Codexis (CDXS) 10-Q 9 Aug 18 2018 Q2 Quarterly report Financial data

Document and Entity Information

Document and Entity Information - shares	6 Months Ended
	Jun. 30, 2018	Jul. 31, 2018
Document and Entity Information [Abstract]
Entity Registrant Name	CODEXIS INC
Entity Central Index Key	1,200,375
Document Type	10-Q
Document Period End Date	Jun. 30, 2018
Amendment Flag	false
Document Fiscal Year Focus	2,018
Document Fiscal Period Focus	Q2
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		53,512,351

Condensed Consolidated Balance

Condensed Consolidated Balance Sheets - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Current assets:
Cash and cash equivalents	$ 53,621	$ 31,219
Accounts receivable, net of allowances of $34 at June 30, 2018 and December 31, 2017	9,910	11,800
Inventories, net	1,036	1,036
Prepaid expenses and other current assets	1,162	984
Contract assets	554	0
Total current assets	66,283	45,039
Restricted cash	1,460	1,557
Marketable securities	676	671
Property and equipment, net	3,883	2,815
Goodwill	3,241	3,241
Other non-current assets	414	302
Total assets	75,957	53,625
Current liabilities:
Accounts payable	3,082	3,545
Accrued compensation	3,817	4,753
Other accrued liabilities	5,051	4,362
Deferred revenue	4,460	12,292
Total current liabilities	16,410	24,952
Deferred revenue, net of current portion	4,994	1,501
Lease incentive obligation, net of current portion	248	460
Financing obligation, net of current portion	183	302
Other long-term liabilities	1,592	1,863
Total liabilities	23,427	29,078
Commitments and Contingencies (Note 11)
Stockholders' equity:
Preferred stock, $0.0001 par value per share; 5,000 shares authorized; none issued and outstanding	0	0
Common stock, $0.0001 par value per share; 100,000 shares authorized; 53,508 shares and 48,365 shares issued and outstanding at June 30, 2018 and December 31, 2017, respectively	5	5
Additional paid-in capital	380,551	340,079
Accumulated other comprehensive loss	0	(472)
Accumulated deficit	(328,026)	(315,065)
Total stockholders' equity	52,530	24,547
Total liabilities and stockholders' equity	$ 75,957	$ 53,625

Condensed Consolidated Balance3

Condensed Consolidated Balance Sheets (Parenthetical) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Statement of Financial Position [Abstract]
Accounts receivable, allowances	$ 34	$ 34
Preferred stock, par value (usd per share)	$ 0.0001	$ 0.0001
Preferred stock, shares authorized (shares)	5,000,000	5,000,000
Preferred stock, shares issued (shares)	0	0
Preferred stock, shares outstanding (shares)	0	0
Common stock, par value (usd per share)	$ 0.0001	$ 0.0001
Common stock, shares authorized (shares)	100,000,000	100,000,000
Common stock, shares, issued (shares)	53,508,000	48,365,000
Common stock, shares outstanding (shares)	53,508,000	48,365,000

Condensed Consolidated Statemen

Condensed Consolidated Statements of Operations - USD ($) shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Revenues:
Product revenue	$ 3,723	$ 6,600	$ 9,886	$ 12,186
Research and development revenue	9,815	3,747	17,694	6,131
Total revenues	13,538	10,347	27,580	18,317
Costs and operating expenses:
Cost of product revenue	2,611	3,790	6,436	6,792
Research and development	7,370	6,348	14,548	12,187
Selling, general and administrative	7,395	6,546	15,141	13,152
Total costs and operating expenses	17,376	16,684	36,125	32,131
Loss from operations	(3,838)	(6,337)	(8,545)	(13,814)
Interest income	174	49	245	68
Other expenses, net	(82)	(34)	(142)	(12)
Loss before income taxes	(3,746)	(6,322)	(8,442)	(13,758)
Benefit from income taxes	(11)	(42)	(13)	(18)
Net loss	$ (3,735)	$ (6,280)	$ (8,429)	$ (13,740)
Net loss per share, basic and diluted (usd per shares)	$ (0.07)	$ (0.13)	$ (0.17)	$ (0.31)
Weighted average common stock shares used in computing net income (loss) per share, basic (shares)	52,787	47,232	50,598	44,258

Condensed Consolidated Stateme5

Condensed Consolidated Statements of Comprehensive Loss - USD ($) $ in Thousands		3 Months Ended		6 Months Ended
		Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Statement of Comprehensive Income [Abstract]
Net loss		$ (3,735)	$ (6,280)	$ (8,429)	$ (13,740)
Other comprehensive income
Unrealized gain on marketable securities, net of tax	[1]	0	194	0	102
Other comprehensive income		0	194	0	102
Total comprehensive loss		$ (3,735)	$ (6,086)	$ (8,429)	$ (13,638)
[1]	No tax benefit (expense) for the three and six months ended June 30, 2018. Net of tax benefit of $60 for the three and six months ended June 30, 2017, respectively.

Condensed Consolidated Stateme6

Condensed Consolidated Statements of Comprehensive Loss (Parenthetical) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Statement of Comprehensive Income [Abstract]
Unrealized gain (loss) on marketable securities, tax benefit	$ 0	$ 60	$ 0	$ 60

Condensed Consolidated Stateme7

Condensed Consolidated Statements of Cash Flows - USD ($) $ in Thousands	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017
Operating activities:
Net loss	$ (8,429)	$ (13,740)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation and amortization	503	554
Gain on disposal of property and equipment	1	(3)
Income tax benefit related to marketable securities	0	(60)
Stock-based compensation	4,437	3,379
Unrealized gain on investment in marketable securities	(5)	0
Changes in operating assets and liabilities:
Accounts receivable, net	2,954	(1,879)
Inventories, net	0	19
Prepaid expenses and other current assets	(132)	(1,824)
Contract Assets	(554)	0
Other assets	79	(44)
Accounts payable	(530)	(446)
Accrued compensation	(936)	(1,394)
Other accrued liabilities	451	271
Long term lease incentive	(212)	(212)
Other long term liabilities	(302)	(56)
Deferred revenue	(9,466)	3,904
Net cash used in operating activities	(12,141)	(11,531)
Investing activities:
Purchase of property and equipment	(1,472)	(680)
Proceeds from disposal of property and equipment	0	3
Net cash used in investing activities	(1,472)	(677)
Financing activities:
Proceeds from exercises of stock options	1,858	142
Proceeds from issuance of common stock in connection with public offering, net of underwriting discounts and commission	37,497	23,782
Costs incurred in connection with public offering	(179)	(491)
Principal payments on capital lease obligations	(118)	(60)
Taxes paid related to net share settlement of equity awards	(3,140)	(1,636)
Net cash provided by financing activities	35,918	21,737
Net increase in cash, cash equivalents and restricted cash	22,305	9,529
Cash, cash equivalents and restricted cash at the beginning of the period	32,776	20,864
Cash, cash equivalents and restricted cash at the end of the period	55,081	30,393
Supplemental disclosure of cash flow information:
Interest paid	42	117
Income taxes paid	5	5
Supplemental non-cash investing and financing activities:
Equipment acquired under capital leases	0	840
Purchase of property and equipment recorded in accounts payable and accrued expenses	67	34
Cash and cash equivalents	53,621	28,817
Total cash, cash equivalents and restricted cash at the end of the period	$ 32,776	$ 20,864

Description of Business

Description of Business	6 Months Ended
	Jun. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Description of Business	Description of Business In these notes to the consolidated financial statements, the "Company," "we," "us," and "our" refers to Codexis, Inc. and its subsidiaries on a consolidated basis. We discover, develop and sell proteins that deliver value to our clients in a growing set of industries. We view proteins as a vast untapped source of value-creating materials, and we are using our proven technologies, which we have been continuously improving over our sixteen -year history, to commercialize an increasing number of novel proteins, both as proprietary Codexis products and in partnership with our customers. We are a pioneer in the harnessing of computational technologies to drive biology advancements. Since our inception in 2002, we have made substantial investments in the development of our CodeEvolver ® protein engineering technology platform, the primary source of our competitive advantage. Our technology platform is powered by proprietary, artificial intelligence-based, computational algorithms that rapidly mine our large and continuously growing library of protein variants’ performance attributes. These computational outputs enable increasingly reliable predictions for next generation protein variants to be engineered, enabling delivery of targeted performance enhancements in a time-efficient manner. In addition to its computational prowess, our CodeEvolver ® protein engineering technology platform integrates additional modular competencies, including robotic high-throughput screening and genomic sequencing, organic chemistry and process development, which are all coordinated to create our novel protein innovations. Our approach to develop commercially viable biocatalytic manufacturing processes begins by conceptually designing the most cost-effective and practical process for a targeted product. We then develop optimized protein catalysts to enable that process design, using our CodeEvolver ® protein engineering platform technology. Engineered protein catalyst candidates - many thousands for each protein engineering project - are then rapidly screened and validated in high throughput under relevant manufacturing operating conditions. This approach results in an optimized protein catalyst enabling cost-efficient processes that typically are relatively simple to run in conventional manufacturing equipment. This also allows for the efficient technical transfer of our process to our manufacturing partners. The successful embodiment of our CodeEvolver ® protein engineering technology platform in commercial manufacturing processes requires well-integrated expertise in a number of technical disciplines. In addition to those directly involved in practicing our CodeEvolver ® protein engineering platform technology, such as molecular biology, enzymology, microbiology, cellular engineering, metabolic engineering, bioinformatics, biochemistry and high throughput analytical chemistry, our process development projects also involve integrated expertise in organic chemistry, chemical process development, chemical engineering, fermentation process development and fermentation engineering. Our integrated, multi-disciplinary approach to biocatalyst and process development is a critical success factor for our company. We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, which remains our primary business focus. Our customers, which include several large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop protein catalysts for use in the fine chemicals market. The fine chemicals market consists of several large market verticals, including food and food ingredients, animal feed, flavors, fragrances and agricultural chemicals. More recently, we have begun using the CodeEvolver ® protein engineering technology platform to develop early stage, novel biotherapeutic product candidates, both for our customers and for our own business, most notably our lead program for the potential treatment of phenylketonuria ("PKU") disease in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we entered into a Global Development, Option and License Agreement (the "Nestlé Agreement") with Nestec Ltd. ("Nestlé Health Science") and, solely for the purpose of the integration and the dispute resolution clauses of the Nestlé Agreement, Nestlé Health Science S.A., to advance CDX-6114, our enzyme biotherapeutic product candidate for the potential treatment of PKU disease. In April 2018, we entered into a strategic collaboration (the "Porton Agreement") with Porton Pharma Solutions, Ltd. ("Porton") to license key elements of Codexis’ biocatalyst technology to Porton’s global custom intermediate and active pharmaceutical ingredients ("API") development and manufacturing business. We also use our technology to develop enzymes for customers using next generation sequencing ("NGS") and polymerase chain reaction ("PCR/qPCR") for in vitro molecular diagnostic and genomic research applications. Below are brief descriptions of our business segments (See Note 13, "Segment, Geographical and Other Revenue Information"): Performance Enzymes We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, and to date this continues to be our largest market served. Our customers, which include many large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop customized enzymes for use in other industrial markets. These markets consist of several large industrial verticals, including food and food ingredients, animal feed, flavors, fragrances, and agricultural chemicals. We also use our technology to develop enzymes for customers using NGS and PCR/qPCR for in vitro molecular diagnostic and molecular biology research applications. In April 2018, we entered into the Porton Agreement related to our strategic collaboration with Porton to license key elements of Codexis’ world-leading biocatalyst technology for use in Porton’s global custom intermediate and API development and manufacturing business. Novel Biotherapeutics We are also targeting new opportunities in the pharmaceutical industry to discover, improve, and/or develop biotherapeutic drug candidates. We believe that our CodeEvolver ® protein engineering platform technology can be used to discover novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. Similarly, we believe that we can deploy our platform technology to improve specific characteristics of a customer’s pre-existing biotherapeutic drug candidate, such as its activity, stability or immunogenicity. Most notable is our lead program for the potential treatment of PKU in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we announced a strategic collaboration with Nestlé Health Science to advance CDX-6114, our own novel orally administrable enzyme therapeutic candidate for the potential treatment of PKU disease. We have also developed a pipeline of other biotherapeutic drug candidates in which we expect to continue to make additional investments with the aim of advancing additional product candidates targeting other therapeutic areas.

Basis of Presentation and Summa

Basis of Presentation and Summary of Significant Accounting Policies	6 Months Ended
	Jun. 30, 2018
Accounting Policies [Abstract]
Basis of Presentation and Summary of Significant Accounting Policies	Basis of Presentation and Summary of Significant Accounting Policies Basis of Presentation and Principles of Consolidation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America ("GAAP") and the applicable rules and regulations of the Securities and Exchange Commission ("SEC") for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim unaudited condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December 31, 2017 . The condensed consolidated balance sheet at December 31, 2017 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of June 30, 2018 and results of our operations and comprehensive loss for the three and six months ended June 30, 2018 and 2017 , and cash flows for the six months ended June 30, 2018 and 2017 . The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Certain prior period amounts have been reclassified to conform to current period presentation. In connection with the adoption of Accounting Standard Update ("ASU") 2016-01, "Financial Instruments-Overall: Recognition and Measurement of Financial Assets and Financial Liabilities," unrealized losses on equity investments in marketable securities, net of taxes, previously included in accumulated other comprehensive loss have been reclassified to beginning accumulated deficit. See "Recently Adopted Accounting Pronouncements" for details regarding the adoption of ASU 2016-01. Comprehensive loss is equivalent to net loss during the three and six months ended June 30, 2018 because after adopting ASC 2016-01, we do not have any transactions recorded under comprehensive loss. Prior to our adoption of ASU 2016-01, and during the three and six months ended June 30, 2017 , comprehensive loss included unrealized losses from our equity investments in marketable securities. The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly owned subsidiaries in the United States, India and the Netherlands. All significant intercompany balances and transactions have been eliminated in consolidation. Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenue and expenses during the reporting period. We regularly assess these estimates which primarily affect revenue recognition, accounts receivable, inventories, the valuation of marketable securities, goodwill arising out of business acquisitions, accrued liabilities, stock awards, and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements. Segment Reporting We report two business segments, Performance Enzymes and Novel Biotherapeutics, which are based on our operating segments. Operating segments are defined as components of an enterprise about which separate financial information is available that is evaluated regularly by the chief operating decision maker ("CODM"), or decision making group, in deciding how to allocate resources, and in assessing performance. Our CODM is our Chief Executive Officer. Our business segments are primarily based on our organizational structure and our operating results as used by our CODM in assessing performance and allocating resources for our company. We do not allocate or evaluate assets by segment. Previously, we had managed our business under one business segment. As our biotherapeutics business has emerged as a significant opportunity for us, effective in 2018, we formed Novel Biotherapeutics as a new business segment. The Novel Biotherapeutics segment focuses on new opportunities in the pharmaceutical industry to discover or improve novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. The Performance Enzymes segment consists of the existing protein catalyst products and services with focus on pharmaceutical, food, molecular diagnostics, and other industrial markets. In the second quarter of 2018, we made a change in the segment measurement for allocating operating expenses between our two reporting segments: Performance Enzymes and Novel Biotherapeutics. This change in measurement only impacts our segment disclosures, and it has no impact on our overall consolidated financial statements. Segment results for the three and six months ended June 30, 2018 reflect the change in operating segment measurement. Refer to Note 13 , "Segment, Geographical and Other Revenue Information" for more details. Foreign Currency Translation The United States dollar is the functional currency for our operations outside the United States. Accordingly, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in other expense in the unaudited condensed consolidated statements of operations. Gains and losses realized from non-U.S. dollar transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity's functional currency are included in other expense in the accompanying unaudited condensed consolidated statements of operations. Revenue Recognition On January 1, 2018, we adopted the provisions of ASU 2014-09, "Revenue from Contracts with Customers (Topic 606) ("ASC 606"). The guidance provides a unified model to determine how revenue is recognized. Our revenues are derived primarily from product revenue and collaborative research and development agreements. The majority of our contracts with customers typically contain multiple products and services. We account for individual products and services separately if they are distinct-that is, if a product or service is separately identifiable from other items in the contract and if a customer can benefit from it on its own or with other resources that are readily available to the customer. In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our product revenue and collaborative research and development agreements, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) we satisfy each performance obligation. The majority of our collaborative contracts contain multiple revenue streams such as up-front and/or annual license fees, fees for full time employee ("FTE") research and development services, contingent milestone payments upon achievement of contractual criteria, and royalty fees based on the licensees' product revenue or usage, among others. We determine the stand-alone selling price ("SSP") and allocate consideration to distinct performance obligations. Typically, we base our SSPs on our historical sales. If an SSP is not directly observable, then we estimate the SSP taking into consideration market conditions, forecasted sales, entity-specific factors and available information about the customer. We account for a contract with a customer when there is approval and commitment from both parties, the rights of the parties are identified, payment terms are identified, the contract has commercial substance and collectability of consideration is probable. Non-cancellable purchase orders received from customers to deliver a specific quantity of product, when combined with our order confirmation, in exchange for future consideration, create enforceable rights and obligations on both parties and constitute a contract with a customer. We measure revenue based on the consideration specified in the contract with each customer, net of any sales incentives and taxes collected on behalf of government authorities. We recognize revenue in a manner that best depicts the transfer of promised goods or services to the customer, when control of the product or service is transferred to a customer. We make significant judgments when determining the appropriate timing of revenue recognition. The following is a description of principal activities from which we generate revenue: Product Revenue Product revenue consist of sales of protein catalysts, pharmaceutical intermediates and Codex ® Biocatalyst Panels and Kits. A majority of our product revenue is made pursuant to purchase orders or supply agreements and is recognized at a point in time when the control of the product has been transferred to the customer typically upon shipment. For some of the products that we develop, we recognize revenue over time as we have a right to payment from the customer under a binding, non-cancellable purchase order, and there is no alternate use of the product for us as it is specifically made for the customer’s use. Certain of our agreements provide options to customers which they can exercise at a future date, such as the option to purchase our product during the contract duration at discounted prices and an option to extend their contract, among others. In accounting for customer options, we determine whether an option is a material right and this requires us to exercise significant judgment. If a contract provides the customer an option to acquire additional goods or services at a discount that exceeds the range of discounts that we typically give for that product or service, or if the option provides the customer certain additional goods or services for free, the option may be considered a material right. If the contract gives the customer the option to acquire additional goods or services at their normal SSPs, we would likely determine that the option is not a material right and, therefore, account for it as a separate performance obligation when the customer exercises the option. We primarily account for options which provide material rights using the alternative approach available under ASC 606, as we concluded we meet the criteria for using the alternative approach. Therefore, the transaction price is calculated as the expected consideration to be received for all the goods and services we expect to provide. We update the transaction price for expected consideration, subject to constraint, each reporting period if our estimate of future goods to be ordered by customers change. Research and Development Revenue We perform research and development activities as specified in each respective customer agreement. We identify each performance obligation in our research and development agreements at contract inception. We allocate the consideration to each distinct performance obligation based on the estimated SSP of each performance obligation. Performance obligations included in our research and services agreements typically include research and development services for a specified term, periodic reports and small samples of enzyme produced. The majority of our research and development agreements are based on a contractual rate per FTE working on the project. The underlying product that we develop for customers does not create an asset with an alternative use to us and the customer receives benefits as we perform the work towards completion. Thus, our performance obligations are generally satisfied over time as the service is performed. We utilize an appropriate method of measuring progress towards the completion of our performance obligations to determine the timing of revenue recognition. For each performance obligation that is satisfied over time, we recognize revenue using a single measure of progress, typically based on FTE hours incurred. Our contracts frequently provide customers with rights to use or access our products or technology, along with other promises or performance obligations. Under ASC 606, we must first determine whether the license is distinct from other promises, such as our promise to manufacture a product. If we determine that the customer cannot benefit from the license without our manufacturing capability, the license will be accounted for as combined with the other performance obligations. If we determine that a license is distinct, we would recognize revenues from non-refundable, up-front license fees when the license is transferred to the customer, and the customer can use and benefit from it. We estimate the SSP for license rights by using an income approach model which includes the following key assumptions: the development timelines, revenue forecasts, commercialization expenses, discount rate, and the probability of technical and regulatory success. For licenses that have been previously sold to other customers, we use historical information to determine SSP. At the inception of each arrangement that includes variable consideration such as development milestone payments, we evaluate whether the milestones are considered probable of being reached and estimate the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within our control or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis, for which we recognize revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, we re-evaluate the probability of achievement of such development milestones and any related constraint, and if necessary, adjust our estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect license, collaboration and other revenues and earnings in the period of adjustment. Our CodeEvolver ® platform technology transfer collaboration agreements typically include license fees, upfront fees, and variable consideration in the form of milestone payments, and sales or usage-based royalties. We recognize revenues from our platform technology transfer agreements over time as our customer learns to use our technology. For agreements that include sales or usage-based royalty payments to us, we do not recognize revenue until the underlying sales of the product or usage has occurred. At the end of each reporting period, we estimate the royalty amount. We recognize revenue at the later of (i) when the related sale of the product occurs, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied, or partially satisfied. Contract Assets Contract assets include amounts related to our contractual right to consideration for completed performance obligations not yet invoiced. The contract assets are reclassified to receivables when the rights become unconditional. Contract Liabilities Contract liabilities are recorded as deferred revenues and include payments received in advance of performance under the contract. Contract liabilities are realized when the development services are provided to the customer or control of the products has been transferred to the customer. A portion of our contract liabilities relate to supply arrangements that contain material rights that are recognized using the alternative method, under which the aggregate amount invoiced to the customer for shipped products, including annual fees, is higher than the amount of revenue recognized based on the transaction price allocated to the shipped products. Contract Costs ASC 606 requires the recognition of an asset for the incremental costs of obtaining a contract with a customer if the entity expects to recover such costs. Incremental costs are costs that would not have been incurred if the contract had not been obtained. Examples of contract costs are commissions paid to sales personnel. We do not typically incur significant incremental costs because the compensation of our salespeople are not based on contracts closed but on a mixture of company goals, individual goals, and sales goals. If a commission paid is directly related to obtaining a specific contract, our policy is to capitalize and amortize such costs over the estimated life of the contract. Contract costs are reported in other non-current assets. Cost of Product Revenue Cost of product revenue comprises both internal and third party fixed and variable costs including materials and supplies, labor, facilities, and other overhead costs associated with our product sales. Shipping costs are included in our cost of product revenue. Such charges were not significant in any of the periods presented. Fulfillment costs, such as shipping and handling, are recognized at a point in time and are included in cost of product sales. Cost of Research and Development Services Cost of research and development services related to FTE services under research and development agreements approximate the research funding over the term of the respective agreements and is included in research and development expense. Costs of services provided under license and platform technology transfer agreements are included in research and development expenses and are expensed in the periods in which such costs are incurred. Research and Development Expenses Research and development expenses consist of costs incurred for internal projects and partner-funded collaborative research and development activities, as well as license and platform technology transfer agreements, as mentioned above. These costs include our direct and research-related overhead expenses, which include salaries and other personnel-related expenses (including stock-based compensation), occupancy-related costs, supplies, depreciation of facilities and laboratory equipment and amortization of acquired technologies, as well as external costs, and are expensed as incurred. Costs to acquire technologies that are utilized in research and development and that have no alternative future use are expensed when incurred. Advertising Advertising costs are expensed as incurred and included in selling, general and administrative expenses in the unaudited condensed consolidated statements of operations. Advertising costs were $0.1 million for the three months ended June 30, 2018 and 2017 and $0.2 million for the six months ended June 30, 2018 and 2017 . Stock-Based Compensation We use the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under our equity incentive plans. The Black-Scholes-Merton option pricing model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. The expected term is based on historical exercise behavior on similar awards, giving consideration to the contractual terms, vesting schedules and expectations of future employee behavior. We use historical volatility to estimate expected stock price volatility. The risk-free rate assumption is based on United States Treasury instruments whose terms are consistent with the expected term of the stock options. The expected dividend assumption is based on our history and expectation of dividend payouts. Restricted Stock Units ("RSUs"), Restricted Stock Awards ("RSAs"), performance based options ("PBOs"), and performance-contingent restricted stock units ("PSUs") are measured based on the fair market values of the underlying stock on the dates of grant. The vesting of PBOs and PSUs awarded is conditioned upon the attainment of one or more performance objectives over a specified period and upon continued employment through the applicable vesting date. At the end of the performance period, shares of stock subject to the PBOs and PSUs vest based upon both the level of achievement of performance objectives within the performance period and continued employment through the applicable vesting date. Stock-based compensation expense is calculated based on awards ultimately expected to vest and is reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. The estimated annual forfeiture rates for stock options, RSUs, PSUs, PBOs, and RSAs are based on historical forfeiture experience. The estimated fair value of stock options, RSUs, and RSAs are expensed on a straight-line basis over the vesting term of the grant and the estimated fair value of PSUs and PBOs are expensed using an accelerated method over the term of the award once management has determined that it is probable that the performance objective will be achieved. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. Management assesses the probability of the performance milestones being met on a continuous basis. Cash and Cash Equivalents We consider all highly liquid investments with maturity dates of three months or less at the date of purchase to be cash equivalents. Our cash and cash equivalents consist of cash on deposit with banks and money market funds. The majority of cash and cash equivalents is maintained with major financial institutions in North America. Deposits with these financial institutions may exceed the amount of insurance provided on such deposits. Cash and cash equivalents totaled $ 53.6 million at June 30, 2018 and were comprised of cash of $22.7 million and money market funds of $30.9 million . At December 31, 2017 , cash and cash equivalents totaled $31.2 million and were comprised of cash of $24.4 million and money market funds of $6.8 million . Restricted Cash In 2016, we began the process of liquidating our Indian subsidiary. The local legal requirements for liquidation required us to maintain our subsidiary's cash balance in an account managed by a legal trustee to satisfy our financial obligations. This balance is recorded as non-current restricted cash on the consolidated balance sheets and totaled $0.8 million at June 30, 2018 and December 31, 2017 . In addition, pursuant to the terms of the lease agreement for our Redwood City, CA facilities, our letters of credit are collateralized by deposit balances of $0.7 million as of June 30, 2018 and December 31, 2017 , which is recorded as non-current restricted cash on the unaudited condensed consolidated balance sheets (see Note 11, "Commitments and Contingencies" for details). Marketable Securities We invest in equity securities that are carried at estimated fair value (see Note 6, "Cash Equivalents and Marketable Securities"), with changes in fair value recognized within earnings. Equity securities with remaining maturities of greater than one year or which we currently do not intend to sell are classified as long-term. Unrealized holding gains and losses (the adjustment to fair value) and realized gains and losses are included in other income (expense) in the unaudited condensed consolidated statement of operations. Fair Value Measurements Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. In determining fair value, we utilize valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible and we consider counterparty credit risk in our assessment of fair value. Carrying amounts of financial instruments, including cash equivalents, marketable investments, accounts receivable, accounts payable, and accrued liabilities, approximate their fair values as of the balance sheet dates because of their short maturities. The fair value hierarchy distinguishes between (1) market participant assumptions developed based on market data obtained from independent sources (observable inputs) and (2) an entity's own assumptions about market participant assumptions developed based on the best information available in the circumstances (unobservable inputs). The fair value hierarchy consists of three broad levels, giving the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1) and the lowest priority to unobservable inputs (Level 3). The three levels of the fair value hierarchy are described below: • Level 1: Inputs that are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date. • Level 2: Inputs that are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life. • Level 3: Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities and which reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date. See Note 7, "Fair Value Measurements" to our unaudited condensed consolidated financial statements. Concentrations of Credit Risk Financial instruments that potentially subject us to significant concentrations of credit risk consist primarily of cash and cash equivalents, accounts receivable, marketable securities, and restricted cash. Cash that is not required for immediate operating needs is invested principally in money market funds. Cash and cash equivalents are invested through banks and other financial institutions in the United States, India, and the Netherlands. Such deposits in those countries may be in excess of insured limits. Accounts Receivable and Allowance for Doubtful Accounts We currently sell primarily to pharmaceutical and fine chemicals companies throughout the world by the extension of trade credit terms based on an assessment of each customer's financial condition. Trade credit terms are generally offered without collateral and may include a discount for prompt payment for specific customers. To manage our credit exposure, we perform ongoing evaluations of our customers' financial conditions. In addition, accounts receivable includes amounts owed to us under our collaborative research and development agreements. We recognize accounts receivable at invoiced amounts and we maintain a valuation allowance for doubtful accounts. We estimate an allowance for doubtful accounts through specific identification of potentially uncollectible accounts receivable based on an analysis of our accounts receivable aging. Uncollectible accounts receivable are written off against the allowance for doubtful accounts when all efforts to collect them have been exhausted. Recoveries are recognized when they are received. Actual collection losses may differ from our estimates and could be material to our consolidated financial position, results of operations, and cash flows. Inventories Inventories are stated at the lower of cost or net realizable value. Cost is determined using a weighted-average approach, assuming full absorption of direct and indirect manufacturing costs, or based on cost of purchasing from our vendors. If inventory costs exceed expected net realizable value due to obsolescence or lack of demand, valuation adjustments are recorded for the difference between the cost and the expected net realizable value. These valuation adjustments are determined based on significant estimates. Concentrations of Supply Risk We rely on a limited number of suppliers for our products. We believe that other vendors would be able to provide similar products; however, the qualification of such vendors may require substantial start-up time. In order to mitigate any adverse impacts from a disruption of supply, we attempt to maintain an adequate supply of critical single-sourced materials. For certain materials, our vendors maintain a supply for us. We outsource the large scale manufacturing of our products to contract manufacturers with facilities in Austria and Italy. Impairment of Long-Lived Assets Our long-lived assets consist of property and equipment. We evaluate the carrying value of long-lived assets, including property and equipment, whenever events, changes in business circumstances or our planned use of long-lived assets indicate that their carrying amounts may not be fully recoverable or that their useful lives are no longer appropriate. If these facts and circumstances exist, we assess for recovery by comparing the carrying values of long-lived assets with their future net undiscounted cash flows. If the comparison indicates that impairment exists, long-lived assets are written down to their respective fair values based on discounted cash flows. Significant management judgment is required in the forecast of future operating results that are used in the preparation of unexpected undiscounted cash flows. As of June 30, 2018 and December 31, 2017 , there were no events or changes in circumstances which indicated that the carrying amount of our long-lived assets might not be recoverable. No impairment charges for long-lived assets were recorded during the six months ended June 30, 2018 and 2017 . Goodwill As of June 30, 2018 and December 31, 2017 , the carrying amount of our goodwill was $3.2 million . All of our goodwill relates to the Performance Enzymes segment. There were no indicators of impairment identified related to our Performance Enzymes segment during the six months ended June 30, 2018 and 2017 . Income Taxes We use the liability method of accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized. We make certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenue and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to our tax provision in a subsequent period. In assessing the realizability of deferred tax assets, we consider whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. We have recorded a valuation allowance against these deferred tax assets in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur. As of June 30, 2018 and December 31, 2017 , we maintained a full valuation allowance in all jurisdictions against th

Revenue Recognition

Revenue Recognition	6 Months Ended
	Jun. 30, 2018
Revenue from Contract with Customer [Abstract]
Revenue Recognition	Revenue Recognition On January 1, 2018, we adopted Topic 606, applying the modified retrospective method to all contracts that were not completed as of that date. Results for reporting periods beginning after January 1, 2018 are presented under Topic 606, while prior period results are not adjusted and continue to be reported under the accounting standards in effect for the prior period. We recorded an increase to opening accumulated deficit of $4.1 million as of January 1, 2018 due to the cumulative impact of adopting Topic 606. The impact on revenue for the three and six months ended June 30, 2018 was an increase of $1.6 million and $5.4 million , respectively, as a result of adopting Topic 606. The increase in revenues from the adoption of ASC 606 was primarily due to revenue from a product that was recognized over time as we have a right to payment from the customer under a binding, non-cancellable purchase order, and there is no alternate use of the product for us as it is specifically for the customer’s use, and revenues from research and development contracts that were recognized when we had the right to invoice our customers for monthly services completed to date. Also revenue from a distinct, functional license granted on January 1, 2018 contributed to the increase in revenue from the adoption of ASC 606. Disaggregation of Revenue The following table provides information about disaggregated revenue from contracts with customers into the nature of the products and services, and geographic regions, and includes a reconciliation of the disaggregated revenue with reportable segments. The geographic regions that are tracked are the Americas (United States, Canada, Latin America), EMEA (Europe, Middle East, Africa), and APAC (Australia, New Zealand, Southeast Asia, China). Three months ended June 30, 2018 Three months ended June 30, 2017 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 3,723 $ — $ 3,723 $ 6,600 $ — $ 6,600 Research and development revenue 7,442 2,373 9,815 3,747 — 3,747 Total revenues $ 11,165 $ 2,373 $ 13,538 $ 10,347 $ — $ 10,347 Primary geographical markets: Americas $ 6,058 $ — $ 6,058 $ 4,401 $ — $ 4,401 EMEA 1,435 2,373 3,808 1,959 — 1,959 APAC 3,672 — 3,672 3,987 — 3,987 Total revenues $ 11,165 $ 2,373 $ 13,538 $ 10,347 $ — $ 10,347 Six months ended June 30, 2018 Six months ended June 30, 2017 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 9,886 $ — $ 9,886 $ 12,186 $ — $ 12,186 Research and development revenue 12,008 5,686 17,694 6,131 — 6,131 Total revenues $ 21,894 $ 5,686 $ 27,580 $ 18,317 $ — $ 18,317 Primary geographical markets: Americas $ 9,655 $ — $ 9,655 $ 6,189 $ — $ 6,189 EMEA 3,114 5,686 8,800 5,166 — 5,166 APAC 9,125 — 9,125 6,962 — 6,962 Total revenues $ 21,894 $ 5,686 $ 27,580 $ 18,317 $ — $ 18,317 The following table shows the reconciliation of contract liabilities from what was disclosed in the Form 10-K for the year ended December 31, 2017 and gives effect to the modified retrospective adoption of the revenue guidance on January 1, 2018 (in thousands): Balance Deferred Revenue, balance at December 31, 2017 $ 13,793 Changes in estimated consideration — Unsatisfied performance obligations $ 5,173 Deferred Revenue, balance at January 1, 2018 $ 18,966 Contract Balances Contract assets primarily relate to our rights to consideration for custom products with no alternate use and under binding non-cancellable purchase orders. Our contract assets are transferred to receivables when our rights to the consideration become unconditional. Contract costs relate to incremental costs of obtaining a contract with a customer. Deferred contract costs are amortized along with the associated revenue over the term of the contract. The contract liabilities primarily relate to development agreements with upfront payments and supply agreements under which the customer makes upfront payments and the customer has options with material rights which are recognized using the alternative method. The advance consideration received from customers is a contract liability until development services are provided to the customer or control of the products has been transferred to the customer. The following table presents changes in the contract assets, deferred contract costs, and liabilities (in thousands): June 30, 2018 January 1, 2018 balance Additions Deductions (1) Ending balance Contract Assets $ — $ 3,047 $ (2,493 ) $ 554 Contract Costs 239 — (80 ) 159 Contract Liabilities: Deferred Revenue 18,966 1,965 (11,477 ) 9,454 (1) The asset or liability balances are presented as a net position per contract and accordingly the deductions column includes the netting effect of presenting each contract on a net position basis as either a net liability or asset. Accounts receivable are recorded when the right to consideration becomes unconditional. Contract assets include amounts related to our contractual right to consideration for completed performance obligations not yet invoiced. Contract liabilities include payments received in advance of performance under the contract and are realized with the associated revenue recognized under the contract. A portion of our contract liabilities relate to arrangements that contain material rights that are recognized using the alternative method, under which the aggregate amount invoiced to the customer for shipped products, including annual fees, is higher than the amount of revenue recognized based on the transaction price allocated to the shipped products. We had no asset impairment charges related to contract assets in the period. During the three and six months ended June 30, 2018 , we recognized the following revenues (in thousands): Revenue recognized in the period from: Three months ended June 30, 2018 Six months ended June 30, 2018 Amounts included in contract liabilities at the beginning of the period: Performance obligations satisfied $ 2,994 $ 8,822 Changes in the period: Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods 64 64 Performance obligations satisfied from new activities in the period - contract revenue 10,480 18,694 Total revenue $ 13,538 $ 27,580 Performance Obligations The following table includes estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied or partially unsatisfied at the end of the reporting period, in thousands. The estimated revenue does not include contracts with original durations of one year or less, amounts of variable consideration attributable to royalties, or contract renewals that are unexercised as of June 30, 2018 . We did not recognize any revenue from performance obligations satisfied in previous periods. The balances in the table below are partially based on judgments involved in estimating future orders from customers subject to the exercise of material rights pursuant to respective contracts. (in thousands) 2018 2019 2020 2021 and Thereafter Total Product Revenue $ 664 $ 2,753 $ 2,183 $ 1,623 $ 7,223 Research and development revenue 1,756 475 — — 2,231 Total $ 2,420 $ 3,228 $ 2,183 $ 1,623 $ 9,454 Practical Expedients, Elections, and Exemptions We used a practical expedient available under ASC 606-10-65-1(f)4 that permits us to consider the aggregate effect of all contract modifications that occurred before the beginning of the earliest period presented when identifying satisfied and unsatisfied performance obligations, transaction price, and allocating the transaction price to the satisfied and unsatisfied performance obligations. We also used a practical expedient available under ASC 606-10-32-18 that permits us not to adjust the amount of consideration for the effects of a significant financing component if, at contract inception, the expected period between the transfer of promised goods or services and customer payment is one year or less. We perform monthly services under our research and development agreements and we use a practical expedient available under ASC 606-10-55-18 that permits us to recognize revenue at the same time that we have the right to invoice our customer for monthly services completed to date. We have elected to treat shipping and handling activities as fulfillment costs. Additionally, we have elected to record revenue net of sales and other similar taxes. Impacts on Financial Statements In accordance with Topic 606, the disclosure of the impact of adoption to our unaudited condensed consolidated statements of operations and balance sheets was as follows (in thousands, except per share amounts): Three months ended June 30, 2018 Six months ended June 30, 2018 As reported Adjustments Balances without adoption of Topic 606 As reported Adjustments Balances without adoption of Topic 606 Revenues: Product revenue $ 3,723 $ (454 ) $ 3,269 $ 9,886 $ (2,970 ) $ 6,916 Research and development revenue 9,815 (1,148 ) 8,667 17,694 (2,470 ) 15,224 Total revenues 13,538 (1,602 ) 11,936 27,580 (5,440 ) 22,140 Costs and operating expenses: Cost of product revenue 2,611 (69 ) 2,542 6,436 (1,355 ) 5,081 Research and development 7,370 (33 ) 7,337 14,548 (80 ) 14,468 Selling, general and administrative 7,395 — 7,395 15,141 — 15,141 Total costs and operating expenses 17,376 (102 ) 17,274 36,125 (1,435 ) 34,690 Loss from operations (3,838 ) (1,500 ) (5,338 ) (8,545 ) (4,005 ) (12,550 ) Interest income 174 — 174 245 — 245 Other expenses (82 ) — (82 ) (142 ) — (142 ) Loss before income taxes (3,746 ) (1,500 ) (5,246 ) (8,442 ) (4,005 ) (12,447 ) Provision (benefit) from income taxes (11 ) — (11 ) (13 ) — (13 ) Net loss $ (3,735 ) $ (1,500 ) $ (5,235 ) $ (8,429 ) $ (4,005 ) $ (12,434 ) Net loss per share, basic and diluted $ (0.07 ) $ (0.03 ) $ (0.10 ) $ (0.17 ) $ (0.08 ) $ (0.25 ) Weighted average common shares used in computing net loss per share, basic and diluted 52,787 52,787 50,598 50,598 June 30, 2018 As reported Adjustments Balances without adoption of Topic 606 Assets Accounts Receivable $ 9,910 $ (1,136 ) $ 8,774 Contract Assets 554 (554 ) — Other non-current assets 414 (159 ) 255 Liabilities Other accrued liabilities 5,051 (1,591 ) 3,460 Deferred revenue - current 4,460 2,909 7,369 Deferred revenue - non-current 4,994 (3,220 ) 1,774 Stockholders' equity Accumulated deficit (328,026 ) 55 (327,971 )

Net Loss per Share

Net Loss per Share	6 Months Ended
	Jun. 30, 2018
Earnings Per Share [Abstract]
Net Loss per Share	Net Loss per Share Basic net loss per share is computed by dividing the net loss by the weighted-average number of shares of common stock outstanding, less RSAs subject to forfeiture. Diluted net loss per share is computed by dividing net loss by the weighted average number of shares of common stock outstanding plus all additional common stock shares that would have been outstanding, assuming dilutive potential common stock shares had been issued for other dilutive securities. For periods of net loss, diluted and basic net loss per share are identical since potential common stock shares are excluded from the calculation, as their effect was anti-dilutive. Anti-Dilutive Securities In periods of net loss, the weighted average number of shares outstanding related to potentially dilutive securities, prior to the application of the treasury stock method, are excluded from the computation of diluted net loss per common share because including such shares would have an anti-dilutive effect. The following shares were not included in the computation of diluted net loss per share (in thousands): Three months ended June 30, Six months ended June 30, 2018 2017 2018 2017 Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan 7,462 7,621 7,462 7,621 Shares of common stock issuable upon exercise of outstanding warrants — 73 — 73 Total shares excluded as anti-dilutive 7,462 7,694 7,462 7,694

Collaborative Arrangements

Collaborative Arrangements	6 Months Ended
	Jun. 30, 2018
Research and Development [Abstract]
Collaborative Arrangements	Collaborative Arrangements GSK Platform Technology Transfer, Collaboration and License Agreement In July 2014, we entered into a CodeEvolver ® protein engineering platform technology transfer collaboration and license agreement (the "GSK CodeEvolver ® Agreement") with GlaxoSmithKline ("GSK"). Pursuant to the terms of the agreement, we granted GSK a non-exclusive license to use the CodeEvolver ® protein engineering platform technology to develop novel enzymes for use in the manufacture of GSK's pharmaceutical and health care products. We received an upfront fee upon the execution of the agreement in July 2014 and milestone payments in each of the years from 2014 through April 2016. We completed the transfer of the CodeEvolver ® protein engineering platform technology to GSK in April 2016 and all revenues relating to the technology transfer have been recognized as of April 2016. We have the potential to receive additional cumulative contingent payments that range from $5.75 million to $38.5 million per project based on GSK’s successful application of the licensed technology. We are also eligible to receive royalties based on net sales of GSK’s sales of licensed enzyme products that are currently constrained. Merck Platform Technology Transfer and License Agreement In August 2015, we entered into a CodeEvolver ® platform technology transfer collaboration and license agreement (the "Merck CodeEvolver ® Agreement") with Merck, Sharp & Dohme ("Merck") which allows Merck to use the CodeEvolver ® protein engineering technology platform in the field of human and animal healthcare. We received a $5.0 million up-front license fee upon execution of the Merck CodeEvolver ® Agreement, and milestone payments in September 2015 and in September 2016, when we completed the transfer of the engineering platform technology. Additionally, we recognized research and development revenues of $1.0 million and $1.9 million for the three and six months ended June 30, 2018 , respectively, compared to $0.9 million and $1.8 million for the three and six months ended June 30, 2017 , respectively, for various research projects under our collaborative arrangement. We have the potential to receive payments of up to a maximum of $15.0 million for each commercial active pharmaceutical ingredient ("API") that is manufactured by Merck using one or more novel enzymes developed by Merck using the CodeEvolver ® protein engineering technology platform. The API payments, which are currently fully constrained, are based on quantity of API developed and manufactured by Merck and will be recognized as usage-based royalties. Merck Sitagliptin Catalyst Supply Agreement In February 2012, we entered into a five -year Sitagliptin Catalyst Supply Agreement ("Sitagliptin Catalyst Supply Agreement") with Merck whereby Merck may obtain commercial scale substance for use in the manufacture of Januvia ® , its product based on the active ingredient sitagliptin. In December 2015, Merck exercised its option under the terms of the Sitagliptin Catalyst Supply Agreement to extend the agreement for an additional five years through February 2022. Effective as of January 2016, we and Merck amended the Sitagliptin Catalyst Supply Agreement to prospectively provide for variable pricing based on the cumulative volume of sitagliptin catalyst purchased by Merck and to allow Merck to purchase a percentage of its requirements for sitagliptin catalyst from a specified third-party supplier. Merck received a distinct, functional license to manufacture a portion of its demand beginning January 1, 2018, which we recognized as research and development revenue. We recognized research and development revenue of zero and $1.3 million for the three and six months ended June 30, 2018 , respectively, and $0.3 million and $0.7 million for the three and six months ended June 30, 2017 , respectively. We have determined that the variable pricing based on the cumulative volume of sitagliptin catalyst purchased by Merck provides Merck material rights and we are recognizing product revenues using the alternative method. Under the alternative approach, we estimate the total expected consideration and allocate it proportionately with the expected sales. The Sitagliptin Catalyst Supply Agreement requires Merck to pay an annual fee for the rights to the sitagliptin technology each year for the term of the Sitagliptin Catalyst Supply Agreement. Amounts of annual license fees are based on contractually agreed prices and are on a declining scale. We had a deferred revenue balance from Merck of $5.2 million at June 30, 2018 and $1.5 million at December 31, 2017 . In addition, pursuant to the terms of the Sitagliptin Catalyst Supply Agreement, Merck may purchase supply from us for a fee based on contractually stated prices and we recognized $2.7 million and $7.2 million for the three and six months ended June 30, 2018 , respectively, compared to $3.2 million and $5.0 million for the three and six months ended June 30, 2017 , respectively, in product revenue under this agreement. Enzyme Supply Agreement In November 2016, we entered into a supply agreement whereby our customer may purchase quantities of one of our proprietary enzymes for use in its commercial manufacture of a product. Pursuant to the supply agreement, we received an upfront payment of $0.8 million in December 2016, which we accordingly recorded as deferred revenue. Such upfront payment will be recognized over the period of the supply agreement as the customer purchases our proprietary enzyme. We have determined that the volume discounts under the supply agreement provides the customer material rights and we are recognizing revenues using the alternative method. As of June 30, 2018 and December 31, 2017 , we had deferred revenue from the supply agreement of $2.0 million and $0.7 million , respectively. Research and Development Agreement In March 2017, we entered into a multi-year research and development services agreement with Tate & Lyle Ingredients Americas LLC ("Tate & Lyle"). Under the agreement, we have the potential to receive research and development revenue and milestone payments based on the customer's decision to continue the development process. We received an upfront payment of $3.0 million , which was recognized ratably over the maximum term of the services period of 21 months. Beginning January 1, 2018, we are recognizing revenue using a single measure of progress that faithfully depicts our performance in transferring the services. During the second quarter of 2018, Tate & Lyle opted to obtain additional development services that we completed by June 30, 2018 and we earned milestone payments upon completion of the services. We recognized $4.5 million and $5.9 million for the three and six months ended June 30, 2018 , respectively, compared to $0.9 million of revenue for the three and six months ended June 30, 2017 , respectively, for research and development services under the agreement. As of June 30, 2018 and December 31, 2017 , we had deferred revenue from the development services agreement of $1.1 million and $3.1 million , respectively. Global Development, Option and License Agreement and Strategic Collaboration Agreement In October 2017, we entered into a Global Development, Option and License Agreement (the "Nestlé Agreement") with Nestec Ltd. ("Nestlé Health Science") and, solely for the purpose of the integration and the dispute resolution clauses of the Nestlé Agreement, Nestlé Health Science S.A., to advance CDX-6114, our enzyme biotherapeutic product candidate for the potential treatment of PKU. We received an upfront cash payment of $14.0 million upon the execution of the Nestlé Agreement of which we recognized development fees of $1.8 million and $4.5 million for the three and six months ended June 30, 2018 , respectively, as research and development revenue and no research and development revenue for the three and six months ended June 30, 2017 . We had deferred revenue related to the development fees of $2.3 million at June 30, 2018 and $6.8 million at December 31, 2017 . We are eligible to receive a $4.0 million progress payment after the commencement of a Phase 1a clinical trial of CDX-6114 for the potential treatment of PKU disease. On July 9, 2018, we announced that we have dosed the first subjects in a first-in-human Phase 1a dose-escalation trial with CDX-6114. The initiation of the trial triggers the $4.0 million milestone payment to Codexis from Nestlé Health Science which is payable within 60 days of the initiation of the trial. In the event Nestlé Health Science exercises an option under the Nestlé Agreement to take an exclusive license under certain of our patents and know-how, they will be obligated to pay us $3.0 million within 60 days after the exercise of the option. The upfront payment and the variable consideration of $4.0 million progress payment are being recognized over time as the development work is being performed. The progress payment variable consideration is estimated using the most likely amount. Revenue is being recognized using a single measure of progress that faithfully depicts our performance in transferring control of the services, which is based on the ratio of level of effort incurred to date compared to the total estimated level of effort required to complete all performance obligations under the agreement. Upon exercise of the option, we are eligible to receive payments from Nestlé Health Science under the Nestlé Agreement that include (i) development and approval milestones of up to $86.0 million , (ii) sales-based milestones of up to $250.0 million in the aggregate, which aggregate amount is achievable if net sales exceed $1.0 billion in a single year, and (iii) tiered royalties, at percentages ranging from the middle single digits to low double-digits, of net sales of product. In addition to the Nestlé Agreement, we and Nestlé Health Science concurrently entered into a Strategic Collaboration Agreement (the "Strategic Collaboration Agreement") pursuant to which we and Nestlé Health Science will collaborate to leverage the CodeEvolver ® protein engineering technology platform to develop novel enzymes for Nestlé Health Science’s established Consumer Care and Medical Nutrition business areas. Under the Strategic Collaboration Agreement, we recognized research and development fees of $0.6 million and $1.2 million for the three and six months ended June 30, 2018 , respectively, and no research and development fees for the three and six months ended June 30, 2017 . We had deferred revenue of $0.8 million and $1.1 million at June 30, 2018 and December 31, 2017 , respectively. Strategic Collaboration Agreement In April 2018, we entered into the Porton Agreement with Porton to license key elements of Codexis’ biocatalyst technology for use in Porton’s global custom intermediate and API development and manufacturing business. Under the Porton Agreement, we are eligible to receive annual collaboration fees and research and development revenues. We received an initial collaboration fee of $0.5 million within 30 days of the effective date of the agreement, and we recognized no research and development revenue for the three and six months ended June 30, 2018 and 2017 . We had deferred revenue of $0.5 million and none at June 30, 2018 and December 31, 2017 , respectively.

Cash Equivalents and Marketable

Cash Equivalents and Marketable Securities	6 Months Ended
	Jun. 30, 2018
Cash Equivalents and Marketable Securities [Abstract]
Cash Equivalents and Marketable Securities	Cash Equivalents and Marketable Securities Cash equivalents and marketable securities at June 30, 2018 and at December 31, 2017 consisted of the following (in thousands): June 30, 2018 Adjusted Cost Gross Unrealized Gross Unrealized Estimated Money market funds (1) $ 30,913 $ — $ — $ 30,913 Common shares of CO2 Solutions (2) 563 113 — 676 Total $ 31,476 $ 113 $ — $ 31,589 December 31, 2017 Adjusted Cost Gross Unrealized Gross Unrealized Estimated Money market funds (1) $ 6,778 $ — $ — $ 6,778 Common shares of CO2 Solutions (2) 563 108 — 671 Total $ 7,341 $ 108 $ — $ 7,449 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified as marketable securities, and included in non-current assets on our unaudited condensed consolidated balance sheets. The marketable securities were in an unrealized gain position at June 30, 2018 and December 31, 2017 .

Fair Value Measurements

Fair Value Measurements	6 Months Ended
	Jun. 30, 2018
Fair Value, Assets, Liabilities and Stockholders' Equity Measured on Recurring Basis [Abstract]
Fair Value Measurements	Fair Value Measurements The following tables present the financial instruments that were measured at fair value on a recurring basis at June 30, 2018 and December 31, 2017 by level within the fair value hierarchy (in thousands): June 30, 2018 Level 1 Level 2 Level 3 Total Money market funds (1) $ 30,913 $ — $ — $ 30,913 Common shares of CO2 Solutions (2) — 676 — 676 Total $ 30,913 $ 676 $ — $ 31,589 December 31, 2017 Level 1 Level 2 Level 3 Total Money market funds (1) $ 6,778 $ — $ — $ 6,778 Common shares of CO2 Solutions (2) — 671 — 671 Total $ 6,778 $ 671 $ — $ 7,449 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified as marketable securities, and included in non-current assets on our unaudited condensed consolidated balance sheets. We determine the fair value of Level 1 assets using quoted prices in active markets for identical assets. We estimated the fair value of our investment in 10,000,000 common shares of CO 2 Solutions using the market value of common shares as determined by trading on the TSX Venture Exchange, and we classified our investment in CO 2 Solutions as Level 2 assets due to the volatile and low trading volume. There were no transfers between Level 1 and Level 2 securities in the periods presented. (See also Note 6, "Cash Equivalents and Marketable Securities.") During the three and six months ended June 30, 2018 , unrealized loss of $20 thousand and unrealized gain of $5 thousand , respectively, related to our investment in CO 2 Solutions were included in other expense, net, in the unaudited condensed consolidated statements of operations. Prior to our adoption of ASU 2016-01, we recorded unrealized gains and losses from our investment in CO 2 Solutions in accumulated other comprehensive loss in stockholders' equity. During the six months ended June 30, 2017 , unrealized losses related to our investment in CO 2 Solutions was $0.1 million and was included in other comprehensive loss.

Balance Sheets Details

Balance Sheets Details	6 Months Ended
	Jun. 30, 2018
Balance Sheets Details [Abstract]
Balance Sheets Details	Balance Sheets Details Inventories Inventories consisted of the following (in thousands): June 30, 2018 December 31, 2017 Raw materials $ 214 $ 215 Work-in-process 62 53 Finished goods 2,157 2,147 Less: reserve (1,397 ) (1,379 ) Inventories, net $ 1,036 $ 1,036 Property and Equipment, net Property and equipment, net consisted of the following (in thousands): June 30, 2018 December 31, 2017 Laboratory equipment (1) $ 20,636 $ 19,777 Leasehold improvements 10,358 10,327 Computer equipment and software 3,770 3,695 Office equipment and furniture 1,195 1,185 Construction in progress (2) 457 85 Property and equipment 36,416 35,069 Less: accumulated depreciation and amortization (32,533 ) (32,254 ) Property and equipment, net $ 3,883 $ 2,815 (1) Fully depreciated laboratory equipment with a cost of $0.2 million and $0.2 million was retired during six months ended June 30, 2018 and the fiscal year ended December 31, 2017, respectively. (2) Construction in progress includes equipment received but not yet placed into service pending installation. Goodwill Goodwill had a carrying value of approximately $3.2 million at June 30, 2018 and December 31, 2017 . Other Accrued liabilities Other accrued liabilities consisted of the following (in thousands): June 30, 2018 December 31, 2017 Accrued purchases (1) $ 834 $ 941 Accrued professional and outside service fees 1,666 2,393 Accrued expenses - cost of sales 1,387 — Deferred rent 297 258 Lease incentive obligation 425 425 Other 442 345 Total $ 5,051 $ 4,362 (1) Amount represents products and services received but not billed as of June 30, 2018 and December 31, 2017 .

Stock-Based Compensation

Stock-Based Compensation	6 Months Ended
	Jun. 30, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Stock-Based Compensation	Stock-Based Compensation Equity Incentive Plans In March 2010, our board of directors (the "Board") and stockholders approved the 2010 Equity Incentive Award Plan (the "2010 Plan"), which became effective upon the completion of our initial public offering in April 2010. The number of shares of our common stock available for issuance under the 2010 Plan is equal to 1,100,000 shares plus any shares of common stock reserved for future grant or issuance under our 2002 Stock Plan (the "2002 Plan") that remained unissued at the time of completion of the initial public offering. The 2010 Plan also provides for automatic annual increases in the number of shares reserved for future issuance. All grants will reduce the 2010 Plan reserve by one share for every share granted. The 2010 Plan provides for the grant of incentive stock options, non-statutory stock options, RSUs, RSAs, PSUs, PBOs, stock appreciation rights, and stock purchase rights to our employees, non-employee directors and consultants. Stock Options The option exercise price for incentive stock options is at least 100% of the fair value of our common stock on the date of grant and the option exercise price for non-statutory stock options is at least 85% of the fair value of our common stock on the date of grant, as determined by the Board. If, at the time of a grant, the optionee directly or by attribution owns stock possessing more than 10% of the total combined voting power of all of our outstanding capital stock, the exercise price for these options must be at least 110% of the fair value of the underlying common stock. Stock options granted to employees generally have a maximum term of 10 years and vest over a four year period from the date of grant, of which 25% vest at the end of one year, and 75% vest monthly over the remaining three years. We may grant options with different vesting terms from time to time. Unless an employee's termination of service is due to disability or death, upon termination of service, any unexercised vested options will be forfeited at the end of three months or the expiration of the option, whichever is earlier. Restricted Stock Units (RSUs) We also grant employees RSUs, which generally vest over either a three year period with one-third of the shares subject to the RSUs vesting on each yearly anniversary of the vesting commencement date or over a four year period with 25% of the shares subject to the RSU vesting on each yearly anniversary of the vesting commencement date, in each case contingent upon such employee’s continued service on such vesting date. RSUs are generally subject to forfeiture if employment terminates prior to the release of vesting restrictions. We may grant RSUs with different vesting terms from time to time. Performance-contingent Restricted Stock Units (PSUs) and Performance Based Options (PBOs) The compensation committee of the Board approved, solely in respect of non-executive employees, delegated to our Chief Executive Officer the authority to approve grants of PSUs. The compensation committee of the Board also approved grants of PBOs and PSUs to our executives. The PSUs and PBOs vest based upon both the successful achievement of certain corporate operating milestones in specified timelines and continued employment through the applicable vesting date. When the performance goals are deemed to be probable of achievement for these types of awards, recognition of stock-based compensation expense commences. Once the number of shares eligible to vest is determined, those shares vest in two equal installments with 50% vesting upon achievement and the remaining 50% vesting on the first anniversary of achievement, in each case, subject to the recipient’s continued service through the applicable vesting date. If the performance goals are achieved at the threshold level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to half the number of PSUs granted and one-quarter the number of shares underlying the PBOs granted. If the performance goals are achieved at the target level, the number of shares eligible to vest in respect of the PSUs and PBOs would be equal to the number of PSUs granted and half of the shares underlying the PBOs granted. If the performance goals are achieved at the superior level, the number of shares eligible to vest in respect of the PSUs would be equal to two times the number of PSUs granted and equal to the number of PBOs granted. The number of shares issuable upon achievement of the performance goals at the levels between the threshold and target levels for the PSUs and PBOs or between the target level and superior levels for the PSUs would be determined using linear interpolation. Achievement below the threshold level would result in no shares being eligible to vest in respect of the PSUs and PBOs. In the first quarter of 2018, we awarded PSUs ("2018 PSUs") and PBOs ("2018 PBOs"), each of which commence vesting based upon the achievement of various weighted performance goals, including revenue growth, non-GAAP net income growth, new licensing collaborations, new research and development service revenue arrangements and novel therapeutic enzymes advancement. As of June 30, 2018 , we estimated that the 2018 PSUs and 2018 PBOs performance goals would be achieved at 143% of the target level, and recognized expenses accordingly. In 2017, we awarded PSUs ("2017 PSUs") and PBOs ("2017 PBOs"), each of which commence vesting based upon the achievement of various weighted performance goals, including revenue growth, fundraising, service revenue, new platform license revenue, and strategic advancement of biotherapeutics pipeline. In the first quarter of 2018, we determined that the 2017 PSU and PBO performance goals had been achieved at 134.2% of the target level, and recognized expenses accordingly. Accordingly, one-half of the shares underlying the 2017 PSUs and PBOs vested in the first quarter of 2018 and one-half of the shares underlying the 2017 PSUs and PBOs will vest in the first quarter of 2019, in each case subject to the recipient’s continued service on each vesting date. In 2016, we awarded PSUs ("2016 PSUs") based upon the achievement of various weighted performance goals, including revenue growth, non-GAAP net income growth, new licensing collaborations, new research and development service revenue arrangements and novel therapeutic enzymes advancement. In the first quarter of 2017, we determined that the 2016 PSU performance goals had been achieved at 142.3% of the target level, and recognized expenses accordingly. Accordingly, one-half of the shares underlying the 2016 PSUs vested in the first quarter of each of 2017 and 2018, in each case subject to the recipient’s continued service on each vesting date. No PBOs were awarded in 2016. Stock-Based Compensation Expense Stock-based compensation expense is included in the consolidated statements of operations as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Research and development $ 567 $ 342 $ 1,003 $ 664 Selling, general and administrative 1,890 1,369 3,434 2,715 Total $ 2,457 $ 1,711 $ 4,437 $ 3,379 The following table presents total stock-based compensation expense by security types included in the unaudited condensed consolidated statements of operations for the three and six months ended June 30, 2018 and 2017 (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Stock options $ 535 $ 380 $ 1,015 $ 714 RSUs and RSAs 436 484 878 943 PSUs 426 348 844 988 PBOs 1,060 499 1,700 734 Total $ 2,457 $ 1,711 $ 4,437 $ 3,379 As of June 30, 2018 , unrecognized stock-based compensation expense, net of expected forfeitures, was $4.5 million related to unvested employee stock options, $1.8 million related to unvested RSUs and RSAs, $1.5 million related to unvested PSUs, and $3.7 million related to unvested PBOs based on current estimates of the level of achievement. Stock-based compensation expense will be recognized over the vesting periods. Valuation Assumptions The weighted-average assumptions used to estimate the fair value of employee stock options and PBOs granted were as follows: Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 (1) (1) Expected term (in years) — — 5.6 5.3 Volatility — — 60 % 62 % Risk-free interest rate — — 2.70 % 2.00 % Dividend yield — — — % — % Weighted-average estimated fair value of stock options granted — — $ 5.02 $ 2.52 (1) The Company did not grant employee stock options or PBOs in the three months ended June 30, 2018 and 2017.

Capital Stock

Capital Stock	6 Months Ended
	Jun. 30, 2018
Equity [Abstract]
Capital Stock	Capital Stock Exercise of Options For the six months ended June 30, 2018 and 2017 , 302,703 and 55,780 shares, respectively, were exercised at a weighted-average exercise price of $6.14 and $2.55 per share, respectively, with net cash proceeds of $1.9 million and $0.1 million , respectively. Public Offering In April 2018 , we completed an underwritten public offering of 4,312,500 shares of our common stock, including the exercise in full by the underwriters of their option to purchase 562,500 of our shares, at a public offering price of $9.25 per share. After deducting the underwriting discounts and commissions and estimated offering expenses, net proceeds were approximately $37.3 million . Unaudited consolidated statements of stockholders' equity as of June 30, 2018 and 2017 are as follows (in thousands): Common Stock Additional Accumulated Other Accumulated Deficit Total Stockholders' Equity Shares Amount Balance at December 31, 2016 41,255 $ 4 $ 311,164 $ — $ (292,069 ) $ 19,099 Exercise of stock options 56 — 142 — — 142 Release of stock awards 1,079 — — — — — Employee stock-based compensation — — 3,379 — — 3,379 Net shares settlements for taxes (391 ) — (1,636 ) — — (1,636 ) Issuance of common stock, net of issuance costs 6,325 1 23,290 — — 23,291 Total comprehensive loss — — — 102 (13,740 ) (13,638 ) Balance at June 30, 2017 48,324 $ 5 $ 336,339 $ 102 $ (305,809 ) $ 30,637 Balance at December 31, 2017 48,365 $ 5 $ 340,079 $ (472 ) $ (315,065 ) $ 24,547 Exercise of stock options 303 — 1,858 — — 1,858 Release of stock awards 824 — — — — — Employee stock-based compensation — — 4,413 — — 4,413 Non-employee stock-based compensation — — 24 — — 24 Net shares settlements for taxes (297 ) — (3,140 ) — — (3,140 ) Issuance of common stock, net of issuance costs of $179 4,313 — 37,317 — — 37,317 ASC 606 Adjustments — — — — (4,060 ) (4,060 ) ASU 2016-01 Adjustments — — — 472 (472 ) — Net loss — — — — (8,429 ) (8,429 ) Balance at June 30, 2018 53,508 $ 5 $ 380,551 $ — $ (328,026 ) $ 52,530

Commitments and Contingencies

Commitments and Contingencies	6 Months Ended
	Jun. 30, 2018
Commitments and Contingencies Disclosure [Abstract]
Commitments and Contingencies	Commitments and Contingencies Operating Leases Our headquarters are located in Redwood City, California, where we occupy approximately 107,200 square feet of office and laboratory space in four buildings within the same business park of Metropolitan Life Insurance Company ("MetLife"). We entered into the initial lease with MetLife for a portion of this space in 2004 and the lease has been amended multiple times since then to adjust space and amend the terms of the lease, with the latest amendment ("Seventh Amendment") in October 2016 which, for one of our buildings, waived our existing asset retirement obligation, and extended the lease term to January 2022. The various terms for the spaces under the lease have expiration dates that range from January 2020 through January 2022. Beginning in February 2014, we have subleased office space to different subtenants with separate options to extend the subleases. If all such options to extend were exercised, these agreements would expire at various dates through November 2019. We incurred $3.6 million of capital improvement costs related to the facilities leased from MetLife through December 31, 2012. During 2011 and 2012, we requested and received $3.1 million of reimbursements from the landlord for the tenant improvement and HVAC allowances for the completed construction. The reimbursements were recorded once cash was received and are amortized on a straight line basis over the term of the lease as a reduction in rent expense. The remaining lease incentive obligations were $0.7 million and $0.9 million at June 30, 2018 and December 31, 2017 , respectively, and are reflected as liabilities on the consolidated balance sheet. Rent expense for the Redwood City properties is recognized on a straight-line basis over the term of the lease. We are required to restore certain areas of the Redwood City facilities that we are renting to their original form. We are expensing the asset retirement obligation over the terms of the respective leases. We review the estimated obligation each reporting period and make adjustments if our estimates change. We recorded asset retirement obligations of $0.2 million as of both June 30, 2018 and December 31, 2017 , which are included in other liabilities on the consolidated balance sheets. Accretion expense related to our asset retirement obligations was nominal in the three and six months ended June 30, 2018 and June 30, 2017 . Pursuant to the terms of the amended lease agreement, we exercised our right to deliver a letter of credit in lieu of a security deposit. The letters of credit are collateralized by deposit balances held by the bank in the amount of $0.7 million as of June 30, 2018 and December 31, 2017 . These deposits are recorded as restricted cash on the consolidated balance sheets. Rent expense was $0.8 million and $1.6 million during the three and six months ended June 30, 2018 , respectively, partially offset by sublease income of $0.3 million and $0.6 million , respectively. Rent expense was $0.8 million and $1.5 million during three and six months ended June 30, 2017 , respectively, partially offset by sublease income of $0.3 million and $0.7 million , respectively. Capital Leases In December 2016, we entered into a three -year financing lease agreement with a third party supplier for the purchase of laboratory equipment that was partially financed through a capital lease of approximately $0.4 million . The lease became effective upon delivery of the equipment, which occurred in February 2017, and the term of the lease is three years from the effective date. This financing agreement was accounted for as a capital lease due to the bargain purchase option at the end of the lease. In April 2017, we entered into a three -year financing lease agreement with a third party supplier for the purchase of information technology equipment for approximately $0.3 million . The effective date of the lease was May 19, 2017 and the term of the lease is three years. This financing agreement was accounted for as a capital lease due to the bargain purchase option at the end of the lease. Leases Future minimum payments under non-cancellable capital and operating leases at June 30, 2018 are as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2018 (remaining 6 months) $ 126 $ 1,598 2019 252 3,280 2020 61 712 2021 — 490 2022 — 41 Total minimum lease payments (1) 439 $ 6,121 Less: amount representing interest (19 ) Present value of capital lease obligations 420 Less: current portion (237 ) Long-term portion of capital leases $ 183 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases at June 30, 2018 . Other Commitments We enter into supply and service arrangements in the normal course of business. Supply arrangements are primarily for fixed-price manufacture and supply. Service agreements are primarily for the development of manufacturing processes and certain studies. Commitments under service agreements are subject to cancellation at our discretion which may require payment of certain cancellation fees. The timing of completion of service arrangements is subject to variability in estimates of the time required to complete the work. The following table provides quantitative data regarding our other commitments. Future minimum payments reflect amounts that we expect to pay including potential obligations under services agreements subject to risk of cancellation by us (in thousands): Other Commitment Agreement Type Agreement Date Future Minimum Payment Manufacture and supply agreement with expected future payment date of December 2022 April 2016 $ 1,693 Service agreement for the development of manufacturing process April 2017 2 Service agreement for stability study July 2017 439 Service agreement for clinical trial December 2017 $ 2,116 Total other commitments $ 4,250 Credit Facility Effective June 30, 2017, we entered into a credit facility (the "Credit Facility") consisting of term loans ("Term Debt") totaling up to $10.0 million , and advances ("Advances") under a revolving line of credit ("Revolving Line of Credit") totaling up to $5.0 million with an accounts receivable borrowing base of 80% of eligible accounts receivable. At June 30, 2018 , we have not drawn from the Credit Facility. In June 2018, we entered into a Third Amendment to the Credit Facility whereby the draw period on the term debt was extended to September 30, 2018. We may draw on the Term Debt at any time prior to September 30, 2018, subject to customary conditions for funding including, among others, that no event of default exists. We may draw on the Revolving Line of Credit at any time prior to the maturity date. On July 1, 2021 , any loans for Term Debt mature and the Revolving Line of Credit terminates. Term Debt bears interest through maturity at a variable rate based on the London Interbank Offered Rate plus 3.60% . Advances under the Revolving Line of Credit bear interest at a variable annual rate equal to the greater of (i) 1.00% above the prime rate and (ii) 5.00% . The Credit Facility allows for interest-only payments on Term Debt through August 1, 2019 . Monthly payments of principal and interest on the Term Debt are required following the applicable amortization date. We may elect to prepay in full the Term Debt and Advances under the Revolving Line of Credit at any time. Our obligations under the Credit Facility are secured by a lien on substantially all of our personal property other than our intellectual property. The Credit Facility includes a number of customary covenants and restrictions which require us to comply with certain financial covenants including achieving consolidated product revenues levels at minimum levels as set forth in the Credit Facility through December 2018 and on and after January 2019 , in each case unless we maintain certain minimum cash levels with the lender in an amount equal to or greater than six times the sum of the average six -month trailing operating cash flow net outlay plus the average monthly principal due and payable in the immediately succeeding three -month period. The Credit Facility places various restrictions on our transferring collateral, incurring additional indebtedness, engaging in mergers or acquisitions, paying dividends or making other distributions, making investments, creating liens, and selling assets and permitted assets to be held at foreign subsidiaries above specified caps, in each case subject to certain exceptions. A failure to comply with these covenants could permit the lender to exercise remedies against us and the collateral securing the Credit Facility, including foreclosure of our properties securing the Credit Facility and our cash. At June 30, 2018 , we were in compliance with the covenants for the Credit Facility. Legal Proceedings We are not currently a party to any material pending litigation or other material legal proceedings. In February 2018, we and EnzymeWorks, Inc. (U.S.), Suzhou Hanmei Biotechnology Co. Ltd, d/b/a EnzymeWorks, Inc. (China) (collectively, "EnzymeWorks"), Junhua Tao, and Andrew Tao reached a settlement concerning the lawsuit filed by us in February 2016 against EnzymeWorks, Junhua Tao, and Andrew Tao in the United States District Court for the Northern District of California. The parties have entered into a settlement agreement, the terms of which are confidential. The parties have also stipulated to a judgment of patent infringement of all asserted patents against EnzymeWorks, and a permanent injunction barring any future infringement. The remaining claims against EnzymeWorks, and all claims against Junhua Tao, and Andrew Tao including trade secret misappropriation, breach of contract and voidable transfer have been dismissed with prejudice. EnzymeWorks appealed the sanctions levied against them by Judge Orrick to the Federal Circuit and filed its opening brief on May 30, 2018. On July 9, 2018, Codexis filed its response brief, and EnzymeWorks filed its reply on July 30, 2018. Indemnifications We are required to recognize a liability for the fair value of any obligations we assume upon the issuance of a guarantee. We have certain agreements with licensors, licensees, and collaborators that contain indemnification provisions. In such provisions, we typically agree to indemnify the licensor, licensee and collaborator against certain types of third party claims. The maximum amount of the indemnifications is not limited. We accrue for known indemnification issues when a loss is probable and can be reasonably estimated. There were no accruals for expenses related to indemnification issues for any periods presented.

Related Party Transactions

Related Party Transactions	6 Months Ended
	Jun. 30, 2018
Related Party Transaction, Due from (to) Related Party [Abstract]
Related Party Transactions	Related Party Transactions Exela PharmSci, Inc. We entered into a commercialization agreement with Exela in 2007. Under the license agreement, as amended, we and Exela cross-licensed certain technology relating to the manufacture of argatroban, an API, in exchange for rights to certain sublicensing fees or development payments and profit sharing. The revenue sharing arrangement was terminated in December 2017. Thomas R. Baruch, one of our directors, serves on the board of directors of Exela, and is a retired general partner in Presidio Partners 2007, LP which owns over 10% of Exela’s outstanding capital stock. As such, Mr. Baruch has an indirect pecuniary interest in the shares of Exela held by Presidio Partners 2007, L.P. We recognized no revenue for the three and six months ended June 30, 2018 , compared to $0.4 million and $0.7 million in revenues for the three and six months ended June 30, 2017 , respectively, shown in the unaudited condensed consolidated statement of operations as research and development revenue. We had $0.6 million and $1.6 million of receivables from Exela at June 30, 2018 and December 31, 2017 , respectively. AstraZeneca PLC Pam P. Cheng, a member of our board of directors, joined AstraZeneca PLC as Executive Vice President, Operations and Information Technology in June 2015. We sell biocatalyst products to AstraZeneca PLC, to Alfa Aesar, which is a purchasing agent of AstraZeneca PLC, and also to Asymchem Life Science Co, Ltd, which is a contract manufacturer for AstraZeneca PLC. In the three and six months ended June 30, 2018 , we recognized $55 thousand and $0.4 million in revenue from AstraZeneca PLC, compared to $24 thousand and $50 thousand in the three and six months ended June 30, 2017 , respectively. We recognized nil and de minimis revenue from Asymchem in the three and six months ended June 30, 2018 , respectively, and no revenue in the three and six months ended June 30, 2017 , respectively. We recognized no revenue from Alfa Aesar in the three and six months ended June 30, 2018 and 2017 , respectively. At June 30, 2018 and December 31, 2017 , we had $45 thousand and $86 thousand accounts receivables from AstraZeneca, PLC, respectively, zero and $0.4 million of accounts receivables from Alfa Aesar, respectively, and no accounts receivables from Asymchem. In the three and six months ended June 30, 2018 , we performed a proof of concept screening service using AstraZeneca’s substrate. This service was related to an option for additional services which AstraZeneca had exercised in June. We had completed the additional services and recognized $45 thousand in revenue at June 30, 2018.

Segment, Geographical and Other

Segment, Geographical and Other Revenue Information	6 Months Ended
	Jun. 30, 2018
Segment Reporting [Abstract]
Segment, Geographical and Other Revenue Information	Segment, Geographical and Other Revenue Information Segment Information As discussed in Note 2, "Basis of Presentation and Summary of Significant Accounting Policies," beginning in 2018, we identified our biotherapeutics business as a standalone business segment. Our two reportable business segments as of January 1, 2018, consisted of Performance Enzymes and Novel Biotherapeutics. We report corporate-related expenses such as legal, accounting, information technology, and other costs that are not otherwise included in our reportable business segments as "Corporate costs." All items not included in income (loss) from operations are excluded from the business segments. We manage our assets on a total company basis, not by business segment, as the majority of our operating assets are shared or commingled. Our CODM does not review asset information by business segment in assessing performance or allocating resources, and accordingly, we do not report asset information by business segment. Performance Enzymes We initially commercialized our CodeEvolver ® protein engineering technology platform and products in the pharmaceuticals market, and to date this continues to be our largest market served. Our customers, which include many large global pharmaceutical companies, use our technology, products and services in their manufacturing processes and process development. We have also used the technology to develop customized enzymes for use in other industrial markets. These markets consist of several large industrial verticals, including food and food ingredients, animal feed, flavors, fragrances, and agricultural chemicals. We also use our technology to develop enzymes for customers using NGS and PCR/qPCR for in vitro molecular diagnostic and molecular biology research applications. Novel Biotherapeutics We are also targeting new opportunities in the pharmaceutical industry to discover, improve, and/or develop biotherapeutic drug candidates. We believe that our CodeEvolver ® protein engineering platform technology can be used to discover novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. Similarly, we believe that we can deploy our platform technology to improve specific characteristics of a customer’s pre-existing biotherapeutic drug candidate, such as its activity, stability or immunogenicity. Most notable is our lead program for the potential treatment of PKU in humans. PKU is an inherited metabolic disorder in which the enzyme that converts the essential amino acid phenylalanine into tyrosine is deficient. In October 2017, we announced a strategic collaboration with Nestlé Health Science to advance CDX-6114, our own novel orally administrable enzyme therapeutic candidate for the potential treatment of PKU disease. We have also developed a pipeline of other biotherapeutic drug candidates in which we expect to continue to make additional investments with the aim of advancing additional product candidates targeting other therapeutic areas. For the three and six months ended June 30, 2018 , all revenues related to the Novel Biotherapeutics segment were generated from our collaboration with Nestlé Health Science. There was no revenue related to the Novel Biotherapeutics segment for the three and six months ended June 30, 2017 . Our CODM regularly reviews our segments and the approach provided by management for performance evaluation and resource allocation. In the second quarter of 2018, we made a change in the segment measurement for allocating operating expenses between our two reporting segments. The remaining expenses have been allocated to corporate costs. This change in measurement only impacts our segment disclosures, and it has no impact on our overall consolidated financial statements. We revised the allocation of operating expenses between the two segments based on better insight and improved judgment during the second quarter of 2018. Operating expenses that directly support the segment activity are allocated based on segment headcount, revenue contribution or activity of the business units within the segments, based on the corporate activity type provided to the segment. The expense allocation excludes certain corporate costs that are separately managed from the segments. Management believes that the current allocation of research and development expenses provides a more accurate presentation of how the segments utilize research and development support activities as compared to the method previously used. This provides the CODM with more meaningful segment profitability reporting to support operating decisions and allocate resources. Following the change, we reclassified the research and development cost of $ 0.3 million from Performance Enzyme to Novel Biotherapeutics for the three months ended March 31, 2018 and we reclassified the research and development cost of $ 0.1 million from Novel Biotherapeutics to Performance Enzyme for the three months ended March 31, 2017. Segment results for the three and six months ended June 30, 2018 have been revised to reflect this change in operating segment measurement. The following table provides financial information by our reportable business segments along with a reconciliation to consolidated loss before income taxes (in thousands): Three months ended June 30, 2018 Three months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 3,723 $ — $ 3,723 $ 6,600 $ — $ 6,600 Research and development revenue 7,442 2,373 9,815 3,747 — 3,747 Total revenues 11,165 2,373 13,538 10,347 — 10,347 Costs and operating expenses: Cost of product revenue 2,611 — 2,611 3,790 — 3,790 Research and development (1) 4,724 2,442 7,166 4,023 2,149 6,172 Selling, general and administrative 1,729 304 2,033 1,777 — 1,777 Total segment costs and operating expenses 9,064 2,746 11,810 9,590 2,149 11,739 Income (loss) from operations $ 2,101 $ (373 ) $ 1,728 $ 757 $ (2,149 ) $ (1,392 ) Corporate costs (2) (5,209 ) (4,702 ) Depreciation and amortization (265 ) (228 ) Loss before income taxes $ (3,746 ) $ (6,322 ) (1) Research and development expenses exclude depreciation and amortization. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. Six months ended June 30, 2018 Six months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 9,886 $ — $ 9,886 $ 12,186 $ — $ 12,186 Research and development revenue 12,008 5,686 17,694 6,131 — 6,131 Total revenues 21,894 5,686 27,580 18,317 — 18,317 Costs and operating expenses: Cost of product revenue 6,436 — 6,436 6,792 — 6,792 Research and development (1) 9,790 4,374 14,164 8,172 3,660 11,832 Selling, general and administrative 3,825 450 4,275 3,589 — 3,589 Total segment costs and operating expenses 20,051 4,824 24,875 18,553 3,660 22,213 Income (loss) from operations $ 1,843 $ 862 $ 2,705 $ (236 ) $ (3,660 ) $ (3,896 ) Corporate costs (2) (10,644 ) (9,308 ) Depreciation and amortization (503 ) (554 ) Loss before income taxes $ (8,442 ) $ (13,758 ) (1) Research and development expenses exclude depreciation and amortization. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. The following table provides stock-based compensation expense included in income (loss) from operations by segment (in thousands): Three months ended June 30, 2018 Three months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 768 $ 83 $ 851 $ 434 $ 47 $ 481 Six months ended June 30, 2018 Six months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 1,326 $ 146 $ 1,472 $ 789 $ 100 $ 889 Significant Customers Customers that each contributed 10% or more of our total revenues were as follows: Percentage of Total Revenues for the Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Customer A 27% 45% 38% 42% Customer B 34% 21% 22% 12% Customer C 18% * 21% * Customers that each contributed 10% or more of our total accounts receivable had the following balances as of the periods presented: Percentage of Accounts Receivables at June 30, 2018 December 31, 2017 Customer A 46% 31% Customer B 27% 16% Customer D 11% 15% Customer E * 14% * Less than 10% of the period presented Geographical Information Geographic revenues are identified by the location of the customer and consist of the following (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Revenues Americas $ 6,058 $ 4,401 $ 9,655 $ 6,189 EMEA 3,808 1,959 8,800 5,166 APAC 3,672 3,987 9,125 6,962 Total revenues $ 13,538 $ 10,347 $ 27,580 $ 18,317 Identifiable long-lived assets as follows (in percentage): Long-lived assets: June 30, 2018 December 31, 2017 United States 100 % 100 %

Basis of Presentation and Sum21

Basis of Presentation and Summary of Significant Accounting Policies (Policies)	6 Months Ended
	Jun. 30, 2018
Accounting Policies [Abstract]
Basis of Presentation and Principles of Consolidation	Basis of Presentation and Principles of Consolidation The accompanying unaudited condensed consolidated financial statements have been prepared in accordance with generally accepted accounting principles in the United States of America ("GAAP") and the applicable rules and regulations of the Securities and Exchange Commission ("SEC") for interim financial information. Accordingly, they do not include all of the information and notes required by GAAP for complete financial statements. These interim unaudited condensed consolidated financial statements should be read in conjunction with the consolidated financial statements and notes thereto contained in our Annual Report on Form 10-K for the year ended December 31, 2017 . The condensed consolidated balance sheet at December 31, 2017 has been derived from the audited consolidated financial statements at that date, but does not include all disclosures, including notes, required by GAAP for complete financial statements. The unaudited interim condensed consolidated financial statements have been prepared on the same basis as the audited consolidated financial statements and, in the opinion of management, reflect all adjustments of a normal recurring nature considered necessary to present fairly our financial position as of June 30, 2018 and results of our operations and comprehensive loss for the three and six months ended June 30, 2018 and 2017 , and cash flows for the six months ended June 30, 2018 and 2017 . The interim results are not necessarily indicative of the results for any future interim period or for the entire year. Certain prior period amounts have been reclassified to conform to current period presentation. In connection with the adoption of Accounting Standard Update ("ASU") 2016-01, "Financial Instruments-Overall: Recognition and Measurement of Financial Assets and Financial Liabilities," unrealized losses on equity investments in marketable securities, net of taxes, previously included in accumulated other comprehensive loss have been reclassified to beginning accumulated deficit. See "Recently Adopted Accounting Pronouncements" for details regarding the adoption of ASU 2016-01. Comprehensive loss is equivalent to net loss during the three and six months ended June 30, 2018 because after adopting ASC 2016-01, we do not have any transactions recorded under comprehensive loss. Prior to our adoption of ASU 2016-01, and during the three and six months ended June 30, 2017 , comprehensive loss included unrealized losses from our equity investments in marketable securities. The unaudited interim condensed consolidated financial statements include the accounts of Codexis, Inc. and its wholly owned subsidiaries in the United States, India and the Netherlands. All significant intercompany balances and transactions have been eliminated in consolidation.
Use of Estimates	Use of Estimates The preparation of financial statements in conformity with GAAP requires management to make estimates and assumptions that affect the reported amounts of assets and liabilities, disclosures of contingent liabilities at the date of the condensed consolidated financial statements, and the reported amounts of revenue and expenses during the reporting period. We regularly assess these estimates which primarily affect revenue recognition, accounts receivable, inventories, the valuation of marketable securities, goodwill arising out of business acquisitions, accrued liabilities, stock awards, and the valuation allowances associated with deferred tax assets. Actual results could differ from those estimates and such differences may be material to the condensed consolidated financial statements.
Segment Reporting	Segment Reporting We report two business segments, Performance Enzymes and Novel Biotherapeutics, which are based on our operating segments. Operating segments are defined as components of an enterprise about which separate financial information is available that is evaluated regularly by the chief operating decision maker ("CODM"), or decision making group, in deciding how to allocate resources, and in assessing performance. Our CODM is our Chief Executive Officer. Our business segments are primarily based on our organizational structure and our operating results as used by our CODM in assessing performance and allocating resources for our company. We do not allocate or evaluate assets by segment. Previously, we had managed our business under one business segment. As our biotherapeutics business has emerged as a significant opportunity for us, effective in 2018, we formed Novel Biotherapeutics as a new business segment. The Novel Biotherapeutics segment focuses on new opportunities in the pharmaceutical industry to discover or improve novel biotherapeutic drug candidates that will target human diseases that are in need of improved therapeutic interventions. The Performance Enzymes segment consists of the existing protein catalyst products and services with focus on pharmaceutical, food, molecular diagnostics, and other industrial markets.
Foreign Currency Translation	Foreign Currency Translation The United States dollar is the functional currency for our operations outside the United States. Accordingly, nonmonetary assets and liabilities originally acquired or assumed in other currencies are recorded in United States dollars at the exchange rates in effect at the date they were acquired or assumed. Monetary assets and liabilities denominated in other currencies are translated into United States dollars at the exchange rates in effect at the balance sheet date. Translation adjustments are recorded in other expense in the unaudited condensed consolidated statements of operations. Gains and losses realized from non-U.S. dollar transactions, including intercompany balances not considered as permanent investments, denominated in currencies other than an entity's functional currency are included in other expense in the accompanying unaudited condensed consolidated statements of operations.
Revenue Recognition	Revenue Recognition On January 1, 2018, we adopted the provisions of ASU 2014-09, "Revenue from Contracts with Customers (Topic 606) ("ASC 606"). The guidance provides a unified model to determine how revenue is recognized. Our revenues are derived primarily from product revenue and collaborative research and development agreements. The majority of our contracts with customers typically contain multiple products and services. We account for individual products and services separately if they are distinct-that is, if a product or service is separately identifiable from other items in the contract and if a customer can benefit from it on its own or with other resources that are readily available to the customer. In determining the appropriate amount of revenue to be recognized as we fulfill our obligations under our product revenue and collaborative research and development agreements, we perform the following steps: (i) identification of the promised goods or services in the contract; (ii) determination of whether the promised goods or services are performance obligations including whether they are distinct in the context of the contract; (iii) measurement of the transaction price, including the constraint on variable consideration; (iv) allocation of the transaction price to the performance obligations based on estimated selling prices; and (v) recognition of revenue when (or as) we satisfy each performance obligation. The majority of our collaborative contracts contain multiple revenue streams such as up-front and/or annual license fees, fees for full time employee ("FTE") research and development services, contingent milestone payments upon achievement of contractual criteria, and royalty fees based on the licensees' product revenue or usage, among others. We determine the stand-alone selling price ("SSP") and allocate consideration to distinct performance obligations. Typically, we base our SSPs on our historical sales. If an SSP is not directly observable, then we estimate the SSP taking into consideration market conditions, forecasted sales, entity-specific factors and available information about the customer. We account for a contract with a customer when there is approval and commitment from both parties, the rights of the parties are identified, payment terms are identified, the contract has commercial substance and collectability of consideration is probable. Non-cancellable purchase orders received from customers to deliver a specific quantity of product, when combined with our order confirmation, in exchange for future consideration, create enforceable rights and obligations on both parties and constitute a contract with a customer. We measure revenue based on the consideration specified in the contract with each customer, net of any sales incentives and taxes collected on behalf of government authorities. We recognize revenue in a manner that best depicts the transfer of promised goods or services to the customer, when control of the product or service is transferred to a customer. We make significant judgments when determining the appropriate timing of revenue recognition. The following is a description of principal activities from which we generate revenue: Product Revenue Product revenue consist of sales of protein catalysts, pharmaceutical intermediates and Codex ® Biocatalyst Panels and Kits. A majority of our product revenue is made pursuant to purchase orders or supply agreements and is recognized at a point in time when the control of the product has been transferred to the customer typically upon shipment. For some of the products that we develop, we recognize revenue over time as we have a right to payment from the customer under a binding, non-cancellable purchase order, and there is no alternate use of the product for us as it is specifically made for the customer’s use. Certain of our agreements provide options to customers which they can exercise at a future date, such as the option to purchase our product during the contract duration at discounted prices and an option to extend their contract, among others. In accounting for customer options, we determine whether an option is a material right and this requires us to exercise significant judgment. If a contract provides the customer an option to acquire additional goods or services at a discount that exceeds the range of discounts that we typically give for that product or service, or if the option provides the customer certain additional goods or services for free, the option may be considered a material right. If the contract gives the customer the option to acquire additional goods or services at their normal SSPs, we would likely determine that the option is not a material right and, therefore, account for it as a separate performance obligation when the customer exercises the option. We primarily account for options which provide material rights using the alternative approach available under ASC 606, as we concluded we meet the criteria for using the alternative approach. Therefore, the transaction price is calculated as the expected consideration to be received for all the goods and services we expect to provide. We update the transaction price for expected consideration, subject to constraint, each reporting period if our estimate of future goods to be ordered by customers change. Research and Development Revenue We perform research and development activities as specified in each respective customer agreement. We identify each performance obligation in our research and development agreements at contract inception. We allocate the consideration to each distinct performance obligation based on the estimated SSP of each performance obligation. Performance obligations included in our research and services agreements typically include research and development services for a specified term, periodic reports and small samples of enzyme produced. The majority of our research and development agreements are based on a contractual rate per FTE working on the project. The underlying product that we develop for customers does not create an asset with an alternative use to us and the customer receives benefits as we perform the work towards completion. Thus, our performance obligations are generally satisfied over time as the service is performed. We utilize an appropriate method of measuring progress towards the completion of our performance obligations to determine the timing of revenue recognition. For each performance obligation that is satisfied over time, we recognize revenue using a single measure of progress, typically based on FTE hours incurred. Our contracts frequently provide customers with rights to use or access our products or technology, along with other promises or performance obligations. Under ASC 606, we must first determine whether the license is distinct from other promises, such as our promise to manufacture a product. If we determine that the customer cannot benefit from the license without our manufacturing capability, the license will be accounted for as combined with the other performance obligations. If we determine that a license is distinct, we would recognize revenues from non-refundable, up-front license fees when the license is transferred to the customer, and the customer can use and benefit from it. We estimate the SSP for license rights by using an income approach model which includes the following key assumptions: the development timelines, revenue forecasts, commercialization expenses, discount rate, and the probability of technical and regulatory success. For licenses that have been previously sold to other customers, we use historical information to determine SSP. At the inception of each arrangement that includes variable consideration such as development milestone payments, we evaluate whether the milestones are considered probable of being reached and estimate the amount to be included in the transaction price using the most likely amount method. If it is probable that a significant revenue reversal would not occur, the associated milestone value is included in the transaction price. Milestone payments that are not within our control or the licensee, such as regulatory approvals, are not considered probable of being achieved until those approvals are received. The transaction price is then allocated to each performance obligation on a relative stand-alone selling price basis, for which we recognize revenue as or when the performance obligations under the contract are satisfied. At the end of each subsequent reporting period, we re-evaluate the probability of achievement of such development milestones and any related constraint, and if necessary, adjust our estimate of the overall transaction price. Any such adjustments are recorded on a cumulative catch-up basis, which would affect license, collaboration and other revenues and earnings in the period of adjustment. Our CodeEvolver ® platform technology transfer collaboration agreements typically include license fees, upfront fees, and variable consideration in the form of milestone payments, and sales or usage-based royalties. We recognize revenues from our platform technology transfer agreements over time as our customer learns to use our technology. For agreements that include sales or usage-based royalty payments to us, we do not recognize revenue until the underlying sales of the product or usage has occurred. At the end of each reporting period, we estimate the royalty amount. We recognize revenue at the later of (i) when the related sale of the product occurs, or (ii) when the performance obligation to which some or all of the royalty has been allocated has been satisfied, or partially satisfied. Contract Assets Contract assets include amounts related to our contractual right to consideration for completed performance obligations not yet invoiced. The contract assets are reclassified to receivables when the rights become unconditional. Contract Liabilities Contract liabilities are recorded as deferred revenues and include payments received in advance of performance under the contract. Contract liabilities are realized when the development services are provided to the customer or control of the products has been transferred to the customer. A portion of our contract liabilities relate to supply arrangements that contain material rights that are recognized using the alternative method, under which the aggregate amount invoiced to the customer for shipped products, including annual fees, is higher than the amount of revenue recognized based on the transaction price allocated to the shipped products. Contract Costs ASC 606 requires the recognition of an asset for the incremental costs of obtaining a contract with a customer if the entity expects to recover such costs. Incremental costs are costs that would not have been incurred if the contract had not been obtained. Examples of contract costs are commissions paid to sales personnel. We do not typically incur significant incremental costs because the compensation of our salespeople are not based on contracts closed but on a mixture of company goals, individual goals, and sales goals. If a commission paid is directly related to obtaining a specific contract, our policy is to capitalize and amortize such costs over the estimated life of the contract. Contract costs are reported in other non-current assets.
Cost of Product Sales	Cost of Product Revenue Cost of product revenue comprises both internal and third party fixed and variable costs including materials and supplies, labor, facilities, and other overhead costs associated with our product sales. Shipping costs are included in our cost of product revenue. Such charges were not significant in any of the periods presented.
Cost of Research and Development Services and Research and Development Expenses	Cost of Research and Development Services Cost of research and development services related to FTE services under research and development agreements approximate the research funding over the term of the respective agreements and is included in research and development expense. Costs of services provided under license and platform technology transfer agreements are included in research and development expenses and are expensed in the periods in which such costs are incurred. Research and Development Expenses Research and development expenses consist of costs incurred for internal projects and partner-funded collaborative research and development activities, as well as license and platform technology transfer agreements, as mentioned above. These costs include our direct and research-related overhead expenses, which include salaries and other personnel-related expenses (including stock-based compensation), occupancy-related costs, supplies, depreciation of facilities and laboratory equipment and amortization of acquired technologies, as well as external costs, and are expensed as incurred. Costs to acquire technologies that are utilized in research and development and that have no alternative future use are expensed when incurred
Advertising	Advertising Advertising costs are expensed as incurred and included in selling, general and administrative expenses in the unaudited condensed consolidated statements of operations.
Stock-Based Compensation	Stock-Based Compensation We use the Black-Scholes-Merton option pricing model to estimate the fair value of options granted under our equity incentive plans. The Black-Scholes-Merton option pricing model requires the use of assumptions, including the expected term of the award and the expected stock price volatility. The expected term is based on historical exercise behavior on similar awards, giving consideration to the contractual terms, vesting schedules and expectations of future employee behavior. We use historical volatility to estimate expected stock price volatility. The risk-free rate assumption is based on United States Treasury instruments whose terms are consistent with the expected term of the stock options. The expected dividend assumption is based on our history and expectation of dividend payouts. Restricted Stock Units ("RSUs"), Restricted Stock Awards ("RSAs"), performance based options ("PBOs"), and performance-contingent restricted stock units ("PSUs") are measured based on the fair market values of the underlying stock on the dates of grant. The vesting of PBOs and PSUs awarded is conditioned upon the attainment of one or more performance objectives over a specified period and upon continued employment through the applicable vesting date. At the end of the performance period, shares of stock subject to the PBOs and PSUs vest based upon both the level of achievement of performance objectives within the performance period and continued employment through the applicable vesting date. Stock-based compensation expense is calculated based on awards ultimately expected to vest and is reduced for estimated forfeitures at the time of grant and revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates. The estimated annual forfeiture rates for stock options, RSUs, PSUs, PBOs, and RSAs are based on historical forfeiture experience. The estimated fair value of stock options, RSUs, and RSAs are expensed on a straight-line basis over the vesting term of the grant and the estimated fair value of PSUs and PBOs are expensed using an accelerated method over the term of the award once management has determined that it is probable that the performance objective will be achieved. Compensation expense is recorded over the requisite service period based on management's best estimate as to whether it is probable that the shares awarded are expected to vest. Management assesses the probability of the performance milestones being met on a continuous basis.
Cash and Cash Equivalents	Cash and Cash Equivalents We consider all highly liquid investments with maturity dates of three months or less at the date of purchase to be cash equivalents. Our cash and cash equivalents consist of cash on deposit with banks and money market funds. The majority of cash and cash equivalents is maintained with major financial institutions in North America. Deposits with these financial institutions may exceed the amount of insurance provided on such deposits.
Restricted Cash	Restricted Cash In 2016, we began the process of liquidating our Indian subsidiary. The local legal requirements for liquidation required us to maintain our subsidiary's cash balance in an account managed by a legal trustee to satisfy our financial obligations.
Marketable Securities	Marketable Securities We invest in equity securities that are carried at estimated fair value (see Note 6, "Cash Equivalents and Marketable Securities"), with changes in fair value recognized within earnings. Equity securities with remaining maturities of greater than one year or which we currently do not intend to sell are classified as long-term. Unrealized holding gains and losses (the adjustment to fair value) and realized gains and losses are included in other income (expense) in the unaudited condensed consolidated statement of operations.
Fair Value Measurements	Fair Value Measurements Fair value is defined as the price that would be received to sell an asset or paid to transfer a liability in an orderly transaction between market participants at the measurement date. In determining fair value, we utilize valuation techniques that maximize the use of observable inputs and minimize the use of unobservable inputs to the extent possible and we consider counterparty credit risk in our assessment of fair value. Carrying amounts of financial instruments, including cash equivalents, marketable investments, accounts receivable, accounts payable, and accrued liabilities, approximate their fair values as of the balance sheet dates because of their short maturities. The fair value hierarchy distinguishes between (1) market participant assumptions developed based on market data obtained from independent sources (observable inputs) and (2) an entity's own assumptions about market participant assumptions developed based on the best information available in the circumstances (unobservable inputs). The fair value hierarchy consists of three broad levels, giving the highest priority to unadjusted quoted prices in active markets for identical assets or liabilities (Level 1) and the lowest priority to unobservable inputs (Level 3). The three levels of the fair value hierarchy are described below: • Level 1: Inputs that are unadjusted, quoted prices in active markets for identical assets or liabilities at the measurement date. • Level 2: Inputs that are either directly or indirectly observable for the asset or liability through correlation with market data at the measurement date and for the duration of the instrument’s anticipated life. • Level 3: Unobservable inputs that are supported by little or no market activity and that are significant to the fair value of the assets or liabilities and which reflect management’s best estimate of what market participants would use in pricing the asset or liability at the measurement date.
Concentrations of Credit Risk	Concentrations of Credit Risk Financial instruments that potentially subject us to significant concentrations of credit risk consist primarily of cash and cash equivalents, accounts receivable, marketable securities, and restricted cash. Cash that is not required for immediate operating needs is invested principally in money market funds. Cash and cash equivalents are invested through banks and other financial institutions in the United States, India, and the Netherlands. Such deposits in those countries may be in excess of insured limits.
Accounts Receivable and Allowance for Doubtful Accounts	Accounts Receivable and Allowance for Doubtful Accounts We currently sell primarily to pharmaceutical and fine chemicals companies throughout the world by the extension of trade credit terms based on an assessment of each customer's financial condition. Trade credit terms are generally offered without collateral and may include a discount for prompt payment for specific customers. To manage our credit exposure, we perform ongoing evaluations of our customers' financial conditions. In addition, accounts receivable includes amounts owed to us under our collaborative research and development agreements. We recognize accounts receivable at invoiced amounts and we maintain a valuation allowance for doubtful accounts. We estimate an allowance for doubtful accounts through specific identification of potentially uncollectible accounts receivable based on an analysis of our accounts receivable aging. Uncollectible accounts receivable are written off against the allowance for doubtful accounts when all efforts to collect them have been exhausted. Recoveries are recognized when they are received. Actual collection losses may differ from our estimates and could be material to our consolidated financial position, results of operations, and cash flows.
Inventories	Inventories Inventories are stated at the lower of cost or net realizable value. Cost is determined using a weighted-average approach, assuming full absorption of direct and indirect manufacturing costs, or based on cost of purchasing from our vendors. If inventory costs exceed expected net realizable value due to obsolescence or lack of demand, valuation adjustments are recorded for the difference between the cost and the expected net realizable value. These valuation adjustments are determined based on significant estimates.
Concentrations of Supply Risk	Concentrations of Supply Risk We rely on a limited number of suppliers for our products. We believe that other vendors would be able to provide similar products; however, the qualification of such vendors may require substantial start-up time. In order to mitigate any adverse impacts from a disruption of supply, we attempt to maintain an adequate supply of critical single-sourced materials. For certain materials, our vendors maintain a supply for us. We outsource the large scale manufacturing of our products to contract manufacturers with facilities in Austria and Italy.
Impairment of Long-Lived Assets	Impairment of Long-Lived Assets Our long-lived assets consist of property and equipment. We evaluate the carrying value of long-lived assets, including property and equipment, whenever events, changes in business circumstances or our planned use of long-lived assets indicate that their carrying amounts may not be fully recoverable or that their useful lives are no longer appropriate. If these facts and circumstances exist, we assess for recovery by comparing the carrying values of long-lived assets with their future net undiscounted cash flows. If the comparison indicates that impairment exists, long-lived assets are written down to their respective fair values based on discounted cash flows. Significant management judgment is required in the forecast of future operating results that are used in the preparation of unexpected undiscounted cash flows.
Goodwill	Goodwill As of June 30, 2018 and December 31, 2017 , the carrying amount of our goodwill was $3.2 million . All of our goodwill relates to the Performance Enzymes segment. There were no indicators of impairment identified related to our Performance Enzymes segment during the six months ended June 30, 2018 and 2017 .
Income Taxes	Income Taxes We use the liability method of accounting for income taxes, whereby deferred tax asset or liability account balances are calculated at the balance sheet date using current tax laws and rates in effect for the year in which the differences are expected to affect taxable income. Valuation allowances are provided when necessary to reduce deferred tax assets to the amount that will more likely than not be realized. We make certain estimates and judgments in determining income tax expense for financial statement purposes. These estimates and judgments occur in the calculation of tax credits, benefits and deductions and in the calculation of certain tax assets and liabilities, which arise from differences in the timing of recognition of revenue and expenses for tax and financial statement purposes. Significant changes to these estimates may result in an increase or decrease to our tax provision in a subsequent period. In assessing the realizability of deferred tax assets, we consider whether it is more likely than not that some portion or all of the deferred tax assets will be realized on a jurisdiction by jurisdiction basis. The ultimate realization of deferred tax assets is dependent upon the generation of taxable income in the future. We have recorded a valuation allowance against these deferred tax assets in jurisdictions where ultimate realization of deferred tax assets is more likely than not to occur. As of June 30, 2018 and December 31, 2017 , we maintained a full valuation allowance in all jurisdictions against the net deferred tax assets as we believe that it is more likely than not that the majority of deferred tax assets will not be realized. We make estimates and judgments about our future taxable income that are based on assumptions that are consistent with our plans and estimates. Should the actual amounts differ from our estimates, the amount of our valuation allowance may be materially impacted. Any adjustment to the deferred tax asset valuation allowance would be recorded in the income statement for the periods in which the adjustment is determined to be required. We account for uncertainty in income taxes as required by the provisions of ASC Topic 740, which clarifies the accounting for uncertainty in income taxes recognized in an enterprise’s financial statements. The first step is to evaluate the tax position for recognition by determining if the weight of available evidence indicates that it is more likely than not that the position will be sustained on audit, including resolution of related appeals or litigation processes, if any. The second step is to estimate and measure the tax benefit as the largest amount that is more than 50% likely of being realized upon ultimate settlement. It is inherently difficult and subjective to estimate such amounts, as this requires us to determine the probability of various possible outcomes. We consider many factors when evaluating and estimating our tax positions and tax benefits, which may require periodic adjustments and may not accurately anticipate actual outcomes. The Tax Reform Act of 1986 and similar state provisions limit the use of net operating loss ("NOL") carryforwards in certain situations where equity transactions result in a change of ownership as defined by Internal Revenue Code Section 382. In the event we should experience such a change of ownership, utilization of our federal and state NOL carryforwards could be limited. The adoption of ASC 606 primarily resulted in less revenue recognized as of January 1, 2018, which in turn generated a decrease in net deferred tax assets. As we fully reserve our net deferred tax assets in the jurisdictions impacted by the adoption of ASC 606, this impact was offset by a corresponding decrease to the valuation allowance. We recognized income tax benefit of $11 thousand and $13 thousand for the three and six months ended June 30, 2018 , respectively. We recognized income tax benefit of $42 thousand and $18 thousand for three and six months ended June 30, 2017 , respectively. The income tax benefits were due to decreases in income from our foreign operations. We continue to maintain a full valuation allowance against our net deferred tax assets as we believe that it is more likely than not that the majority of our deferred tax assets will not be realized.
Recently Adopted and Issued Accounting Pronouncements	Recently Adopted Accounting Pronouncements In May 2014, the FASB issued ASU 2014-09, " Revenue from Contracts with Customers (Topic 606)" ("ASC 606"), amending revenue recognition guidance and requiring more detailed disclosures to enable users of financial statements to understand the nature, amount, timing, and uncertainty of revenue and cash flows arising from contracts with customers is effective for annual and interim reporting periods beginning after December 15, 2017, with early adoption permitted for public companies effective for annual and interim reporting periods beginning after December 15, 2016. We have adopted ASC 606, effective January 1, 2018, using the modified retrospective transition method. We recognized the cumulative effect of applying the new revenue standard as an adjustment to the opening balance of retained earnings at the beginning of 2018. The comparative information has not been restated and continues to be reported under the accounting standards in effect for the period presented. See Note 3, "Revenue Recognition" for more details. In January 2016, the FASB issued ASU No. 2016-01, " Financial Instruments-Overall: Recognition and Measurement of Financial Assets and Financial Liabilities ." This guidance principally affects accounting standards for equity investments, financial liabilities where the fair value option has been elected, and the presentation and disclosure requirements for financial instruments. Upon the effective date of this new guidance, all equity investments in unconsolidated entities, other than those accounted for using the equity method of accounting, will generally be measured at fair value through earnings. There will no longer be an available-for-sale classification and therefore no changes in fair value will be reported in other comprehensive income (loss) for equity securities with readily determinable fair values. This new guidance primarily impacts our accounting for equity investments. In February 2018, the FASB issued ASU 2018-03, " Technical Corrections and Improvements to Financial Instruments—Overall (Subtopic 825-10): Recognition and Measurement of Financial Assets and Financial Liabilities, that clarifies the guidance in ASU No. 2016-01, Financial Instruments—Overall (Subtopic 825-10) ." Prior to the adoption of ASU 2016-01, we recognized unrealized holding gains and losses from our equity investment in CO 2 Solutions in other comprehensive loss. We adopted ASU 2016-01 in the first quarter of 2018 using a modified retrospective approach by means of a cumulative-effect adjustment to accumulated deficit. Upon adoption of ASU 2016-01, we reclassified $0.5 million of unrealized loss (net of $0.6 million tax) from other accumulated comprehensive loss to beginning accumulated deficit. Any changes in the fair value of our equity investments, except those accounted for under the equity method, will be recognized in earnings on a prospective basis. In August 2016, the FASB issued ASU 2016-15, " Statement of Cash Flows (Topic 230): Classification of Certain Cash Receipts and Cash Payments ," which provides the FASB's guidance on certain cash flow statements items. ASU 2016-15 is effective for fiscal reporting periods beginning after December 15, 2017, including interim periods within those fiscal years. We adopted ASU 2016-15 in the first quarter of 2018, and the adoption had no impact on our unaudited condensed consolidated financial statements. In November 2016, the FASB issued ASU No. 2016-18, " Statement of Cash Flows (Topic 230) Restricted Cash a consensus of the FASB Emerging Issues Task Force ." The standard requires restricted cash and restricted cash equivalents to be included with cash and cash equivalents on the statement of cash flows. We adopted ASU 2016-18 in the first quarter of 2018 and the adoption had no material impact on our unaudited condensed consolidated financial statements. The effect of the adoption of ASU 2016-18 on our unaudited condensed consolidated statements of cash flows was to include restricted cash balances in the beginning and end of period balances of cash and cash equivalents and restricted cash. The change in restricted cash was previously disclosed in operating and investing activities in the unaudited condensed consolidated statements of cash flows. In January 2017, the FASB issued ASU No. 2017-01 " Business Combinations (Topic 805): Clarifying the Definition of a Business." The guidance requires the use of a framework to determine whether a set of assets and activities constitutes an acquired or a sold business. The guidance is effective for fiscal reporting periods beginning after December 15, 2017, including interim periods within those fiscal years. The amendments should be applied prospectively as of the beginning of the period of adoption. We adopted ASU 2017-01 in the first quarter of 2018, and the adoption had no impact on our unaudited condensed consolidated financial statements. In May 2017, the FASB issued ASU No. 2017-09, " Compensation-Stock Compensation (Topic 718): Scope of Modification Accounting ." The amendments provide guidance on determining which changes to the terms and conditions of share-based payment awards require an entity to apply modification accounting under Topic 718. The new standard is effective for annual periods, including interim periods within those annual periods, beginning after December 15, 2017 with early adoption permitted. We adopted ASU 2017-09 in the first quarter of 2018 and the adoption had no impact on our unaudited condensed consolidated financial statements. Recently Issued Accounting Pronouncements From time to time, new accounting pronouncements are issued by the FASB or other standards setting bodies that are adopted by us as of the specified effective date. Unless otherwise discussed, we believe that the impact of recently issued standards that are not yet effective will not have a material impact on our consolidated financial statements upon adoption. In February 2016, the FASB issued ASU 2016-02, " Leases (Topic 842)," which replaces prior lease guidance (Topic 840). This guidance establishes a right-of-use ("ROU") model that requires a lessee to record a ROU asset and lease liability on the balance sheet for all leases with terms longer than 12 months. Leases will be classified as either finance or operating, with classification affecting the pattern of expense recognition in the Consolidated Statement of Operations. The guidance also eliminates today’s real estate-specific provisions for all entities. For lessors, the guidance modifies the classification criteria and the accounting for sales-type and direct financing leases. Entities are required to use a modified retrospective approach for leases that exist or are entered into after the beginning of the earliest comparative period in the financial statements. Entities have the option to use certain practical expedients. Full retrospective application is prohibited. This ASU is effective for public business entities for fiscal years beginning after December 15, 2018, and interim periods within those fiscal years. Early adoption is permitted. We are currently evaluating the impact of this accounting standards update on our Consolidated Financial Statements. We expect that upon adoption, ROU assets and lease liabilities will be recognized in the balance sheet in amounts that will be material. In June 2016, the FASB issued ASU 2016-13, " Financial Instruments - Credit Losses (Topic 326): Measurement of Credit Losses on Financial Instruments," which amends the FASB's guidance on the impairment of financial instruments. The ASU adds to GAAP an impairment model (known as the "current expected credit loss model") that is based on expected losses rather than incurred losses. ASU 2016-13 is effective for annual reporting periods ending after December 15, 2019, including interim periods within those fiscal years. Early adoption is permitted for fiscal years beginning after December 15, 2018, including interim periods within those fiscal years. The adoption of ASU 2016-13 is not expected to have a material impact on our consolidated financial statements and related disclosures. In January 2017, the FASB issued ASU No. 2017-04, " Intangibles - Goodwill and Other (Topic 350): Simplifying the Test for Goodwill Impairment." The amendments eliminate Step 2 from the goodwill impairment test. The annual, or interim, goodwill impairment test is performed by comparing the fair value of a reporting unit with its carrying amount. An impairment charge should be recognized for the amount by which the carrying amount exceeds the reporting unit’s fair value; however, the loss recognized should not exceed the total amount of goodwill allocated to that reporting unit. In addition, income tax effects from any tax deductible goodwill on the carrying amount of the reporting unit should be considered when measuring the goodwill impairment loss, if applicable. The amendments also eliminate the requirements for any reporting unit with a zero or negative carrying amount to perform a qualitative assessment and, if it fails that qualitative test, to perform Step 2 of the goodwill impairment test. An entity still has the option to perform the qualitative assessment for a reporting unit to determine if the quantitative impairment test is necessary. The new standard is effective for fiscal years beginning after December 15, 2019, with early adoption permitted. We do not expect the adoption of ASU 2017-04 to have a material impact on our consolidated financial statements and related disclosures. In February 2018, the FASB issued ASU No. 2018-02, Income Statement - Reporting Comprehensive Income (Topic 220) - Reclassification of Certain Tax Effects from Accumulated Other Comprehensive Income. This standard allows a reclassification from accumulated other comprehensive income to retained earnings for stranded tax effects resulting from the Tax Cuts and Jobs Act and requires certain disclosures about stranded tax effects. This standard will be effective for us beginning January 1, 2019 and should be applied either in the period of adoption or retrospectively. Early adoption is permitted. We do not expect this standard to have any impact on our consolidated financial statements. In June 2018, the FASB issued ASU 2018-07, " Compensation-Stock Compensation (Topic 718): Improvements to Nonemployee Share-Based Payment Accounting ". These amendments expand the scope of Topic 718, Compensation—Stock Compensation (which currently only includes share-based payments to employees) to include share-based payments issued to nonemployees for goods or services. Consequently, the accounting for share-based payments to nonemployees and employees will be substantially aligned. The ASU supersedes Subtopic 505-50, Equity—Equity-Based Payments to Non-Employees. The new standard is effective for fiscal years beginning after December 15, 2018, with early adoption permitted. We do not expect the adoption of ASU 2018-07 to have a material impact on our consolidated financial statements and related disclosures.

Revenue Recognition (Tables)

Revenue Recognition (Tables)	6 Months Ended
	Jun. 30, 2018
Revenue from Contract with Customer [Abstract]
Disaggregation of revenue	The following table provides information about disaggregated revenue from contracts with customers into the nature of the products and services, and geographic regions, and includes a reconciliation of the disaggregated revenue with reportable segments. The geographic regions that are tracked are the Americas (United States, Canada, Latin America), EMEA (Europe, Middle East, Africa), and APAC (Australia, New Zealand, Southeast Asia, China). Three months ended June 30, 2018 Three months ended June 30, 2017 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 3,723 $ — $ 3,723 $ 6,600 $ — $ 6,600 Research and development revenue 7,442 2,373 9,815 3,747 — 3,747 Total revenues $ 11,165 $ 2,373 $ 13,538 $ 10,347 $ — $ 10,347 Primary geographical markets: Americas $ 6,058 $ — $ 6,058 $ 4,401 $ — $ 4,401 EMEA 1,435 2,373 3,808 1,959 — 1,959 APAC 3,672 — 3,672 3,987 — 3,987 Total revenues $ 11,165 $ 2,373 $ 13,538 $ 10,347 $ — $ 10,347 Six months ended June 30, 2018 Six months ended June 30, 2017 (in thousands) Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Major products and service: Product Revenue $ 9,886 $ — $ 9,886 $ 12,186 $ — $ 12,186 Research and development revenue 12,008 5,686 17,694 6,131 — 6,131 Total revenues $ 21,894 $ 5,686 $ 27,580 $ 18,317 $ — $ 18,317 Primary geographical markets: Americas $ 9,655 $ — $ 9,655 $ 6,189 $ — $ 6,189 EMEA 3,114 5,686 8,800 5,166 — 5,166 APAC 9,125 — 9,125 6,962 — 6,962 Total revenues $ 21,894 $ 5,686 $ 27,580 $ 18,317 $ — $ 18,317
Contract with customer	The following table presents changes in the contract assets, deferred contract costs, and liabilities (in thousands): June 30, 2018 January 1, 2018 balance Additions Deductions (1) Ending balance Contract Assets $ — $ 3,047 $ (2,493 ) $ 554 Contract Costs 239 — (80 ) 159 Contract Liabilities: Deferred Revenue 18,966 1,965 (11,477 ) 9,454 (1) The asset or liability balances are presented as a net position per contract and accordingly the deductions column includes the netting effect of presenting each contract on a net position basis as either a net liability or asset. The following table shows the reconciliation of contract liabilities from what was disclosed in the Form 10-K for the year ended December 31, 2017 and gives effect to the modified retrospective adoption of the revenue guidance on January 1, 2018 (in thousands): Balance Deferred Revenue, balance at December 31, 2017 $ 13,793 Changes in estimated consideration — Unsatisfied performance obligations $ 5,173 Deferred Revenue, balance at January 1, 2018 $ 18,966 During the three and six months ended June 30, 2018 , we recognized the following revenues (in thousands): Revenue recognized in the period from: Three months ended June 30, 2018 Six months ended June 30, 2018 Amounts included in contract liabilities at the beginning of the period: Performance obligations satisfied $ 2,994 $ 8,822 Changes in the period: Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods 64 64 Performance obligations satisfied from new activities in the period - contract revenue 10,480 18,694 Total revenue $ 13,538 $ 27,580
Performance obligation, expected timing of satisfaction	The following table includes estimated revenue expected to be recognized in the future related to performance obligations that are unsatisfied or partially unsatisfied at the end of the reporting period, in thousands. The estimated revenue does not include contracts with original durations of one year or less, amounts of variable consideration attributable to royalties, or contract renewals that are unexercised as of June 30, 2018 . We did not recognize any revenue from performance obligations satisfied in previous periods. The balances in the table below are partially based on judgments involved in estimating future orders from customers subject to the exercise of material rights pursuant to respective contracts. (in thousands) 2018 2019 2020 2021 and Thereafter Total Product Revenue $ 664 $ 2,753 $ 2,183 $ 1,623 $ 7,223 Research and development revenue 1,756 475 — — 2,231 Total $ 2,420 $ 3,228 $ 2,183 $ 1,623 $ 9,454
Impact of adoption on financial statements	In accordance with Topic 606, the disclosure of the impact of adoption to our unaudited condensed consolidated statements of operations and balance sheets was as follows (in thousands, except per share amounts): Three months ended June 30, 2018 Six months ended June 30, 2018 As reported Adjustments Balances without adoption of Topic 606 As reported Adjustments Balances without adoption of Topic 606 Revenues: Product revenue $ 3,723 $ (454 ) $ 3,269 $ 9,886 $ (2,970 ) $ 6,916 Research and development revenue 9,815 (1,148 ) 8,667 17,694 (2,470 ) 15,224 Total revenues 13,538 (1,602 ) 11,936 27,580 (5,440 ) 22,140 Costs and operating expenses: Cost of product revenue 2,611 (69 ) 2,542 6,436 (1,355 ) 5,081 Research and development 7,370 (33 ) 7,337 14,548 (80 ) 14,468 Selling, general and administrative 7,395 — 7,395 15,141 — 15,141 Total costs and operating expenses 17,376 (102 ) 17,274 36,125 (1,435 ) 34,690 Loss from operations (3,838 ) (1,500 ) (5,338 ) (8,545 ) (4,005 ) (12,550 ) Interest income 174 — 174 245 — 245 Other expenses (82 ) — (82 ) (142 ) — (142 ) Loss before income taxes (3,746 ) (1,500 ) (5,246 ) (8,442 ) (4,005 ) (12,447 ) Provision (benefit) from income taxes (11 ) — (11 ) (13 ) — (13 ) Net loss $ (3,735 ) $ (1,500 ) $ (5,235 ) $ (8,429 ) $ (4,005 ) $ (12,434 ) Net loss per share, basic and diluted $ (0.07 ) $ (0.03 ) $ (0.10 ) $ (0.17 ) $ (0.08 ) $ (0.25 ) Weighted average common shares used in computing net loss per share, basic and diluted 52,787 52,787 50,598 50,598 June 30, 2018 As reported Adjustments Balances without adoption of Topic 606 Assets Accounts Receivable $ 9,910 $ (1,136 ) $ 8,774 Contract Assets 554 (554 ) — Other non-current assets 414 (159 ) 255 Liabilities Other accrued liabilities 5,051 (1,591 ) 3,460 Deferred revenue - current 4,460 2,909 7,369 Deferred revenue - non-current 4,994 (3,220 ) 1,774 Stockholders' equity Accumulated deficit (328,026 ) 55 (327,971 )

Net Loss per Share (Tables)

Net Loss per Share (Tables)	6 Months Ended
	Jun. 30, 2018
Earnings Per Share [Abstract]
Securities not included in the net loss per common share calculations	The following shares were not included in the computation of diluted net loss per share (in thousands): Three months ended June 30, Six months ended June 30, 2018 2017 2018 2017 Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan 7,462 7,621 7,462 7,621 Shares of common stock issuable upon exercise of outstanding warrants — 73 — 73 Total shares excluded as anti-dilutive 7,462 7,694 7,462 7,694

Cash Equivalents and Marketab24

Cash Equivalents and Marketable Securities (Tables)	6 Months Ended
	Jun. 30, 2018
Cash Equivalents and Marketable Securities [Abstract]
Schedule of cash equivalents and marketable securities	Cash equivalents and marketable securities at June 30, 2018 and at December 31, 2017 consisted of the following (in thousands): June 30, 2018 Adjusted Cost Gross Unrealized Gross Unrealized Estimated Money market funds (1) $ 30,913 $ — $ — $ 30,913 Common shares of CO2 Solutions (2) 563 113 — 676 Total $ 31,476 $ 113 $ — $ 31,589 December 31, 2017 Adjusted Cost Gross Unrealized Gross Unrealized Estimated Money market funds (1) $ 6,778 $ — $ — $ 6,778 Common shares of CO2 Solutions (2) 563 108 — 671 Total $ 7,341 $ 108 $ — $ 7,449 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified as marketable securities, and included in non-current assets on our unaudited condensed consolidated balance sheets.

Fair Value Measurements (Tables

Fair Value Measurements (Tables)	6 Months Ended
	Jun. 30, 2018
Fair Value, Assets, Liabilities and Stockholders' Equity Measured on Recurring Basis [Abstract]
Summary of financial instruments measured at fair value on a recurring basis	The following tables present the financial instruments that were measured at fair value on a recurring basis at June 30, 2018 and December 31, 2017 by level within the fair value hierarchy (in thousands): June 30, 2018 Level 1 Level 2 Level 3 Total Money market funds (1) $ 30,913 $ — $ — $ 30,913 Common shares of CO2 Solutions (2) — 676 — 676 Total $ 30,913 $ 676 $ — $ 31,589 December 31, 2017 Level 1 Level 2 Level 3 Total Money market funds (1) $ 6,778 $ — $ — $ 6,778 Common shares of CO2 Solutions (2) — 671 — 671 Total $ 6,778 $ 671 $ — $ 7,449 (1) Money market funds are classified in cash and cash equivalents on our unaudited condensed consolidated balance sheets. (2) Common shares of CO 2 Solutions are classified as marketable securities, and included in non-current assets on our unaudited condensed consolidated balance sheets.

Balance Sheets Details (Tables)

Balance Sheets Details (Tables)	6 Months Ended
	Jun. 30, 2018
Balance Sheets Details [Abstract]
Schedule of inventory components	Inventories consisted of the following (in thousands): June 30, 2018 December 31, 2017 Raw materials $ 214 $ 215 Work-in-process 62 53 Finished goods 2,157 2,147 Less: reserve (1,397 ) (1,379 ) Inventories, net $ 1,036 $ 1,036
Schedule of property and equipment, net	Property and equipment, net consisted of the following (in thousands): June 30, 2018 December 31, 2017 Laboratory equipment (1) $ 20,636 $ 19,777 Leasehold improvements 10,358 10,327 Computer equipment and software 3,770 3,695 Office equipment and furniture 1,195 1,185 Construction in progress (2) 457 85 Property and equipment 36,416 35,069 Less: accumulated depreciation and amortization (32,533 ) (32,254 ) Property and equipment, net $ 3,883 $ 2,815 (1) Fully depreciated laboratory equipment with a cost of $0.2 million and $0.2 million was retired during six months ended June 30, 2018 and the fiscal year ended December 31, 2017, respectively. (2) Construction in progress includes equipment received but not yet placed into service pending installation.
Schedule of accrued liabilities	Other accrued liabilities consisted of the following (in thousands): June 30, 2018 December 31, 2017 Accrued purchases (1) $ 834 $ 941 Accrued professional and outside service fees 1,666 2,393 Accrued expenses - cost of sales 1,387 — Deferred rent 297 258 Lease incentive obligation 425 425 Other 442 345 Total $ 5,051 $ 4,362 (1) Amount represents products and services received but not billed as of June 30, 2018 and December 31, 2017 .

Stock-Based Compensation (Table

Stock-Based Compensation (Tables)	6 Months Ended
	Jun. 30, 2018
Disclosure of Compensation Related Costs, Share-based Payments [Abstract]
Schedule of stock-based compensation expense	Stock-based compensation expense is included in the consolidated statements of operations as follows (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Research and development $ 567 $ 342 $ 1,003 $ 664 Selling, general and administrative 1,890 1,369 3,434 2,715 Total $ 2,457 $ 1,711 $ 4,437 $ 3,379
Schedule of stock-based compensation expense by security types	The following table presents total stock-based compensation expense by security types included in the unaudited condensed consolidated statements of operations for the three and six months ended June 30, 2018 and 2017 (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Stock options $ 535 $ 380 $ 1,015 $ 714 RSUs and RSAs 436 484 878 943 PSUs 426 348 844 988 PBOs 1,060 499 1,700 734 Total $ 2,457 $ 1,711 $ 4,437 $ 3,379
Valuation assumptions	The weighted-average assumptions used to estimate the fair value of employee stock options and PBOs granted were as follows: Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 (1) (1) Expected term (in years) — — 5.6 5.3 Volatility — — 60 % 62 % Risk-free interest rate — — 2.70 % 2.00 % Dividend yield — — — % — % Weighted-average estimated fair value of stock options granted — — $ 5.02 $ 2.52 (1) The Company did not grant employee stock options or PBOs in the three months ended June 30, 2018 and 2017.

Commitments and Contingencies (

Commitments and Contingencies (Tables)	6 Months Ended
	Jun. 30, 2018
Commitments and Contingencies Disclosure [Abstract]
Schedule of future minimum payments under non-cancellable operating leases	Future minimum payments under non-cancellable capital and operating leases at June 30, 2018 are as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2018 (remaining 6 months) $ 126 $ 1,598 2019 252 3,280 2020 61 712 2021 — 490 2022 — 41 Total minimum lease payments (1) 439 $ 6,121 Less: amount representing interest (19 ) Present value of capital lease obligations 420 Less: current portion (237 ) Long-term portion of capital leases $ 183 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases at June 30, 2018 .
Schedule of future minimum lease payments for capital leases	Future minimum payments under non-cancellable capital and operating leases at June 30, 2018 are as follows (in thousands): Years ending December 31, Capital Leases Operating Leases 2018 (remaining 6 months) $ 126 $ 1,598 2019 252 3,280 2020 61 712 2021 — 490 2022 — 41 Total minimum lease payments (1) 439 $ 6,121 Less: amount representing interest (19 ) Present value of capital lease obligations 420 Less: current portion (237 ) Long-term portion of capital leases $ 183 (1) Minimum payments have not been reduced by future minimum sublease rentals of $0.9 million to be received under non-cancellable subleases at June 30, 2018 .
Schedule of supply and service commitments	The following table provides quantitative data regarding our other commitments. Future minimum payments reflect amounts that we expect to pay including potential obligations under services agreements subject to risk of cancellation by us (in thousands): Other Commitment Agreement Type Agreement Date Future Minimum Payment Manufacture and supply agreement with expected future payment date of December 2022 April 2016 $ 1,693 Service agreement for the development of manufacturing process April 2017 2 Service agreement for stability study July 2017 439 Service agreement for clinical trial December 2017 $ 2,116 Total other commitments $ 4,250

Segment, Geographical and Oth29

Segment, Geographical and Other Revenue Information (Tables)	6 Months Ended
	Jun. 30, 2018
Segment Reporting [Abstract]
Schedule of segment reporting	The following table provides financial information by our reportable business segments along with a reconciliation to consolidated loss before income taxes (in thousands): Three months ended June 30, 2018 Three months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 3,723 $ — $ 3,723 $ 6,600 $ — $ 6,600 Research and development revenue 7,442 2,373 9,815 3,747 — 3,747 Total revenues 11,165 2,373 13,538 10,347 — 10,347 Costs and operating expenses: Cost of product revenue 2,611 — 2,611 3,790 — 3,790 Research and development (1) 4,724 2,442 7,166 4,023 2,149 6,172 Selling, general and administrative 1,729 304 2,033 1,777 — 1,777 Total segment costs and operating expenses 9,064 2,746 11,810 9,590 2,149 11,739 Income (loss) from operations $ 2,101 $ (373 ) $ 1,728 $ 757 $ (2,149 ) $ (1,392 ) Corporate costs (2) (5,209 ) (4,702 ) Depreciation and amortization (265 ) (228 ) Loss before income taxes $ (3,746 ) $ (6,322 ) (1) Research and development expenses exclude depreciation and amortization. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. Six months ended June 30, 2018 Six months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Revenues: Product revenue $ 9,886 $ — $ 9,886 $ 12,186 $ — $ 12,186 Research and development revenue 12,008 5,686 17,694 6,131 — 6,131 Total revenues 21,894 5,686 27,580 18,317 — 18,317 Costs and operating expenses: Cost of product revenue 6,436 — 6,436 6,792 — 6,792 Research and development (1) 9,790 4,374 14,164 8,172 3,660 11,832 Selling, general and administrative 3,825 450 4,275 3,589 — 3,589 Total segment costs and operating expenses 20,051 4,824 24,875 18,553 3,660 22,213 Income (loss) from operations $ 1,843 $ 862 $ 2,705 $ (236 ) $ (3,660 ) $ (3,896 ) Corporate costs (2) (10,644 ) (9,308 ) Depreciation and amortization (503 ) (554 ) Loss before income taxes $ (8,442 ) $ (13,758 ) (1) Research and development expenses exclude depreciation and amortization. (2) Corporate costs include unallocated selling, general and administrative expense, interest income, and other income and expenses. The following table provides stock-based compensation expense included in income (loss) from operations by segment (in thousands): Three months ended June 30, 2018 Three months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 768 $ 83 $ 851 $ 434 $ 47 $ 481 Six months ended June 30, 2018 Six months ended June 30, 2017 Performance Enzymes Novel Biotherapeutics Total Performance Enzymes Novel Biotherapeutics Total Stock-based compensation $ 1,326 $ 146 $ 1,472 $ 789 $ 100 $ 889
Schedule of customers that contributed 10% or more of total accounts receivable	Customers that each contributed 10% or more of our total revenues were as follows: Percentage of Total Revenues for the Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Customer A 27% 45% 38% 42% Customer B 34% 21% 22% 12% Customer C 18% * 21% * Customers that each contributed 10% or more of our total accounts receivable had the following balances as of the periods presented: Percentage of Accounts Receivables at June 30, 2018 December 31, 2017 Customer A 46% 31% Customer B 27% 16% Customer D 11% 15% Customer E * 14% * Less than 10% of the period presented
Schedule of revenues by geographical area	Geographic revenues are identified by the location of the customer and consist of the following (in thousands): Three Months Ended June 30, Six Months Ended June 30, 2018 2017 2018 2017 Revenues Americas $ 6,058 $ 4,401 $ 9,655 $ 6,189 EMEA 3,808 1,959 8,800 5,166 APAC 3,672 3,987 9,125 6,962 Total revenues $ 13,538 $ 10,347 $ 27,580 $ 18,317
Schedule of long-lived assets by geographical area	Identifiable long-lived assets as follows (in percentage): Long-lived assets: June 30, 2018 December 31, 2017 United States 100 % 100 %

Description of Business - Textu

Description of Business - Textual (Details)	6 Months Ended
	Jun. 30, 2018
Organization, Consolidation and Presentation of Financial Statements [Abstract]
Number of years company has been in business	16 years

Basis of Presentation and Sum31

Basis of Presentation and Summary of Significant Accounting Policies - Textual (Details)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2018USD ($)	Jun. 30, 2017USD ($)	Jun. 30, 2018USD ($)segment	Jun. 30, 2017USD ($)	Dec. 31, 2017USD ($)segment
Loss Contingencies [Line Items]
Number of operating segments | segment			2		1
Advertising expense	$ 100,000	$ 100,000	$ 200,000	$ 200,000
Cash and cash equivalents	53,621,000	28,817,000	53,621,000	28,817,000	$ 31,219,000
Cash, cash equivalents, and short-term investments					7,449,000
Impairment of long-lived assets			0	0
Goodwill	3,241,000		3,241,000		3,241,000
Expense (benefit) from income taxes	(11,000)	$ (42,000)	(13,000)	$ (18,000)
Provisional reduction to offsetting valuation allowance			34,100,000
Accounting Standards Update 2016-01 [Member]
Loss Contingencies [Line Items]
Reclassified unrealized loss			500,000
Tax related to unrealized loss			600,000
Cash [Member]
Loss Contingencies [Line Items]
Cash, cash equivalents, and short-term investments	22,700,000		22,700,000		24,400,000
Money Market Funds [Member]
Loss Contingencies [Line Items]
Cash, cash equivalents, and short-term investments	$ 30,900,000		$ 30,900,000		$ 6,778,000

Basis of Presentation and Sum32

Basis of Presentation and Summary of Significant Accounting Policies - Restricted Cash Narrative (Details) - USD ($) $ in Millions	Jun. 30, 2018	Dec. 31, 2017
Trustee Deposit [Member]
Restricted Cash and Cash Equivalents Items [Line Items]
Non-current restricted cash	$ 0.8	$ 0.8
Demand Deposits [Member]
Restricted Cash and Cash Equivalents Items [Line Items]
Non-current restricted cash	$ 0.7	$ 0.7

Revenue Recognition - Addition

Revenue Recognition - Additional Information (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Accumulated deficit	$ (328,026,000)		$ (328,026,000)		$ (315,065,000)
Revenues	13,538,000	$ 10,347,000	27,580,000	$ 18,317,000
Impairment charges related to contract assets			0
Difference between Revenue Guidance in Effect before and after Topic 606 [Member] | Accounting Standards Update 2014-09 [Member]
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Accumulated deficit	55,000		55,000		$ (4,100,000)
Revenues	$ (1,602,000)		$ (5,440,000)

Revenue Recognition - Disaggre

Revenue Recognition - Disaggregation of Revenue (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Disaggregation of Revenue [Line Items]
Revenue	$ 13,538	$ 10,347	$ 27,580	$ 18,317
Americas [Member]
Disaggregation of Revenue [Line Items]
Revenue	6,058	4,401	9,655	6,189
EMEA [Member]
Disaggregation of Revenue [Line Items]
Revenue	3,808	1,959	8,800	5,166
APAC [Member]
Disaggregation of Revenue [Line Items]
Revenue	3,672	3,987	9,125	6,962
Product Sales [Member]
Disaggregation of Revenue [Line Items]
Revenue	3,723	6,600	9,886	12,186
Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Revenue	9,815	3,747	17,694	6,131
Performance Enzymes [Member]
Disaggregation of Revenue [Line Items]
Revenue	11,165	10,347	21,894	18,317
Performance Enzymes [Member] | Americas [Member]
Disaggregation of Revenue [Line Items]
Revenue	6,058	4,401	9,655	6,189
Performance Enzymes [Member] | EMEA [Member]
Disaggregation of Revenue [Line Items]
Revenue	1,435	1,959	3,114	5,166
Performance Enzymes [Member] | APAC [Member]
Disaggregation of Revenue [Line Items]
Revenue	3,672	3,987	9,125	6,962
Performance Enzymes [Member] | Product Sales [Member]
Disaggregation of Revenue [Line Items]
Revenue	3,723	6,600	9,886	12,186
Performance Enzymes [Member] | Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Revenue	7,442	3,747	12,008	6,131
Novel Biotherapeutics [Member]
Disaggregation of Revenue [Line Items]
Revenue	2,373	0	5,686	0
Novel Biotherapeutics [Member] | Americas [Member]
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Novel Biotherapeutics [Member] | EMEA [Member]
Disaggregation of Revenue [Line Items]
Revenue	2,373	0	5,686	0
Novel Biotherapeutics [Member] | APAC [Member]
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Novel Biotherapeutics [Member] | Product Sales [Member]
Disaggregation of Revenue [Line Items]
Revenue	0	0	0	0
Novel Biotherapeutics [Member] | Research and Development Revenue [Member]
Disaggregation of Revenue [Line Items]
Revenue	$ 2,373	$ 0	$ 5,686	$ 0

Revenue Recognition - Contract

Revenue Recognition - Contracts with Customer (Details) - USD ($)	3 Months Ended	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2018
Movement in Deferred Revenue [Roll Forward]
Deferred Revenue, balance at December 31, 2017		$ 13,793,000
Changes in estimated consideration		0
Unsatisfied performance obligations		5,173,000
Deferred Revenue, balance at January 1, 2018	$ 18,966,000	18,966,000
Contract Assets
January 1, 2018 balance		0
Additions		3,047,000
Deductions		(2,493,000)
Ending balance	554,000	554,000
Contract Costs
January 1, 2018 balance		239,000
Additions		0
Deductions		(80,000)
Ending balance	159,000	159,000
Contract Liabilities: Deferred Revenue
January 1, 2018 balance		18,966,000
Additions		1,965,000
Deductions		(11,477,000)
Ending balance	9,454,000	9,454,000
Impairment charges related to contract assets		0
Change in Contract with Customer, Liability [Abstract]
Performance obligations satisfied	2,994,000	8,822,000
Changes in the estimated transaction price allocated to performance obligations satisfied in prior periods	64,000	64,000
Performance obligations satisfied from new activities in the period - contract revenue	10,480,000	18,694,000
Total revenue	$ 13,538,000	$ 27,580,000

Revenue Recognition - Performa

Revenue Recognition - Performance Obligation (Details) $ in Thousands	6 Months Ended
	Jun. 30, 2018USD ($)
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-07-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 2,420
Expected timing of satisfaction, period	6 months
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 3,228
Expected timing of satisfaction, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 2,183
Expected timing of satisfaction, period	1 year
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,623
Expected timing of satisfaction, period
Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 9,454
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-07-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 664
Expected timing of satisfaction, period	6 months
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 2,753
Expected timing of satisfaction, period	1 year
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 2,183
Expected timing of satisfaction, period	1 year
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,623
Expected timing of satisfaction, period
Product Sales [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 7,223
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2018-07-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 1,756
Expected timing of satisfaction, period	6 months
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2019-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 475
Expected timing of satisfaction, period	1 year
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2020-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 0
Expected timing of satisfaction, period	1 year
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: 2021-01-01
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 0
Expected timing of satisfaction, period
Research and Development Revenue [Member] | Revenue, Remaining Performance Obligation, Expected Timing of Satisfaction, Start Date [Axis]: (nil)
Revenue, Initial Application Period Cumulative Effect Transition [Line Items]
Performance obligation	$ 2,231

Revenue Recognition - Impact t

Revenue Recognition - Impact to Financial Statements (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Revenues:
Product revenue	$ 3,723	$ 6,600	$ 9,886	$ 12,186
Research and development revenue	9,815	3,747	17,694	6,131
Total revenues	13,538	10,347	27,580	18,317
Costs and operating expenses:
Cost of product revenue	2,611	3,790	6,436	6,792
Research and development	7,370	6,348	14,548	12,187
Selling, general and administrative	7,395	6,546	15,141	13,152
Total costs and operating expenses	17,376	16,684	36,125	32,131
Loss from operations	(3,838)	(6,337)	(8,545)	(13,814)
Interest income	174	49	245	68
Other expenses	(82)	(34)	(142)	(12)
Loss before income taxes	(3,746)	(6,322)	(8,442)	(13,758)
Provision (benefit) from income taxes	(11)	(42)	(13)	(18)
Net loss	$ (3,735)	$ (6,280)	$ (8,429)	$ (13,740)
Net loss per share, basic and diluted (usd per shares)	$ (0.07)	$ (0.13)	$ (0.17)	$ (0.31)
Weighted average common stock shares used in computing net income (loss) per share, basic (shares)	52,787	47,232	50,598	44,258
Assets
Accounts Receivable	$ 9,910		$ 9,910		$ 11,800
Contract assets	554		554		0
Other non-current assets	414		414		302
Liabilities
Other accrued liabilities	5,051		5,051		4,362
Deferred revenue	4,460		4,460		12,292
Deferred revenue - non-current	4,994		4,994		1,501
Stockholders' equity:
Accumulated deficit	(328,026)		(328,026)		(315,065)
Balances without adoption of Topic 606 [Member]
Revenues:
Product revenue	3,269		6,916
Research and development revenue	8,667		15,224
Total revenues	11,936		22,140
Costs and operating expenses:
Cost of product revenue	2,542		5,081
Research and development	7,337		14,468
Selling, general and administrative	7,395		15,141
Total costs and operating expenses	17,274		34,690
Loss from operations	(5,338)		(12,550)
Interest income	174		245
Other expenses	(82)		(142)
Loss before income taxes	(5,246)		(12,447)
Provision (benefit) from income taxes	(11)		(13)
Net loss	$ (5,235)		$ (12,434)
Net loss per share, basic and diluted (usd per shares)	$ (0.10)		$ (0.25)
Weighted average common stock shares used in computing net income (loss) per share, basic (shares)	52,787		50,598
Assets
Accounts Receivable	$ 8,774		$ 8,774
Contract assets	0		0
Other non-current assets	255		255
Liabilities
Other accrued liabilities	3,460		3,460
Deferred revenue	7,369		7,369
Deferred revenue - non-current	1,774		1,774
Stockholders' equity:
Accumulated deficit	(327,971)		(327,971)
Accounting Standards Update 2014-09 [Member] | Adjustments [Member]
Revenues:
Product revenue	(454)		(2,970)
Research and development revenue	(1,148)		(2,470)
Total revenues	(1,602)		(5,440)
Costs and operating expenses:
Cost of product revenue	(69)		(1,355)
Research and development	(33)		(80)
Selling, general and administrative	0		0
Total costs and operating expenses	(102)		(1,435)
Loss from operations	(1,500)		(4,005)
Interest income	0		0
Other expenses	0		0
Loss before income taxes	(1,500)		(4,005)
Provision (benefit) from income taxes	0		0
Net loss	$ (1,500)		$ (4,005)
Net loss per share, basic and diluted (usd per shares)	$ (0.03)		$ (0.08)
Assets
Accounts Receivable	$ (1,136)		$ (1,136)
Contract assets	(554)		(554)
Other non-current assets	(159)		(159)
Liabilities
Other accrued liabilities	(1,591)		(1,591)
Deferred revenue	2,909		2,909
Deferred revenue - non-current	(3,220)		(3,220)
Stockholders' equity:
Accumulated deficit	$ 55		$ 55		$ (4,100)

Net Loss per Share - Anti-Dilut

Net Loss per Share - Anti-Dilutive Securities (Details) - shares shares in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded as anti-dilutive (shares)	7,462	7,694	7,462	7,694
Shares of common stock issuable pursuant to equity awards outstanding under the Equity Incentive Plan [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded as anti-dilutive (shares)	7,462	7,621	7,462	7,621
Shares of common stock issuable upon exercise of outstanding warrants [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Total shares excluded as anti-dilutive (shares)	0	73	0	73

Collaborative Arrangements - Te

Collaborative Arrangements - Textual (Details) - USD ($)	1 Months Ended						3 Months Ended		6 Months Ended
	Apr. 30, 2018	Oct. 31, 2017	Mar. 31, 2017	Dec. 31, 2016	Aug. 31, 2015	Feb. 29, 2012	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Deferred revenue							$ 18,966,000		$ 18,966,000		$ 13,793,000
Research and development revenue							9,815,000	$ 3,747,000	17,694,000	$ 6,131,000
Deferred revenue							4,460,000		4,460,000		12,292,000
Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Sales revenue							2,700,000	3,200,000	7,200,000	5,000,000
Merck [Member] | Collaborative Arrangement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Proceeds from license fees received					$ 5,000,000
License and services revenue							1,000,000	900,000	1,900,000	1,800,000
Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Deferred revenue							2,300,000		2,300,000		6,800,000
Milestone revenue		$ 14,000,000
Revenue recognized							1,800,000	0	4,500,000	0
Progress payment amount									4,000,000
Event of counterparty exercising alternative option		$ 3,000,000
Duration to pay after license effective date		60 days
Nestec Ltd. (Nestle Health Sciences) [Member] | Collaborative Arrangement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Research and development revenue							600,000	0	1,200,000	0
Deferred revenue							800,000		800,000		1,100,000
Porton [Member] | Porton Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Deferred revenue							500,000		500,000		0
Milestone revenue	$ 500,000
Research and development revenue							0	0	0	0
Technology Transfer, Collaboration and License Agreement [Member] | Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Maximum milestone receivable					$ 15,000,000
Technology Transfer, Collaboration and License Agreement [Member] | Minimum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License revenue, contingent receivables							5,750,000		5,750,000
Technology Transfer, Collaboration and License Agreement [Member] | Maximum [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License revenue, contingent receivables							38,500,000		38,500,000
Supply Agreement [Member] | Merck [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
License and services revenue							0	300,000	1,300,000	700,000
Term of collaborative research and development agreement						5 years
Optional extension period						5 years
Deferred revenue							5,200,000		5,200,000		1,500,000
Supply Agreement [Member] | Customer [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Deferred revenue							2,000,000		2,000,000		700,000
Milestone revenue				$ 800,000
Research and Development Agreement [Member] | Fine chemical customer [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Term of collaborative research and development agreement			21 months
Deferred revenue							1,100,000		1,100,000		$ 3,100,000
Milestone revenue			$ 3,000,000
Research and development revenue							$ 4,500,000	$ 900,000	$ 5,900,000	$ 900,000
Research and Development Agreement [Member] | Maximum [Member] | Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue		$ 86,000,000
Sales-Based Milestone [Member] | Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Target sales for sales milestone		1,000,000,000
Sales-Based Milestone [Member] | Maximum [Member] | Nestec Ltd. (Nestle Health Sciences) [Member] | Global Development, Option and License Agreement [Member]
Collaborative Arrangements and Non-collaborative Arrangement Transactions [Line Items]
Milestone revenue		$ 250,000,000

Cash Equivalents and Marketab40

Cash Equivalents and Marketable Securities - Components of Cash Equivalents and Marketable Securities (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Cash Equivalents and Marketable Securities [Line Items]
Adjusted Cost	$ 31,476
Gross Unrealized Gains	113
Gross Unrealized Losses	0
Estimated Fair Value	31,589
Adjusted Cost		$ 7,341
Gross Unrealized Gains		108
Gross Unrealized Losses		0
Estimated Fair Value		7,449
Common shares of CO2 Solution [Member]
Cash Equivalents and Marketable Securities [Line Items]
Adjusted Cost	563
Gross Unrealized Gains	113
Gross Unrealized Losses	0
Estimated Fair Value	676
Adjusted Cost		563
Gross Unrealized Gains		108
Gross Unrealized Losses		0
Estimated Fair Value		671
Money Market Funds [Member]
Cash Equivalents and Marketable Securities [Line Items]
Adjusted Cost	30,913
Gross Unrealized Gains	0
Gross Unrealized Losses	0
Estimated Fair Value	30,913
Adjusted Cost		6,778
Gross Unrealized Gains		0
Gross Unrealized Losses		0
Estimated Fair Value	$ 30,900	$ 6,778

Fair Value Measurements - Sche

Fair Value Measurements - Schedule of Financial Instruments Measured at Fair Value on Recurring Basis (Details) - USD ($) $ in Thousands	3 Months Ended	6 Months Ended
	Jun. 30, 2018	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	$ 31,589	$ 31,589		$ 7,449
Unrealized gains (losses)		5	$ 0
Other Expense [Member]
Summary of financial instruments measured at fair value on a recurring basis
Unrealized gains (losses)	(20)	5
Other Comprehensive Income (Loss) [Member]
Summary of financial instruments measured at fair value on a recurring basis
Unrealized gains (losses)			$ 100
Common Shares of Co Two Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	676	676		671
Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	30,913	30,913		6,778
Level 1 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	30,913	30,913		6,778
Level 1 [Member] | Common Shares of Co Two Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	0	0		0
Level 1 [Member] | Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	30,913	30,913		6,778
Level 2 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	676	676		671
Level 2 [Member] | Common Shares of Co Two Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	$ 676	$ 676		671
Investment owned (shares)	10,000,000	10,000,000
Level 2 [Member] | Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	$ 0	$ 0		0
Level 3 [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	0	0		0
Level 3 [Member] | Common Shares of Co Two Solution [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	0	0		0
Level 3 [Member] | Money Market Funds [Member]
Summary of financial instruments measured at fair value on a recurring basis
Financial assets	$ 0	$ 0		$ 0

Balance Sheets Details - Inven

Balance Sheets Details - Inventories (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Schedule of Inventory Components
Raw materials	$ 214	$ 215
Work-in-process	62	53
Finished goods	2,157	2,147
Less: reserve	(1,397)	(1,379)
Inventories, net	$ 1,036	$ 1,036

Balance Sheets Details - Prope

Balance Sheets Details - Property and Equipment, net (Details) - USD ($) $ in Thousands	6 Months Ended	12 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Property, Plant and Equipment [Line Items]
Property and equipment	$ 36,416	$ 35,069
Less: accumulated depreciation and amortization	(32,533)	(32,254)
Property and equipment, net	3,883	2,815
Equipment retired during period	200	200
Laboratory equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	20,636	19,777
Leasehold improvements [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	10,358	10,327
Computer equipment and software [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	3,770	3,695
Office equipment and furniture [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	1,195	1,185
Construction in progress [Member]
Property, Plant and Equipment [Line Items]
Property and equipment	$ 457	$ 85

Balance Sheets Details - Goodw

Balance Sheets Details - Goodwill (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Balance Sheet Details [Abstract]
Goodwill	$ 3,241	$ 3,241

Balance Sheets Details - Accru

Balance Sheets Details - Accrued Liabilities (Details) - USD ($) $ in Thousands	Jun. 30, 2018	Dec. 31, 2017
Balance Sheets Details [Abstract]
Accrued purchases	$ 834	$ 941
Accrued professional and outside service fees	1,666	2,393
Accrued expenses - cost of sales	1,387	0
Deferred rent	297	258
Lease incentive obligation	425	425
Other	442	345
Total	$ 5,051	$ 4,362

Stock-Based Compensation - Tex

Stock-Based Compensation - Textual (Details) $ in Millions	1 Months Ended	3 Months Ended			6 Months Ended	12 Months Ended
	Mar. 31, 2010shares	Mar. 31, 2019	Mar. 31, 2018	Mar. 31, 2017	Jun. 30, 2018USD ($)	Dec. 31, 2016shares	Dec. 31, 2017
Incentive Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock	100.00%
Non-Statutory Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Purchase price of common stock	85.00%
Stock options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Percent of voting interests	10.00%
Purchase price of common stock above minimum threshold	110.00%
Expiration period	10 years
Award vesting period	4 years
Compensation not yet recognized, stock options					$ 4.5
Stock options [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights	25.00%
Stock options [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights	75.00%
Restricted Stock Units (RSUs) [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period	3 years
Award vesting rights	33.3333%
Restricted Stock Units (RSUs) [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting period	4 years
Award vesting rights	25.00%
Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Performance awards, threshold level, number of shares, multiplier					0
Performance Shares [Member] | Tranche One [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Future vesting rights percentage					50.00%
Performance Shares [Member] | Tranche Two [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Future vesting rights percentage					50.00%
RSAs and RSUs [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options					$ 1.8
Performance Stock Units (PSUs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options					1.5
Performance Based Options (PBOs) [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Compensation not yet recognized, share-based awards other than options					$ 3.7
2017 PSU Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights			50.00%
2017 PSU Plan [Member] | Performance Shares [Member] | Scenario, Forecast [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights		50.00%
2010 Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares reserved for future issuance (shares) | shares	1,100,000
2018 PSU and PBO Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated performance goal achievement rate					143.00%
2017 PSU and PBO Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Estimated performance goal achievement rate							134.20%
2016 PSU Plan [Member] | Performance Shares [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Award vesting rights			50.00%	50.00%
Estimated performance goal achievement rate						142.30%
PBOs granted in period (shares) | shares						0

Stock-Based Compensation - Sto

Stock-Based Compensation - Stock-Based Compensation Expense (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Schedule of stock-based compensation expense
Stock-based compensation	$ 2,457	$ 1,711	$ 4,437	$ 3,379
Stock options [Member]
Schedule of stock-based compensation expense
Stock-based compensation	535	380	1,015	714
RSAs and RSUs [Member]
Schedule of stock-based compensation expense
Stock-based compensation	436	484	878	943
Performance Stock Units (PSUs) [Member]
Schedule of stock-based compensation expense
Stock-based compensation	426	348	844	988
Performance Based Options (PBOs) [Member]
Schedule of stock-based compensation expense
Stock-based compensation	1,060	499	1,700	734
Research and development [Member]
Schedule of stock-based compensation expense
Stock-based compensation	567	342	1,003	664
Selling, General and Administrative Expenses [Member]
Schedule of stock-based compensation expense
Stock-based compensation	$ 1,890	$ 1,369	$ 3,434	$ 2,715

Stock-Based Compensation - Val

Stock-Based Compensation - Valuation Assumptions (Details) - Stock options [Member] - $ / shares	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Expected term (in years)	0 years	0 years	5 years 7 months 17 days	5 years 3 months 18 days
Volatility	0.00%	0.00%	60.00%	62.00%
Risk-free interest rate	0.00%	0.00%	2.70%	2.00%
Dividend yield	0.00%	0.00%	0.00%	0.00%
Weighted-average estimated fair value of stock options granted (usd per share)	$ 0	$ 0	$ 5.02	$ 2.52

Capital Stock - Textual (Detai

Capital Stock - Textual (Details) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	6 Months Ended
	Apr. 30, 2018	Jun. 30, 2018	Jun. 30, 2017
Class of Stock [Line Items]
Stock options exercised (shares)		302,703	55,780
Weighted average exercise price of stock options exercised (usd per share)		$ 6.14	$ 2.55
Proceeds from exercises of stock options		$ 1,858	$ 142
Public offering price (usd per share)	$ 9.25
Proceeds from issuance of common stock, net of costs	$ 37,300
Underwritten Public Offering [Member]
Class of Stock [Line Items]
Issuance of common stock, net of issuance costs (shares)	4,312,500
Over-Allotment Option [Member]
Class of Stock [Line Items]
Issuance of common stock, net of issuance costs (shares)	562,500

Capital Stock - Stockholders'

Capital Stock - Stockholders' Equity (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Beginning balance			$ 24,547	$ 19,099
Exercise of stock options (shares)			302,703	55,780
Exercise of stock options			$ 1,858	$ 142
Employee stock-based compensation			4,413	3,379
Non-employee stock-based compensation			24
Net shares settlements for taxes			(3,140)	(1,636)
Issuance of common stock, net of issuance costs			37,317	23,291
Issuance costs			179
Total comprehensive loss	$ (3,735)	$ (6,086)	(8,429)	(13,638)
Net loss	(3,735)	(6,280)	(8,429)	(13,740)
Ending balance	$ 52,530	$ 30,637	$ 52,530	$ 30,637
Accounting Standards Update 2014-09 [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Effect of new accounting principle					$ (4,060)
Accounting Standards Update 2016-01 [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Effect of new accounting principle					0
Common Stock [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Beginning balance (shares)			48,365,000	41,255,000
Beginning balance			$ 5	$ 4
Exercise of stock options (shares)			303,000	56,000
Release of stock awards (shares)			824,000	1,079,000
Net shares settlements for taxes (shares)			(297,000)	(391,000)
Issuance of common stock, net of issuance costs (shares)			4,313,000	6,325,000
Issuance of common stock, net of issuance costs				$ 1
Ending balance (shares)	53,508,000	48,324,000	53,508,000	48,324,000
Ending balance	$ 5	$ 5	$ 5	$ 5
Additional Paid-in Capital [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Beginning balance			340,079	311,164
Exercise of stock options			1,858	142
Employee stock-based compensation			4,413	3,379
Non-employee stock-based compensation			24
Net shares settlements for taxes			(3,140)	(1,636)
Issuance of common stock, net of issuance costs			37,317	23,290
Ending balance	380,551	336,339	380,551	336,339
AOCI Attributable to Parent [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Beginning balance			(472)	0
Total comprehensive loss				102
Ending balance	0	102	0	102
AOCI Attributable to Parent [Member] | Accounting Standards Update 2016-01 [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Effect of new accounting principle					472
Accumulated Deficit [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Beginning balance			(315,065)	(292,069)
Total comprehensive loss				(13,740)
Net loss			(8,429)
Ending balance	$ (328,026)	$ (305,809)	$ (328,026)	$ (305,809)
Accumulated Deficit [Member] | Accounting Standards Update 2014-09 [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Effect of new accounting principle					(4,060)
Accumulated Deficit [Member] | Accounting Standards Update 2016-01 [Member]
Increase (Decrease) in Stockholders' Equity [Roll Forward]
Effect of new accounting principle					$ (472)

Commitments and Contingencies

Commitments and Contingencies - Textual (Details)	Jun. 30, 2017USD ($)	Apr. 30, 2017USD ($)	Feb. 28, 2017USD ($)	Dec. 31, 2016	Jun. 30, 2018USD ($)ft²building	Jun. 30, 2017USD ($)	Jun. 30, 2018USD ($)ft²building	Jun. 30, 2017USD ($)	Dec. 31, 2012USD ($)	Dec. 31, 2012USD ($)	Dec. 31, 2017USD ($)
Commitments and Contingencies [Line Items]
Incentive from lessor					$ 700,000		$ 700,000				$ 900,000
Asset retirement obligations					200,000		200,000				200,000
Accretion expense related to asset retirement obligation					0	$ 0	0	$ 0
Rent expense					800,000	800,000	1,600,000	1,500,000
Operating lease, sublease rentals					300,000	300,000	600,000	700,000
Capital leases, term of contract		3 years	3 years	3 years
Capital lease obligations incurred		$ 300,000	$ 400,000
Operating lease, future minimum sublease rentals					$ 900,000		$ 900,000
Fifth Amendment [Member]
Commitments and Contingencies [Line Items]
Payments for capital improvements									$ 3,600,000
Tenant reimbursements										$ 3,100,000
Headquarters, Redwood City [Member] | Sixth Amendment [Member]
Commitments and Contingencies [Line Items]
Lease area space occupancy (square feet) | ft²					107,200		107,200
Number of buildings leased | building					4		4
Number of buildings with waived asset retirement obligation and extended lease term | building					1		1
Term Loan [Member]
Commitments and Contingencies [Line Items]
Borrowing capacity	$ 10,000,000					10,000,000		10,000,000
Revolving Credit Facility [Member]
Commitments and Contingencies [Line Items]
Borrowing capacity	$ 5,000,000					$ 5,000,000		$ 5,000,000
Accounts receivable borrowing base percentage	80.00%
Stated interest rate	5.00%					5.00%		5.00%
LIBOR [Member] | Term Loan [Member]
Commitments and Contingencies [Line Items]
Basis spread on variable rate	3.60%
Prime Rate [Member] | Revolving Credit Facility [Member]
Commitments and Contingencies [Line Items]
Basis spread on variable rate	1.00%
Indemnification Agreement [Member]
Commitments and Contingencies [Line Items]
Loss contingency accrual					$ 0		$ 0				0
Demand Deposits [Member]
Commitments and Contingencies [Line Items]
Non-current restricted cash					$ 700,000		$ 700,000				$ 700,000

Commitments and Contingencies52

Commitments and Contingencies - Future Minimum Lease Payments (Details) $ in Thousands	Jun. 30, 2018USD ($)
Capital Leases
2018 (remaining 6 months)	$ 126
2,019	252
2,020	61
2,021	0
2,022	0
Total minimum lease payments (1)	439
Less: amount representing interest	(19)
Present value of capital lease obligations	420
Less: current portion	(237)
Long-term portion of capital leases	183
Operating Leases
2018 (remaining 6 months)	1,598
2,019	3,280
2,020	712
2,021	490
2,022	41
Total minimum lease payments (1)	$ 6,121

Commitments and Contingencies53

Commitments and Contingencies - Other Commitments (Details) - Supply Commitment [Member] $ in Thousands	Jun. 30, 2018USD ($)
Other Commitments [Line Items]
Future Minimum Payment	$ 4,250
April 2016 [Member]
Other Commitments [Line Items]
Future Minimum Payment	1,693
April 2017 [Member]
Other Commitments [Line Items]
Future Minimum Payment	2
July 2017 [Member]
Other Commitments [Line Items]
Future Minimum Payment	439
December 2017 [Member]
Other Commitments [Line Items]
Future Minimum Payment	$ 2,116

Related Party Transactions - Te

Related Party Transactions - Textual (Details) - USD ($)	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2017
Related Party Transaction [Line Items]
Revenue sharing arrangement	$ 0	$ 400,000	$ 0	$ 700,000
Exela PharmSci, Inc [Member]
Related Party Transaction [Line Items]
Accounts receivable from related parties	600,000		600,000		$ 1,600,000
AstraZeneca [Member]
Related Party Transaction [Line Items]
Accounts receivable from related parties	45,000		45,000		86,000
Revenue from related parties	55,000	24,000	400,000	50,000
Estimated value of option	45,000		45,000
Asymchem [Member]
Related Party Transaction [Line Items]
Accounts receivable from related parties	0		0		0
Revenue from related parties	0	0	0	0
Alfa Aesar [Member]
Related Party Transaction [Line Items]
Accounts receivable from related parties	0		0		$ 400,000
Revenue from related parties	$ 0	$ 0	$ 0	$ 0
Presidio Partners 2007, L.P. [Member] | Exela PharmSci, Inc [Member] | Affiliated Entity [Member]
Related Party Transaction [Line Items]
Ownership percentage	10.00%		10.00%

Segment, Geographical and Oth55

Segment, Geographical and Other Revenue Information - Segment Reporting (Details) $ in Thousands	3 Months Ended				6 Months Ended		12 Months Ended
	Jun. 30, 2018USD ($)	Mar. 31, 2018USD ($)	Jun. 30, 2017USD ($)	Mar. 31, 2017USD ($)	Jun. 30, 2018USD ($)segment	Jun. 30, 2017USD ($)	Dec. 31, 2017segment
Segment Reporting Information [Line Items]
Number of operating segments | segment					2		1
Revenue	$ 13,538		$ 10,347		$ 27,580	$ 18,317
Cost of product revenue	2,611		3,790		6,436	6,792
Research and development	7,370		6,348		14,548	12,187
Selling, general and administrative	7,395		6,546		15,141	13,152
Total segment costs and operating expenses	17,376		16,684		36,125	32,131
Income (loss) from operations	(3,838)		(6,337)		(8,545)	(13,814)
Loss before income taxes	(3,746)		(6,322)		(8,442)	(13,758)
Stock-based compensation	2,457		1,711		4,437	3,379
Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	11,165		10,347		21,894	18,317
Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	2,373		0		5,686	0
Operating Segments [Member]
Segment Reporting Information [Line Items]
Revenue	13,538		10,347		27,580	18,317
Cost of product revenue	2,611		3,790		6,436	6,792
Research and development	7,166		6,172		14,164	11,832
Selling, general and administrative	2,033		1,777		4,275	3,589
Total segment costs and operating expenses	11,810		11,739		24,875	22,213
Income (loss) from operations	1,728		(1,392)		2,705	(3,896)
Stock-based compensation	851		481		1,472	889
Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	11,165		10,347		21,894	18,317
Cost of product revenue	2,611		3,790		6,436	6,792
Research and development	4,724		4,023		9,790	8,172
Selling, general and administrative	1,729		1,777		3,825	3,589
Total segment costs and operating expenses	9,064		9,590		20,051	18,553
Income (loss) from operations	2,101		757		1,843	(236)
Stock-based compensation	768		434		1,326	789
Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	2,373		0		5,686	0
Cost of product revenue	0		0		0	0
Research and development	2,442		2,149		4,374	3,660
Selling, general and administrative	304		0		450	0
Total segment costs and operating expenses	2,746		2,149		4,824	3,660
Income (loss) from operations	(373)		(2,149)		862	(3,660)
Stock-based compensation	83		47		146	100
Corporate [Member]
Segment Reporting Information [Line Items]
Total segment costs and operating expenses	(5,209)		(4,702)		(10,644)	(9,308)
Depreciation and amortization	(265)		(228)		(503)	(554)
Product Sales [Member]
Segment Reporting Information [Line Items]
Revenue	3,723		6,600		9,886	12,186
Product Sales [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	3,723		6,600		9,886	12,186
Product Sales [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	0		0		0	0
Product Sales [Member] | Operating Segments [Member]
Segment Reporting Information [Line Items]
Revenue	3,723		6,600		9,886	12,186
Product Sales [Member] | Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	3,723		6,600		9,886	12,186
Product Sales [Member] | Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	0		0		0	0
Research and Development Revenue [Member]
Segment Reporting Information [Line Items]
Revenue	9,815		3,747		17,694	6,131
Research and Development Revenue [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	7,442		3,747		12,008	6,131
Research and Development Revenue [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	2,373		0		5,686	0
Research and Development Revenue [Member] | Operating Segments [Member]
Segment Reporting Information [Line Items]
Revenue	9,815		3,747		17,694	6,131
Research and Development Revenue [Member] | Operating Segments [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Revenue	7,442		3,747		12,008	6,131
Research and Development Revenue [Member] | Operating Segments [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Revenue	$ 2,373		$ 0		$ 5,686	$ 0
Segment Operating Expense Allocation [Member] | Performance Enzymes [Member]
Segment Reporting Information [Line Items]
Research and development		$ (300)
Segment Operating Expense Allocation [Member] | Novel Biotherapeutics [Member]
Segment Reporting Information [Line Items]
Research and development				$ (100)

Segment, Geographical and Oth56

Segment, Geographical and Other Revenue Information - Concentration Risk (Details)	3 Months Ended		6 Months Ended		12 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017	Dec. 31, 2016
Customer Concentration Risk [Member] | Customer A [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	27.00%	45.00%	38.00%	42.00%
Customer Concentration Risk [Member] | Customer B [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	34.00%	21.00%	22.00%	12.00%
Customer Concentration Risk [Member] | Customer C [Member] | Sales [Member]
Concentration Risk [Line Items]
Concentration risk, percentage	18.00%		21.00%
Credit Concentration Risk [Member] | Customer A [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			46.00%		31.00%
Credit Concentration Risk [Member] | Customer B [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			27.00%		16.00%
Credit Concentration Risk [Member] | Customer D [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage			11.00%		15.00%
Credit Concentration Risk [Member] | Customer E [Member] | Accounts Receivable [Member]
Concentration Risk [Line Items]
Concentration risk, percentage					14.00%

Segment, Geographical and Oth57

Segment, Geographical and Other Revenue Information - Revenues by Geographic Area (Details) - USD ($) $ in Thousands	3 Months Ended		6 Months Ended
	Jun. 30, 2018	Jun. 30, 2017	Jun. 30, 2018	Jun. 30, 2017
Schedule of revenues by geographical area
Revenue	$ 13,538	$ 10,347	$ 27,580	$ 18,317
Americas [Member]
Schedule of revenues by geographical area
Revenue	6,058	4,401	9,655	6,189
EMEA [Member]
Schedule of revenues by geographical area
Revenue	3,808	1,959	8,800	5,166
APAC [Member]
Schedule of revenues by geographical area
Revenue	3,672	3,987	9,125	6,962
Core Segment [Member]
Schedule of revenues by geographical area
Revenue	11,165	10,347	21,894	18,317
Core Segment [Member] | Americas [Member]
Schedule of revenues by geographical area
Revenue	6,058	4,401	9,655	6,189
Core Segment [Member] | EMEA [Member]
Schedule of revenues by geographical area
Revenue	1,435	1,959	3,114	5,166
Core Segment [Member] | APAC [Member]
Schedule of revenues by geographical area
Revenue	$ 3,672	$ 3,987	$ 9,125	$ 6,962

Segment, Geographical and Oth58

Segment, Geographical and Other Revenue Information - Long-Lived Assets by Geographic Area (Details)	6 Months Ended	12 Months Ended
	Jun. 30, 2018	Dec. 31, 2017
Net Assets, Geographic Area [Member] | United States [Member]
Schedule of long-lived assets by geographical area
Long-lived assets	100.00%	100.00%