústria Química (or "SMA"), a joint venture with Sao Martinho S.A. (or "SMSA") (formerly Usina São Martinho S.A.), to build a production facility in Brazil. SMA is located at the SMSA 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 SMSA 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 would fund the construction costs of the new facility and SMSA would reimburse the Company up to R$61.8 million (approximately US$28.1 million based on the exchange rate as of June 30, 2014) of the construction costs after SMA commences production. After commercialization, the Company would market and distribute Amyris renewable products produced by SMA and SMSA 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 SMSA 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 SMSA’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 SMSA, then SMSA has the right to acquire the Company’s interest in SMA. If SMSA becomes controlled, directly or indirectly, by a competitor of the Company, then the Company has the right to sell its interest in SMA to SMSA. 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 variable interest entity (or "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 SMSA’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 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 SMSA which updated and documented certain preexisting business plan requirements related to the start-up of construction at the joint venture operated plant and set 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, which shall occur no later than March 31, 2017, and (ii) the extension of an option held by SMSA 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.
	Glycotech
	In January 2011, the Company entered into a production service agreement (referred to as 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 (referred to as 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 June 30, 2014, the carrying amounts of the consolidated VIE'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 June 30, 2014, the assets include $22.9 million in property, plant and equipment, $4.1 million in other assets and $0.5 million in current assets. The liabilities include $0.2 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.
		June 30,			December 31,
	(In thousands)	2014			2013
	Assets	$	27,509		$	25,730
	Liabilities	$	421		$	229
	The change in noncontrolling interest for the six months ended June 30, 2014 and 2013, is summarized below (in thousands):
		2014			2013
	Balance at January 1	$	(584	)	$	(877	)
	Foreign currency translation adjustment	(42		)	54
	Gain (loss) attributable to noncontrolling interest	(60		)	261
	Balance at June 30	$	(686	)	$	(562	)

Significant_Agreements

Significant Agreements	6 Months Ended
	Jun. 30, 2014
Significant Agreements [Abstract]	'
Significant Agreements	'
	Significant Agreements
	Collaboration Agreement with Michelin and Braskem
	In September 2011, the Company entered into a collaboration agreement with Manufacture Francaise des Pneumatiques 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 agreed to pay an upfront payment to the Company of $5.0 million.
	In June 2014, the Company entered into a collaboration agreement with Braskem S.A. and Braskem America, Inc. (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 (3) 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 June 30, 2014, the $5.0 million from Michelin is still recorded as "Deferred Revenue" in the condensed consolidated balance sheet .
	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 revenue for the three and six months ended June 30, 2014 of $0.8 million and $1.0 million, respectively, and zero for the three and six months ended June 30, 2013, respectively, under this agreement.
	Collaboration Partner Master Collaboration and Joint Development Agreement
	In March 2013, the Company entered into a Master Collaboration Agreement with the collaboration partner to establish a collaboration for the development and commercialization of multiple renewable flavors and fragrances (referred to as "F&F") 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 F&F 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 provides 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. The initial payment of $10.0 million was received by the Company in March 2013 and the second payment was received in March 2014. The Company recognized revenue under this agreement for the three months ended June 30, 2014 and 2013, of $2.5 million and $2.8 million, respectively, and for the six months ended June 30, 2014 and 2013, of $5.0 million and $3.2 million, respectively. The agreement contemplates 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.
	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 will pay the Company $4.0 million in two (2) equal installments of $2.0 million. The first installment was paid on April 30, 2014 and the second installment is 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.

Goodwill_and_Intangible_Assets

Goodwill and Intangible Assets	6 Months Ended
	Jun. 30, 2014
Goodwill and Intangible Assets Disclosure [Abstract]	'
Goodwill and Intangible Assets	'
	Goodwill and Intangible Assets
	The following table presents the components of the Company's intangible assets (in thousands):
				30-Jun-14								31-Dec-13
		Useful Life in Years		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value			Gross Carrying Amount			Accumulated Amortization			Net Carrying Value
	In-process research and development	Indefinite		$	8,560	$	—		$	8,560		$	8,560		$	—		$	8,560
	Acquired licenses and permits	2		772		(772		)	—			772			(772		)	—
	Goodwill	Indefinite		560		—			560			560			—			560
				$	9,892	$	(772	)	$	9,120		$	9,892		$	(772	)	$	9,120
	The following table presents the activity of intangible assets for the six months ended June 30, 2014 (in thousands):
			31-Dec-13														30-Jun-14
			Net Carrying Value			Additions				Adjustments			Amortization				Net Carrying Value
	In-process research and development		$	8,560		$	—			$	—		$	—			$	8,560
	Acquired licenses and permits		—			—				—			—				—
	Goodwill		560			—				—			—				560
			$	9,120		$	—			$	—		$	—			$	9,120
	The intangible assets acquired through the Draths Corporation acquisition in October 2011 of in-process research and development of $8.6 million and goodwill of $0.6 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 year in which the related impairment charges occur. As of June 30, 2014 and December 31, 2013, no impairment of the goodwill and intangible assets was recorded.
	Acquired licenses and permits are amortized using a straight-line method over its estimated useful life. Amortization expense for this intangible was zero and $32,000 for the six months ended June 30, 2014 and 2013, respectively. As of June 30, 2014, acquired licenses and permits were fully amortized.

Stockholders_Deficit

Stockholders' Deficit	6 Months Ended
	Jun. 30, 2014
Stockholders' Equity Note [Abstract]	'
Stockholders' Deficit	'
	Stockholders’ Deficit
	Private Placement
	In March 2014, the Company completed a private placement of 943,396 shares of its common stock at a price of $4.24 per share for aggregate proceeds of $4.0 million (see Note 8, "Significant Agreements").
	Evergreen Shares for 2010 Equity Plan and 2010 ESPP
	In January 2014, the Company's Board of Directors (or "Board") approved an increase to the number of shares available for issuance under the Company's 2010 Equity Incentive Plan (or "Equity Plan") and the 2010 Employee Stock Purchase Plan (or "ESPP"). These shares represent an automatic annual increase in the number of shares available for issuance under the Equity Plan and the ESPP of 3,833,141 and 766,628, respectively. These increases equal 5% and 1%, respectively, of 76,662,812 shares, the total outstanding shares of the Company’s common stock as of December 31, 2013. This automatic increase was effective as of January 1, 2014. Shares available for issuance under the Equity Plan and ESPP were initially registered on a registration statement on Form S-8 filed with the Securities and Exchange Commission on October 1, 2010 (Registration No. 333-169715). The Company filed registration statements on Form S-8 on April 14, 2014 (Registration No. 333-195259) with respect to the shares added by the automatic increase on January 1, 2014.
	Common Stock
	As of June 30, 2014, the Company was authorized to issue 300,000,000 shares of common stock pursuant to the Company’s amended and restated certificate of incorporation. Holders of the Company’s common stock are entitled to dividends as and when declared by the Board, subject to the rights of holders of all classes of stock outstanding having priority rights as to dividends. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.
	Preferred Stock
	Pursuant to the Company’s amended and restated certificate of incorporation, the Company is authorized to issue 5,000,000 shares of preferred stock. The Board has the authority, without action by its stockholders, to designate and issue shares of preferred stock in one or more series and to fix the rights, preferences, privileges and restrictions thereof. As of June 30, 2014 and December 31, 2013, the Company had no convertible preferred stock outstanding.
	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 June 30, 2014.
	In October 2013, in connection with the issuance of the Temasek Tranche I Notes (see Note 5, "Debt"), the Company issued 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 remain unexercised and outstanding as of June 30, 2014.
	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 six months ended June 30, 2014 and 2013, no warrants were exercised through the cashless exercise provision.

StockBased_Compensation

Stock-Based Compensation	6 Months Ended
	Jun. 30, 2014
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]	'
Stock-Based Compensation Plans	'
	Stock-Based Compensation
	The Company’s stock option activity and related information for the six months ended June 30, 2014 was as follows:
				Number			Weighted-				Weighted-Average		Aggregate
				Outstanding			Average				Remaining		Intrinsic
							Exercise				Contractual		Value
							Price				Life (Years)
													(in thousands)
	Outstanding - December 31, 2013			8,409,605			$	7.39			7.4		$	12,393
		Options granted		2,909,183			$	3.51
		Options exercised		(337,110	)		$	3.06
		Options cancelled		(485,971	)		$	7.09
	Outstanding - June 30, 2014			10,495,707			$	6.47			7.72		$	3,709
	Vested and Expected to vest after June 30, 2014			9,590,575			$	6.72			7.58		$	3,326
	Exercisable at June 30, 2014			4,554,010			$	9.29			6.13		$	1,027
	The aggregate intrinsic value of options exercised under all option plans was $33,000 and $0.1 million for the three months ended June 30, 2014 and 2013, respectively, and was $0.5 million and $0.3 million for the six months ended June 30, 2014 and 2013, 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 six months ended June 30, 2014 was as follows:
			RSUs			Weighted-Average Grant-Date Fair Value				Weighted Average Remaining Contractual Life (Years)
	Outstanding - December 31, 2013		2,316,437			$	4.3			0.88
	Awarded		1,049,300			$	3.51			—
	Vested		(1,158,585	)		$	4.68			—
	Forfeited		(98,863	)		$	3.17			—
	Outstanding - June 30, 2014		2,108,289			$	3.75			1.39
	Expected to vest after June 30, 2014		1,803,053			$	3.75			1.31
	The following table summarizes information about stock options outstanding as of June 30, 2014:
		Options Outstanding									Options Exercisable
	Exercise Price	Number of Options			Weighted-		Weighted-Average Exercise Price				Number of Options			Weighted-Average Exercise Price
					Average
					Remaining
					Contractual Life
					(Years)
	$0.10—$2.79	1,580,682			8.2		$	2.66			476,896			$	2.52
	$2.81—$2.94	1,056,600			8.94		$	2.88			279,097			$	2.87
	$2.96—$3.44	945,057			8.55		$	3.14			304,429			$	3.07
	$3.51—$3.51	2,489,199			9.75		$	3.51			—			$	—
	$3.55—$3.93	1,700,908			5.75		$	3.88			1,247,160			$	3.89
	$4.06—$16.00	1,555,854			5.94		$	10.11			1,281,705			$	9.88
	$16.50—$24.50	724,345			5.97		$	20.1			625,057			$	20.11
	$25.43—$25.43	15,000			7.07		$	25.43			15,000			$	25.43
	$26.84—$26.84	368,062			6.64		$	26.84			264,666			$	26.84
	$30.17—$30.17	60,000			6.71		$	30.17			60,000			$	30.17
	$0.10—$30.17	10,495,707			7.72		$	6.47			4,554,010			$	9.29
	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 June 30,								Six Months Ended June 30,
		2014				2013				2014				2013
	Research and development	$	909			$	1,049			$	1,707			$	2,296
	Sales, general and administrative	2,774				3,936				5,490				6,882
	Total stock-based compensation expense	$	3,683			$	4,985			$	7,197			$	9,178
	As of June 30, 2014, there was unrecognized compensation expense of $15.0 million related to stock options, and the Company expects to recognize this expense over a weighted average period of 2.93 years. As of June 30, 2014, there was unrecognized compensation expense of $4.9 million related to RSUs, and the Company expects to recognize this expense over a weighted average period of 2.07 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 June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Expected dividend yield	—	%		—	%		—	%		—	%
	Risk-free interest rate	2	%		1	%		2	%		1	%
	Expected term (in years)	6.09			6.1			6.1			6.1
	Expected volatility	75	%		82	%		75	%		82	%
	Expected Dividend Yield—The Company has never paid dividends and does not expect to pay dividends.
	Risk-Free Interest Rate—The risk-free interest rate was based on the market yield currently available on United States Treasury securities with maturities approximately equal to the option’s expected term.
	Expected Term—Expected term represents the period that the Company’s stock-based awards are expected to be outstanding. The Company’s assumptions about the expected term have been based on that of companies that have similar industry, life cycle, revenue, and market capitalization and the historical data on employee exercises.
	Expected Volatility—The expected volatility is based on a combination of historical volatility for the Company's stock and the historical stock volatilities of several of the Company’s publicly listed comparable companies over a period equal to the expected terms of the options, as the Company does not have a long trading history.
	Forfeiture Rate—The Company estimates its forfeiture rate based on an analysis of its actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior, and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated by the Company, the Company may be required to record adjustments to stock-based compensation expense in future periods.
	Each of the inputs discussed above is subjective and generally requires significant management and director judgment.
	Nonemployee Stock–Based Compensation
During the three months ended June 30, 2014 and 2013, there were no options granted to nonemployees, and for each of the six months ended June 30, 2014 and 2013, the Company granted options to purchase 20,000 shares of its common stock, respectively, to nonemployees in exchange for services. Compensation expense of $0.1 million and $8,000 was recorded for the three months ended June 30, 2014 and 2013, respectively, and $0.1 million and $22,000 was recorded for the six months ended June 30, 2014 and 2013, respectively, for stock-based options granted to nonemployees. The nonemployee options were valued using the Black-Scholes option pricing model.
During the three and six months ended June 30, 2014 and 2013, no restricted stock units, were granted to nonemployees. Stock-based compensation expense of $12,000 and $15,000 was recorded by the Company for the three months ended June 30, 2014 and 2013, respectively, and $9,000 and $39,000 for the six months ended June 30, 2014 and 2013, respectively, for the restricted stocks granted to nonemployees.
The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:
	Three Months Ended June 30,						Six Months Ended June 30,
	2014			2013			2014			2013
Expected dividend yield	—	%		—	%		—	%		—	%
Risk-free interest rate	2	%		2	%		2	%		2	%
Expected term (in years)	5.8			6.1			5.94			6.4
Expected volatility	75	%		82	%		76	%		83	%

Employee_Benefit_Plan

Employee Benefit Plan	6 Months Ended
	Jun. 30, 2014
Compensation and Retirement Disclosure [Abstract]	'
Employee Benefit Plan	'
	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 (referred to as 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 six months ended June 30, 2014 was $0.1 million and $0.2 million, respectively.

Related_Party_Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2014
Related Party Transactions [Abstract]	'
Related Party Transactions	'
	Related Party Transactions
	Letter Agreements with Total
	In March 2013 and March 2014, respectively, the Company entered into letter agreements with Total that reduced the respective conversion prices of certain convertible promissory notes issuable under the Total Purchase Agreement, as described under “Related Party Convertible Notes” in Note 5, "Debt."
	Related Party Financings
	In March 2013, the Company completed a private placement of 1,533,742 shares of its common stock to an existing stockholder, Biolding Investment SA ("Biolding"), at a price of $3.26 per share for aggregate proceeds of $5.0 million. This private placement represented the final tranche of Biolding's preexisting contractual obligation to fund $15.0 million upon satisfaction by the Company of certain criteria associated with the commissioning of the Company's production plant in Brotas, Brazil.
	In June 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $10.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."
	In July 2013, the Company sold and issued a 1.5% Senior Unsecured Convertible Note to Total in the face amount of $20.0 million with a March 1, 2017 maturity date pursuant to the Total Purchase Agreement as discussed above under “Related Party Convertible Notes” in Note 5, “Debt."
	In August 2013, the Company entered into a securities purchase agreement by and among the Company, Total and Temasek, each a beneficial owner of more than 5% of the Company's existing common stock at the time of the transaction, for a private placement of convertible promissory notes in an aggregate principal amount of $73.0 million. The initial closing of the August 2013 Financing was completed in October 2013 for the sale of approximately$42.6 million of these Tranche I Notes and the second closing of the August 2013 Financing for the sale of approximately $30.4 million of these Tranche II Notes was completed in January 2014.
	In September 2013, the Company entered into a bridge loan agreement with an existing investor to provide additional cash availability of up to $5.0 million as needed before the initial closing of the August 2013 Financing. The Company did not use this facility and it expired in October 2013 in accordance with its terms.
	In October 2013, the Company sold and issued a senior secured promissory note to Temasek for a bridge loan of $35.0 million. The note was due on February 2, 2014 and accrued interest at a rate of 5.5% each four months from October 4, 2013 (with a rate of 2% per month if a default occurred). The note was cancelled as payment for the investor’s purchase of Tranche I Notes in the August 2013 Financing.
	In December 2013, the Company agreed to issue to Temasek $25.0 million of Tranche II Notes for cash. Total purchased approximately $6.0 million of Tranche II Notes through cancellation of the same amount of principal of previously outstanding convertible promissory notes held by Total (in respect of Total’s preexisting contractual right to maintain its pro rata ownership position through such cancellation). Such financing transactions closed in January 2014 (see Note 5, "Debt").
	In December 2013, the Company agreed (i) to exchange the $69.0 million outstanding Total unsecured convertible notes and issue a replacement 1.5% senior secured convertible notes, in principal amounts equal to the principal amount of each cancelled note (see Note 5, "Debt") and (ii) that all notes issued in connection with a third closing under the Total Purchase Agreement will be senior secured convertible notes instead of senior unsecured convertible notes (see Note 5, "Debt").
	In May 2014, the Company sold and issued 144A Notes pursuant to the Rule 144A Convertible Note Offering. In connection with obtaining a waiver from one of its existing investors, Total, of its preexisting contractual right to exchange certain senior secured convertible notes previously issued by Amyris for new notes issued in the Rule 144A Convertible Note Offering, Amyris used approximately $9.7 million of the net proceeds of the Rule 144A Convertible Note Offering to repay such amount of previously issued notes (representing the amount of notes purchased by Total from the Initial Purchaser under the Rule 144A Convertible Note Offering). Additionally, Foris Ventures, LLC (a fund affiliated with John Doerr) and Temasek each participated in the Rule 144A Convertible Note Offering and purchased $5.0 million and $10.0 million, respectively, of the convertible promissory notes sold thereunder (see Note 5, “Debt").
	As of June 30, 2014 and December 31, 2013, convertible notes with related parties were outstanding in aggregate principal of $100.5 million and $89.5 million, respectively, net of debt discount of $55.3 million and $23.9 million, respectively. The Company recorded a loss from extinguishment of debt from the settlement, exchange and cancellation of related party convertible notes for the three months ended June 30, 2014 and 2013, of $1.1 million and zero, respectively, and $10.5 million and zero for the six months ended June 30, 2014 and 2013, respectively (see Note 5, "Debt").
	The fair value of the derivative liability related to the related party convertible notes as of June 30, 2014 and December 31, 2013 is $107.2 million and $116.8 million, respectively. The Company recognized for the three months ended June 30, 2014 and 2013, a $4.0 million loss from change in fair value of the derivative instruments and $1.4 million gain from change in fair value of the derivative instruments, respectively, and $53.1 million and $2.5 million gain from change in fair value of the derivative instruments for the six months ended June 30, 2014 and 2013, respectively, related to these derivative liabilities (see Note 3, "Fair Value of Financial Instruments").
	Related Party Revenue
	The Company recognized related party revenue from Novvi of zero and $0.3 million for the three months ended June 30, 2014 and 2013, respectively, and zero and $2.8 million for the six months ended June 30, 2014 and 2013, respectively, from the research and development activities that it has performed on behalf of Novvi. The related party accounts receivables from Novvi as of June 30, 2014 and December 31, 2013, was $20,604 and $0.3 million, respectively.
	The Company recognized related party revenue from Total of $30,625 and $32,441 for the three months ended June 30, 2014 and 2013, respectively, and $33,250 and $35,294 for the six months ended June 30, 2014 and 2013, respectively, from product sales. The related party accounts receivables from Total as of June 30, 2014 and December 31, 2013, was $30,625 and $0.2 million, respectively.
	Joint Venture
	In November 2013, the Company and Total formed JVCO as discussed above under “Joint Venture and Noncontrolling Interest” in Note 7.
	Pilot Plant Agreements
	In May 2014, the Company received the final consents necessary for the Pilot Plant Services Agreement ("Pilot Plant Services Agreement") and a Sublease Agreement (the "Sublease Agreement"), each dated as of April 4, 2014 (collectively the “Pilot Plant Agreements”), between the Company and Total for a term of 5 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. As of June 30, 2014, the Company received $0.3 million in cash under the Pilot Plant Agreements from Total which was recorded as "Other Current Liability" on the condensed consolidated balance sheet.

Income_Taxes

Income Taxes	6 Months Ended
	Jun. 30, 2014
Income Tax Disclosure [Abstract]	'
Income Taxes	'
	Income Taxes
	For the three months ended June 30, 2014 and 2013, the Company recorded a provision for income taxes of $0.1 million and $0.2 million, respectively, and $0.2 million and $0.5 million for the six months ended June 30, 2014 and 2013, respectively. The provision for income taxes for the six months ended June 30, 2014 and 2013 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.
	As of June 30, 2014, the US Internal Revenue Service (the "IRS") has 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.

Reporting_Segments

Reporting Segments	6 Months Ended
	Jun. 30, 2014
Segment Reporting [Abstract]	'
Reporting Segments	'
	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 June 30,				Six Months Ended June 30,
		2014		2013		2014		2013
	United States	$	2,815	$	4,458	$	4,788	$	10,022
	Brazil	1,402		1,259		2,050		2,077
	Europe	2,985		4,005		6,338		4,230
	Asia	2,105		1,127		2,172		2,389
	Total	$	9,307	$	10,849	$	15,348	$	18,718
	Long-Lived Assets
		June 30, 2014		December 31, 2013
	United States	$	49,628	$	54,015
	Brazil	90,375		85,891
	Europe	653		685
	Total	$	140,656	$	140,591

Comprehensive_Income_Loss

Comprehensive Income (Loss)	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Comprehensive Income (Loss)	'
	Comprehensive Income (Loss)
	Comprehensive income (loss) represents all changes in stockholders’ equity (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):
		June 30, 2014			31-Dec-13
	Foreign currency translation adjustment, net of tax	$	(15,634	)	$	(20,087	)
	Total accumulated other comprehensive loss	$	(15,634	)	$	(20,087	)

Net_Income_Loss_Attributable_t

Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share	6 Months Ended
	Jun. 30, 2014
Earnings Per Share [Abstract]	'
Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share	'
	Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share
	The Company computes net income (loss) per share in accordance with ASC 260, “Earnings per Share.” Basic net income (loss) per share of common stock is computed by dividing the Company’s net income (loss) attributable to Amyris, Inc. common stockholders by the weighted average number of shares of common stock outstanding during the period. Diluted net income (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 months ended June 2014 and 2013 and for the six months ended June 30, 2013, 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 are the same.
	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 June 30,							Six Months Ended June 30,
		2014				2013			2014			2013
	Numerator:
	Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)		$	(38,876	)	$	(19,094	)	$	(71,490	)
	Interest on convertible debt	—				—			3,169			—
	Accretion of debt discount	—				—			2,518			—
	Gain from change in fair value of derivative instruments	—				—			(59,995		)	—
	Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(35,479	)		$	(38,876	)	$	(73,402	)	$	(71,490	)
	Denominator:
	Weighted average shares of common stock outstanding for basic EPS	78,604,692				75,959,228			77,722,437			74,640,314
	Basic loss per share	$	(0.45	)		$	(0.51	)	$	(0.25	)	$	(0.96	)
	Weighted average shares of common stock outstanding	78,604,692				75,959,228			77,722,437			74,640,314
	Effect of dilutive securities:
	Convertible promissory notes	—				—			32,909,641			—
	Weighted common stock equivalents	—				—			32,909,641			—
	Diluted weighted-average common shares	78,604,692				75,959,228			110,632,078			74,640,314
	Diluted loss per share	$	(0.45	)		$	(0.51	)	$	(0.66	)	$	(0.96	)
	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 June 30,						Six Months Ended June 30,
		2014			2013			2014		2013
	Period-end stock options to purchase common stock	10,495,707			8,803,300			10,495,707		8,803,300
	Convertible promissory notes	69,727,211			13,617,144			36,643,102		13,617,144
	Period-end common stock subject to repurchase	—			1			—		1
	Period-end common stock warrants	1,021,087			21,087			1,021,087		21,087
	Period-end restricted stock units	2,108,289			2,770,516			2,108,289		2,770,516
	Total	83,352,294			25,212,048			50,268,185		25,212,048

Subsequent_Events

Subsequent Events	6 Months Ended
	Jun. 30, 2014
Subsequent Events [Abstract]	'
Subsequent Events	'
	Subsequent Events
	In July 2014, the Company closed on the initial installment of the remaining $21.7 million in convertible notes to be issued to Total under the July 2012 Agreements as described in in Note 5, "Debt", in the amount of $10.85 million and expect the second installment to occur by January 2015.

Summary_of_Significant_Account1

Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2014
Accounting Policies [Abstract]	'
Basis of Presentation	'
	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 filed with the Securities and Exchange Commission (“SEC”) on April 2, 2014. 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.
Principles of Consolidations	'
	Principles of Consolidation
	The Company has interests in joint venture entities that are variable interest entities (“VIEs”). Determining whether to consolidate a variable interest entity 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.
	The condensed consolidated financial statements of the Company include the accounts of Amyris, Inc., its subsidiaries and two consolidated 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."
Use of Estimates	'
	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 revenue and expenses during the reporting period. Actual results could differ from those estimates.
Recent Accounting Pronouncements	'
	Recent Accounting Pronouncements
	In July 2013, the Financial Accounting Standards Board ("FASB") issued an amended accounting standard update on the financial statement presentation of unrecognized tax benefits. The amended guidance provides that a liability related to an unrecognized tax benefit would be presented as a reduction of a deferred tax asset for a net operating loss carryforward, a similar tax loss or a tax credit carryforward if such settlement is required or expected in the event the uncertain tax position is disallowed. The new guidance became effective for the Company on January 1, 2014 and will be applied prospectively to unrecognized tax benefits that exist at the effective date with retrospective applications permitted. The Company's current presentation of unrecognized tax benefits conforms with the amended guidance. Accordingly, there was no significant impact to the Company resulting from the guidance.
	In May 2014, the FASB issued a 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 standard 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. This guidance will be effective for the Company beginning January 1, 2017 and can be applied either retrospectively to each period presented or as a cumulative-effect adjustment as of the date of adoption. The Company is currently assessing the impact of adopting this new accounting standard on its financial statements.

Fair_Value_of_Financial_Instru1

Fair Value of Financial Instruments (Tables)	6 Months Ended
	Jun. 30, 2014
Fair Value Disclosures [Abstract]	'
Schedule of Fair Value, Assets and Liabilities Measured on Recurring Basis	'
	The Company’s financial assets and financial liabilities as of December 31, 2013 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, 2013
	Financial Assets
	Money market funds	$	398			$	—			$	—			$	398
	Certificates of deposit	1,428				—				—				1,428
	Total financial assets	$	1,826			$	—			$	—			$	1,826
	Financial Liabilities
	Loans payable	$	—			$	18,491			$	—			$	18,491
	Credit facilities	—				7,571				—				7,571
	Convertible notes	—				—				131,952				131,952
	Compound embedded derivative liability	—				—				131,117				131,117
	Currency interest rate swap derivative liability	—				3,600				—				3,600
	Total financial liabilities	$	—			$	29,662			$	263,069			$	292,731
	As of June 30, 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 June 30, 2014
	Financial Assets
	Money market funds	$	74,765			$	—			$	—			$	74,765
	Certificates of deposit	1,453				—				—				1,453
	Total financial assets	$	76,218			$	—			$	—			$	76,218
	Financial Liabilities
	Loans payable (1)	$	—			$	20,360			$	—			$	20,360
	Credit facilities  (1)	—				39,864				—				39,864
	Convertible notes (1)	—				—				227,638				227,638
	Compound embedded derivative liability	—				—				145,032				145,032
	Currency interest rate swap derivative liability	—				2,808				—				2,808
	Total financial liabilities	$	—			$	63,032			$	372,670			$	435,702
	________
	(1) These liabilities are carried on the condensed consolidated balance sheet on a historical basis.
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation	'
	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):
		2014
	Balance at January 1	$	131,952
	Additions to convertible notes	93,295
	Change in fair value of convertible notes	2,391
	Balance at June 30	$	227,638
Schedule of Derivative Instruments in Statement of Financial Position, Fair Value	'
	The following table provides a reconciliation of the beginning and ending balances for the compound embedded derivative liability measured at fair value using significant unobservable inputs (Level 3) (in thousands):
		2014
	Balance at January 1	$	131,117
	Transfers in to Level 3 net of cancellation (1)	86,551
	Total (income) loss from change in fair value of derivative liability	(72,636		)
	Balance at June 30	$	145,032
	________
	(1) Includes $1.1 million removal of derivative liability related to debt extinguishment.
	Derivative instruments measured at fair value as of June 30, 2014 and December 31, 2013, and their classification on the condensed consolidated balance sheets and condensed consolidated statements of operations, are presented in the following tables (in thousands except contract amounts):
			Liability as of
			30-Jun-14							31-Dec-13
	Type of Derivative Contract		Quantity of			Fair Value				Quantity of			Fair Value
			Short							Short
			Contracts							Contracts
	Currency interest rate swap, included as net liability in derivative liability		1			$	2,808			1			$	3,600
Schedule of Derivative Instruments, Gain (Loss) in Statement of Financial Performance	'
			Income	Three Months Ended June 30,								Six Months Ended June 30,
	Type of Derivative Contract		Statement Classification	2014				2013				2014		2013
				Gain (Loss) Recognized								Gain (Loss) Recognized
	Currency interest rate swap (1)		Gain (loss) from change in fair value of derivative instruments	$	722			$	(1,639	)		$1,056		$	(1,651	)
	___________
	(1)	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Balance_Sheet_Components_Table

Balance Sheet Components (Tables)	6 Months Ended
	Jun. 30, 2014
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'
Schedule of Inventory, Current	'
	Inventories are stated at the lower of cost or market and consist of the following (in thousands):
		June 30,			December 31,
		2014			2013
	Raw materials	$	2,468		$	1,796
	Work-in-process	6,536			7,292
	Finished goods	5,749			1,800
	Inventories, net	$	14,753		$	10,888
Schedule of Prepaid and Other Current Assets	'
	Prepaid expenses and other current assets is comprised of the following (in thousands):
		June 30,			December 31,
		2014			2013
	Maintenance (1)	$	393		$	258
	Prepaid insurance(1)	603			894
	Manufacturing catalysts	1,715			1,536
	Recoverable VAT and other taxes	2,776			5,125
	Other (1)	1,651			1,705
	Prepaid expenses and other current assets	$	7,138		$	9,518
	______________
	(1)	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.
Property, Plant and Equipment	'
	Property, plant and equipment, net is comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Leasehold improvements	$	39,208		$	39,034
	Machinery and equipment	101,383			96,585
	Computers and software	8,946			8,509
	Furniture and office equipment	2,584			2,535
	Buildings	7,606			7,148
	Vehicles	436			488
	Construction in progress	44,635			41,387
		204,798			195,686
	Less: accumulated depreciation and amortization	(64,142		)	(55,095		)
	Property, plant and equipment, net	$	140,656		$	140,591
Schedule of Other Assets, Noncurrent	'
	Other assets are comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Deposits on property and equipment, including taxes	$	2,095		$	1,970
	Recoverable taxes from Brazilian government entities	9,064			6,599
	Debt issuance cost (2)	978			454
	Investments in joint venture (1)	2,170			68
	Other (2)	1,519			1,494
	Total other assets	$	15,826		$	10,585
Schedule Of Accrued And Other Current Liabilities	'
	Accrued and other current liabilities are comprised of the following (in thousands):
		June 30, 2014			31-Dec-13
	Professional services	$	2,093		$	2,279
	Accrued vacation	2,516			2,274
	Payroll and related expenses	3,939			5,066
	Tax-related liabilities	157			825
	Deferred rent, current portion	1,111			1,111
	Accrued interest	1,246			3,176
	Contractual obligations to contract manufacturers	853			4,241
	Other	846			2,249
	Total accrued and other current liabilities	$	12,761		$	21,221
Schedule of Derivative Liability	'
	Derivative liability is comprised of the following (in thousands):
		June 30, 2014			December 31, 2013
	Fair market value of swap obligation	$	2,808		$	3,600
	Fair value of compound embedded derivative liability(1)	145,032			131,117
	Total derivative liability	$	147,840		$	134,717
	______________
	(1)	The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

Debt_Tables

Debt (Tables)	6 Months Ended
	Jun. 30, 2014
Debt Disclosure [Abstract]	'
Schedule of Debt	'
	Debt is comprised of the following (in thousands):
		June 30, 2014			December 31, 2013
	Credit facilities	$	37,972		$	8,767
	Convertible notes	57,904			28,537
	Related party convertible notes	100,480			89,499
	Loans payable	25,999			25,259
	Total debt	222,355			152,062
	Less: current portion	(9,923		)	(6,391		)
	Long-term debt	$	212,432		$	145,671
Schedule of Long-term Debt Instruments	'
	Future minimum payments under the debt agreements as of June 30, 2014 are as follows (in thousands):
	Years ending December 31:	Related Party Convertible Debt			Convertible Debt			Loans Payable			Credit Facility
	2014 (remaining six months)	$	744		$	1,891		$	4,080		$	2,539
	2015	1,606			4,020			4,114			15,426
	2016	1,606			4,020			3,935			20,301
	2017	58,849			28,715			3,772			7,822
	2018	74,485			15,685			3,612			472
	Thereafter	75,825			56,798			11,751			131
	Total future minimum payments	213,115			111,129			31,264			46,691
	Less: amount representing interest(1)	(112,635		)	(53,225		)	(5,265		)	(8,719		)
	Present value of minimum debt payments	100,480			57,904			25,999			37,972
	Less: current portion	—			—			(5,218		)	(4,705		)
	Noncurrent portion of debt	$	100,480		$	57,904		$	20,781		$	33,267
	______________
	(1) Including debt discount of $83.9 million related to the embedded derivative 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.

Commitments_and_Contingencies_

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2014
Commitments and Contingencies Disclosure [Abstract]	'
Schedule of Future Minimum Payments For Lease Obligations	'
	Future minimum payments under the Company's lease obligations as of June 30, 2014, are as follows (in thousands):
	Years ending December 31:	Capital			Operating		Total Lease Obligations
		Leases			Leases
	2014 (remaining six months)	$	557		$	3,182	$	3,739
	2015	462			6,606		7,068
	2016	159			6,614		6,773
	2017	—			6,588		6,588
	2018	—			6,675		6,675
	Thereafter	—			32,320		32,320
	Total future minimum lease payments	1,178			$	61,985	$	63,163
	Less: amount representing interest	(68		)
	Present value of minimum lease payments	1,110
	Less: current portion	(882		)
	Long-term portion	$	228

Joint_Ventures_and_Noncontroll1

Joint Ventures and Noncontrolling Interest (Tables)	6 Months Ended
	Jun. 30, 2014
Joint Ventures and Noncontrolling Interest [Abstract]	'
Schedule of Variable Interest Entities	'
	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 June 30, 2014, the assets include $22.9 million in property, plant and equipment, $4.1 million in other assets and $0.5 million in current assets. The liabilities include $0.2 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.
		June 30,			December 31,
	(In thousands)	2014			2013
	Assets	$	27,509		$	25,730
	Liabilities	$	421		$	229
Noncontrolling Interest	'
	The change in noncontrolling interest for the six months ended June 30, 2014 and 2013, is summarized below (in thousands):
		2014			2013
	Balance at January 1	$	(584	)	$	(877	)
	Foreign currency translation adjustment	(42		)	54
	Gain (loss) attributable to noncontrolling interest	(60		)	261
	Balance at June 30	$	(686	)	$	(562	)

Goodwill_and_Intangible_Assets1

Goodwill and Intangible Assets (Tables)	6 Months Ended
	Jun. 30, 2014
Goodwill and Intangible Assets Disclosure [Abstract]	'
Schedule of Intangible Assets and Goodwill	'
	The following table presents the components of the Company's intangible assets (in thousands):
				30-Jun-14								31-Dec-13
		Useful Life in Years		Gross Carrying Amount		Accumulated Amortization			Net Carrying Value			Gross Carrying Amount			Accumulated Amortization			Net Carrying Value
	In-process research and development	Indefinite		$	8,560	$	—		$	8,560		$	8,560		$	—		$	8,560
	Acquired licenses and permits	2		772		(772		)	—			772			(772		)	—
	Goodwill	Indefinite		560		—			560			560			—			560
				$	9,892	$	(772	)	$	9,120		$	9,892		$	(772	)	$	9,120
	The following table presents the activity of intangible assets for the six months ended June 30, 2014 (in thousands):
			31-Dec-13														30-Jun-14
			Net Carrying Value			Additions				Adjustments			Amortization				Net Carrying Value
	In-process research and development		$	8,560		$	—			$	—		$	—			$	8,560
	Acquired licenses and permits		—			—				—			—				—
	Goodwill		560			—				—			—				560
			$	9,120		$	—			$	—		$	—			$	9,120

StockBased_Compensation_Tables

Stock-Based Compensation (Tables)	6 Months Ended
	Jun. 30, 2014
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Compensation, Stock Options and Stock Appreciation Rights Award Activity	'
	The Company’s stock option activity and related information for the six months ended June 30, 2014 was as follows:
				Number			Weighted-				Weighted-Average		Aggregate
				Outstanding			Average				Remaining		Intrinsic
							Exercise				Contractual		Value
							Price				Life (Years)
													(in thousands)
	Outstanding - December 31, 2013			8,409,605			$	7.39			7.4		$	12,393
		Options granted		2,909,183			$	3.51
		Options exercised		(337,110	)		$	3.06
		Options cancelled		(485,971	)		$	7.09
	Outstanding - June 30, 2014			10,495,707			$	6.47			7.72		$	3,709
	Vested and Expected to vest after June 30, 2014			9,590,575			$	6.72			7.58		$	3,326
	Exercisable at June 30, 2014			4,554,010			$	9.29			6.13		$	1,027
Schedule of Share-based Compensation, Restricted Stock and Restricted Stock Units Activity	'
	The Company’s restricted stock units (or RSUs) and restricted stock activity and related information for the six months ended June 30, 2014 was as follows:
			RSUs			Weighted-Average Grant-Date Fair Value				Weighted Average Remaining Contractual Life (Years)
	Outstanding - December 31, 2013		2,316,437			$	4.3			0.88
	Awarded		1,049,300			$	3.51			—
	Vested		(1,158,585	)		$	4.68			—
	Forfeited		(98,863	)		$	3.17			—
	Outstanding - June 30, 2014		2,108,289			$	3.75			1.39
	Expected to vest after June 30, 2014		1,803,053			$	3.75			1.31
Schedule of Share-based Compensation, Shares Authorized under Stock Option Plans, by Exercise Price Range	'
	The following table summarizes information about stock options outstanding as of June 30, 2014:
		Options Outstanding									Options Exercisable
	Exercise Price	Number of Options			Weighted-		Weighted-Average Exercise Price				Number of Options			Weighted-Average Exercise Price
					Average
					Remaining
					Contractual Life
					(Years)
	$0.10—$2.79	1,580,682			8.2		$	2.66			476,896			$	2.52
	$2.81—$2.94	1,056,600			8.94		$	2.88			279,097			$	2.87
	$2.96—$3.44	945,057			8.55		$	3.14			304,429			$	3.07
	$3.51—$3.51	2,489,199			9.75		$	3.51			—			$	—
	$3.55—$3.93	1,700,908			5.75		$	3.88			1,247,160			$	3.89
	$4.06—$16.00	1,555,854			5.94		$	10.11			1,281,705			$	9.88
	$16.50—$24.50	724,345			5.97		$	20.1			625,057			$	20.11
	$25.43—$25.43	15,000			7.07		$	25.43			15,000			$	25.43
	$26.84—$26.84	368,062			6.64		$	26.84			264,666			$	26.84
	$30.17—$30.17	60,000			6.71		$	30.17			60,000			$	30.17
	$0.10—$30.17	10,495,707			7.72		$	6.47			4,554,010			$	9.29
Schedule of Employee Service Share-based Compensation, Allocation of Recognized Period Costs	'
	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 June 30,								Six Months Ended June 30,
		2014				2013				2014				2013
	Research and development	$	909			$	1,049			$	1,707			$	2,296
	Sales, general and administrative	2,774				3,936				5,490				6,882
	Total stock-based compensation expense	$	3,683			$	4,985			$	7,197			$	9,178
Employee Share Based Compensation [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions	'
	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 June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Expected dividend yield	—	%		—	%		—	%		—	%
	Risk-free interest rate	2	%		1	%		2	%		1	%
	Expected term (in years)	6.09			6.1			6.1			6.1
	Expected volatility	75	%		82	%		75	%		82	%
Non Employee Share Based Compensation [Member]	'
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]	'
Schedule of Share-based Payment Award, Stock Options, Valuation Assumptions	'
	The fair value of nonemployee stock options was estimated using the following weighted-average assumptions:
		Three Months Ended June 30,						Six Months Ended June 30,
		2014			2013			2014			2013
	Expected dividend yield	—	%		—	%		—	%		—	%
	Risk-free interest rate	2	%		2	%		2	%		2	%
	Expected term (in years)	5.8			6.1			5.94			6.4
	Expected volatility	75	%		82	%		76	%		83	%

Reporting_Segments_Tables

Reporting Segments (Tables)	6 Months Ended
	Jun. 30, 2014
Segment Reporting [Abstract]	'
Schedule of Revenue from External Customers and Long-Lived Assets, by Geographical Areas	'
	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 June 30,				Six Months Ended June 30,
		2014		2013		2014		2013
	United States	$	2,815	$	4,458	$	4,788	$	10,022
	Brazil	1,402		1,259		2,050		2,077
	Europe	2,985		4,005		6,338		4,230
	Asia	2,105		1,127		2,172		2,389
	Total	$	9,307	$	10,849	$	15,348	$	18,718
	Long-Lived Assets
		June 30, 2014		December 31, 2013
	United States	$	49,628	$	54,015
	Brazil	90,375		85,891
	Europe	653		685
	Total	$	140,656	$	140,591

Comprehensive_Income_Loss_Tabl

Comprehensive Income (Loss) (Tables)	6 Months Ended
	Jun. 30, 2014
Equity [Abstract]	'
Schedule of Accumulated Other Comprehensive Income (Loss)	'
	The components of accumulated other comprehensive loss are as follows (in thousands):
		June 30, 2014			31-Dec-13
	Foreign currency translation adjustment, net of tax	$	(15,634	)	$	(20,087	)
	Total accumulated other comprehensive loss	$	(15,634	)	$	(20,087	)

Net_Income_Loss_Attributable_t1

Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share (Tables)	6 Months Ended
	Jun. 30, 2014
Earnings Per Share [Abstract]	'
Schedule of Calculation of Basic and Diluted Net Loss Per Share of Common Stock Attributable to Amyris, Inc. Common Stockholders	'
	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 June 30,							Six Months Ended June 30,
		2014				2013			2014			2013
	Numerator:
	Net loss attributable to Amyris, Inc. common stockholders	$	(35,479	)		$	(38,876	)	$	(19,094	)	$	(71,490	)
	Interest on convertible debt	—				—			3,169			—
	Accretion of debt discount	—				—			2,518			—
	Gain from change in fair value of derivative instruments	—				—			(59,995		)	—
	Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	$	(35,479	)		$	(38,876	)	$	(73,402	)	$	(71,490	)
	Denominator:
	Weighted average shares of common stock outstanding for basic EPS	78,604,692				75,959,228			77,722,437			74,640,314
	Basic loss per share	$	(0.45	)		$	(0.51	)	$	(0.25	)	$	(0.96	)
	Weighted average shares of common stock outstanding	78,604,692				75,959,228			77,722,437			74,640,314
	Effect of dilutive securities:
	Convertible promissory notes	—				—			32,909,641			—
	Weighted common stock equivalents	—				—			32,909,641			—
	Diluted weighted-average common shares	78,604,692				75,959,228			110,632,078			74,640,314
	Diluted loss per share	$	(0.45	)		$	(0.51	)	$	(0.66	)	$	(0.96	)
Schedule of Antidilutive Securities Excluded from Computation of Earnings Per Share	'
	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 June 30,						Six Months Ended June 30,
		2014			2013			2014		2013
	Period-end stock options to purchase common stock	10,495,707			8,803,300			10,495,707		8,803,300
	Convertible promissory notes	69,727,211			13,617,144			36,643,102		13,617,144
	Period-end common stock subject to repurchase	—			1			—		1
	Period-end common stock warrants	1,021,087			21,087			1,021,087		21,087
	Period-end restricted stock units	2,108,289			2,770,516			2,108,289		2,770,516
	Total	83,352,294			25,212,048			50,268,185		25,212,048

The_Company_Details

The Company (Details) (USD $)	6 Months Ended
	Jun. 30, 2014	Dec. 31, 2013
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'	'
Expected Capital Expenditures During Next Fiscal Year	$9,000,000	'
Retained Earnings (Accumulated Deficit)	-840,532,000	-821,438,000
Cash, Cash Equivalents, and Short-term Investments	90,200,000	'
Debt Instrument, Unamortized Discount	83,900,000	'
Long-term Debt	222,355,000	152,062,000
Debt, current portion	$9,923,000	$6,391,000

Summary_of_Significant_Account2

Summary of Significant Accounting Policies - Principles of Consolidations (Details)	6 Months Ended
	Jun. 30, 2014
	consolidated_VIE
Accounting Policies [Abstract]	'
Variable Interest Entity Number of Entities (in VIEs)	2

Fair_Value_of_Financial_Instru2

Fair Value of Financial Instruments - Hierarchy (Details) (Fair Value, Measurements, Recurring [Member], USD $)	Jun. 30, 2014		Dec. 31, 2013
In Thousands, unless otherwise specified
Quoted Prices in Active Markets for Identical Assets (Level 1) [Member]	'		'
Financial Assets	'		'
Money market funds	$74,765		$398
Certificates of deposit	1,453		1,428
Total financial assets	76,218		1,826
Financial Liabilities	'		'
Loans payable	0	[1]	0
Credit facilities	0	[1]	0
Convertible notes	0	[1]	0
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	0		0
Total financial liabilities	0		0
Other Observable Inputs (Level 2) [Member]	'		'
Financial Assets	'		'
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities	'		'
Loans payable	20,360	[1]	18,491
Credit facilities	39,864	[1]	7,571
Convertible notes	0	[1]	0
Compound embedded derivative liability	0		0
Currency interest rate swap derivative liability	2,808		3,600
Total financial liabilities	63,032		29,662
Significant Unobservable Inputs (Level 3) [Member]	'		'
Financial Assets	'		'
Money market funds	0		0
Certificates of deposit	0		0
Total financial assets	0		0
Financial Liabilities	'		'
Loans payable	0	[1]	0
Credit facilities	0	[1]	0
Convertible notes	227,638	[1]	131,952
Compound embedded derivative liability	145,032		131,117
Currency interest rate swap derivative liability	0		0
Total financial liabilities	372,670		263,069
Balance as of June 30 [Member]	'		'
Financial Assets	'		'
Money market funds	74,765		398
Certificates of deposit	1,453		1,428
Total financial assets	76,218		1,826
Financial Liabilities	'		'
Loans payable	20,360	[1]	18,491
Credit facilities	39,864	[1]	7,571
Convertible notes	227,638	[1]	131,952
Compound embedded derivative liability	145,032		131,117
Currency interest rate swap derivative liability	2,808		3,600
Total financial liabilities	$435,702		$292,731
[1]	These liabilities are carried on the condensed consolidated balance sheet on a historical basis.

Fair_Value_of_Financial_Instru3

Fair Value of Financial Instruments - Fair Value Using Significant Unobservable Inputs (Level 3) (Details) (Convertible Notes Payable [Member], Significant Unobservable Inputs (Level 3) [Member], USD $)	6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014
Convertible Notes Payable [Member] | Significant Unobservable Inputs (Level 3) [Member]	'
Fair Value, Liabilities Measured on Recurring Basis, Unobservable Input Reconciliation, Calculation [Roll Forward]	'
Fair value, beginning of period	$131,952
Additions to convertible notes	93,295
Change in fair value of convertible notes	2,391
Fair value, end of period	$227,638

Fair_Value_of_Financial_Instru4

Fair Value of Financial Instruments - Banco Pine Textuals (Details) (Banco Pine July 2012 Loan Agreement [Member])	Jul. 30, 2012	Jun. 30, 2014	Jun. 30, 2014
In Millions, unless otherwise specified	BRL	Interest Rate Swap [Member]	Interest Rate Swap [Member]
		USD ($)	BRL
Fair Value, Assets and Liabilities Measured on Recurring and Nonrecurring Basis [Line Items]	'	'	'
Notional Amount of Interest Rate Derivatives	'	$10	22
Debt Instrument, Face Amount	22	'	'
Derivative, Fixed Interest Rate	'	3.94%	3.94%

Derivative_Disclosures_Details

- Derivative Disclosures (Details) (USD $)

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

In Thousands, unless otherwise specified

Future [Member]

Future [Member]

Currency interest rate swap [Member]

Currency interest rate swap [Member]

Currency interest rate swap [Member]

Currency interest rate swap [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Significant Unobservable Inputs (Level 3) [Member]

Significant Unobservable Inputs (Level 3) [Member]

Derivative Financial Instruments, Liabilities [Member]

Fair Value Measurement [Domain]

Not Designated as Hedging Instrument [Member]

Not Designated as Hedging Instrument [Member]

Not Designated as Hedging Instrument [Member]

Not Designated as Hedging Instrument [Member]

Not Designated as Hedging Instrument [Member]

Not Designated as Hedging Instrument [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Significant Unobservable Inputs (Level 3) [Member]

Significant Unobservable Inputs (Level 3) [Member]

Currency interest rate swap, included as net liability in other long term liability [Member]

Currency interest rate swap, included as net liability in other long term liability [Member]

Other income (expense), net [Member]

Other income (expense), net [Member]

Other income (expense), net [Member]

Other income (expense), net [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Contracts

Contracts

Derivative [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Quantity of Short Contracts (in contracts)

'

'

1

1

'

'

'

'

'

'

'

'

'

'

'

'

Fair Value

($2,808)

($3,600)

$2,808

$3,600

'

'

'

'

'

'

'

'

'

'

'

'

Derivative contracts, gain (loss)

'

'

'

'

722

[1]

-1,639

[1]

1,056

[1]

-1,651

[1]

'

'

'

'

'

'

'

'

Fair value, beginning of period

'

'

'

'

'

'

'

'

'

'

'

'

145,032

131,117

'

'

Transfer in to Level 3 net of cancellation

'

'

'

'

'

'

'

'

'

1,400

1,100

'

'

'

86,551

[2]

'

Total (income) loss from change in fair value of derivative liability

'

'

'

'

'

'

'

'

4,000

'

-53,100

-2,500

'

'

'

72,636

Fair value, end of period

'

'

'

'

'

'

'

'

'

'

'

'

$145,032

$131,117

'

'

[1]

Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

[2]

Includes $1.1 million removal of derivative liability related to debt extinguishment.

Balance_Sheet_Components_Inven

Balance Sheet Components - Inventory (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'	'
Raw materials	$2,468	$1,796
Work-in-process	6,536	7,292
Finished goods	5,749	1,800
Inventories, net	$14,753	$10,888

Balance_Sheet_Components_Prepa

Balance Sheet Components - Prepaid and Other Current Assets (Details) (USD $)	Jun. 30, 2014		Dec. 31, 2013
In Thousands, unless otherwise specified
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'		'
Maintenance (1)	$393	[1]	$258	[1]
Prepaid insurance(1)	603	[1]	894	[1]
Manufacturing catalysts	1,715		1,536
Recoverable VAT and other taxes	2,776		5,125
Other (1)	1,651	[1]	1,705	[1]
Prepaid expenses and other current assets	$7,138		$9,518
[1]	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.

Balance_Sheet_Components_Prope

Balance Sheet Components - Property, Plant and Equipment, net (Details) (USD $)

6 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Capital Lease Obligations [Member]

Capital Lease Obligations [Member]

Leasehold improvements [Member]

Leasehold improvements [Member]

Machinery and equipment [Member]

Machinery and equipment [Member]

Computer and software [Member]

Computer and software [Member]

Furniture and office equipment [Member]

Furniture and office equipment [Member]

Buildings [Member]

Buildings [Member]

Vehicles [Member]

Vehicles [Member]

Construction in progress [Member]

Construction in progress [Member]

Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member]

Machinery and Equipment and Furniture and Office Equipment Under Capital Lease [Member]

Property Plant and Equipment Including Capital Leases [Member]

Property Plant and Equipment Including Capital Leases [Member]

Property Plant and Equipment Including Capital Leases [Member]

Property Plant and Equipment Including Capital Leases [Member]

Capital Lease Obligations [Member]

Capital Lease Obligations [Member]

Property, Plant and Equipment [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Property, Plant and Equipment, Gross

$204,798,000

'

$195,686,000

'

'

$39,208,000

$39,034,000

$101,383,000

$96,585,000

$8,946,000

$8,509,000

$2,584,000

$2,535,000

$7,606,000

$7,148,000

$436,000

$488,000

$44,635,000

$41,387,000

$3,800,000

$3,400,000

'

'

'

'

Less: accumulated depreciation and amortization

-64,142,000

'

-55,095,000

-1,800,000

-1,500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Property, plant and equipment, net

140,656,000

'

140,591,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Depreciation and amortization expense

7,539,000

8,491,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,700,000

4,100,000

7,500,000

8,500,000

Interest Costs Capitalized

$500,000

'

$500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Balance_Sheet_Components_Other

Balance Sheet Components - Other Assets (Details) (USD $)	Jun. 30, 2014		Dec. 31, 2013
Deposits on property and equipment, including taxes	$2,095,000		$1,970,000
Recoverable taxes from Brazilian government entities	9,064,000		6,599,000
Debt issuance cost (2)	978,000	[1]	454,000	[1]
Investments in joint venture (1)	2,170,000	[2]	68,000	[2]
Other (2)	1,519,000	[1]	1,494,000	[1]
Total other assets	15,826,000		10,585,000
Novvi LLC [Member]	'		'
Investments in joint venture (1)	2,100,000		0
Total Amyris Biosolutions B.V [Member]	'		'
Investments in joint venture (1)	$100,000		$100,000
[1]	Certain classifications of prior period amounts have been made to conform to the current period presentation. Such reclassifications did not materially change previously reported consolidated financial statements.
[2]	The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

Balance_Sheet_Components_Accru

Balance Sheet Components - Accrued and Other Current Liabilities (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'	'
Professional services	$2,093	$2,279
Accrued vacation	2,516	2,274
Payroll and related expenses	3,939	5,066
Tax-related liabilities	157	825
Deferred rent, current portion	1,111	1,111
Accrued interest	1,246	3,176
Contractual obligations to contract manufacturers	853	4,241
Other	846	2,249
Total accrued and other current liabilities	$12,761	$21,221

Balance_Sheet_Components_Deriv

Balance Sheet Components - Derivative Liability (Details) (USD $)	Jun. 30, 2014		Dec. 31, 2013
In Thousands, unless otherwise specified
Organization, Consolidation and Presentation of Financial Statements [Abstract]	'		'
Fair market value of swap obligation	$2,808		$3,600
Fair value of compound embedded derivative liability(1)	145,032	[1]	131,117	[1]
Total derivative liability	$147,840		$134,717
[1]	The compound embedded derivative liability represents the fair value of the bifurcated conversion options that contain "make-whole" provisions or down round conversion price adjustment provisions included in the outstanding Total Notes, Tranche I Notes, Tranche II Notes and the Rule 144A Convertible Note Offering (see Note 3, "Fair value of financial instruments" and Note 5, "Debt").

Debt_Details

Debt (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Dec. 02, 2013
In Thousands, unless otherwise specified
Debt Instrument [Line Items]	'	'	'
Long-term Debt	$222,355	$152,062	'
Less: current portion	-9,923	-6,391	'
Long-term debt	212,432	145,671	'
Credit Facility [Member]	'	'	'
Debt Instrument [Line Items]	'	'	'
Long-term Debt	37,972	8,767	'
Years ending December 31: [Abstract]	'	'	'
2014	2,539	'	'
2015	15,426	'	'
2016	20,301	'	'
2017	7,822	'	'
2018	472	'	'
Thereafter	131	'	'
Total future minimum payments	46,691	'	'
Less: amount representing interest	-8,719	'	'
Present value of minimum debt payments	37,972	'	'
Less: current portion	-4,705	'	'
Noncurrent portion of debt	33,267	'	'
Convertible Debt [Member]	'	'	'
Debt Instrument [Line Items]	'	'	'
Long-term Debt	57,904	28,537	'
Years ending December 31: [Abstract]	'	'	'
2014	1,891	'	'
2015	4,020	'	'
2016	4,020	'	'
2017	28,715	'	'
2018	15,685	'	'
Thereafter	56,798	'	'
Total future minimum payments	111,129	'	'
Less: amount representing interest	-53,225	'	'
Present value of minimum debt payments	57,904	'	'
Less: current portion	0	'	'
Noncurrent portion of debt	57,904	'	'
Related Party Convertible Notes [Member]	'	'	'
Debt Instrument [Line Items]	'	'	'
Long-term Debt	100,480	89,499	25,000
Years ending December 31: [Abstract]	'	'	'
2014	744	'	'
2015	1,606	'	'
2016	1,606	'	'
2017	58,849	'	'
2018	74,485	'	'
Thereafter	75,825	'	'
Total future minimum payments	213,115	'	'
Less: amount representing interest	-112,635	'	'
Present value of minimum debt payments	100,480	'	'
Less: current portion	0	'	'
Noncurrent portion of debt	100,480	'	'
Loans Payable [Member]	'	'	'
Debt Instrument [Line Items]	'	'	'
Long-term Debt	25,999	25,259	'
Years ending December 31: [Abstract]	'	'	'
2014	4,080	'	'
2015	4,114	'	'
2016	3,935	'	'
2017	3,772	'	'
2018	3,612	'	'
Thereafter	11,751	'	'
Total future minimum payments	31,264	'	'
Less: amount representing interest	-5,265	'	'
Present value of minimum debt payments	25,999	'	'
Less: current portion	-5,218	'	'
Noncurrent portion of debt	$20,781	'	'

Debt_FINEP_Credit_Facility_Det

Debt - FINEP Credit Facility (Details) (FINEP Credit Facility [Member])	0 Months Ended	6 Months Ended		6 Months Ended
In Millions, unless otherwise specified	Nov. 30, 2010	Jun. 30, 2014	Nov. 30, 2010	Jun. 30, 2014	Jun. 30, 2014	Nov. 30, 2010	Jun. 30, 2014	Jun. 30, 2014	Dec. 31, 2013	Dec. 31, 2013	Nov. 30, 2010
			Minimum [Member]	Maximum [Member]	FINEP Project [Member]	FINEP Project [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]	Chattel Mortgage [Member]
					USD ($)	BRL	USD ($)	BRL	USD ($)	BRL	BRL
Line of Credit Facility [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Line of Credit Facility, Maximum Borrowing Capacity	'	'	'	'	'	'	$2.90	'	'	'	6.4
Debt Instrument, Interest Rate, Stated Percentage	5.00%	'	'	'	'	'	'	'	'	'	'
Long-term Debt, Percentage Bearing Fixed Interest, Percentage Rate	'	'	6.00%	'	'	'	'	'	'	'	'
Debt Instrument, Basis Spread on Variable Rate	'	5.00%	'	'	'	'	'	'	'	'	'
Long-term Debt, Percentage Bearing Variable Interest, Percentage Rate	11.00%	'	'	'	'	'	'	'	'	'	'
Debt Instrument Debt Default Fine Percentage	10.00%	'	'	'	'	'	'	'	'	'	'
Debt Instrument Interest On Late Balance Percentage Per Month	1.00%	'	'	'	'	'	'	'	'	'	'
Period Credit Line Is Available	'	'	'	'81 months	'	'	'	'	'	'	'
Line of Credit Facility, Amount Outstanding	'	'	'	'	'	'	2.2	4.8	2.2	5.2	'
Research and Development Project, Amount To Be Contributed From Company Funds	'	'	'	'	6.6	14.5	'	'	'	'	'
Research and Development Project Amount To Be Contributed From Company Prior To Release Of Second Tranche	'	'	'	'	'	11.1	'	'	'	'	'
Guaranty Liabilities	'	'	'	'	'	'	$1.50	'	'	'	3.3
Period Of Time Amounts Released Must Be Used	'30 months	'	'	'	'	'	'	'	'	'	'

Debt_BNDES_Credit_Facility_Det

Debt - BNDES Credit Facility (Details) (BNDES Credit Facility [Member], BNDES [Member])	1 Months Ended						1 Months Ended
In Millions, unless otherwise specified	Dec. 31, 2011	Jun. 30, 2014	Jun. 30, 2014	Mar. 31, 2014	Dec. 31, 2013	Dec. 31, 2013	Dec. 31, 2011
	BRL	USD ($)	BRL	BRL	USD ($)	BRL	Maximum [Member]
	Monthly_installment						BRL
Line of Credit Facility [Line Items]	'	'	'	'	'	'	'
Line of Credit Facility, Maximum Borrowing Capacity	'	$10.20	'	'	'	'	22.4
Line of Credit Facility, Initial Tranche	19.1	'	'	'	'	'	'
Line of Credit Facility, Additional Tranche, Available Upon Delivery of Additional Guarantees	3.3	'	'	'	'	'	'
Period Credit Line Is Available	'	'	'	'	'	'	'12 months
Line of Credit Facility Number of Monthly Payments (in monthly installment)	60	'	'	'	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	7.00%	'	'	'	'	'	'
Line of Credit Facility, Unused Capacity, Commitment Fee Percentage	0.10%	'	'	'	'	'	'
Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount	'	11.3	'	24.9	'	'	'
Line of Credit Facility, Bank Guarantee, Percentage	10.00%	'	'	'	'	'	'
Line of Credit Facility, Bank Guarantee, Percentage, Second Tranche	90.00%	'	'	'	'	'	'
Guarantor Obligations, Liquidation Proceeds, Percentage	130.00%	'	'	'	'	'	'
Line of Credit Facility, Amount Outstanding	'	$6.10	13.4	'	$6.50	15.3	'

Debt_Hercules_Loan_Facility_De

Debt - Hercules Loan Facility (Details) (USD $)	6 Months Ended
	Jun. 30, 2014	29-May-14	Mar. 31, 2014
Line of Credit Facility [Line Items]	'	'	'
Debt Instrument, Unamortized Discount	83,900,000	'	'
Hercules Loan Facility [Member]	'	'	'
Line of Credit Facility [Line Items]	'	'	'
Loans Payable	'	'	25,000,000
Debt Instrument, Interest Rate, Stated Percentage	'	9.50%	'
Debt Instrument, Covenant Compliance	'15.0	'	'
Debt Instrument, Financing Transaction, Additional Cash Proceeds	'	50,000,000	'
Debt Instrument, End of Term Fee Amount, Percentage	'	10.00%	'
Forbearance Fee Due	'	10,000,000	10,000,000
Prime Rate [Member] | Hercules Loan Facility [Member]	'	'	'
Line of Credit Facility [Line Items]	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	'	6.25%	'
Funding Tranche [Domain] | Hercules Loan Facility [Member]	'	'	'
Line of Credit Facility [Line Items]	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	8.50%	'	'
Convertible Notes Payable	29,700,000	'	'
Debt Instrument, Unamortized Discount	273,000	'	'
Debt Instrument, Financing Transaction, Additional Cash Proceeds	5,000,000	'	'
Funding Tranche [Domain] | Prime Rate [Member] | Hercules Loan Facility [Member]	'	'	'
Line of Credit Facility [Line Items]	'	'	'
Debt Instrument, Interest Rate, Stated Percentage	5.25%	'	'

Debt_Notes_Payable_Details

Debt - Notes Payable (Details) (Notes Payable, Other Payables-Lessor [Member], USD $)	Oct. 31, 2008	Apr. 30, 2013
In Millions, unless otherwise specified		Amendment of Lease Agreement - Emeryville [Member]
Debt Instrument [Line Items]	'	'
Debt Instrument, Face Amount	$3.30	'
Debt Instrument, Interest Rate, Stated Percentage	9.50%	'
Lease Incentive, Elimination of Debt, Amount	'	$1.40

Debt_Convertible_Notes_Details

Debt - Convertible Notes (Details) (USD $)

3 Months Ended

0 Months Ended

0 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

0 Months Ended

1 Months Ended

Jun. 30, 2014

22-May-14

Dec. 31, 2013

Jan. 31, 2014

Dec. 02, 2013

Mar. 31, 2014

Dec. 31, 2013

Sep. 30, 2013

Feb. 29, 2012

Jul. 30, 2012

Jun. 30, 2014

Dec. 31, 2013

Dec. 02, 2013

Oct. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

Oct. 31, 2013

Aug. 31, 2013

Dec. 31, 2013

Dec. 02, 2013

Jan. 31, 2014

Aug. 31, 2013

22-May-14

Oct. 31, 2013

Aug. 31, 2013

Dec. 24, 2012

Jul. 31, 2013

Jun. 30, 2013

Jul. 30, 2012

First Tranche [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Rule 144A Convertible Notes [Member]

Maximum [Member]

Maximum [Member]

Private Placement [Member]

Initial Installment [Member]

Initial Installment [Member]

Initial Installment [Member]

August 2013 Convertible Notes [Member]

Fidelity [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Rule 144A Convertible Notes [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

l

Debt Instrument [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Convertible Note Offering

'

$15,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$75,000,000

'

'

'

'

'

'

Proceeds from Convertible Debt

72,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

24,700,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Unamortized Discount

83,900,000

'

'

'

'

'

'

'

'

'

83,900,000

'

'

'

'

'

'

31,600,000

'

'

6,300,000

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible Promissory Note, Held by Third Party

'

'

'

'

48,300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future Proceeds from Convertible Debt

'

'

'

'

'

'

'

'

'

21,700,000

'

'

'

'

'

60,000,000

9,700,000

'

'

35,000,000

'

6,000,000

6,000,000

25,000,000

'

'

'

'

'

'

'

Convertible Note Offering [Abstract]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Face Amount

'

'

'

34,000,000

'

'

'

'

25,000,000

105,000,000

'

'

'

'

'

'

'

'

'

42,600,000

'

'

3,000,000

30,400,000

'

51,800,000

73,000,000

'

20,000,000

10,000,000

30,000,000

Debt Instrument, Interest Rate, Stated Percentage

'

'

'

'

'

'

'

'

3.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price

'

'

'

'

$2.20

'

'

$7.07

'

$7.07

'

'

'

'

'

'

'

'

$2.44

'

'

'

$2.87

'

$3.74

'

'

$2.98

'

'

$3.08

Debt Instrument, Convertible, Common Stock, Shares

'

'

'

'

'

'

'

'

3,536,968

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,677,852

'

'

'

Percentage of Principal Amount of Notes, Required to Be Repaid In An Acquisition

'

'

'

'

'

'

'

'

101.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Outstanding Debt, Maximum

'

'

'

'

'

'

'

'

200,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum

'

'

'

'

'

'

'

'

50.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum

'

'

'

'

'

'

'

'

'

125,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum

'

'

'

'

'

'

'

'

'

30.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Bridge Loan

'

'

'

'

'

'

'

'

'

'

'

'

'

35,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Amended Additional Investor Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

7,600,000

'

'

'

'

'

'

'

'

'

'

'

Long-term Debt

222,355,000

'

152,062,000

'

'

29,300,000

28,500,000

'

'

'

100,480,000

89,499,000

25,000,000

'

'

'

'

46,200,000

'

'

37,900,000

'

'

'

'

'

'

'

'

'

'

Future Cancellation Of Debt, Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

44,200,000

13,000,000

'

'

'

'

'

'

'

5,400,000

'

'

'

'

'

'

'

Debt Instrument, Trailing Sixty Day Discount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15.00%

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Event Date Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$2.15

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Volume

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,000,000

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'45 days

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Product Sales, Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Milestone Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$1.87

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Six Months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Three Months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6.50%

'

'

'

13.00%

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'30 months

'

'

'

'36 months

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

8.00%

'

'

'

16.00%

'

'

'

'

'

'

'

'

Debt Instrument, Unamortized Discount (Premium), Net

'

'

'

'

'

$3,700,000

$4,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt_Related_Party_Convertible

Debt - Related Party Convertible Notes (Details)

3 Months Ended

6 Months Ended

0 Months Ended

1 Months Ended

1 Months Ended

3 Months Ended

3 Months Ended

0 Months Ended

1 Months Ended

0 Months Ended

1 Months Ended

1 Months Ended

3 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 31, 2014

Dec. 31, 2013

Jun. 30, 2014

Jul. 13, 2012

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Oct. 31, 2012

Mar. 31, 2014

Dec. 31, 2013

Mar. 31, 2014

Dec. 31, 2013

Dec. 02, 2013

Sep. 30, 2013

Jul. 30, 2012

Jan. 31, 2014

Jun. 30, 2014

Dec. 31, 2013

Dec. 02, 2013

Oct. 31, 2013

Dec. 24, 2012

Oct. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Sep. 14, 2012

Jul. 30, 2012

Jul. 26, 2013

Jun. 06, 2013

Dec. 31, 2013

Dec. 31, 2010

Dec. 24, 2012

Dec. 31, 2013

Jul. 31, 2013

Jun. 30, 2013

Jul. 30, 2012

Jul. 30, 2012

Jul. 30, 2012

Jan. 31, 2014

Jun. 30, 2014

Jan. 31, 2014

Oct. 31, 2013

Aug. 31, 2013

Dec. 31, 2013

Dec. 02, 2013

Jan. 31, 2014

Aug. 31, 2013

Oct. 31, 2013

Mar. 24, 2013

Mar. 24, 2013

Aug. 31, 2013

Oct. 31, 2013

Aug. 31, 2013

Aug. 31, 2013

Feb. 29, 2012

Oct. 31, 2013

Sep. 30, 2013

Aug. 31, 2013

Jul. 31, 2013

Jun. 30, 2013

Jun. 30, 2012

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Loans Payable Lessor Emeryville Plant [Member]

Loans Payable Lessor Emeryville Plant [Member]

Private Placement [Member]

Private Placement [Member]

Initial Installment [Member]

Initial Installment [Member]

Initial Installment [Member]

Initial Installment [Member]

Second Installment [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

First and Second Tranche [Member]

May 15th 2013 [Member]

June 15th 2013 [Member]

Maximum [Member]

Maximum [Member]

Common Stock [Member]

Common Stock [Member]

Fidelity [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Bridge Loan [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

USD ($)

BRL

USD ($)

USD ($)

USD ($)

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

Temasek Bridge Note [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Rule 144A Convertible Notes [Member]

Unsecured Debt [Member]

Unsecured Debt [Member]

Unsecured Debt [Member]

Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]

Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]

July 2013 Convertible Notes [Member]

July 2013 Convertible Notes [Member]

USD ($)

USD ($)

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Private Placement [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Temasek Bridge Note [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Banco Pine S.A Loan Agreement June 2012 [Member]

Related Party Convertible Notes [Member]

Temasek [Member]

Total [Member]

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

Unsecured Senior Convertible Notes 1.5% Due 2017 [Member]

USD ($)

USD ($)

USD ($)

July 2014 Convertible Notes [Member]

January 2015 Convertible Notes [Member]

USD ($)

USD ($)

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

USD ($)

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

USD ($)

USD ($)

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Related Party Convertible Notes [Member]

USD ($)

USD ($)

USD ($)

July 2013 Convertible Notes [Member]

July 2013 Convertible Notes [Member]

BRL

Rule 144A Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

August 2013 Convertible Notes [Member]

USD ($)

USD ($)

USD ($)

Rule 144A Convertible Notes [Member]

Rule 144A Convertible Notes [Member]

l

USD ($)

USD ($)

USD ($)

Debt Instrument [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Face Amount

'

'

'

'

'

'

$23,600,000

52,000,000

'

$600,000

'

'

'

'

'

'

'

'

$105,000,000

'

'

'

'

'

'

'

'

'

'

'

$69,000,000

'

$15,000,000

'

$20,000,000

$10,000,000

'

$0

'

$5,000,000

$20,000,000

$10,000,000

$30,000,000

'

'

$34,000,000

'

'

'

$42,600,000

'

'

$3,000,000

$30,400,000

'

'

'

$73,000,000

$51,800,000

'

$110,000,000

$25,000,000

'

'

$73,000,000

$20,000,000

$10,000,000

52,000,000

'

'

'

Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount

'

'

'

'

'

'

30,900,000

68,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Interest Rate, Stated Percentage

'

'

'

'

'

'

'

5.50%

'

'

'

3.24%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1.50%

'

'

1.50%

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3.00%

5.50%

'

'

1.50%

1.50%

'

'

'

'

Proceeds from Convertible Debt

72,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

24,700,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5,000,000

10,000,000

9,700,000

Future Proceeds from Convertible Debt

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

21,700,000

'

'

'

'

'

'

'

'

60,000,000

9,700,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10,850,000

10,850,000

'

'

'

'

35,000,000

'

6,000,000

6,000,000

25,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$2.20

$7.07

$7.07

'

'

'

'

'

'

'

'

'

'

'

$4.11

'

'

'

$3.08

'

'

'

$2.98

'

'

'

$3.08

'

'

'

'

'

$2.44

'

'

'

$2.87

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Convertible Debt

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

75,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Common Stock, Shares

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,677,852

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3,536,968

'

'

'

'

'

'

'

'

'

Collaboration Agreement, Funding Obligation Advanced Installments

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10,000,000

10,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Private Placement Convertible Notes, Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'24 months

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Closing Price Plus Incremental Rate

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$0.01

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Interest Rate, Default Rate, Stated Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2.50%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Period Prior to Maturity to Eligible For Conversion

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'10 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period of Lock-up Upon Conversion of Debt

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'6 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Loss from extinguishment of debt

-1,100,000

0

-10,512,000

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-9,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

900,000

'

'

'

'

'

'

'

-19,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Convertible Debt, Amount Outstanding

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

53,300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Early Repayment, Percentage of Principal

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

101.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Outstanding Debt, Maximum

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

200,000,000

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Percentage of Consolidated Total Assets, Maximum

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Outstanding Secured Debt, Maximum

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

125,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Debt Convenant, Secured Debt, Percentage of Consolidated Total Assets, Maximum

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

30.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Bridge Loan

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

35,000,000

'

35,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5,000,000

'

'

'

'

'

'

'

Debt Instrument, Amended Additional Investor Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

7,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Amended Promissory Note, Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

14,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

9,200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future Cancellation Of Debt, Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

44,200,000

13,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Class of Warrant or Right, Number of Securities Called by Warrants or Rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,000,000

'

'

'

'

'

'

'

'

'

'

'

Class of Warrant or Right, Exercise Price of Warrants or Rights

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0.01

'

'

'

'

'

'

'

'

'

'

'

Export Financing Agreement

'

'

'

'

2,200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Long-term Debt

222,355,000

'

222,355,000

'

'

152,062,000

'

'

25,999,000

'

25,259,000

'

23,600,000

22,200,000

29,300,000

28,500,000

'

'

'

'

100,480,000

89,499,000

25,000,000

'

'

'

'

'

'

40,300,000

'

51,500,000

'

'

'

'

0

'

'

'

'

'

'

'

'

'

46,200,000

'

'

'

37,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Unamortized Discount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-55,300,000

23,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Unamortized Discount

$83,900,000

'

$83,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$83,900,000

'

'

'

'

'

'

'

'

$13,100,000

'

$17,600,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$31,600,000

'

'

'

$6,300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Event Date Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$2.15

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Volume

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'45 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Plant Manufacturing Production, Product Sales, Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Milestone Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$1.87

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Six Months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued for Three Months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

6.50%

'

'

'

13.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'30 months

'

'

'

'36 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued Thereafter

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

8.00%

'

'

'

16.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Term

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'12 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price, Interest Accrued

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

12.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

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

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

101.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt_Loans_Payable_Details

Debt - Loans Payable (Details)

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Jun. 30, 2012

Jul. 31, 2012

Jun. 30, 2014

Jul. 13, 2012

Jul. 30, 2012

Jul. 30, 2012

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Oct. 31, 2012

Mar. 31, 2014

Dec. 31, 2013

Dec. 31, 2009

Dec. 31, 2013

Dec. 31, 2010

Jun. 30, 2014

Mar. 18, 2013

Mar. 31, 2014

USD ($)

USD ($)

USD ($)

Banco Pine S.A Loan Agreement June 2012 [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Banco Pine July 2012 Loan Agreement [Member]

Nossa Caixa Loan Agreement [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable [Member]

Loans Payable Lessor Emeryville Plant [Member]

Loans Payable Lessor Emeryville Plant [Member]

Loans Payable Lessor Emeryville Plant [Member]

Interest Rate Swap [Member]

ABC Brasil Agreement [Member]

ABC Brasil Agreement [Member]

Bridge Loan [Member]

USD ($)

BRL

BRL

BRL

USD ($)

USD ($)

USD ($)

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

USD ($)

USD ($)

Banco Pine July 2012 Loan Agreement [Member]

USD ($)

USD ($)

BRL

USD ($)

USD ($)

Debt Instrument [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Face Amount

'

'

'

52,000,000

'

$23,600,000

52,000,000

22,000,000

30,000,000

'

$600,000

'

'

'

'

'

'

$0

'

'

'

Debt Instrument, Interest Rate, Stated Percentage

'

'

'

'

'

'

5.50%

'

'

'

'

'

3.24%

'

'

'

'

10.00%

'

'

'

Repayment Period

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'96 months

'

'

'

'

'

Long-term Debt

222,355,000

'

152,062,000

'

'

'

'

'

'

25,999,000

'

25,259,000

'

23,600,000

22,200,000

'

0

'

'

'

'

Derivative, Fixed Interest Rate

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

3.94%

'

'

Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount

'

'

'

'

'

30,900,000

68,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Period of Interest Only Quarterly Payments

'

'

'

'

'2 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Loans Payable to Bank

'

'

'

'

'

'

'

'

'

0

'

400,000

'

'

'

'

'

'

'

'

'

Other Loans Payable

100,000

200,000

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Export Financing Agreement

'

$2,200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$2,500,000

$2,200,000

Export Funding Agreement, Term

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'1 year

'1 year

Debt_Letters_of_Credit_Details

Debt - Letters of Credit (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2012
Debt Instrument [Line Items]	'	'	'
Restricted cash	$1,721,000	$1,648,000	'
Letter of Credit [Member]	'	'	'
Debt Instrument [Line Items]	'	'	'
Letters of Credit Outstanding, Amount	'	'	1,000,000
Restricted cash	$1,700,000	$900,000	'

Commitments_and_Contingencies_1

Commitments and Contingencies (Details) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013
Commitments and Contingencies Disclosure [Abstract]	'	'	'	'	'
Operating Leases, Rent Expense	$1,300,000	$2,100,000	$2,700,000	$1,400,000	'
Capital Leases, Future Minimum Payments Due [Abstract]	'	'	'	'	'
2014	557,000	'	557,000	'	'
2015	462,000	'	462,000	'	'
2016	159,000	'	159,000	'	'
2017	0	'	0	'	'
2018	0	'	0	'	'
Thereafter	0	'	0	'	'
Total future minimum lease payments	1,178,000	'	1,178,000	'	'
Less: amount representing interest	-68,000	'	-68,000	'	'
Present value of minimum lease payments	1,110,000	'	1,110,000	'	'
Less: current portion	-882,000	'	-882,000	'	-956,000
Long-term portion	228,000	'	228,000	'	287,000
Operating Leases, Future Minimum Payments Due, Fiscal Year Maturity [Abstract]	'	'	'	'	'
2014	3,182,000	'	3,182,000	'	'
2015	6,606,000	'	6,606,000	'	'
2016	6,614,000	'	6,614,000	'	'
2017	6,588,000	'	6,588,000	'	'
2018	6,675,000	'	6,675,000	'	'
Thereafter	32,320,000	'	32,320,000	'	'
Total future minimum lease payments	61,985,000	'	61,985,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Next Twelve Months	3,739,000	'	3,739,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Two Years	7,068,000	'	7,068,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Three Years	6,773,000	'	6,773,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Four Years	6,588,000	'	6,588,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Due in Five Years	6,675,000	'	6,675,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due, Due Thereafter	32,320,000	'	32,320,000	'	'
Capital Leases And Operating Leases, Future Minimum Payments Due	$63,163,000	'	$63,163,000	'	'

Commitments_and_Contingencies_2

Commitments and Contingencies - Guarantor Arrangements/Purchase Obligations and Other Matters (Details)

Jun. 30, 2014

Mar. 31, 2014

Nov. 30, 2010

Jun. 30, 2014

Mar. 31, 2014

Nov. 15, 2011

Mar. 31, 2014

Dec. 31, 2013

Nov. 15, 2011

Nov. 15, 2011

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2011

Jun. 30, 2014

Jul. 13, 2012

Dec. 02, 2013

Sep. 30, 2013

Jul. 30, 2012

Mar. 31, 2014

29-May-14

Mar. 31, 2014

Mar. 18, 2013

Mar. 31, 2014

In Millions, except Per Share data, unless otherwise specified

USD ($)

USD ($)

FINEP Credit Facility [Member]

FINEP Credit Facility [Member]

FINEP Credit Facility [Member]

Performance Guarantee [Member]

Performance Guarantee [Member]

Performance Guarantee [Member]

Performance Guarantee [Member]

Performance Guarantee [Member]

BNDES Credit Facility [Member]

BNDES Credit Facility [Member]

BNDES Credit Facility [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Pine and Nossa Caixa Loan Agreement [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Hercules Loan Facility [Member]

Hercules Loan Facility [Member]

ABC Brasil Agreement [Member]

ABC Brasil Agreement [Member]

Chattel Mortgage [Member]

Chattel Mortgage [Member]

Payment Guarantee [Member]

Payment Guarantee [Member]

Payment Guarantee [Member]

Payment Guarantee [Member]

BNDES [Member]

BNDES [Member]

BNDES [Member]

USD ($)

BRL

USD ($)

USD ($)

USD ($)

Unsecured Debt [Member]

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

BRL

USD ($)

USD ($)

USD ($)

BRL

USD ($)

BRL

USD ($)

Loss Contingencies [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

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

'

'

'

$2.70

6

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Collateral Provided By Company, Certain Equipment and Other Tangible Assets, Amount

'

'

'

'

'

'

'

'

'

'

11.3

24.9

'

30.9

68

'

'

'

'

'

'

'

'

Export Financing Agreement

'

2.2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2.5

2.2

Export Funding Agreement, Term

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'1 year

'1 year

Period Required For Restricted Cash

'

'

'

'

'

'3 months

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Restricted Cash and Cash Equivalents

'

'

'

'

'

'

0.8

0.7

0.1

0.2

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Convertible Promissory Note, Held by Third Party

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

48.3

'

'

'

'

'

'

'

Debt Instrument, Convertible, Conversion Price

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$2.20

$7.07

$7.07

$4.11

'

'

'

'

Debt Instrument, Face Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

23.6

52

'

'

105

69

'

'

'

'

Debt Instrument, Interest Rate, Stated Percentage

'

'

5.00%

'

'

'

'

'

'

'

'

'

7.00%

'

5.50%

'

'

'

1.50%

9.50%

'

'

'

Loans Payable

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

25

'

'

Purchase Obligation

6.8

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

21.7

'

'

'

'

Purchase Obligation, Due in Second Year

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10.85

'

'

'

'

Forbearance Fee Due

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10

10

'

'

Debt Instrument, Financing Transaction, Additional Cash Proceeds

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

50

'

'

'

Contractual Obligation

5.9

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Loss on Purchase Commitments

$2.40

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Joint_Ventures_and_Noncontroll2

Joint Ventures and Noncontrolling Interest - Narrative (Details)	Mar. 31, 2014	Mar. 26, 2013	Mar. 31, 2013	Jun. 30, 2011	Mar. 26, 2013	Mar. 26, 2013	Jun. 30, 2014	Apr. 30, 2010	Apr. 14, 2010	Jun. 30, 2014	Mar. 31, 2014
	EUR (€)	Joint Venture with Cosan [Member]	Joint Venture with Cosan [Member]	Joint Venture with Cosan [Member]	Joint Venture with Cosan [Member]	Joint Venture with Cosan [Member]	Joint Venture with Cosan [Member]	SMA Industria Quimica S.A. [Member]	SMA Industria Quimica S.A. [Member]	Maximum [Member]	Maximum [Member]
		USD ($)	Corporate Joint Venture [Member]	Corporate Joint Venture [Member]	Corporate Joint Venture [Member]	Amyris Brasil S.A. Subsidiary [Member]	Amyris Brasil S.A. Subsidiary [Member]	Corporate Joint Venture [Member]	Corporate Joint Venture [Member]	SMA Industria Quimica S.A. [Member]	SMA Industria Quimica S.A. [Member]
						BRL	BRL		member	Corporate Joint Venture [Member]	Corporate Joint Venture [Member]
									Y	USD ($)	BRL
Redeemable Noncontrolling Interest [Line Items]	'	'	'	'	'	'	'	'	'	'	'
Initial Term of Joint Venture	'	'	'20 years	'20 years	'	'	'	'20 years	'	'	'
Initial Term Shareholders Agreement	'	'	'	'10 years	'	'	'	'	'	'	'
Equity Method Investment Number of Members of Executive Committee	'	'	'	'	'	'	'	'	3	'	'
Equity Method Investment Number of Company Appointed Members of Executive Committee	'	'	'	'	'	'	'	'	2	'	'
Equity Method Investment Number of Members of Board of Directors	'	'	'	'	'	'	'	'	4	'	'
Equity Method Investment Number of Members of Board of Directors Appointed by Each Venture	'	'	'	'	'	'	'	'	2	'	'
Due from Joint Ventures	'	'	'	'	'	'	'	'	'	$28,100,000	61,800,000
Equity Method Investment Period Company is required to Purchase Output of SMA	'	'	'	'	'	'	'	'	4	'	'
Equity Method Investment, Ownership Percentage	'	'	'	50.00%	50.00%	'	'	'	50.00%	'	'
Obligation to Fund Agreement, Cash Portion	'	10,000,000	'	'	'	'	'	'	'	'	'
Equity Method Investment Ownership Percentage Required	'	'	'	10.00%	'	'	'	'	'	'	'
Agreement to Sell Equity Ownership	'	'	'	'	'	22,000	9,989	'	'	'	'
Capitalization, Long-term Debt and Equity	€ 100,000	'	'	'	'	'	'	'	'	'	'

Joint_Ventures_and_Noncontroll3

Joint Ventures and Noncontrolling Interest - Variable Interest Entity (Details)

3 Months Ended

6 Months Ended

3 Months Ended

1 Months Ended

0 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 31, 2014

Dec. 31, 2013

Mar. 31, 2014

Jun. 30, 2014

Dec. 31, 2013

Jan. 31, 2011

Jan. 31, 2011

Jun. 30, 2014

Mar. 26, 2013

Mar. 26, 2013

Jun. 30, 2011

Mar. 26, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Dec. 31, 2013

Apr. 14, 2010

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

USD ($)

USD ($)

USD ($)

USD ($)

EUR (€)

USD ($)

Variable Interest Entity, Primary Beneficiary [Member]

Variable Interest Entity, Primary Beneficiary [Member]

Variable Interest Entity, Primary Beneficiary [Member]

Glycotech Agreement [Member]

Glycotech Agreement [Member]

Glycotech Agreement [Member]

Joint Venture with Cosan [Member]

Joint Venture with Cosan [Member]

Joint Venture with Cosan [Member]

Joint Venture with Cosan [Member]

Joint Venture with Cosan [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

SMA Industria Quimica S.A. [Member]

SMA Industria Quimica S.A. [Member]

SMA Industria Quimica S.A. [Member]

Novvi LLC [Member]

consolidated_VIE

USD ($)

USD ($)

USD ($)

Variable Interest Entity, Primary Beneficiary [Member]

Variable Interest Entity, Primary Beneficiary [Member]

USD ($)

Corporate Joint Venture [Member]

Corporate Joint Venture [Member]

Amyris Brasil S.A. Subsidiary [Member]

Amyris Brasil S.A. Subsidiary [Member]

USD ($)

USD ($)

USD ($)

USD ($)

USD ($)

Corporate Joint Venture [Member]

Maximum [Member]

Maximum [Member]

USD ($)

consolidated_VIE

USD ($)

BRL

BRL

Corporate Joint Venture [Member]

Corporate Joint Venture [Member]

USD ($)

BRL

Variable Interest Entity [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Equity Method Investment Ownership Percentage Required

'

'

'

'

'

'

'

'

'

'

'

'

'

'

10.00%

'

'

'

'

'

'

'

'

'

'

'

Equity Method Investment, Ownership Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

50.00%

50.00%

'

'

'

'

'

'

'

50.00%

'

'

'

Agreement to Sell Equity Ownership

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

22,000

9,989

'

'

'

'

'

'

'

'

'

Due from Joint Ventures

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

28,100,000

61,800,000

'

Variable Interest Entity, Consolidated, Carrying Amount, Assets

'

'

'

'

'

'

27,509,000

'

25,730,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Period of Initial Term of Collaboration Agreement

'

'

'

'

'

'

'

'

'

'2 years

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Additional Year Periods of Collaboration Agreement

'

'

'

'

'

'

'

'

'

'1 year

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity, Financial or Other Support, Percentage

'

'

'

'

'

'

'

'

'

'

100.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity Number of Entities (in VIEs)

'

'

2

'

'

'

2

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity, Consolidated, Carrying Amount, Other Assets

'

'

'

'

'

'

'

4,100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity, Consolidated, Carrying Amount, Current Assets

'

'

'

'

'

'

500,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity, Consolidated, Carrying Amount, Accounts Payable And Accrued Liabilities

'

'

'

'

'

'

'

200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Variable Interest Entity, Consolidated, Carrying Amount, Loan Obligations

'

'

'

'

'

'

'

'

'

'

'

100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Assets

'

'

'

'

'

'

'

22,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Liabilities

'

'

'

'

'

'

421,000

'

229,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Obligation to Fund Agreement, Cash Portion

'

'

'

'

'

'

'

'

'

'

'

'

10,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

Investments in joint venture (1)

2,170,000

[1]

'

2,170,000

[1]

'

'

68,000

[1]

'

'

'

'

'

'

'

'

'

'

'

2,100,000

'

2,100,000

'

0

'

'

'

200,000

Equity Method Investment, Summarized Financial Information, Gross Profit (Loss)

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

0

'

'

'

'

'

'

Related party grants and collaborations revenue

0

109,000

0

2,647,000

'

'

'

'

'

'

'

'

'

'

'

'

'

0

300,000

0

2,800,000

'

'

'

'

'

Capitalization, Long-term Debt and Equity

'

'

'

'

€ 100,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

[1]

The investments in joint venture represents the Company's investments in the joint venture with Novvi LLC and Total Amyris Biosolutions B.V. of $2.1 million and $0.1 million as of June 30, 2014, respectively, and zero and $0.1 million as of December 31, 2013, respectively.

Joint_Ventures_and_Noncontroll4

Joint Ventures and Noncontrolling Interest - Noncontrolling Interest (Details) (USD $)	3 Months Ended		6 Months Ended		3 Months Ended		6 Months Ended	3 Months Ended	1 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Mar. 31, 2014	Mar. 31, 2013	Jun. 30, 2014	Mar. 31, 2014	Jan. 31, 2011	Apr. 14, 2010
			consolidated_VIE		Noncontrolling Interest [Member]	Noncontrolling Interest [Member]	Noncontrolling Interest [Member]	Variable Interest Entity, Primary Beneficiary [Member]	Variable Interest Entity, Primary Beneficiary [Member]	SMA Industria Quimica S.A. [Member]
								consolidated_VIE	Glycotech Agreement [Member]	Corporate Joint Venture [Member]
										member
Noncontrolling Interest [Line Items]	'	'	'	'	'	'	'	'	'	'
Equity Method Investment Number of Members of Executive Committee that are Senior Executive	'	'	'	'	'	'	'	'	'	1
Variable Interest Entity, Consolidated, Carrying Amount, Current Assets	'	'	'	'	'	'	'	$500,000	'	'
Variable Interest Entity Number of Entities (in VIEs)	'	'	2	'	'	'	'	2	'	'
Variable Interest Entity, Financial or Other Support, Percentage	'	'	'	'	'	'	'	'	100.00%	'
Stockholders' Equity Attributable to Noncontrolling Interest [Roll Forward]	'	'	'	'	'	'	'	'	'	'
Beginning Balance	'	'	-584,000	'	-584,000	-877,000	-584,000	'	'	'
Foreign currency translation adjustment	'	'	4,411,000	'	-42,000	54,000	-42,000	'	'	'
Income (loss) attributable to noncontrolling interest	31,000	38,000	60,000	-261,000	60,000	-261,000	'	'	'	'
Ending Balance	($686,000)	'	($686,000)	'	($686,000)	($562,000)	'	'	'	'

Significant_Agreements_Narrati

Significant Agreements - Narrative (Details) (USD $)

6 Months Ended

0 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Apr. 04, 2014

Apr. 23, 2013

Mar. 13, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Mar. 31, 2014

Mar. 31, 2014

Jun. 30, 2014

International Flavors & Fragrances Inc Agreement [Member]

Firmenich SA Agreement [Member]

Firmenich SA Agreement [Member]

Firmenich SA Agreement [Member]

Firmenich SA Agreement [Member]

Firmenich SA Agreement [Member]

Firmenich SA Agreement [Member]

Kuraray Securities Purchase Agreement [Member]

Kuraray Securities Purchase Agreement, Equal Installment Amount [Member]

Common Stock [Member]

Common Stock [Member]

Common Stock [Member]

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

'

'

'

'

'

'

'

'

'

'

'

'

'

Collaboration Agreement, Range of Funding, First Phase of Collaberation

'

'

'

$6,000,000

'

'

'

'

'

'

'

'

'

Collaboration Agreement, Annual Funding

'

'

'

'

'

'

'

10,000,000

'

'

'

'

'

Collaboration Agreement, Period

'

'

'

'

'

'

'

'3 years

'

'

'

'

'

Revenue Reognized, Including Portion Related to Milestone Method

'

'

'

'

'

2,500,000

2,800,000

'

5,000,000

3,200,000

'

'

'

Revenue Recognition, Milestone Method, Potential Revenue to be Recognized

'

'

'

'

5,000,000

'

'

'

'

'

'

'

'

Proceeds from issuance of common stock in private placements, net of issuance costs

4,000,000

19,980,000

'

'

'

'

'

'

'

'

4,000,000

2,000,000

'

Stock Issued During Period, Shares, New Issues

'

'

'

'

'

'

'

'

'

'

'

'

943,396

Stock Issued During Period, Price Per Share, New Issues

'

'

'

'

'

'

'

'

'

'

$4.24

'

'

Pilot plant service agreement

'

'

900,000

'

'

'

'

'

'

'

'

'

'

Sublease agreement

'

'

100,000

'

'

'

'

'

'

'

'

'

'

Accrued Liabilities

$300,000

'

'

'

'

'

'

'

'

'

'

'

'

Goodwill_and_Intangible_Assets2

Goodwill and Intangible Assets (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013	Jun. 30, 2014	Jun. 30, 2013	Dec. 31, 2013	Jun. 30, 2014	Dec. 31, 2013	Oct. 31, 2011
			Acquired Licenses and Permits [Member]	Acquired Licenses and Permits [Member]	Acquired Licenses and Permits [Member]	In Process Research and Development [Member]	In Process Research and Development [Member]	Draths Corporation [Member]
Schedule of Finite-Lived and Indefinite-Lived Intangible Assets [Line Items]	'	'	'	'	'	'	'	'
Indefinite-Lived Intangible Assets (Excluding Goodwill)	'	'	'	'	'	$8,560,000	$8,560,000	'
Finite-Lived Intangible Asset, Useful Life	'	'	'2 years	'	'	'	'	'
Finite-Lived Intangible Assets, Gross	'	'	772,000	'	772,000	'	'	'
Finite-Lived Intangible Assets, Accumulated Amortization	-772,000	-772,000	-772,000	'	-772,000	'	'	'
Finite-Lived Intangible Assets, Net	9,120,000	9,120,000	0	'	0	'	'	'
Goodwill	560,000	560,000	'	'	'	'	'	'
Goodwill and Intangible Assets, Gross	9,892,000	9,892,000	'	'	'	'	'	'
Goodwill and Intangible Assets, Net	9,120,000	9,120,000	'	'	'	'	'	'
Business Acquisition, Purchase Price Allocation, In-Process Research and Development	'	'	'	'	'	'	'	8,600,000
Business Acquisition, Purchase Price Allocation, Goodwill and Other Intangible Assets, Amount	'	'	'	'	'	'	'	600,000
Amortization of Intangible Assets	'	'	$0	($32,000)	'	'	'	'

Stockholders_Deficit_Details

Stockholders' Deficit (Details) (USD $)

3 Months Ended

6 Months Ended

1 Months Ended

1 Months Ended

6 Months Ended

3 Months Ended

In Thousands, except Share data, unless otherwise specified

Mar. 31, 2014

Jun. 30, 2014

Dec. 31, 2013

Sep. 30, 2010

Jan. 31, 2014

Dec. 31, 2013

Jan. 31, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

Dec. 31, 2013

Mar. 31, 2014

votes

Equity Incentive Plan, 2010 [Member]

Equity Incentive Plan, 2010 [Member]

Employee Stock Purchase Plan, 2010 [Member]

Employee Stock Purchase Plan, 2010 [Member]

Additional Paid-in Capital [Member]

Common Stock [Member]

Common Stock [Member]

Kuraray Securities Purchase Agreement [Member]

Common Stock [Member]

Class of Stock [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

Issuance of common stock in a private placement, shares

'

'

'

'

'

'

'

'

'

943,396

'

'

Stock Issued During Period, Price Per Share, New Issues

'

'

'

'

'

'

'

'

'

'

'

$4.24

Issuance of common stock in a private placement

'

$4,000

'

'

'

'

'

'

$4,000

$4,000

'

'

Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized

'

'

'

'

3,833,141

'

766,628

'

'

'

'

'

Share-based Compensation Arrangement by Share-based Payment Award, Number of Additional Shares Authorized, Percentage Increase of Common Stock, Shares, Outstanding

'

'

'

'

'

'

'

1.00%

'

'

'

'

Shares Available For Issuance Percentage Of Total Outstanding Shares

'

'

'

'

'

5.00%

'

'

'

'

'

'

Common Stock, Shares, Outstanding

'

78,914,451

76,662,812

'

'

'

'

'

'

78,914,451

76,662,812

'

Common stock, shares authorized

'

300,000,000

200,000,000

'

'

'

'

'

'

'

'

'

Common Stock, Number of Votes Entitled to Holder of each share

1

'

'

'

'

'

'

'

'

'

'

'

Preferred stock, shares authorized

'

5,000,000

5,000,000

5,000,000

'

'

'

'

'

'

'

'

Stockholders_Deficit_Common_St

Stockholders' Deficit - Common Stock Warrants (Details) (Common Stock [Member], USD $)	3 Months Ended	12 Months Ended		3 Months Ended
In Millions, except Share data, unless otherwise specified	Mar. 31, 2014	Dec. 31, 2013	Dec. 31, 2012	Mar. 31, 2014	Oct. 31, 2013
	Warrants In Connection With Capital Lease Arrangement [Member]	Warrants In Connection With Capital Lease Arrangement [Member]	Warrants In Connection With Capital Lease Arrangement [Member]	Warrants In Connection With Issuance of Tranche I Convertible Promissory Notes [Member]	Warrants In Connection With Issuance of Tranche I Convertible Promissory Notes [Member]
Class of Warrant or Right [Line Items]	'	'	'	'	'
Class of Warrant or Right, Outstanding	'	'	21,087	'	1,000,000
Class of Warrant or Right, Exercise Price of Warrants or Rights	'	'	10.67	'	0.01
Warrants and Rights Outstanding	'	'	$0.20	'	$1.30
Contractual term (in years)	'	'10 years	'	'3 years 5 months	'
Risk-free interest rate	2.00%	'	'	0.77%	'
Expected volatility	86.00%	'	'	45.00%	'
Expected dividend yield	0.00%	'	'	0.00%	'

StockBased_Compensation_Stock_

Stock-Based Compensation - Stock Option Activity (Details) (USD $)

3 Months Ended

6 Months Ended

12 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Dec. 31, 2013

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Mar. 31, 2014

Jun. 30, 2014

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

Employee Stock Option [Member]

$0.10—$2.79

$0.10—$2.79

$2.81—$2.94

$2.81—$2.94

$2.96—$3.44

$2.96—$3.44

$3.51—$3.51

$3.51—$3.51

$3.55—$3.93

$3.55—$3.93

$4.06—$16.00

$4.06—$16.00

$16.50—$24.50

$16.50—$24.50

$25.43—$25.43

$25.43—$25.43

$26.84—$26.84

$26.84—$26.84

$30.17—$30.17

$30.17—$30.17

$0.10—$30.17

$0.10—$30.17

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding [Roll Forward]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Oustanding, Beginning Balance

'

'

'

'

8,409,605

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Options granted

'

'

'

'

2,909,183

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Options exercised

'

'

'

'

-337,110

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Options cancelled

'

'

'

'

-485,971

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Ending Balance

'

'

'

'

10,495,707

8,409,605

'

1,580,682

'

1,056,600

'

945,057

'

2,489,199

'

1,700,908

'

1,555,854

'

724,345

'

15,000

'

368,062

'

60,000

'

10,495,707

Share-based Compensation Arrangement by Share-based Payment Award, Options, Outstanding, Weighted Average Exercise Price [Roll Forward]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Weighted Average Exercise Price, Beginning Balance

'

'

'

'

$7.39

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Weighted Average Exercise Price, Options granted

'

'

'

'

$3.51

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Weighted Average Exercise Price, Options exercised

'

'

'

'

$3.06

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Weighted Average Exercise Price, Options cancelled

'

'

'

'

$7.09

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options Outstanding, Weighted Average Exercise Price, Ending Balance

'

'

'

'

$6.47

$7.39

'

$2.66

'

$2.88

'

$3.14

'

$3.51

'

$3.88

'

$10.11

'

$20.10

'

$25.43

'

$26.84

'

$30.17

'

$6.47

Options Outstanding, Weighted Average Remaining Contractual Life (Years)

'

'

'

'

'7 years 8 months 19 days

'7 years 4 months 24 days

'

'8 years 2 months 12 days

'

'8 years 11 months 9 days

'

'8 years 6 months 18 days

'

'9 years 9 months

'

'5 years 9 months

'

'5 years 11 months 9 days

'

'5 years 11 months 19 days

'

'7 years 0 months 26 days

'

'6 years 7 months 21 days

'

'6 years 8 months 16 days

'

'7 years 8 months 19 days

Options Outstanding, Aggregate Intrinsic Value

'

'

'

'

$3,709,000

$12,393,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Vested and Expected to Vest, Number Outstanding

'

'

'

'

9,590,575

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Vested and Expected to Vest, Weighted Average Exercise Price

'

'

'

'

$6.72

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Vested and Expected to Vest, Weighted Average Remaining Contractual Life (Years)

'

'

'

'

'7 years 6 months 29 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Vested and Expected to Vest, Aggregate Intrinsic Value

'

'

'

'

3,326,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Exercisable, Number Outstanding

'

'

'

'

4,554,010

'

'

476,896

'

279,097

'

304,429

'

0

'

1,247,160

'

1,281,705

'

625,057

'

15,000

'

264,666

'

60,000

'

4,554,010

Options, Exercisable, Weighted Average Exercise Price

'

'

'

'

$9.29

'

'

$2.52

'

$2.87

'

$3.07

'

$0

'

$3.89

'

$9.88

'

$20.11

'

$25.43

'

$26.84

'

$30.17

'

$9.29

Options, Exercisable, Weighted Average Remaining Contractual Life (Years)

'

'

'

'

'6 years 1 month 17 days

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Options, Exercisable, Aggregate Intrinsic Value

'

'

'

'

1,027,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Aggregate intrinsic value of options exercised under all option plans

$0

$100,000

$500,000

$300,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Exercise Price Range, Lower Range Limit

'

'

'

'

'

'

$0.10

'

$2.81

'

$2.96

'

$3.51

'

$3.55

'

$4.06

'

$16.50

'

$25.43

'

$26.84

'

$30.17

'

$0.10

'

Exercise Price Range, Upper Range Limit

'

'

'

'

'

'

$2.79

'

$2.94

'

$3.44

'

$3.51

'

$3.93

'

$16

'

$24.50

'

$25.43

'

$26.84

'

$30.17

'

$30.17

'

StockBased_Compensation_Restri

Stock-Based Compensation - Restricted Stock Units and Restricted Stock Activity (Details) (Restricted Stock Units (RSUs) [Member], USD $)	6 Months Ended	12 Months Ended
	Jun. 30, 2014	Dec. 31, 2013
Restricted Stock Units (RSUs) [Member]	'	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Number of Shares [Roll Forward]	'	'
RSU's Outstanding, Beginning Balance	2,316,437	'
RSU's Oustanding, Units awarded	1,049,300	'
RSU's Outstanding, Units vested	-1,158,585	'
RSU's Outstanding, Units forfeited	-98,863	'
RSU's Outstanding, Ending Balance	2,108,289	2,316,437
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Nonvested, Weighted Average Grant Date Fair Value [Roll Forward]	'	'
RSU's Outstanding, Weighted Average Grant Date Fair Value, Beginning Balance	$4.30	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Grants in Period, Weighted Average Grant Date Fair Value	$3.51	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Vested in Period, Weighted Average Grant Date Fair Value	$4.68	'
Share-based Compensation Arrangement by Share-based Payment Award, Equity Instruments Other than Options, Forfeited in Period, Weighted Average Grant Date Fair Value	$3.17	'
RSU's Outstanding, Weighted Average Grant Date Fair Value, Ending Balance	$3.75	$4.30
RSU's Outstanding, Weighted Average Remaining Contractual Life (Years)	'1 year 4 months 21 days	'10 months 17 days
RSU's Outstanding, Expected to Vest	1,803,053	'
RSU's Outstanding, Expected to Vest, Weighted Average Grant Date Fair Value	$3.75	'
RSU's Outstanding, Expected to Vest , Weighted Average Remaining Contractual Life (Years)	'1 year 3 months 22 days	'

StockBased_Compensation_StockB

Stock-Based Compensation - Stock-Based Compensation Expense (Details) (USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	$3,683,000	$4,985,000	$7,197,000	$9,178,000
Employee Share Based Compensation [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Weighted average period expense is to be recognized	'	'	'2 years 0 months 26 days	'
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	2.00%	1.00%	2.00%	1.00%
Expected term (in years)	'6 years 1 month 2 days	'6 years 1 month 6 days	'6 years 1 month 6 days	'6 years 1 month 6 days
Expected volatility	75.00%	82.00%	75.00%	82.00%
Employee Share Based Compensation [Member] | Common Stock [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Unrecognized compensation expense	15,000,000	'	15,000,000	'
Weighted average period expense is to be recognized	'	'	'2 years 11 months 5 days	'
Employee Share Based Compensation [Member] | Restricted Stock Units (RSUs) [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Unrecognized compensation expense	4,900,000	'	4,900,000	'
Research and Development [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	909,000	1,049,000	1,707,000	2,296,000
Sales General and Administrative [Member]	'	'	'	'
Employee Service Share-based Compensation, Allocation of Recognized Period Costs [Line Items]	'	'	'	'
Allocated Share-based Compensation Expense	$2,774,000	$3,936,000	$5,490,000	$6,882,000

StockBased_Compensation_Nonemp

Stock-Based Compensation - Nonemployee Stock-Based Compensation (Details) (Non Employee Share Based Compensation [Member], USD $)	3 Months Ended		6 Months Ended
	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Stock Options [Member]	'	'	'	'
Share-based Goods and Nonemployee Services Transaction [Line Items]	'	'	'	'
Granted options to purchase, common stock	'	'	20,000	20,000
Compensation expense	$97,226	$8,000	$138,900	$22,000
Expected dividend yield	0.00%	0.00%	0.00%	0.00%
Risk-free interest rate	2.00%	2.00%	2.00%	2.00%
Expected term (in years)	'5 years 9 months 18 days	'6 years 1 month 6 days	'5 years 11 months 9 days	'6 years 4 months 24 days
Expected volatility	75.00%	82.00%	76.00%	83.00%
Restricted Stock Units (RSUs) [Member]	'	'	'	'
Share-based Goods and Nonemployee Services Transaction [Line Items]	'	'	'	'
Compensation expense	$12,000	$15,000	$9,000	$39,000

Employee_Benefit_Plan_Details

Employee Benefit Plan (Details) (USD $)	3 Months Ended		6 Months Ended
In Millions, unless otherwise specified	Jun. 30, 2014	Mar. 31, 2014	Jun. 30, 2014
Compensation and Retirement Disclosure [Abstract]	'	'	'
401K Voluntary Contributions, Percentage of Eligible Compensation	'	90.00%	'
Defined Contribution Plan, Minimum Service Vesting Period	'	'1 year	'
Defined Contribution Plan, Employer Discretionary Contribution Amount	$0.10	'	$0.20

Related_Party_Transactions_Det

Related Party Transactions (Details) (USD $)

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

3 Months Ended

6 Months Ended

6 Months Ended

0 Months Ended

1 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

3 Months Ended

1 Months Ended

0 Months Ended

1 Months Ended

1 Months Ended

3 Months Ended

6 Months Ended

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Apr. 04, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Dec. 31, 2013

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Jul. 30, 2012

Jan. 31, 2014

Jun. 30, 2014

Dec. 31, 2013

Dec. 02, 2013

Oct. 31, 2013

Jul. 26, 2013

Jun. 06, 2013

Oct. 31, 2013

Aug. 31, 2013

Oct. 31, 2013

Jun. 30, 2014

Mar. 31, 2014

Dec. 31, 2013

Jun. 30, 2014

Jun. 30, 2014

Jun. 30, 2014

Sep. 30, 2013

Aug. 31, 2013

Oct. 31, 2013

Jul. 31, 2013

Jun. 30, 2013

Oct. 31, 2013

Jun. 30, 2014

Jan. 31, 2014

Jun. 30, 2014

Jan. 31, 2014

Aug. 31, 2013

Dec. 31, 2013

Dec. 02, 2013

Jan. 31, 2014

Aug. 31, 2013

Mar. 31, 2013

Mar. 26, 2013

Aug. 31, 2013

Aug. 31, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Jun. 30, 2013

Jun. 30, 2014

Dec. 31, 2013

Jun. 30, 2014

Dec. 31, 2013

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Novvi LLC [Member]

Total Gas And Power USA Biotech Agreement [Member]

Total Gas And Power USA Biotech Agreement [Member]

Total Gas And Power USA Biotech Agreement [Member]

Total Gas And Power USA Biotech Agreement [Member]

Total Gas And Power USA Biotech Agreement [Member]

Common Stock [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Total [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Related Party Financings [Member]

Temasek [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

First Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Second Tranche [Member]

Private Placement [Member]

Private Placement [Member]

Private Placement [Member]

Private Placement [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

Derivative Liability - Compound Embedded Derivatives [Member]

July 2013 Convertible Notes [Member]

July 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Unsecured Debt [Member]

Unsecured Debt [Member]

Unsecured Debt [Member]

Rule 144A Convertible Notes [Member]

Rule 144A Convertible Notes [Member]

Related Party Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Unsecured Senior Convertible Promissory Notes [Member]

Cancellation of the Temasek Bridge Note [Member]

Related Party Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Related Party Convertible Notes [Member]

Biolding Investment SA [Member]

Biolding Investment SA [Member]

Related Party Convertible Notes [Member]

Related Party Financings [Member]

Significant Unobservable Inputs (Level 3) [Member]

Significant Unobservable Inputs (Level 3) [Member]

Significant Unobservable Inputs (Level 3) [Member]

Significant Unobservable Inputs (Level 3) [Member]

Related Party Financings [Member]

Rule 144A Convertible Notes [Member]

July 2013 Convertible Notes [Member]

July 2013 Convertible Notes [Member]

Temasek Bridge Note [Member]

Rule 144A Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

August 2013 Convertible Notes [Member]

Common Stock [Member]

Common Stock [Member]

Wolverine [Member]

Wolverine [Member]

Related Party Financings [Member]

Related Party Financings [Member]

August 2013 Convertible Notes [Member]

Related Party Transaction [Line Items]

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Stock Issued During Period, Shares, New Issues

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

943,396

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,533,742

'

'

'

'

'

'

'

'

'

'

'

Stock Issued During Period, Price Per Share, New Issues

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$3.26

'

'

'

'

'

'

'

'

'

'

'

Proceeds from issuance of common stock in private placements, net of issuance costs

'

'

$4,000,000

$19,980,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

$5,000,000

'

'

'

'

'

'

'

'

'

'

'

Commitment to purchase company common stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

15,000,000

'

'

'

'

'

'

'

'

'

'

Benefical Owner, Ownership Percentage of Common Stock

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

5.00%

'

'

'

'

'

'

'

'

Debt Instrument, Interest Rate, Stated Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1.50%

'

'

'

'

'

'

5.50%

1.50%

1.50%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Face Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

105,000,000

'

'

'

'

'

20,000,000

10,000,000

'

'

'

'

69,000,000

'

'

'

'

'

73,000,000

'

20,000,000

10,000,000

'

'

34,000,000

'

'

42,600,000

'

'

3,000,000

30,400,000

'

'

110,000,000

'

'

'

'

'

'

'

'

'

Bridge Loan

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

35,000,000

'

'

'

'

35,000,000

'

'

'

'

'

'

5,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future Cancellation Of Debt, Amount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

44,200,000

13,000,000

'

'

'

'

'

'

'

'

'

'

'

'

35,000,000

'

'

'

'

'

'

'

'

5,400,000

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Interest Rate, Stated Default Percentage

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

2.00%

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Future Proceeds from Convertible Debt

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

21,700,000

'

'

'

'

'

'

'

'

60,000,000

'

'

'

'

9,700,000

'

'

'

'

'

'

'

'

'

'

'

'

35,000,000

'

6,000,000

6,000,000

25,000,000

'

'

'

'

'

'

'

'

'

'

'

'

Proceeds from Convertible Debt

72,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

24,700,000

5,000,000

9,700,000

'

'

'

'

'

'

10,000,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Long-term Debt

222,355,000

'

222,355,000

'

'

152,062,000

'

'

'

'

'

'

'

'

'

'

'

'

29,300,000

28,500,000

'

'

100,480,000

89,499,000

25,000,000

'

'

'

'

'

'

40,300,000

'

51,500,000

'

'

'

'

'

'

'

'

'

'

'

46,200,000

'

'

37,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Debt Instrument, Unamortized Discount

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-55,300,000

23,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Gains (Losses) on Extinguishment of Debt

-1,100,000

0

-10,512,000

0

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-9,400,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-19,900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Fair Value, Measurement with Unobservable Inputs Reconciliations, Recurring Basis, Liability Value

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

145,032,000

131,117,000

107,200,000

116,800,000

Fair Value, Measurement with Unobservable Inputs Reconciliation, Liability, Transfers Into Level 3

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

1,400,000

1,100,000

'

'

'

'

'

Fair Value, Measurement with Unobservable Inputs Reconciliation, Recurring Basis, Liability, Gain (Loss) Included in Earnings

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

-4,000,000

'

53,100,000

2,500,000

'

'

'

'

Related party grants and collaborations revenue

0

109,000

0

2,647,000

'

'

0

300,000

0

2,800,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Revenue from Related Parties

'

'

'

'

'

'

'

'

'

'

'

'

30,625

32,441

33,250

35,294

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Related party accounts receivable

'

'

'

'

'

'

'

'

'

'

20,604

300,000

30,625

'

30,625

'

200,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

Pilot plant service agreement

'

'

'

'

900,000

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

'

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Sublease agreement

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100,000

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Accrued Liabilities

$300,000

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$300,000

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Income_Taxes_Details

Income Taxes (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Income Tax Disclosure [Abstract]	'	'	'	'
Income Tax Expense (Benefit), Continuing Operations	$125	$246	$236	$482

Reporting_Segments_Details

Reporting Segments (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013	Mar. 31, 2014	Dec. 31, 2013
					businessactivities
					segmentmanagers
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'
Segment Reporting, Number of Business Activities	'	'	'	'	1	'
Segment Reporting, Number of Segment Managers Held Accountable	'	'	'	'	0	'
Revenues	$9,307	$10,849	$15,348	$18,718	'	'
Long-Lived Assets	140,656	'	140,656	'	'	140,591
United States [Member]	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'
Revenues	2,815	4,458	4,788	10,022	'	'
Long-Lived Assets	49,628	'	49,628	'	'	54,015
Brazil [Member]	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'
Revenues	1,402	1,259	2,050	2,077	'	'
Long-Lived Assets	90,375	'	90,375	'	'	85,891
Europe [Member]	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'
Revenues	2,985	4,005	6,338	4,230	'	'
Long-Lived Assets	653	'	653	'	'	685
Asia [Member]	'	'	'	'	'	'
Revenues from External Customers and Long-Lived Assets [Line Items]	'	'	'	'	'	'
Revenues	$2,105	$1,127	$2,172	$2,389	'	'

Comprehensive_Income_Loss_Deta

Comprehensive Income (Loss) (Details) (USD $)	Jun. 30, 2014	Dec. 31, 2013
In Thousands, unless otherwise specified
Equity [Abstract]	'	'
Foreign currency translation adjustment, net of tax	($15,634)	($20,087)
Total accumulated other comprehensive loss	($15,634)	($20,087)

Net_Income_Loss_Attributable_t2

Net Income (Loss) Attributable to Common Stockholders and Net Income (Loss) per Share (Details) (USD $)	3 Months Ended		6 Months Ended
In Thousands, except Share data, unless otherwise specified	Jun. 30, 2014	Jun. 30, 2013	Jun. 30, 2014	Jun. 30, 2013
Earnings Per Share [Abstract]	'	'	'	'
Net loss attributable to Amyris, Inc. common stockholders	($35,479)	($38,876)	($19,094)	($71,490)
Interest on convertible debt	0	0	3,169	0
Accretion of debt discount	0	0	2,518	0
Gain from change in fair value of derivative instruments	0	0	-59,995	0
Net loss attributable to Amyris, Inc. common stockholders after assumed conversion	($35,479)	($38,876)	($73,402)	($71,490)
Weighted average shares of common stock outstanding for basic EPS (in shares)	78,604,692	75,959,228	77,722,437	74,640,314
Basic earnings (loss) per share (in dollars per share)	($0.45)	($0.51)	($0.25)	($0.96)
Effect of dilutive securities:	'	'	'	'
Convertible promissory notes	0	0	32,909,641	0
Weighted common stock equivalents	0	0	32,909,641	0
Diluted weighted-average common shares	78,604,692	75,959,228	110,632,078	74,640,314
Diluted earnings (loss) per share (in dollars per share)	($0.45)	($0.51)	($0.66)	($0.96)
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	83,352,294	25,212,048	50,268,185	25,212,048
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 (in shares)	10,495,707	8,803,300	10,495,707	8,803,300
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 (in shares)	69,727,211	13,617,144	36,643,102	13,617,144
Common Stock Subject to Repurchase [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	0	1	0	1
Common Stock Warrants [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	1,021,087	21,087	1,021,087	21,087
Restricted Stock Units [Member]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]	'	'	'	'
Antidilutive Securities Excluded from Computation of Earnings Per Share, Amount (in shares)	2,108,289	2,770,516	2,108,289	2,770,516

Subsequent_Events_Details

Subsequent Events (Details) (Related Party Convertible Notes [Member], USD $)	0 Months Ended		1 Months Ended
In Millions, unless otherwise specified	Jul. 30, 2012	Jul. 30, 2012	Jul. 31, 2014	Jul. 31, 2014
		Initial Installment [Member]	Subsequent Event [Member]	Subsequent Event [Member]
		July 2014 Convertible Notes [Member]	July 2014 Convertible Notes [Member]	Initial Installment [Member]
				July 2014 Convertible Notes [Member]
Subsequent Event [Line Items]	'	'	'	'
Future Proceeds from Convertible Debt	$21.70	$10.85	$21.70	$10.85