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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2012	Mar. 07, 2013	Jun. 30, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
Entity Central Index Key	0001299130
Document Type	10-K
Document Period End Date	Dec. 31, 2012
Amendment Flag	false
Document Fiscal Year Focus	2012
Document Fiscal Period Focus	FY
Current Fiscal Year End Date	--12-31
Entity Well-known Seasoned Issuer	No
Entity Voluntary Filers	No
Entity Current Reporting Status	Yes
Entity Filer Category	Accelerated Filer
Entity Public Float			$ 89,575,000
Entity Common Stock, Shares Outstanding		57,497,327

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Current assets
Cash and cash equivalents	$ 46,540	$ 58,865
Investments	54,040	118,569
Accounts receivable	2,822	4,557
Inventory, net	9,592	15,517
Prepaid expenses and other current assets	2,006	2,093
Total current assets	115,000	199,601
Property and equipment, net	14,329	18,398
Long-term assets	354	317
Total assets	129,683	218,316
Current liabilities
Accounts payable	2,988	4,742
Accrued expenses and other current liabilities	8,204	10,258
Deferred revenue, current	3,378	4,236
Facility financing obligation, current	173	140
Total current liabilities	14,743	19,376
Deferred revenue, non-current	800	1,616
Lease incentives and other long-term liabilities	2,145	3,075
Facility financing obligation, non-current	2,613	2,786
Total liabilities	20,301	26,853
Commitments and contingencies (Note 6)
Stockholders' equity
Convertible Preferred Stock, $0.001 par value: Authorized 50,000 shares; No shares issued or outstanding at December 31, 2012 and 2011
Common Stock and additional paid-in-capital, $0.001 par value: Authorized 1,000,000 shares; Issued and outstanding 56,170 and 54,964 shares at December 31, 2012 and 2011, respectively	645,372	632,961
Accumulated other comprehensive income	30	57
Accumulated deficit	(536,020)	(441,555)
Total stockholders' equity	109,382	191,463
Total liabilities and stockholders' equity	$ 129,683	$ 218,316

Consolidated Balance Sheets (Parenthetical) - $ / shares	Dec. 31, 2012	Dec. 31, 2011
Consolidated Balance Sheets [Abstract]
Convertible Preferred Stock, par value	$ 0.001	$ 0.001
Convertible Preferred Stock, shares authorized	50,000	50,000
Convertible Preferred Stock, shares issued
Convertible Preferred Stock, shares outstanding
Common Stock, par value	$ 0.001	$ 0.001
Common Stock, shares authorized	1,000,000	1,000,000
Common Stock, shares issued	56,170	54,964
Common Stock, shares outstanding	56,170	54,964

Consolidated Statements of Operations and Comprehensive Loss - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Revenue:
Product revenue	$ 20,089	$ 31,486
Service and other revenue	4,959	1,487
Grant revenue	935	890	$ 1,674
Total revenue	25,983	33,863	1,674
Cost of Revenue:
Cost of product revenue	18,796	18,725
Cost of service and other revenue	6,247	2,104
Total cost of revenue	25,043	20,829
Gross profit	940	13,034	1,674
Operating Expense:
Research and development	47,623	76,080	111,821
Sales, general and administrative	47,655	46,710	30,087
Total operating expense	95,278	122,790	141,908
Operating loss	(94,338)	(109,756)	(140,234)
Other income (expense), net	(127)	368	68
Net loss	(94,465)	(109,388)	(140,166)
Other comprehensive income (loss):
Unrealized gain/(loss) on investments	(27)	78	(22)
Comprehensive loss	$ (94,492)	$ (109,310)	$ (140,188)
Net loss per share:
Basic and diluted net loss per share	$ (1.69)	$ (2.03)	$ (14.10)
Shares used in computing basic and diluted net loss per share	55,733	53,874	9,938

Consolidated Statements of Stockholders' Equity (Deficit) - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-in Capital	Accumulated Other Comprehensive Income (Loss)	Accumulated Deficit
Balance at Dec. 31, 2009	$ (177,123)	$ 0	$ 14,877	$ 1	$ (192,001)
Balance, shares at Dec. 31, 2009		656
Components of Comprehensive loss:
Other comprehensive loss	(22)			(22)
Net loss	(140,166)				(140,166)
Total comprehensive loss	(140,188)
Conversion of redeemable convertible preferred stock to common stock at initial public offering	374,964	$ 37	374,927
Conversion of redeemable convertible preferred stock to common stock at initial public offering, shares		37,184
Conversion of warrants from warrants for preferred stock to warrants for common stock	326		326
Elimination of fractional shares resulting from reverse stock split	(1)		(1)
Elimination of fractional shares resulting from reverse stock split, shares		(1)
Issuance of common stock from Initial public offering, net of issuance costs	210,781	$ 15	210,766
Issuance of common stock from Initial public offering, net of issuance costs, shares		14,375
Issuance of Common Stock upon exercise of stock options	708	$ 1	707
Issuance of Common Stock upon exercise of stock options, shares		607
Issuance of Common Stock to consultant	281		281
Issuance of Common Stock to consultant, shares		21
Issuance of Common Stock in connection with exercise of warrants, shares		13
Vesting of Common Stock options early exercised	428		428
Employee stock-based compensation expense recorded under the intrinsic value method	845		845
Employee stock-based compensation expense recorded under the fair value method	7,880		7,880
Nonemployee stock-based compensation expense	965		965
Balance at Dec. 31, 2010	279,866	$ 53	612,001	(21)	(332,167)
Balance, shares at Dec. 31, 2010		52,855
Components of Comprehensive loss:
Other comprehensive loss	78			78
Net loss	(109,388)				(109,388)
Total comprehensive loss	(109,310)
Issuance of Common Stock	7,743	$ 2	7,741
Issuance of Common Stock, shares		2,109
Vesting of Common Stock options early exercised	780		780
Employee stock-based compensation expense recorded under the fair value method	12,146		12,146
Nonemployee stock-based compensation expense	238		238
Balance at Dec. 31, 2011	$ 191,463	$ 55	632,906	57	(441,555)
Balance, shares at Dec. 31, 2011	54,964	54,964
Components of Comprehensive loss:
Other comprehensive loss	$ (27)			(27)
Net loss	(94,465)				(94,465)
Total comprehensive loss	(94,492)
Issuance of Common Stock	$ 2,705	$ 1	2,704
Issuance of Common Stock, shares		1,206
Issuance of common stock from Initial public offering, net of issuance costs, shares	3,900,000
Issuance of Common Stock upon exercise of stock options, shares	373
Employee stock-based compensation expense recorded under the fair value method	$ 9,627		9,627
Nonemployee stock-based compensation expense	79		79
Balance at Dec. 31, 2012	$ 109,382	$ 56	$ 645,316	$ 30	$ (536,020)
Balance, shares at Dec. 31, 2012	56,170	56,170

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Cash flows from operating activities
Net loss	$ (94,465)	$ (109,388)	$ (140,166)
Adjustments to reconcile net loss to net cash used in operating activities
Depreciation and amortization	6,649	5,803	5,160
Stock-based compensation	9,705	12,384	9,690
Other items	287	226	459
Changes in assets and liabilities
Accounts receivable	1,735	(4,216)	(341)
Inventory	4,761	(11,409)	(6,864)
Prepaid expenses and other assets	1,058	1,874	(1,336)
Accounts payable	(1,754)	(4,773)	3,637
Accrued expenses and other current liabilities	(2,054)	3,044	4,245
Deferred revenue	(1,674)	2,631	3,221
Lease incentives and other long-term liabilities	(1,070)	850	299
Net cash used in operating activities	(76,822)	(102,974)	(121,996)
Cash flows from investing activities
Purchase of property and equipment	(1,703)	(9,284)	(5,259)
Purchase of investments	(87,889)	(264,071)	(180,964)
Sales of investments	7,896	36,520
Maturities of investments	143,488	243,281	47,973
Net cash provided by (used in) investing activities	61,792	6,446	(138,250)
Cash flows from financing activities
Proceeds from issuance of Convertible Preferred Stock, net			106,145
Proceeds from issuance of Common Stock	2,705	7,743	212,519
Net cash provided by financing activities	2,705	7,743	318,664
Net (decrease) increase in cash and cash equivalents	(12,325)	(88,785)	58,418
Cash and cash equivalents at beginning of period	58,865	147,650	89,232
Cash and cash equivalents at end of period	46,540	58,865	147,650
Supplemental disclosure of non-cash investing and financing activities
Assets acquired under facility lease			2,971
Additions to property and equipment under tenant improvement allowances			1,910
Inventory transferred to property and equipment for internal use	$ 1,164	2,756
Conversion of convertible preferred stock to common stock upon IPO			374,965
Reclassification of preferred warrants to common stock warrants			326
Issuance of common stock related to convertible preferred stock offering			281
Vesting of stock options related to early exercises		$ 780	$ 428

Overview

12 Months Ended

Dec. 31, 2012

Overview/Balance Sheet Components [Abstract]

Overview

1. Overview

Pacific Biosciences of California, Inc., (“Pacific Biosciences”, “PacBio”, the “Company”, “we”, “us”) has commercialized a platform for single molecule, real-time detection of biological events. Our initial focus is on the DNA sequencing market where we have developed and introduced a third generation sequencing platform.

The names “Pacific Biosciences,” “PacBio,” “SMRT,” “SMRTbell” and our logo are our trademarks.

- Definition

The entire disclosure for organization, consolidation and basis of presentation of financial statements disclosure.

+ References

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+ Details

Summary of Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

Summary of Significant Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation and Consolidation

Our consolidated financial statements have been prepared in conformity with accounting principles generally accepted in the United States, or GAAP, as set forth in the Financial Accounting Standards Board, or FASB, Accounting Standards Codification, or ASC. The consolidated financial statements include the accounts of Pacific Biosciences and our wholly owned subsidiaries. All intercompany transactions and balances have been eliminated. Translation adjustments resulting from translating foreign subsidiaries’ results of operations and assets and liabilities into U.S. dollars are immaterial for all periods presented.

Use of Estimates

The preparation of financial statements in conformity with GAAP requires us to make estimates and assumptions that affect the reported amounts of assets and liabilities and disclosure of contingent assets and liabilities at the date of the financial statements and the reported amounts of revenue and expense during the reporting periods. Our estimates include, but are not limited to, useful lives assigned to long-lived assets, assumptions used in computing stock-based compensation expense, provisions for income taxes, inventory and contingencies. Actual results could differ from our estimates, and such differences could be material to our financial position and results of operations.

Fair Value of Financial Instruments

The carrying amount of our financial assets and liabilities, including accounts receivable, prepaid expenses, other current assets, accounts payable, accrued expenses and other current liabilities, approximate fair value due to their short maturities. The carrying value of our facility financing obligation approximates fair value based on currently available borrowing rates and after consideration of non-performance risk and credit risk.

The fair value hierarchy established under GAAP requires an entity to maximize the use of observable inputs and minimize the use of unobservable inputs when measuring fair value. A financial instrument’s categorization within the fair value hierarchy is based upon the lowest level input that is significant to the fair value measurement. The three levels of inputs that may be used to measure fair value are as follows:

•

Level 1: quoted prices in active markets for identical assets or liabilities;

•

Level 2: inputs other than Level 1 that are observable, either directly or indirectly, such as quoted prices in active markets for similar assets or liabilities, quoted prices for identical or similar assets or liabilities in markets that are not active, or other inputs that are observable or can be corroborated by observable market data for substantially the full term of the assets or liabilities; and

•

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.

We consider an active market as one in which transactions for the asset or liability occurs with sufficient frequency and volume to provide pricing information on an ongoing basis. Conversely, we view an inactive market as one in which there are few transactions for the asset or liability, the prices are not current, or price quotations vary substantially either over time or among market makers. Where appropriate, our non-performance risk, or that of our counterparty, is considered in determining the fair values of liabilities and assets, respectively.

All of our cash deposits and money market funds are classified within Level 1 of the fair value hierarchy because they are valued using bank balances or quoted market prices. Our investments are classified as Level 2 instruments based on market pricing and other observable inputs. None of our investments are classified within Level 3 of the fair value hierarchy.

Assets and liabilities measured at fair value are classified in their entirety based on the lowest level input that is significant to the fair value measurement. Our assessment of the significance of a particular input to the entire fair value measurement requires management to make judgments and consider factors specific to the asset or liability.

The following table sets forth the fair value of our financial assets that were measured on a recurring basis as of December 31, 2012 and 2011, respectively (in thousands):


	December 31, 2012						December 31, 2011
	Level 1		Level 2		Total		Level 1		Level 2		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	11,847	$	—	$	11,847	$	49,267	$	—	$	49,267
Commercial paper		—		34,693		34,693		—		9,598		9,598

Investments:
Commercial paper		—		28,866		28,866		—		29,772		29,772
Corporate debt securities		—		13,203		13,203		—		37,387		37,387
Asset backed securities		—		955		955		—		9,909		9,909
Certificates of deposit		—		2,008		2,008		—		4,034		4,034
U.S. government and agency securities		—		9,008		9,008		—		37,467		37,467

Total assets measured at fair value	$	11,847	$	88,733	$	100,580	$	49,267	$	128,167	$	177,434

The estimated fair value of marketable debt securities (commercial paper, corporate debt securities, asset backed securities, certificates of deposit, and U.S. government and agency securities) as of December 31, 2012, by contractual maturity, are as follows:


	Fair Value
Due in one year or less	$	87,778
Due after one year through 3 years		955

Total investments in debt securities	$	88,733

Actual maturities may differ from contractual maturities because issuers may have the right to call or prepay obligations without call or prepayment penalties.

Cash and cash equivalents

We consider all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents.

Investments

We have designated all investments as available-for-sale and therefore, such investments are reported at fair value, with unrealized gains and losses recorded in accumulated other comprehensive income (loss) (“OCI”) in stockholders’ equity. The cost of marketable securities is adjusted for the amortization of premiums and discounts to expected maturity. Premium and discount amortization is included in other income (expense), net. Realized gains and losses, as well as interest income, on available-for-sale securities are also included in other income (expense), net. The cost of securities sold is based on the specific identification method. We include all of our available-for-sale securities in current assets.

All of our investments are subject to a periodic impairment review. We recognize an impairment charge when a decline in the fair value of our investments below the cost basis is judged to be other-than-temporary. Factors considered in determining whether a loss is temporary included the length of time and extent to which the investments fair value has been less than the cost basis, the financial condition and near-term prospects of the investee, extent of the loss related to credit of the issuer, the expected cash flows from the security, our intent to sell the security and whether or not we will be required to sell the security before the recovery of its amortized cost. During the years ended December 31, 2012, 2011 and 2010, we did not record any impairment charges on our investments as it is more likely than not that we will recover their amortized cost basis upon sale or maturity.

Concentration of Credit Risk

The counterparties to the agreements relating to our investment securities consist of various major corporations, financial institutions, municipalities and government agencies of high credit standing. Our accounts receivable are derived from net revenue to customers and distributors located in the United States and other countries. We perform credit evaluations of our customers’ financial condition and, generally, require no collateral from our customers. We regularly review our accounts receivable including consideration of factors such as historical experience, credit quality, the age of the accounts receivable balances and current economic conditions that may affect a customer’s ability to pay. We have not experienced any significant losses to date. As of December 31, 2012 and 2011, approximately 95% and 62%, respectively, of our accounts receivable were from domestic customers. As of December 31, 2012, approximately 78% of our net accounts receivable were from 3 individual customers, each representing at least 10% of our net accounts receivable. As of December 31, 2011, approximately 85% of our net accounts receivable were from 5 individual customers, each representing at least 10% of our net accounts receivable.

Inventory

Inventory is valued at the lower of the standard cost, which approximates actual cost, or market. Cost is determined using the FIFO (first-in, first-out) method. Adjustments to reduce the cost of inventory to its net realizable value, if required, are made for estimated excess or obsolete balances.

Property and Equipment, Net

Property and equipment are stated at cost, net of accumulated depreciation and any impairment charges. Depreciation is computed using the straight-line method over the estimated useful life of the asset, generally two to three years for computer equipment, three to five years for software, three to seven years for furniture and fixtures, three years for lab equipment and 30 years for buildings. Leasehold improvements are depreciated over the shorter of the lease term or the estimated useful life of the related asset. Major improvements are capitalized, while maintenance and repairs are expensed as incurred.

In connection with build-to-suit lease arrangements that we account for as if we own the facility, we record the facility at the fair value at the date construction commences, prior to significant renovations, plus the costs of the renovations. We determined the fair value of such facilities prior to renovation based on several factors, including an appraisal conducted by an independent licensed appraiser.

Impairment of Long-Lived Assets

We periodically review property and equipment for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset is impaired or the estimated useful lives are no longer appropriate. Fair value is estimated based on discounted future cash flows. If indicators of impairment exist and the undiscounted projected cash flows associated with such assets are less than the carrying amount of the asset, an impairment loss is recorded to write the asset down to its estimated fair values. To date, we have not recorded any impairment charges.

Revenue Recognition

Our revenue is generated primarily from the sale of products and services. Product revenue consists of sales of our PacBio RS instrument and related consumables, and service and other revenue primarily consists of revenue earned from product maintenance agreements. Grant revenue reflects revenue from government grants that generally provide cost reimbursement for certain types of expenditures in return for research and development activities over a contractually defined period. Revenue from grants is recognized in the period during which the related costs are incurred, provided that the conditions under which the grants were provided have been met.

We recognize revenue when persuasive evidence of an arrangement exists, delivery has occurred or services have been rendered, the price is fixed or determinable, and collectability is reasonably assured. In instances where final acceptance of the product or system is required, revenue is deferred until all acceptance criteria have been met. Revenue for product sales is generally recognized upon customer acceptance. Revenue for product maintenance agreements is recognized when earned, which is generally ratably over the service period.

In order to assess whether the price is fixed or determinable, we evaluate whether refund rights exist. If refund rights exist or payment terms are based on future performance, we defer revenue recognition until the price becomes fixed or determinable. We assess collectability based on a number of factors, including customer creditworthiness. If we determine that collection of amounts due is not reasonably assured, revenue recognition is deferred until receipt of payment.

We regularly enter into contracts from which revenue is derived from multiple deliverables including a mix of products and or services. Revenue recognition for contracts with multiple deliverables is based on the individual units of accounting determined to exist in the contract. A delivered item is considered a separate unit of accounting when 1) the delivered item has value to the customer on a stand-alone basis; and 2) when a general right of return exists, the delivery or performance of an undelivered item is considered probable and under our control. Items are considered to have stand-alone value when they are sold separately by any vendor or when the customer could resell the item on a stand-alone basis. Our revenue arrangements generally do not have a general right of return. When a deliverable does not meet the criteria to be considered a separate unit of accounting, we group it with other deliverables that, when combined, meet the criteria, and the appropriate allocation of arrangement consideration and revenue recognition is determined. Consideration is allocated at the inception of the contract to all deliverables based on their relative selling price. In order to determine the relative selling price of a deliverable, we apply, in order, the following hierarchy: 1) vendor-specific objective evidence (“VSOE”); 2) third-party evidence if VSOE is not available; and 3) our best estimate of selling price for the deliverable if neither VSOE nor third-party evidence is available.

In order to establish VSOE, we must regularly sell the product or service on a standalone basis with a substantial majority of sales priced within a relatively narrow range. If an insufficient number of standalone sales exist and VSOE cannot be determined, we then consider whether third party evidence can be used to establish selling price. Due to the lack of similar products and services sold by other companies within our industry, we have not established selling price using third-party evidence. If neither VSOE nor third party evidence of selling price exists, we determine our best estimate of selling price using a combination of prices set by our pricing committee adjusted for applicable discounts and customer orders received to date.

Deferred revenue primarily represents product maintenance agreement revenue that is expected to be recognized over the related service period, generally one to three years.

Cost of Revenue

Cost of revenue reflects the direct cost of product components, third party manufacturing services and our internal manufacturing overhead and customer service infrastructure costs incurred to produce, deliver, maintain and support our instruments, consumables, and services.

Manufacturing overhead, comprised mainly of labor costs, is determined and capitalized into inventory based on management’s estimate of normal manufacturing capacity. Normal capacity is the production level expected to be achieved over a number of periods under normal circumstances with available resources. Our current manufacturing volumes are below expected normal capacities, therefore manufacturing overhead incurred during the period exceeds the amounts absorbed into inventory and included in cost of revenue. As excess manufacturing resources are engaged in next generation product research and development, production of product used internally for R&D, and other R&D support activities, manufacturing costs in excess of amounts reflected in inventory and cost of revenue are expensed as a component of research and development expense during the period in which the expenses are incurred.

Service costs include the direct costs of components used in support, repair and maintenance of customer instruments as well as the cost of personnel, materials and support infrastructure necessary to support the installed customer base. As we are in the early stages of the commercial launch of our products, the capacity of our existing service infrastructure exceeds the number of installed customer instruments. Therefore, management has estimated the capacity of the existing service infrastructure and recognizes service related cost of revenue based on the installed base. As a result, total service infrastructure costs exceed the costs associated with the support of customer instruments and such excess costs are included as a component of sales, general and administrative expense.

Research and Development

We expense research and development costs during the period in which the costs are incurred. However, we defer and capitalize non-refundable advance payments made for research and development activities until the related goods are received or the related services are rendered.

Leases

We categorize leases at their inception as either operating or capital leases. On certain of our lease agreements, we may receive tenant improvement allowances, rent holidays and other incentives. Rent expense is recorded on a straight-line basis over the term of the lease. The difference between rent expense recognized and amounts paid under the lease agreement is recorded as lease incentives in the balance sheets. Leasehold improvements are capitalized at cost and depreciated over the lesser of their expected useful life or the life of the lease. Tenant improvements afforded to us by landlord incentives are recorded as leasehold improvement assets with corresponding lease incentives liabilities.

For build-to-suit lease arrangements, we evaluate the extent of our financial and operational involvement in the tenant improvements to determine whether we are considered the owner of the construction project under GAAP. When we are considered the owner of a project, we record the shell of the facility at its fair value at the date construction commences with a corresponding facility financing obligation. Improvements to the facility during the construction project are capitalized and, to the extent funded by lessor afforded incentives, with corresponding increases to the facility financing obligation. Payments we make under leases in which we are considered the owner of the facility are allocated to land rental expense, based on the relative values of the land and building at the commencement of construction, reductions of the facility financing obligation and interest expense recognized on the outstanding obligation. As the build-out was completed in 2010, the activity in 2012 consisted solely of lease payments. To the extent gross future payments do not equal the recorded liability, the liability is settled upon return of the facility to the lessor. Any difference between the book value of the assets and remaining facility obligation are recorded in other expense, net. For existing arrangements, the differences are expected to be immaterial.

Income Taxes

We account for income taxes under the asset and liability method, which requires, among other things, that deferred income taxes be provided for temporary differences between the tax basis of our assets and liabilities and the amounts reported in the financial statements. In addition, deferred tax assets are recorded for the future benefit of utilizing net operating losses and research and development credit carryforwards. A full valuation allowance is provided against our net deferred tax assets as it is more likely than not that the deferred tax assets will not be fully realized.

We review our positions taken relative to income taxes. To the extent our tax positions are more likely than not to result in the payout of additional taxes, we accrue the estimated amount of tax for such uncertain positions.

Stock-based Compensation

Stock-based compensation expense for all stock-based compensation awards is based on the grant date fair value estimated using the Black-Scholes option pricing model. We have limited historical information available to support the underlying estimates of certain assumptions required to value stock options. The expected term of options is estimated based on the simplified method. We do not have sufficient trading history to solely rely on the volatility of our own common stock for establishing expected volatility. Therefore, we based our expected volatility on the historical stock volatilities of our common stock as well as several comparable publicly listed companies over a period equal to the expected term of the options. The risk-free interest rate is based on the U.S. Treasury yield curve in effect at the time of grant for the expected term of the stock option. We estimate our forfeiture rate based on an analysis of our actual forfeitures and will continue to evaluate the adequacy of the forfeiture rate based on actual forfeiture experience, analysis of employee turnover behavior and other factors. The impact from a forfeiture rate adjustment will be recognized in full in the period of adjustment, and if the actual number of future forfeitures differs from that estimated, we may be required to record adjustments to stock-based compensation expense in future periods. We recognize compensation expense on a straight-line basis over the requisite service period. We have elected to use the simplified method to calculate the beginning pool of excess tax benefits.

We have employee and director stock option plans that are more fully described in Note 10.

Other Comprehensive Income (loss)

Other comprehensive income (loss) is comprised of unrealized gains (losses) on our investment securities.

Recent Accounting Pronouncements

In 2011 the FASB issued Accounting Standards Update No. 2011-04, to modify the definition of and requirements for measurement of and disclosure concerning fair value. We adopted this guidance beginning January 1, 2012. The adoption of this amendment had no impact on our financial position or results of operations.

In 2011 the FASB issued Accounting Standards Update No. 2011-05, requiring companies to present the components of OCI either in a single continuous statement of comprehensive income or in two separate but consecutive statements of net income and other comprehensive income. We adopted this guidance during the first quarter of 2012 and elected to disclose the OCI in a single continuous statement.

Investments

12 Months Ended

Dec. 31, 2012

Investments [Abstract]

Investments

3. Investments

The following table summarizes our investments as of December 31, 2012 and December 31, 2011 (in thousands):


	As of December 31, 2012
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	11,847	$	—	$	—		$	11,847
Commercial paper		34,690		3		—			34,693

Total cash and cash equivalents		46,537		3		—			46,540

Investments:
Commercial paper		28,859		7		—			28,866
Corporate debt securities		13,190		13		—			13,203
Asset backed securities		954		1		—			955
Certificates of deposit		2,005		3		—			2,008
U.S. government and agency securities		9,005		3		—			9,008

Total investments		54,013		27		—			54,040

Total cash, cash equivalents and investments	$	100,550	$	30	$	—		$	100,580


	As of December 31, 2011
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	49,267	$	—	$	—		$	49,267
Commercial paper		9,599		—		(1	)		9,598

Total cash and cash equivalents		58,866		—		(1	)		58,865

Investments:
Commercial paper		29,767		5		—			29,772
Corporate debt securities		37,379		65		(57	)		37,387
Asset backed securities		9,904		7		(2	)		9,909
Certificates of deposit		4,026		9		(1	)		4,034
U.S. government and agency securities		37,435		35		(3	)		37,467

Total investments		118,511		121		(63	)		118,569

Total cash, cash equivalents and investments	$	177,377	$	121	$	(64	)	$	177,434

- Definition

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

+ References

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

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Topic 310
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 3, 19, 20, 21, 22, 137
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Balance Sheet Components

12 Months Ended

Dec. 31, 2012

Overview/Balance Sheet Components [Abstract]

Balance Sheet Components

4. Balance Sheet Components

Accounts Receivable:

As of December 31, 2012 and 2011, our accounts receivable, net consisted of the following components (in thousands):


	December 31,
	2012		2011
Trade receivables	$	2,008	$	4,540
Related party receivables		814		17

Accounts receivable	$	2,822	$	4,557

Related party receivables primarily relate to instrument and other products and services purchased by Stanford University.

Inventory:

As of December 31, 2012 and 2011, our inventory, net consisted of the following components (in thousands):


	December 31,
	2012		2011
Purchased materials	$	3,823	$	5,273
Work in process		3,494		5,347
Finished goods		2,275		4,897

Inventory, net	$	9,592	$	15,517

Property and Equipment:

As of December 31, 2012 and 2011, our property and equipment, net consisted of the following components (in thousands):


	December 31,
	2012			2011
Building	$	1,160		$	1,160
Laboratory equipment and machinery		16,856			15,664
Leasehold improvements		8,035			7,636
Computer equipment		3,681			3,450
Software		4,457			1,577
Furniture and fixtures		854			859
Construction in progress		47			3,222

		35,090			33,568
Less: Accumulated depreciation		(20,761	)		(15,170	)

Property and equipment, net	$	14,329		$	18,398

Depreciation expense during 2012, 2011 and 2010 was $6.6 million, $5.8 million and $5.2 million, respectively.

Software increased from $1.6 million as of December 31, 2011 to $4.5 million as of December 31, 2012, primarily due to enterprise-level business software that we purchased and customized to meet our specific operational needs being placed into service during 2012. The majority of these costs were capitalized as construction in progress as of December 31, 2011. Upon being placed in service, these costs are depreciated over an estimated useful life of 3 to 5 years.

Accrued liabilities and other current liabilities:

As of December 31, 2012 and 2011, our accrued expenses and other current liabilities consisted of the following (in thousands):


	December 31, 2012		December 31, 2011
Salaries and benefits	$	4,660	$	5,284
Professional services		1,093		1,915
Short-term portion of deferred rent		941		844
Customer deposits		685		1,503
Other		825		712

Accrued expenses and other current liabilities	$	8,204	$	10,258

Facility Financing and Debt Obligations

12 Months Ended

Dec. 31, 2012

Facility Financing and Debt Obligations [Abstract]

Facility Financing and Debt Obligations

5. Facility Financing and Debt Obligations

Facility Financing Obligation

In December 2009 we entered into a lease agreement for a manufacturing and office facility. In order for the facility to meet our needs and operating requirements, substantial tenant improvements, including improvements to the structural elements and principal operating systems of the facility, were necessary. The lessor provided a tenant improvement allowance of $1.8 million to apply towards the necessary improvements and we remained obligated for additional amounts over the afforded allowance.

Due to our involvement in and the nature of the renovations made to the facility and our obligations to fund the costs of renovations exceeding the incentives afforded to us, we account for the facility as if we are the owner. Accordingly we recorded $3.0 million of building and leasehold improvement assets, reflecting the $1.2 million fair value of the facility prior to commencing renovations and the $1.8 million of landlord incentives within property and equipment, net and a corresponding liability recorded to facility financing obligation.

Based on the allocation of payments, the facility financing obligation bears an implied interest rate of 9.0%. During 2012 and 2011, we recognized $0.3 million and $0.3 million, respectively, of interest expense in our consolidated statement of operations relating to the facility financing obligation.

As of December 31, 2012, the future minimum payments due under the facility financing obligation were as follows (in thousands):


	Financing obligation
2013	$	629
2014		648
2015		667

Total payments		1,944
Less discounts and interest		(1,309	)

Total net payments under facility financing obligation		635
Property reverting to landlord		2,151

Present value of obligation		2,786
Less current portion of obligation		(173	)

Long-term portion of obligation	$	2,613

Commitments and Contingencies

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies/Litigation Settlements [Abstract]

Commitments and Contingencies

6. Commitments and Contingencies

Operating Lease Commitment

As of December 31, 2012 we have noncancelable operating lease agreements for research and development, office, manufacturing and training facilities in Menlo Park, California that expire at various dates, with the latest expiration in December 2015. Our leases generally have an option to renew at rates approximating the prevailing fair market rental rate at the end of the lease term. As of December 31, 2012, the future annual minimum lease payments under all noncancelable operating leases with an initial term in excess of one year are as follows (in thousands):


Years ending December 31:	Amount
2013	$	3,789
2014		3,860
2015		3,850

Total minimum lease payments	$	11,499

Rent expense for 2012, 2011 and 2010, was $2.4 million, $2.8 million and $2.1 million, respectively. We are also required to pay our share of operating expenses with respect to the facilities in which we operate.

Other commitments include an estimated amount of approximately $7.9 million of all open cancellable purchase orders and contractual obligations that occur in the ordinary course of business, including commitments with suppliers, for which we have not received the goods or services.

Contingencies

We may become subject to claims and assessments from time to time in the ordinary course of business. We accrue liabilities for such matters when it is probable that future expenditures will be made and such expenditures can be reasonably estimated.

Three putative class action lawsuits were filed against us and certain of our officers and directors in the Superior Court of the State of California, County of San Mateo. These actions were brought on behalf of all persons or entities who purchased or otherwise acquired our common stock pursuant or traceable to our initial public offering (“IPO”) of common stock in October 2010. The claims were initiated between October 2011 and April 2012 and have since been consolidated as In re Pacific Biosciences of California Inc. S’holder Litig., Case No. CIV509210 (the “State Court Action”). The plaintiffs in the State Court Action allege violations of several provisions of the federal securities laws in connection with our August 16, 2010, registration statement (effective, as amended, on October 26, 2010) and seek, among other things, compensatory damages, rescission, and attorneys’ fees and costs on behalf of the putative class. The defendants in the State Court Action filed a motion to stay that lawsuit in deference to the Primo action pending in federal district court. On May 25, 2012, the Superior Court denied the defendants’ motion to stay. The defendants in the State Court Action also filed a demurrer to certain of the plaintiffs’ claims, which was sustained in part and overruled in part on October 16, 2012. On October 26, 2012, the plaintiffs in the State Court Action filed a First Amended Consolidated Class Action Complaint, which the defendants answered on November 13, 2012.

On or around December 12, 2012, the parties to the State Court Action reached an agreement on certain terms of a tentative settlement on behalf of the entire class of persons or entities that purchased our common stock between October 27, 2010, and September 20, 2011 (inclusive). On January 18, 2013, the parties in the State Court Action entered into a memorandum of understanding regarding the tentative settlement, which will not become effective until final approval is granted by the Superior Court. As of December 31, 2012, we have accrued for our best estimate to resolve this matter.

On December 21, 2011, we and certain of our officers and directors were named in a putative class action lawsuit filed in United States District Court for the Northern District of California (Primo v. Pacific Biosciences of California, Inc., et al., Case No. 4:11-CV-06599). On April 11, 2012, an amended complaint was filed in the Primo action, which added another plaintiff, Evan Powell. As amended, the complaint alleges violations of several provisions of the federal securities laws in connection with our August 16, 2010 registration statement (effective, as amended, on October 26, 2010), and by us and/or our employees during the class period. The complaint seeks, among other things, compensatory damages, rescission, and attorneys’ fees and costs on behalf of the putative class. On April 6, 2012, Mr. Primo was appointed lead plaintiff in the action. On July 31, 2012, the defendants moved to dismiss the Primo action in its entirety. A hearing on the defendants’ motion to dismiss was held on October 11, 2012. A decision on the motion to dismiss has not yet been issued.

On December 29, 2011, we were named as a nominal defendant, along with certain of our directors as individual defendants, in a purported shareholder derivative lawsuit filed in United States District Court for the Northern District of California (Burlingame v. Martin et al., Case No. 4:11-CV-06703). The complaint alleges that the director defendants breached various fiduciary duties owed to us, engaged in waste of corporate assets, and were, as a result, unjustly enriched. The complaint seeks, among other things, restitution of director profits allegedly obtained as a result of the aforesaid conduct, improvement of our corporate governance procedures, and attorneys’ fees and costs. On February 28, 2012, the Burlingame action was related to the Primo action and transferred to the same judge hearing the Primo action. The parties in the Burlingame action have stipulated that no response to the complaint will be due until resolution of the motion to dismiss the Primo action.

Pursuant to Delaware law, we may have obligations, under certain circumstances, to hold harmless and indemnify each of our directors and certain officers, including those named in the actions, against judgments, fines, settlements and expenses related to claims arising against such directors and officers to the fullest extent permitted under Delaware law, our bylaws and certificate of incorporation. We also enter and have entered into indemnification agreements with our directors and officers that may require us to indemnify them against liabilities that arise by reason of their status or service as directors or officers, except as prohibited by applicable law. Such obligations for indemnification may apply to these lawsuits. In addition, we may have obligations to hold harmless and indemnify each of the underwriters from our initial public offering and their respective affiliates, directors and officers against any and all losses, claims, damages and liabilities related to claims arising against such parties pursuant to the terms of the underwriting agreement between the underwriters and the Company.

We believe that the allegations in each of these pending actions are without merit and intend to vigorously contest the actions. However, there can be no assurance that we will be successful in our defense.

In addition, from time to time, we are a party to litigation and subject to claims incident to the ordinary course of business.

We cannot determine the ultimate outcome of these lawsuits. Except as noted above regarding the tentative settlement of the State Court Action, we cannot provide an estimate of the possible loss or possible range of loss associated with the resolution of these contingencies with certainty or confidence; therefore, except as noted above, we have not provided an estimate and we have not recorded a liability.

Indemnification

In the ordinary course of business, we enter into standard indemnification arrangements. Pursuant to these arrangements, we indemnify, hold harmless, and agree to reimburse the indemnified parties for losses suffered or incurred by the indemnified party in connection with any trade secret, copyright, patent or other intellectual property infringement claim by any third party with respect to its technology, or from claims relating to our performance or non-performance under a contract, any defective products supplied by us, or any negligent acts or omissions, or willful misconduct, committed by us or any of our employees, agents or representatives. The term of these indemnification agreements is generally perpetual after the execution of the agreement. The maximum potential amount of future payments we could be required to make under these agreements is not determinable because it involves claims that may be made against us in future periods, but have not yet been made. To date, we have not incurred costs to defend lawsuits or settle claims related to these indemnification agreements.

Pursuant to Delaware law, we may have obligations, under certain circumstances, to hold harmless and indemnify each of our directors and certain officers against judgments, fines, settlements and expenses related to claims arising against such directors and officers to the fullest extent permitted under Delaware law, our bylaws and certificate of incorporation. We also enter and have entered into indemnification agreements with our directors and certain officers that may require us to indemnify them against liabilities that arise by reason of their status or service as directors or officers, except as prohibited by applicable law. In addition, we may have obligations to hold harmless and indemnify third parties involved with our fund raising efforts and their respective affiliates, directors, officers, employees, agents or other representatives against any and all losses, claims, damages and liabilities related to claims arising against such parties pursuant to the terms of agreements entered into between such third parties and the Company in connection with such fund raising efforts. To the extent that any such indemnification obligations apply to the lawsuits described above, any associated expenses incurred are included within the related accrued litigation expense amounts. No additional liability associated with such indemnification obligations has been recorded at December 31, 2012.

- Definition

The entire disclosure for commitments and contingencies.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 825
-SubTopic 20
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6449706&loc=d3e16207-108621

Reference 2: http://www.xbrl.org/2003/role/presentationRef
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 14
-Paragraph 3
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 5
-Paragraph 9, 10, 11, 12
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Litigation Settlements

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies/Litigation Settlements [Abstract]

Litigation Settlements

7. Litigation Settlements

During April 2012, we entered into a settlement agreement with Life Technologies Corporation to settle a complaint filed by Life Technologies Corporation seeking review of a patent interference decision of the U.S. Patent and Trademark Office. Additionally, during April 2012, we entered into a settlement and release agreement with Helicos Biosciences Corporation, or Helicos, and Arizona Science and Technology Enterprises LLC d/b/a Arizona Technology Enterprises, or AzTE, to resolve all existing patent litigation between the parties. The settlement terms with Helicos and AzTE also include other features such as worldwide, non-exclusive limited licenses for the Company to all patents owned by Helicos and the two asserted patents in-licensed by Helicos from AzTE in the field relevant to our current products, and a perpetual covenant not to sue. The Company determined the principal benefit of the settlement with Helicos and AzTE was the economic benefit of avoiding litigation expenses and that the value attributable to other settlement features was believed to be de minimis. No value was assigned to the licenses from Helicos and AzTE as we do not believe any of our current or future products would fall under any valid and enforceable claims in the licensed applications and patents.

We recorded a $1.8 million charge to selling, general and administrative expense during the first quarter of fiscal 2012. The payment of the $1.8 million was made during the six-month period ended June 30, 2012.

Income Taxes

12 Months Ended

Dec. 31, 2012

Income Taxes [Abstract]

Income Taxes

8. Income Taxes

A reconciliation between the statutory federal income tax and our effective tax rates as a percentage of loss before income taxes are as follows:


	Years Ended December 31,
	2012			2011			2010
Statutory tax rate		35.0	%		35.0	%		35.0	%
State tax rate, net of federal benefit		3.9			5.0			5.7
Stock-based compensation		(1.7	)		(2.0	)		(1.6	)
Federal R&D credit		0.0			2.8			2.0
CA R&D credit		1.1			2.3			1.1
Other		(2.1	)		0.0			(0.2	)
Change in valuation allowance		(36.2	)		(43.1	)		(43.5	)
Change of implied statutory tax rate to prior years		0.0			0.0			1.5

Effective income tax rate		0.0	%		0.0	%		0.0	%

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):


	December 31,
	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	186,906		$	154,118
Research and development credits		18,883			17,814
Depreciation		2,736			2,708
Accruals and reserves		5,678			6,197

Total deferred tax assets		214,203			180,837
Less: Valuation allowance		(213,773	)		(180,810	)

Deferred tax liabilities:
Deferred Rent		(430	)		(27	)

Net deferred tax assets	$	—		$	—

Due to uncertainties surrounding the realization of deferred tax assets through future taxable income, we have provided a full valuation allowance and, therefore, have not recognized any benefits from net operating losses and other deferred tax assets.

Recognition of deferred tax assets is appropriate when realization of such assets is more likely than not. Based upon the weight of available evidence, we believe it is more likely than not that the net deferred tax assets will not be fully realizable. Accordingly, we have provided a full valuation allowance against our net deferred tax assets as of December 31, 2012.

For the year ended December 31, 2012, the Company’s valuation allowance increased to $213.8 million primarily because of an increase in deferred tax assets related to net operating losses, state research and development tax credits, and changes in accruals and reserves. For the year ended December 31, 2011, the Company’s valuation allowance increased to $180.8 million primarily because of an increase in deferred tax assets related to net operating losses, federal and state research and development tax credits, and changes in accruals and reserves.

As of December 31, 2012, we had federal and state net operating loss carryforwards of approximately $476.4 million and $434.9 million, respectively, available to reduce future taxable income, if any. The federal net operating loss carryforward begins expiring in 2024, and the state net operating loss carryforward begins expiring in 2014.

We also had federal and California state research and development credit carryforwards of approximately $15.3 million and $18.0 million, respectively, as of December 31, 2012. The federal research and development credits begin expiring in 2024 if not utilized. The California tax research and development credits can be carried forward indefinitely.

Our 2012 tax provision did not include the benefit of the 2012 federal R&D credit. The federal R&D credit expired as of December 31, 2011. In January 2013, it was retroactively extended through the end of 2013. Under U.S. GAAP, the tax benefit of the 2012 federal R&D credit will be a discrete item in the first quarter of year 2013 when the reenactment occurred. However, due to the full valuation allowance, such additional deferred tax assets are expected to be fully offset.

Tax attributes related to stock option windfall deductions are not recorded until they result in a reduction of cash tax payable. Our federal and state net operating losses from windfall deductions were excluded from our deferred tax asset balance as of December 31, 2012. The benefit of the federal and state net operating loss deferred tax assets of $3.3 million and $0.5 million, respectively, will be recorded to additional paid-in capital when they reduce cash tax payable.

The Tax Reform Act of 1986 limits the use of net operating loss and tax credit 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 experience an ownership change, utilization of our United States net operating loss and tax credit carryforwards could be limited.

As of December 31, 2012, our total unrecognized tax benefit was $10.0 million, of which none of the tax benefit, if recognized, would affect the effective income tax rate due to the valuation allowance that currently offsets deferred tax assets. We do not anticipate the total amount of unrecognized income tax benefits to significantly increase or decrease in the next 12 months.

A reconciliation of the beginning and ending unrecognized tax benefit accounts is as follows (in thousands):


Balance as of December 31, 2009	$	3,937
Increase in balance related to tax positions taken in prior year		198
Increase in balance related to tax positions taken during current year		2,222

Balance as of December 31, 2010		6,357
Increase in balance related to tax positions taken in prior year		832
Increase in balance related to tax positions taken during current year		2,098

Balance as of December 31, 2011		9,287
Increase in balance related to tax positions taken in prior year		—
Increase in balance related to tax positions taken during current year		705

Balance as of December 31, 2012	$	9,992

Our practice is to recognize interest and/or penalties related to income tax matters in income tax expense. As of December 31, 2012 and 2011, we had no accrued interest or penalties due to our net operating losses available to offset any tax adjustment. We file U.S. federal and various state income tax returns. For U.S. federal and state income tax purposes, the statute of limitation currently remains open for the years ending December 31, 2009 to present and December 31, 2008 to present, respectively. In addition, all of the net operating losses and research and development credit carryforwards that may be utilized in future years may be subject to examination. We are not currently under examination by income tax authorities in any jurisdiction.

- Definition

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

+ References

+ Details

Stockholders' Equity

12 Months Ended

Dec. 31, 2012

Stockholders' Equity [Abstract]

Stockholders' Equity

9. Stockholders’ Equity

Our Certificate of Incorporation, as amended and restated in October 2010 in connection with the closing of our IPO, authorizes us to issue 1,000,000,000 shares of $0.001 par value common stock and 50,000,000 shares of $0.001 par value preferred stock. As of December 31, 2012 and 2011, there were no shares of preferred stock issued or outstanding.

Common stockholders are entitled to dividends when and if declared by our board of directors. There have been no dividends declared to date. The holder of each share of common stock is entitled to one vote.

Stock Offering

In April 2012, we filed a shelf registration statement on Form S-3 with the SEC pursuant to which we may, from time to time, sell up to an aggregate of $150 million of our common stock, warrants or debt securities. On May 1, 2012, the registration statement was declared effective by the SEC, which will allow us to access the capital markets for the three year period following this effective date. On October 5, 2012, we entered into a Controlled Equity Offering Sales Agreement (the “Sales Agreement”) with Cantor Fitzgerald & Co. (“Cantor”) pursuant to which we may offer and sell, from time to time, through Cantor shares of our common stock having an aggregate offering price of up to $30.0 million through an “at-the-market” offering. We are not obligated to make any sales of shares under the Sales Agreement. We will pay Cantor a commission equal to 3% of the gross proceeds from the sale of shares of our common stock under the Sales Agreement and reimburse up to $50,000 of legal expenses incurred by Cantor. As of December 31, 2012, no shares of the Company’s common stock had been sold under this Sales Agreement. We commenced selling shares on February 7, 2013 and as of March 12, 2013, we have sold in aggregate approximately 3.9 million shares resulting in net proceeds of approximately $8.6 million.

- Definition

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

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(d),(e))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

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-Topic 310
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-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 4.E)
-URI http://asc.fasb.org/extlink&oid=6228006&loc=d3e74512-122707

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-Name Accounting Standards Codification
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-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6521494

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Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Section B
-Paragraph 7, 11A
-Chapter 1
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 12
-Paragraph 10
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 16: http://www.xbrl.org/2003/role/presentationRef
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-Name Statement of Financial Accounting Standard (FAS)
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 17: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph d
-Article 4

Reference 18: http://www.xbrl.org/2003/role/presentationRef
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-Number 210
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Reference 19: http://www.xbrl.org/2003/role/presentationRef
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-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
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Reference 20: http://www.xbrl.org/2003/role/presentationRef
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-Number 210
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Reference 21: http://www.xbrl.org/2003/role/presentationRef
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-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 23: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Article 3

+ Details

Stock-Based Compensation

12 Months Ended

Dec. 31, 2012

Share Based Compensation [Abstract]

Stock-Based Compensation

10. Stock-Based Compensation

Stock Option Plans

As of December 31, 2012, we had three active equity compensation plans, the 2010 Equity Incentive Plan, or “2010 Plan”, the 2010 Outside Director Equity Incentive Plan, or “2010 Director Plan”, and the 2010 Employee Stock Purchase Plan or “ESPP” all of which we adopted upon the effectiveness of our IPO during October 2010. Prior to the adoption of these plans, we granted options pursuant to the 2004 Equity Incentive Plan, through August 2005, and the 2005 Stock Plan, through October 2010. Upon termination of the predecessor plans, the shares available for grant at the time of termination, and shares subsequently returned to the plans upon forfeiture or option termination, were transferred to the successor plan in effect at the time of share return. We issue new shares of common stock upon exercise of stock options.

2010 Equity Incentive Plan

Stock options granted under the 2010 Plan may be either ISOs or NSOs. ISOs may be granted only to employees. NSOs may be granted to employees, consultants and directors. Stock options under the 2010 Plan may be granted with a term of up to ten years and at prices no less than the fair market value of our common stock on the date of grant. To date, stock options granted generally vest over four years and vest at a rate of 25% upon the first anniversary of the vesting commencement date and 1/48th per month thereafter. As of December 31, 2012 we had reserved 6.5 million shares of common stock for issuance under the 2010 Plan.

2010 Outside Director Equity Incentive Plan

Stock options granted under the 2010 Director Plan provide for the grant of NSOs. Stock options under the 2010 Plan may be granted with a term of up to ten years and at prices no less than the fair market value of our common stock on the date of grant. To date, stock options granted generally vest over one year on a monthly basis or three years at a rate of one-third upon the first anniversary of the vesting commencement date and 1/36th per month thereafter. As of December 31, 2012 we had reserved 1.0 million shares of common stock for issuance under the 2010 Director Plan.

2010 Employee Stock Purchase Plan

We adopted the ESPP in October 2010 under which 0.4 million shares of our common stock have been reserved for issuance as of December 31, 2012. Our ESPP permits eligible employees to purchase common stock at a discount through payroll deductions during defined offering periods. Each offering period will generally consist of four purchase periods, each purchase period being approximately six months. The price at which the stock is purchased is equal to the lower of 85% of the fair market value of the common stock at the beginning of an offering period or at the end of a purchase period. Each offering period will generally end and the shares will be purchased twice yearly on March 1 and September 1.

We issue new shares of common stock upon the purchase of shares under the plan.

Stock Options

The following table summarizes stock option activity for all stock option plans for the year ended December 31, 2012 (in thousands, except per share amounts):


				Common Stock Options Outstanding
	Shares available for grant			Number of shares			Exercise price		Weighted average exercise price
Balances, December 31, 2011		1,441			10,522		$	0.20 – 16.00	$	6.69

Additional shares reserved		3,298
Options granted		(4,720	)		4,720		$	1.16 – 4.79	$	3.13
Options exercised		—			(373	)	$	0.20 – 3.86	$	1.52
Options canceled		2,853			(2,853	)	$	0.26 – 16.00	$	7.03

Balances, December 31, 2012		2,872			12,016		$	0.20 – 16.00	$	5.37

On January 1, 2013, an additional 2.8 million shares were reserved under the 2010 Equity Incentive Plan and 0.6 million shares were reserved under the 2010 Outside Director Equity Incentive Plan.

The following table summarizes information with respect to stock options outstanding and exercisable under the plans at December 31, 2012 (dollars in thousands, except per share values):


	Options Outstanding						Options Exercisable
Exercise price	Number outstanding		Weighted average remaining contractual life (Years)		Weighted average exercise price		Number vested		Weighted average exercise price
$0.00 – 1.00		287,591		2.61	$	0.60		287,591	$	0.60
$1.01 – 1.70		1,171,115		9.87	$	1.18		—	$	—
$1.71 – 2.50		1,110,736		7.21	$	1.96		595,330	$	1.94
$2.51 – 3.00		331,458		5.43	$	2.53		316,299	$	2.52
$3.01 – 4.00		3,184,050		8.85	$	3.23		532,983	$	3.39
$4.01 – 6.00		2,099,204		8.71	$	4.93		295,177	$	5.64
$6.01 – 10.00		1,936,780		6.63	$	7.97		1,515,966	$	7.91
$10.01 – 16.00		1,894,809		7.91	$	12.59		983,230	$	12.54

		12,015,743			$	5.37		4,526,576	$	6.61

The aggregate intrinsic value of the outstanding and exercisable options presented in the table above totaled $0.9 million and $0.3 million, respectively. The aggregate intrinsic value represents the total pretax intrinsic value (i.e., the difference between $1.70, our closing stock price on the last trading day of our fourth quarter of 2012 and the exercise price, multiplied by the number of in-the-money options) that would have been received by the option holders had all option holders exercised their options on December 31, 2012. The amount changes based on the fair market value of the Company’s common stock. The weighted average remaining contractual life for exercisable options is 6.5 years.

The total intrinsic value of options exercised during the years ended December 31, 2012, 2011 and 2010 was $0.7 million, $11.0 million and $6.0 million, respectively.

Options Granted to Non-employees

During the years ended December 31, 2011 and 2010 we granted options to purchase 60,000 and 12,750 shares of common stock, respectively, to non-employees at exercise prices ranging from $3.30 to $13.50 per share.

Stock-based compensation expense will fluctuate as the estimated fair value of the common stock fluctuates over the vesting period. In connection with the grant of stock options to non-employees, we recognized stock-based compensation expense of $0.1 million, $0.2 million and $1.0 million, for the years ended December 31, 2012, 2011 and 2010, respectively.

Stock-based compensation expense related to stock options granted to non-employees is recognized as the stock options are earned. We believe that the estimated fair value of the stock options is more readily measurable than the fair value of the services rendered. The fair value of the stock options granted to non-employees is calculated at each reporting date using the Black-Scholes option pricing model.

Stock-based Compensation

Total stock-based compensation expense consists of the following (in thousands):


	Years Ended December 31,
	2012		2011		2010
Cost of revenue	$	506	$	490	$	—
Research and development		4,562		5,882		5,733
Sales, general and administrative		4,637		6,012		3,112

Total stock-based compensation expense	$	9,705	$	12,384	$	8,845

The tax benefit of stock-based compensation expense was immaterial for the fiscal years ended December 31, 2012, 2011 and 2010. The Black-Scholes option pricing model is used to estimate the fair value of stock options granted under the Company’s stock-based compensation plans and rights to acquire stock granted under the Company’s ESPP. The weighted average estimated fair values of the stock options and rights to acquire stock granted under the Company’s ESPP as well as the weighted average assumptions used in calculating these values during the years ended December 31, 2012, 2011 and 2010, were based on estimates at the date of grant as follows:


	Years ended December 31,
	2012			2011			2010
Stock Option Plans
Expected term (years)		6.1 years			6.1 years			6.0 years
Expected volatility		63.4	%		62.3	%		50.6	%
Risk-free interest rate		1.0	%		1.5	%		2.3	%
Dividend yield		0	%		0	%		0	%
Weighted average fair value at grant date	$	1.84		$	3.33		$	5.49
Total stock-based compensation expense (in thousands)	$	6,865		$	9,424		$	8,266

ESPP
Expected term range (years)		0.5 -2.0			0.5 -2.0			1.3
Expected volatility		90	%		73	%		55	%
Risk-free interest rate		0.2	%		0.2	%		0.3	%
Dividend yield		0	%		0	%		0	%
Weighted average fair value at grant date	$	1.38		$	3.54		$	6.34
Total stock-based compensation expense (in thousands)	$	2,840		$	2,960		$	579

Stock Option Plans — As of December 31, 2012 there was unrecognized compensation costs of $19.4 million related to these stock options. We expect to recognize those costs over a weighted-average period of 2.9 years as of December 31, 2012. Future option grants will increase the amount of compensation expense to be recorded in those future periods. Cash received from option exercises for the years ended December 31, 2012, 2011 and 2010 was $0.6 million, $4.3 million and $1.7 million, respectively.

Employee Stock Purchase Plan — For the years ended December 31, 2012 and 2011, 832,878 and 620,424 shares of common stock were purchased under the Plan, respectively. Cash received from ESPP for the years ended December 31, 2012 and 2011 was $2.1 million, and $3.4 million, respectively. No shares of common stock were purchased under the Plan in 2010.

Fair value of common stock granted prior to September 2010 — The fair values of the common stock underlying stock options granted through September 2010 were estimated by our board of directors, which intended all options granted to be exercisable at a price per share not less than the per share fair value of our common stock underlying those options on the date of grant. The fair value of the shares of common stock underlying the stock options has historically been the responsibility of and determined by our board of directors. Because there has been no public market for our common stock, our board of directors has determined fair value of the common stock at the time of grant of the option by considering a number of objective and subjective factors including independent third-party valuations of our common stock, sales of convertible preferred stock to unrelated third parties, operating and financial performance, the lack of liquidity of capital stock and general and industry specific economic outlook, amongst other factors. The fair value of the underlying common stock shall be determined by our board of directors until such time as our common stock is listed on an established stock exchange or national market system.

Our common stock became publicly listed upon our IPO at which time options granted are issued at a price equal to the closing price on the date of grant.

- Definition

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

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 505
-SubTopic 50
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6406099&loc=d3e25284-112666

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-Name Accounting Standards Codification
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Reference 3: http://www.xbrl.org/2003/role/presentationRef
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Reference 4: http://www.xbrl.org/2003/role/presentationRef
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Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 14

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

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

+ Details

Net Loss Per Share

12 Months Ended

Dec. 31, 2012

Net Loss Per Share [Abstract]

Net Loss Per Share

11. Net Loss Per Share

The following table presents the computation of basic and diluted net loss per share (in thousands, except per share values):


	Years Ended December 31,
	2012			2011			2010
Net loss per share:
Numerator
Net loss	$	(94,465	)	$	(109,388	)	$	(140,166	)

Denominator:
Weighted average shares of common stock outstanding		55,733			53,874			10,024
Less: Shares of common stock subject to repurchase		—			—			(86	)

Weighted average shares used in computation of basic and diluted net loss per share		55,733			53,874			9,938

Basic and diluted net loss per share	$	(1.69	)	$	(2.03	)	$	(14.10	)

The following options outstanding, common stock subject to repurchase, and warrants to purchase common stock were excluded from the computation of diluted net loss per share for the periods presented because the effect of including such shares would have been antidilutive in the periods presented:


	Years Ended December 31, (in thousands)
	2012		2011		2010
Options outstanding		12,016		10,522		9,813
Common Stock subject to repurchase		—		—		169
Warrants to purchase Common Stock		10		10		10

Segment and Geographic Information

12 Months Ended

Dec. 31, 2012

Segment and Geographic Information [Abstract]

Segment and Geographic Information

12. Segment and Geographic Information

The Company is organized as, and operates in, one reportable segment: the development, manufacturing and marketing of an integrated platform for genetic analysis. The Company’s chief operating decision-maker is its Chief Executive Officer. The Chief Executive Officer reviews financial information presented on a consolidated basis for purposes of evaluating financial performance and allocating resources, accompanied by information about revenue by geographic regions. The Company’s assets are primarily located in the United States of America and not allocated to any specific region and it does not measure the performance of its geographic regions based upon asset-based metrics. Therefore, geographic information is presented only for revenue. Revenue by geographic region is based on the ship to address on the customer order.

Revenue in 2012 from the United States of America, Europe and Asia (predominantly Japan) was $11.4 million, $6.6 million and $8.0 million, respectively, for a total of $26.0 million. Revenue in 2011 from the United States of America, Europe and Asia was $27.6 million, $5.1 million and $1.2 million, respectively, for a total of $33.9 million. Revenue for 2010 of $1.7 million was based in the United States of America.

- Definition

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

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
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-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8595-108599

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8380-108599

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-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
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-Section 50
-Paragraph 32
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-Name Accounting Standards Codification
-Topic 280
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-Name Accounting Standards Codification
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-Publisher FASB
-Name Accounting Standards Codification
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-Publisher FASB
-Name Accounting Standards Codification
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Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
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-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
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-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8924-108599

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 280
-SubTopic 10
-Section 50
-Paragraph 30
-URI http://asc.fasb.org/extlink&oid=6534315&loc=d3e8906-108599

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 131
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Restructuring

12 Months Ended

Dec. 31, 2012

Restructuring [Abstract]

Restructuring

13. Restructuring

During September 2011, we implemented a workforce reduction of approximately 130 employees, or 28% of our workforce. The actions taken were in consideration of uncertainties associated with the economic environment and to position the Company for long-term success. The costs associated with this restructuring consisted of termination benefits of approximately $4.9 million, of which $3.5 million is included in research and development expense and $1.4 million is included in sales, general and administrative expense for the year ended December 31, 2011.

A summary of the Company’s restructuring expense and accrued restructuring liability as of December 31, 2011 and December 31, 2012 is as follows (in thousands):


	Expense for Year Ended December 31, 2011		Balance January 1, 2011		Accrued		Paid			Balance December 31, 2011
Salaries and benefits	$	4,592	$	—	$	4,592	$	(4,426	)	$	166
Administrative		347		—		347		(347	)		—

Total Restructuring	$	4,939	$	—	$	4,939	$	(4,773	)	$	166

No additional restructuring expenses were recorded or accrued during the year ended December 31, 2012 and the accrued restructuring balance as of December 31, 2012 is zero, as all related amounts were settled or paid. With respect to our workforce reduction, we do not expect to incur further restructuring charges.

- Definition

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

+ References + Details

Subsequent Event

12 Months Ended

Dec. 31, 2012

Subsequent Event [Abstract]

Subsequent Event

14. Subsequent Event

On February 5, 2013, we entered into a Facility Agreement (the “Facility Agreement”) with entities affiliated with Deerfield Management Company, L.P. (collectively, “Deerfield”), pursuant to which Deerfield agreed to provide $20.5 million in funding to us (the “Facility”). Under the terms of the Facility Agreement, we issued to Deerfield promissory notes in the aggregate principal amount of $20.5 million (the “Notes”). The Notes bear simple interest at a rate of 8.75% per annum, payable quarterly in arrears commencing on April 1, 2013 and on the first business day of each January, April, July and October thereafter. We received net proceeds of $20.0 million, representing $20.5 million of gross proceeds, less a $500,000 facility fee, before deducting other expenses of the transaction.

The Facility has a maximum term of seven years from the date of the Facility Agreement. The Facility Agreement provides for an early repayment of principal in the event we have Net Sales (as defined in the Facility Agreement) of less than $41 million for the twelve-month period from the beginning of the second calendar quarter of 2014 through the first calendar quarter of 2015 (the “Milestone”). If the Milestone is not achieved, at Deerfield’s option, one-third of the original principal balance of the Facility will become due, on each of the third, fourth and fifth anniversaries of the date of the Facility Agreement.

From and after the date of the Facility Agreement, at the election of the holders of Notes representing a majority of the aggregate principal amount of the outstanding Notes, we shall apply 25% of the net proceeds from any financing that includes an equity component, including without limitation, the sale or issuance of our common stock (the “Common Stock”), options, warrants or other securities convertible or exchangeable for shares of Common Stock, to the payment of the Notes. This right is subject to certain exceptions set forth in the Facility Agreement, including that the right will not apply until we have issued 15,000,000 shares (as adjusted for any stock split or reverse stock split) of our Common Stock or rights to acquire our capital stock following the date of the Facility Agreement.

Deerfield has the option to require us to repay the Notes if we complete a Major Transaction (as defined in the Facility Agreement), including a change of control or a sale of all or substantially all of our assets. Additionally, the principal balance of the Facility may become immediately due and payable upon an “Event of Default,” as defined in the Facility Agreement, in which case Deerfield would have the right to require us to repay 100% of the principal amount of the loan, plus any accrued and unpaid interest thereon. The Facility Agreement does not provide for a prepayment of the Facility at our option.

The Facility Agreement also contains various representations and warranties, and affirmative and negative covenants, customary for financings of this type, including restrictions on the ability of the Company and its subsidiaries to incur additional indebtedness or liens on its assets, except as permitted under the Facility Agreement. In addition, we are required to maintain consolidated cash and cash equivalents on the last day of each calendar quarter of not less than $2.0 million. As security for our repayment of our obligations under the Facility Agreement, we granted to Deerfield a security interest in substantially all of our property and interests in property.

In connection with the execution of the Facility Agreement, on February 5, 2013, we issued to Deerfield warrants to purchase an aggregate of 5,500,000 shares of Common Stock immediately exercisable at an exercise price initially equal to $2.63 (the “Warrants”). The number of shares of Common Stock into which the Warrants are exercisable and the exercise price will be adjusted to reflect any stock splits, payment of stock dividends, recapitalizations, reclassifications or other similar adjustments in the number of outstanding shares of Common Stock. The exercise price may also be adjusted to reflect certain dividends or other distributions, including distributions of stock or other securities, property or options by way of a dividend, spin off, reclassification, corporate rearrangement, scheme of arrangement or similar transaction.

Summary of Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Summary of Significant Accounting Policies [Abstract]

Basis of Presentation and Consolidation

Basis of Presentation and Consolidation

Use of Estimates

Use of Estimates

Fair Value of Financial Instruments

Fair Value of Financial Instruments

•

Level 1: quoted prices in active markets for identical assets or liabilities;

•

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.

The following table sets forth the fair value of our financial assets that were measured on a recurring basis as of December 31, 2012 and 2011, respectively (in thousands):


	December 31, 2012						December 31, 2011
	Level 1		Level 2		Total		Level 1		Level 2		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	11,847	$	—	$	11,847	$	49,267	$	—	$	49,267
Commercial paper		—		34,693		34,693		—		9,598		9,598

Investments:
Commercial paper		—		28,866		28,866		—		29,772		29,772
Corporate debt securities		—		13,203		13,203		—		37,387		37,387
Asset backed securities		—		955		955		—		9,909		9,909
Certificates of deposit		—		2,008		2,008		—		4,034		4,034
U.S. government and agency securities		—		9,008		9,008		—		37,467		37,467

Total assets measured at fair value	$	11,847	$	88,733	$	100,580	$	49,267	$	128,167	$	177,434


	Fair Value
Due in one year or less	$	87,778
Due after one year through 3 years		955

Total investments in debt securities	$	88,733

Actual maturities may differ from contractual maturities because issuers may have the right to call or prepay obligations without call or prepayment penalties.

Cash and cash equivalents

Cash and cash equivalents

We consider all highly liquid investments purchased with an original maturity of three months or less to be cash equivalents.

Investments

Investments

Concentration of Credit Risk

Concentration of Credit Risk

Inventory

Inventory

Property and Equipment, Net

Property and Equipment, Net

Impairment of Long-Lived Assets

Impairment of Long-Lived Assets

Revenue Recognition

Revenue Recognition

Deferred revenue primarily represents product maintenance agreement revenue that is expected to be recognized over the related service period, generally one to three years.

Cost of Revenue

Cost of Revenue

Research and Development

Research and Development

Leases

Leases

Income Taxes

Income Taxes

Stock-based Compensation

Stock-based Compensation

We have employee and director stock option plans that are more fully described in Note 10.

Other Comprehensive Income (loss)

Other Comprehensive Income (loss)

Other comprehensive income (loss) is comprised of unrealized gains (losses) on our investment securities.

Recent Accounting Pronouncements

Recent Accounting Pronouncements

Summary of Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

Summary of Significant Accounting Policies [Abstract]

Summary of assets and liabilities measured at fair value classified based on level of input

The following table sets forth the fair value of our financial assets that were measured on a recurring basis as of December 31, 2012 and 2011, respectively (in thousands):


	December 31, 2012						December 31, 2011
	Level 1		Level 2		Total		Level 1		Level 2		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	11,847	$	—	$	11,847	$	49,267	$	—	$	49,267
Commercial paper		—		34,693		34,693		—		9,598		9,598

Investments:
Commercial paper		—		28,866		28,866		—		29,772		29,772
Corporate debt securities		—		13,203		13,203		—		37,387		37,387
Asset backed securities		—		955		955		—		9,909		9,909
Certificates of deposit		—		2,008		2,008		—		4,034		4,034
U.S. government and agency securities		—		9,008		9,008		—		37,467		37,467

Total assets measured at fair value	$	11,847	$	88,733	$	100,580	$	49,267	$	128,167	$	177,434

Estimated fair value of marketable debt securities


	Fair Value
Due in one year or less	$	87,778
Due after one year through 3 years		955

Total investments in debt securities	$	88,733

- Definition

Tabular disclosure related to assets and liabilities by class, including financial instruments measured at fair value that are classified in shareholders' equity, if any, that are measured at fair value on a recurring and/or nonrecurring basis in periods after initial recognition. Disclosures include, but are not limited to: (a) the fair value measurements recorded and the reasons for the measurements and (b) the level within the fair value hierarchy in which the fair value measurements are categorized in their entirety (levels 1, 2, 3) as well as transfers between levels 1 and 2.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=7578670&loc=d3e19279-110258

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

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 2C
-URI http://asc.fasb.org/extlink&oid=7578670&loc=SL7498348-110258

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 820
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=7578670&loc=d3e19190-110258

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 157
-Paragraph 32
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 157
-Paragraph 33
-Subparagraph a, b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 157
-Paragraph 6
-Footnote 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Investments (Tables)

12 Months Ended

Dec. 31, 2012

Investments [Abstract]

Summary of cash and cash equivalents and investments

The following table summarizes our investments as of December 31, 2012 and December 31, 2011 (in thousands):


	As of December 31, 2012
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	11,847	$	—	$	—		$	11,847
Commercial paper		34,690		3		—			34,693

Total cash and cash equivalents		46,537		3		—			46,540

Investments:
Commercial paper		28,859		7		—			28,866
Corporate debt securities		13,190		13		—			13,203
Asset backed securities		954		1		—			955
Certificates of deposit		2,005		3		—			2,008
U.S. government and agency securities		9,005		3		—			9,008

Total investments		54,013		27		—			54,040

Total cash, cash equivalents and investments	$	100,550	$	30	$	—		$	100,580


	As of December 31, 2011
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	49,267	$	—	$	—		$	49,267
Commercial paper		9,599		—		(1	)		9,598

Total cash and cash equivalents		58,866		—		(1	)		58,865

Investments:
Commercial paper		29,767		5		—			29,772
Corporate debt securities		37,379		65		(57	)		37,387
Asset backed securities		9,904		7		(2	)		9,909
Certificates of deposit		4,026		9		(1	)		4,034
U.S. government and agency securities		37,435		35		(3	)		37,467

Total investments		118,511		121		(63	)		118,569

Total cash, cash equivalents and investments	$	177,377	$	121	$	(64	)	$	177,434

Balance Sheet Components (Tables)

12 Months Ended

Dec. 31, 2012

Overview/Balance Sheet Components [Abstract]

Components of accounts receivable net

As of December 31, 2012 and 2011, our accounts receivable, net consisted of the following components (in thousands):


	December 31,
	2012		2011
Trade receivables	$	2,008	$	4,540
Related party receivables		814		17

Accounts receivable	$	2,822	$	4,557

Components of inventory

As of December 31, 2012 and 2011, our inventory, net consisted of the following components (in thousands):


	December 31,
	2012		2011
Purchased materials	$	3,823	$	5,273
Work in process		3,494		5,347
Finished goods		2,275		4,897

Inventory, net	$	9,592	$	15,517

Components of property and equipment, net

As of December 31, 2012 and 2011, our property and equipment, net consisted of the following components (in thousands):


	December 31,
	2012			2011
Building	$	1,160		$	1,160
Laboratory equipment and machinery		16,856			15,664
Leasehold improvements		8,035			7,636
Computer equipment		3,681			3,450
Software		4,457			1,577
Furniture and fixtures		854			859
Construction in progress		47			3,222

		35,090			33,568
Less: Accumulated depreciation		(20,761	)		(15,170	)

Property and equipment, net	$	14,329		$	18,398

Schedule of accrued expenses and other current liabilities

As of December 31, 2012 and 2011, our accrued expenses and other current liabilities consisted of the following (in thousands):


	December 31, 2012		December 31, 2011
Salaries and benefits	$	4,660	$	5,284
Professional services		1,093		1,915
Short-term portion of deferred rent		941		844
Customer deposits		685		1,503
Other		825		712

Accrued expenses and other current liabilities	$	8,204	$	10,258

Facility Financing and Debt Obligations (Tables)

12 Months Ended

Dec. 31, 2012

Facility Financing and Debt Obligations [Abstract]

Future minimum payments due under facility financing obligation

As of December 31, 2012, the future minimum payments due under the facility financing obligation were as follows (in thousands):


	Financing obligation
2013	$	629
2014		648
2015		667

Total payments		1,944
Less discounts and interest		(1,309	)

Total net payments under facility financing obligation		635
Property reverting to landlord		2,151

Present value of obligation		2,786
Less current portion of obligation		(173	)

Long-term portion of obligation	$	2,613

Commitments and Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

Commitments and Contingencies/Litigation Settlements [Abstract]

Schedule of minimum future lease payments receivable

As of December 31, 2012, the future annual minimum lease payments under all noncancelable operating leases with an initial term in excess of one year are as follows (in thousands):


Years ending December 31:	Amount
2013	$	3,789
2014		3,860
2015		3,850

Total minimum lease payments	$	11,499

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income Taxes [Abstract]

Reconciliation of Federal Income Tax Rate

A reconciliation between the statutory federal income tax and our effective tax rates as a percentage of loss before income taxes are as follows:


	Years Ended December 31,
	2012			2011			2010
Statutory tax rate		35.0	%		35.0	%		35.0	%
State tax rate, net of federal benefit		3.9			5.0			5.7
Stock-based compensation		(1.7	)		(2.0	)		(1.6	)
Federal R&D credit		0.0			2.8			2.0
CA R&D credit		1.1			2.3			1.1
Other		(2.1	)		0.0			(0.2	)
Change in valuation allowance		(36.2	)		(43.1	)		(43.5	)
Change of implied statutory tax rate to prior years		0.0			0.0			1.5

Effective income tax rate		0.0	%		0.0	%		0.0	%

Reconciliation of Deferred Tax Assets & Liabilities

Temporary differences and carryforwards that gave rise to significant portions of deferred taxes are as follows (in thousands):


	December 31,
	2012			2011
Deferred tax assets:
Net operating loss carryforwards	$	186,906		$	154,118
Research and development credits		18,883			17,814
Depreciation		2,736			2,708
Accruals and reserves		5,678			6,197

Total deferred tax assets		214,203			180,837
Less: Valuation allowance		(213,773	)		(180,810	)

Deferred tax liabilities:
Deferred Rent		(430	)		(27	)

Net deferred tax assets	$	—		$	—

Reconciliation of unrecognized tax benefit accounts

A reconciliation of the beginning and ending unrecognized tax benefit accounts is as follows (in thousands):


Balance as of December 31, 2009	$	3,937
Increase in balance related to tax positions taken in prior year		198
Increase in balance related to tax positions taken during current year		2,222

Balance as of December 31, 2010		6,357
Increase in balance related to tax positions taken in prior year		832
Increase in balance related to tax positions taken during current year		2,098

Balance as of December 31, 2011		9,287
Increase in balance related to tax positions taken in prior year		—
Increase in balance related to tax positions taken during current year		705

Balance as of December 31, 2012	$	9,992

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2012

Share Based Compensation [Abstract]

Summary of Stock Option Activity

The following table summarizes stock option activity for all stock option plans for the year ended December 31, 2012 (in thousands, except per share amounts):


				Common Stock Options Outstanding
	Shares available for grant			Number of shares			Exercise price		Weighted average exercise price
Balances, December 31, 2011		1,441			10,522		$	0.20 – 16.00	$	6.69

Additional shares reserved		3,298
Options granted		(4,720	)		4,720		$	1.16 – 4.79	$	3.13
Options exercised		—			(373	)	$	0.20 – 3.86	$	1.52
Options canceled		2,853			(2,853	)	$	0.26 – 16.00	$	7.03

Balances, December 31, 2012		2,872			12,016		$	0.20 – 16.00	$	5.37

Reconciliation of Outstanding and Exercisable Stock Options

The following table summarizes information with respect to stock options outstanding and exercisable under the plans at December 31, 2012 (dollars in thousands, except per share values):


	Options Outstanding						Options Exercisable
Exercise price	Number outstanding		Weighted average remaining contractual life (Years)		Weighted average exercise price		Number vested		Weighted average exercise price
$0.00 – 1.00		287,591		2.61	$	0.60		287,591	$	0.60
$1.01 – 1.70		1,171,115		9.87	$	1.18		—	$	—
$1.71 – 2.50		1,110,736		7.21	$	1.96		595,330	$	1.94
$2.51 – 3.00		331,458		5.43	$	2.53		316,299	$	2.52
$3.01 – 4.00		3,184,050		8.85	$	3.23		532,983	$	3.39
$4.01 – 6.00		2,099,204		8.71	$	4.93		295,177	$	5.64
$6.01 – 10.00		1,936,780		6.63	$	7.97		1,515,966	$	7.91
$10.01 – 16.00		1,894,809		7.91	$	12.59		983,230	$	12.54

		12,015,743			$	5.37		4,526,576	$	6.61

Schedule of Stock-Based Compensation Expense

Total stock-based compensation expense consists of the following (in thousands):


	Years Ended December 31,
	2012		2011		2010
Cost of revenue	$	506	$	490	$	—
Research and development		4,562		5,882		5,733
Sales, general and administrative		4,637		6,012		3,112

Total stock-based compensation expense	$	9,705	$	12,384	$	8,845

Schedule of Fair Value of Employee Stock Options

The weighted average estimated fair values of the stock options and rights to acquire stock granted under the Company’s ESPP as well as the weighted average assumptions used in calculating these values during the years ended December 31, 2012, 2011 and 2010, were based on estimates at the date of grant as follows:


	Years ended December 31,
	2012			2011			2010
Stock Option Plans
Expected term (years)		6.1 years			6.1 years			6.0 years
Expected volatility		63.4	%		62.3	%		50.6	%
Risk-free interest rate		1.0	%		1.5	%		2.3	%
Dividend yield		0	%		0	%		0	%
Weighted average fair value at grant date	$	1.84		$	3.33		$	5.49
Total stock-based compensation expense (in thousands)	$	6,865		$	9,424		$	8,266

ESPP
Expected term range (years)		0.5 -2.0			0.5 -2.0			1.3
Expected volatility		90	%		73	%		55	%
Risk-free interest rate		0.2	%		0.2	%		0.3	%
Dividend yield		0	%		0	%		0	%
Weighted average fair value at grant date	$	1.38		$	3.54		$	6.34
Total stock-based compensation expense (in thousands)	$	2,840		$	2,960		$	579

Net Loss Per Share (Tables)

12 Months Ended

Dec. 31, 2012

Net Loss Per Share [Abstract]

Computation of basic and diluted net loss per share

The following table presents the computation of basic and diluted net loss per share (in thousands, except per share values):


	Years Ended December 31,
	2012			2011			2010
Net loss per share:
Numerator
Net loss	$	(94,465	)	$	(109,388	)	$	(140,166	)

Denominator:
Weighted average shares of common stock outstanding		55,733			53,874			10,024
Less: Shares of common stock subject to repurchase		—			—			(86	)

Weighted average shares used in computation of basic and diluted net loss per share		55,733			53,874			9,938

Basic and diluted net loss per share	$	(1.69	)	$	(2.03	)	$	(14.10	)

Anti-dilutive excluded from computation of diluted net loss per share


	Years Ended December 31, (in thousands)
	2012		2011		2010
Options outstanding		12,016		10,522		9,813
Common Stock subject to repurchase		—		—		169
Warrants to purchase Common Stock		10		10		10

Restructuring (Tables)

12 Months Ended

Dec. 31, 2012

Restructuring [Abstract]

Summary of the Company's restructuring expense and accrued restructuring liability

A summary of the Company’s restructuring expense and accrued restructuring liability as of December 31, 2011 and December 31, 2012 is as follows (in thousands):


	Expense for Year Ended December 31, 2011		Balance January 1, 2011		Accrued		Paid			Balance December 31, 2011
Salaries and benefits	$	4,592	$	—	$	4,592	$	(4,426	)	$	166
Administrative		347		—		347		(347	)		—

Total Restructuring	$	4,939	$	—	$	4,939	$	(4,773	)	$	166

Summary of Significant Accounting Policies (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Assets
Total assets measured at fair value	$ 100,580	$ 177,434
Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total assets measured at fair value	11,847	49,267
Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total assets measured at fair value	34,693	9,598
Investments [Member] \| Commercial paper [Member]
Assets
Total assets measured at fair value	28,866	29,772
Investments [Member] \| Corporate debt securities [Member]
Assets
Total assets measured at fair value	13,203	37,387
Investments [Member] \| Asset backed securities [Member]
Assets
Total assets measured at fair value	955	9,909
Investments [Member] \| Certificates of deposit [Member]
Assets
Total assets measured at fair value	2,008	4,034
Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total assets measured at fair value	9,008	37,467
Level 1 [Member]
Assets
Total assets measured at fair value	11,847	49,267
Level 1 [Member] \| Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total assets measured at fair value	11,847	49,267
Level 2 [Member]
Assets
Total assets measured at fair value	88,733	128,167
Level 2 [Member] \| Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total assets measured at fair value	34,693	9,598
Level 2 [Member] \| Investments [Member] \| Commercial paper [Member]
Assets
Total assets measured at fair value	28,866	29,772
Level 2 [Member] \| Investments [Member] \| Corporate debt securities [Member]
Assets
Total assets measured at fair value	13,203	37,387
Level 2 [Member] \| Investments [Member] \| Asset backed securities [Member]
Assets
Total assets measured at fair value	955	9,909
Level 2 [Member] \| Investments [Member] \| Certificates of deposit [Member]
Assets
Total assets measured at fair value	2,008	4,034
Level 2 [Member] \| Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total assets measured at fair value	$ 9,008	$ 37,467

Summary of Significant Accounting Policies (Details 1) $ in Thousands	Dec. 31, 2012 USD ($)
Estimated fair value of marketable debt securities
Due in one year or less	$ 87,778
Due after one year through 3 years	955
Total investments in debt securities	$ 88,733

- Definition

Amount of debt securities categorized neither as held-to-maturity nor trading.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 25
-Paragraph 1
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=7534914&loc=d3e22054-111558

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 45
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6871852&loc=d3e26610-111562

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-Subparagraph (b)-(g)
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 12
-Subparagraph b
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 13
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 137
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS115-1/124-1
-Paragraph 15C
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 16
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 133
-Paragraph 22
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS115-1/124-1
-Paragraph 15D
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Summary of Significant Accounting Policies (Details Textual) - Customer	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Summary of Significant Accounting Policies (Textual) [Abstract]
Accounts receivable percentage from domestic customers	95.00%	62.00%
Net accounts receivable from customers, Description	As of December 31, 2012, approximately 78% of our net accounts receivable were from 3 individual customers, each representing at least 10% of our net accounts receivable	As of December 31, 2011, approximately 85% of our net accounts receivable were from 5 individual customers, each representing at least 10% of our net accounts receivable
Net accounts receivable percentage from individual customers	78.00%	85.00%
Minimum percentage of net accounts receivable from each customer	10.00%	10.00%
Number of individual customers	3	5
Product maintenance agreement service period, Minimum	1 year
Product maintenance agreement service period, Maximum	3 years
Lab equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	3 years
Building [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	30 years
Minimum [Member] \| Computer equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	2 years
Minimum [Member] \| Software [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	3 years
Minimum [Member] \| Furniture and fixtures [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	3 years
Maximum [Member] \| Computer equipment [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	3 years
Maximum [Member] \| Software [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	5 years
Maximum [Member] \| Furniture and fixtures [Member]
Property, Plant and Equipment [Line Items]
Property and equipment estimated useful life	7 years

Investments (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Summary of cash and cash equivalents and investments
Amortized Cost	$ 100,550	$ 177,377
Gross unrealized gains	30	121
Gross unrealized losses		(64)
Fair Value	100,580	177,434
Cash and cash equivalents [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	46,537	58,866
Gross unrealized gains	3
Gross unrealized losses		(1)
Fair Value	46,540	58,865
Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	11,847	49,267
Gross unrealized losses
Fair Value	11,847	49,267
Cash and cash equivalents [Member] \| Commercial paper [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	34,690	9,599
Gross unrealized gains	3
Gross unrealized losses		(1)
Fair Value	34,693	9,598
Investments [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	54,013	118,511
Gross unrealized gains	27	121
Gross unrealized losses		(63)
Fair Value	54,040	118,569
Investments [Member] \| Commercial Paper [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	28,859	29,767
Gross unrealized gains	7	5
Gross unrealized losses
Fair Value	28,866	29,772
Investments [Member] \| Corporate debt securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	13,190	37,379
Gross unrealized gains	13	65
Gross unrealized losses		(57)
Fair Value	13,203	37,387
Investments [Member] \| Asset backed securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	954	9,904
Gross unrealized gains	1	7
Gross unrealized losses		(2)
Fair Value	955	9,909
Investments [Member] \| Certificates of deposit [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	2,005	4,026
Gross unrealized gains	3	9
Gross unrealized losses		(1)
Fair Value	2,008	4,034
Investments [Member] \| U.S. government and agency securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	9,005	37,435
Gross unrealized gains	3	35
Gross unrealized losses		(3)
Fair Value	$ 9,008	$ 37,467

Balance Sheet Components (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Components of accounts receivable net
Trade receivables	$ 2,008	$ 4,540
Related party receivables	814	17
Accounts receivable	$ 2,822	$ 4,557

- Definition

Amount of receivables arising from transactions with related parties due within one year or the normal operating cycle, if longer.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.3(a)(2))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 850
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6457730&loc=d3e39603-107864

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.4-08.(k)(1))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 850
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (d)
-URI http://asc.fasb.org/extlink&oid=6457730&loc=d3e39549-107864

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 850
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6457730&loc=d3e39622-107864

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph k
-Subparagraph 1
-Article 4

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 57
-Paragraph 2
-Subparagraph d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 3
-Subparagraph a
-Article 5

+ Details

Balance Sheet Components (Details 1) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Components of inventory
Purchased materials	$ 3,823	$ 5,273
Work in process	3,494	5,347
Finished goods	2,275	4,897
Inventory, net	$ 9,592	$ 15,517

Balance Sheet Components (Details 2) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Components of property and equipment, net
Capitalized costs of software	$ 35,090	$ 33,568
Less: Accumulated depreciation	(20,761)	(15,170)
Property and equipment, net	14,329	18,398
Building [Member]
Components of property and equipment, net
Capitalized costs of software	1,160	1,160
Laboratory equipment and machinery [Member]
Components of property and equipment, net
Capitalized costs of software	16,856	15,664
Leasehold improvements [Member]
Components of property and equipment, net
Capitalized costs of software	8,035	7,636
Computer equipment [Member]
Components of property and equipment, net
Capitalized costs of software	3,681	3,450
Software [Member]
Components of property and equipment, net
Capitalized costs of software	4,457	1,577
Furniture and fixtures [Member]
Components of property and equipment, net
Capitalized costs of software	854	859
Construction in progress [Member]
Components of property and equipment, net
Capitalized costs of software	$ 47	$ 3,222

Balance Sheet Components (Details 3) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Schedule of accrued expenses and other current liabilities
Salaries and benefits	$ 4,660	$ 5,284
Professional services	1,093	1,915
Short-term portion of deferred rent	941	844
Customer deposits	685	1,503
Other	825	712
Accrued expenses and other current liabilities	$ 8,204	$ 10,258

- Definition

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

+ References + Details

- Definition

Carrying value as of the balance sheet date of obligations incurred through that date and payable for contractual rent under lease arrangements. Used to reflect the current portion of the liabilities (due within one year or within the normal operating cycle if longer).

+ References + Details

Balance Sheet Components (Details Textual) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Property, Plant and Equipment [Line Items]
Capitalized costs of software	$ 35,090	$ 33,568
Balance Sheet Components (Textual) [Abstract]
Depreciation Expense	6,649	5,803	$ 5,160
Software [Member]
Property, Plant and Equipment [Line Items]
Capitalized costs of software	$ 4,457	$ 1,577
Minimum [Member] \| Software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful life	3 years
Maximum [Member] \| Software [Member]
Property, Plant and Equipment [Line Items]
Estimated useful life	5 years

Facility Financing and Debt Obligations (Details) $ in Thousands	Dec. 31, 2012 USD ($)
Future minimum payments due under the facility financing obligation
2013	$ 629
2014	648
2015	667
Total payments	1,944
Less discounts and interest	(1,309)
Total net payments under facility financing obligation	635
Property reverting to landlord	2,151
Present value of obligation	2,786
Less current portion of obligation	(173)
Long-term portion of obligation	$ 2,613

Facility Financing and Debt Obligations (Details Textual) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011
Facility Financing and Debt Obligations (Textual) [Abstract]
Tenant improvement allowance	$ 1.8
Building and leasehold improvement assets	3.0
Fair value of the facility prior to commencing renovations	1.2
Landlord incentives within property and equipment, net	$ 1.8
Implied interest rate	9.00%
Interest expense	$ 0.3	$ 0.3

Commitments and Contingencies (Details) $ in Thousands	Dec. 31, 2012 USD ($)
Schedule of minimum future lease payments receivable
2013	$ 3,789
2014	3,860
2015	3,850
Total minimum lease payments	$ 11,499

Commitments and Contingencies (Details Textual) - USD ($) $ in Millions	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Commitments and Contingencies (Textual) [Abstract]
Rent expense	$ 2.4	$ 2.8	$ 2.1
Other commitments estimated amount	7.9
License and maintenance fees	$ 0.2	$ 0.3	$ 0.2

Litigation Settlements (Details) $ in Millions	3 Months Ended	6 Months Ended
Litigation Settlements (Details) $ in Millions	Mar. 31, 2012 USD ($)	Jun. 30, 2012 USD ($)	Apr. 30, 2012 Entity
Litigation Settlements (Additional Textual) [Abstract]
Selling, general and administrative expenses \| $	$ 1.8	$ 1.8
Helicos Biosciences Corporation [Member]
Litigation Settlements (Textual) [Abstract]
Number of patents owned			2
Helicos Arizona Science and Technology Enterprises LLC [Member]
Litigation Settlements (Textual) [Abstract]
Number of patents owned			2

Income Taxes (Details)	12 Months Ended
Income Taxes (Details)	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Reconciliation of Federal Income Tax Rate
Statutory tax rate	35.00%	35.00%	35.00%
State tax rate, net of federal benefit	3.90%	5.00%	5.70%
Stock-based compensation	(1.70%)	(2.00%)	(1.60%)
Federal R&D credit	0.00%	2.80%	2.00%
CA R&D credit	1.10%	2.30%	1.10%
Other	(2.10%)	0.00%	(0.20%)
Change in valuation allowance	(36.20%)	(43.10%)	(43.50%)
Change of implied statutory tax rate to prior years	0.00%	0.00%	1.50%
Effective income tax rate	0.00%	0.00%	0.00%

Income Taxes (Details 1) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Deferred tax assets:
Net operating loss carryforwards	$ 186,906	$ 154,118
Research and development credits	18,883	17,814
Depreciation	2,736	2,708
Accruals and reserves	5,678	6,197
Total deferred tax assets	214,203	180,837
Less: Valuation allowance	(213,773)	(180,810)
Deferred tax liabilities:
Deferred Rent	(430)	(27)
Net deferred tax assets	$ 0	$ 0

Income Taxes (Details 2) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details 2) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Reconciliation of unrecognized tax benefit accounts
Unrecognized Tax Benefits, Beginning Balance	$ 9,287	$ 6,357	$ 3,937
Increase in balance related to tax positions taken in prior year		832	198
Increase in balance related to tax positions taken during current year	705	2,098	2,222
Unrecognized Tax Benefits, Ending Balance	$ 9,992,000	$ 9,287	$ 6,357

Income Taxes (Details Textual) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details Textual) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Dec. 31, 2009
Income Taxes (Textual) [Abstract]
Expiration of federal net operating loss carryforward	2024
Expiration of state net operating loss carryforward	2014
Expiration of federal research and development credits	2024
Total unrecognized tax benefit	$ 9,992,000	$ 9,287	$ 6,357	$ 3,937
Period of increase or decrease total amount of unrecognized income tax benefits	next 12 months
Benefit of the federal net operating loss deferred tax assets	$ 3,300
Benefit of state net operating loss deferred tax assets	500
Increase in Valuation allowance	213,773	180,810
Accrued interest or penalties	0	$ 0
Domestic Tax Authority [Member]
Income Taxes (Additional Textual) [Abstract]
Federal net operating loss carryforwards	476,400
California state research and development credit carryforwards	15,300
State and Local Jurisdiction [Member]
Income Taxes (Additional Textual) [Abstract]
Federal net operating loss carryforwards	434,900
California state research and development credit carryforwards	$ 18,000

Stockholders' Equity (Details Textual) - USD ($) $ / shares in Units, $ in Thousands	1 Months Ended	12 Months Ended
	Apr. 30, 2012	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Oct. 05, 2012
Stockholders Equity (Additional Textual) [Abstract]
Common stock offering price Cantor shares		$ 645,372	$ 632,961
Stockholders' Equity (Textual) [Abstract]
Common Stock, par value		$ 0.001	$ 0.001	$ 0.001
Common Stock, shares authorized		1,000,000	1,000,000	1,000,000,000
Convertible Preferred Stock, shares authorized		50,000	50,000	50,000,000
Preferred stock shares par value		$ 0.001	$ 0.001	$ 0.001
Preferred stock issued
Preferred stock outstanding
Voting right of common stock share holders		1 vote
Common stock, warrants or debt securities	$ 150,000
Commission to Cantor		3.00%
Shares issued		3,900,000
Proceeds from issuance of common stock		$ 2,705	$ 7,743	$ 212,519
Cantor [Member]
Stockholders Equity (Additional Textual) [Abstract]
Common stock offering price Cantor shares					$ 30,000
legal expenses incurred by Cantor		$ 50,000

Stock-Based Compensation (Details) - $ / shares	12 Months Ended
Stock-Based Compensation (Details) - $ / shares	Dec. 31, 2012	Dec. 31, 2011
Reconciliation of Outstanding and Exercisable Stock Options
Beginning balances, Shares available for grant	1,441
Additional shares reserved, Shares available for grant	3,298
Options granted, Shares available for grant	(4,720)
Options cancelled, Shares available for grant	2,853
Ending balances, Shares available for grant	2,872	1,441
Beginning balances, Number of shares	10,522
Options granted, Number of shares	4,720
Options exercised, Number of shares	(373)
Options cancelled, Number of shares	(2,853)
Ending balances, Number of shares	12,016	10,522
Beginning balances, Weighted average exercise price per share	$ 6.69
Options granted, Weighted average exercise price per share	3.13
Options exercised, Weighted average exercise price per share	1.52
Options cancelled, Weighted average exercise price per share	7.03
Ending balances, Weighted average exercise price per share	5.37	$ 6.69
0.20 - 16.00 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	0.20	0.20
Exercise price, upper range	16.00	$ 16.00
1.16 - 4.79 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	1.16
Exercise price, upper range	4.79
0.20 - 3.86 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	0.20
Exercise price, upper range	3.86
0.26 - 16.00 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	0.26
Exercise price, upper range	$ 16.00

Stock-Based Compensation (Details 1) shares in Thousands	12 Months Ended
Stock-Based Compensation (Details 1) shares in Thousands	Dec. 31, 2012 $ / shares shares
Reconciliation of Outstanding and Exercisable Stock Options
Number outstanding \| shares	12,015,743
Weighted average exercise price	$ 5.37
Number vested \| shares	4,526,576
Weighted average exercise price, vested	$ 6.61
Exercise Price Range One [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	0.00
Exercise price, upper range	$ 1.00
Number outstanding \| shares	287,591
Weighted average remaining contractual life	2 years 7 months 10 days
Weighted average exercise price	$ 0.60
Number vested \| shares	287,591
Weighted average exercise price, vested	$ 0.60
Exercise Price Range Two [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	1.01
Exercise price, upper range	$ 1.70
Number outstanding \| shares	1,171,115
Weighted average remaining contractual life	9 years 10 months 13 days
Weighted average exercise price	$ 1.18
Exercise Price Range Three [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	1.71
Exercise price, upper range	$ 2.50
Number outstanding \| shares	1,110,736
Weighted average remaining contractual life	7 years 2 months 16 days
Weighted average exercise price	$ 1.96
Number vested \| shares	595,330
Weighted average exercise price, vested	$ 1.94
Exercise Price Range Four [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	2.51
Exercise price, upper range	$ 3.00
Number outstanding \| shares	331,458
Weighted average remaining contractual life	5 years 5 months 5 days
Weighted average exercise price	$ 2.53
Number vested \| shares	316,299
Weighted average exercise price, vested	$ 2.52
Exercise Price Range Five [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	3.01
Exercise price, upper range	$ 4.00
Number outstanding \| shares	3,184,050
Weighted average remaining contractual life	8 years 10 months 6 days
Weighted average exercise price	$ 3.23
Number vested \| shares	532,983
Weighted average exercise price, vested	$ 3.39
Exercise Price Range Six [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	4.01
Exercise price, upper range	$ 6.00
Number outstanding \| shares	2,099,204
Weighted average remaining contractual life	8 years 8 months 16 days
Weighted average exercise price	$ 4.93
Number vested \| shares	295,177
Weighted average exercise price, vested	$ 5.64
Exercise Price Range Seven [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	6.01
Exercise price, upper range	$ 10.00
Number outstanding \| shares	1,936,780
Weighted average remaining contractual life	6 years 7 months 17 days
Weighted average exercise price	$ 7.97
Number vested \| shares	1,515,966
Weighted average exercise price, vested	$ 7.91
Exercise Price Range Eight [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	10.01
Exercise price, upper range	$ 16.00
Number outstanding \| shares	1,894,809
Weighted average remaining contractual life	7 years 10 months 28 days
Weighted average exercise price	$ 12.59
Number vested \| shares	983,230
Weighted average exercise price, vested	$ 12.54

Stock-Based Compensation (Details 2) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	$ 9,705	$ 12,384	$ 9,690
Cost of revenue [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	506	490
Research and development [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	4,562	5,882	5,733
Sales, General and Administrative Expenses [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	$ 4,637	$ 6,012	$ 3,112

Stock-Based Compensation (Details 3) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Schedule of Fair Value of Employee Stock Options
Total stock-based compensation expense (in thousand)	$ 9,705	$ 12,384	$ 9,690
ESPP [Member]
Schedule of Fair Value of Employee Stock Options
Expected term in years			1 year 3 months 18 days
Expected volatility	90.00%	73.00%	55.00%
Risk-free interest rate	0.20%	0.20%	0.30%
Dividend yield	0.00%	0.00%	0.00%
Weighted-average fair value at grant date	$ 1.38	$ 3.54	$ 6.34
Total stock-based compensation expense (in thousand)	$ 2,840	$ 2,960	$ 579
Minimum [Member] \| ESPP [Member]
Schedule of Fair Value of Employee Stock Options
Expected term in years	6 months	6 months
Maximum [Member] \| ESPP [Member]
Schedule of Fair Value of Employee Stock Options
Expected term in years	2 years	2 years
Stock Options [Member]
Schedule of Fair Value of Employee Stock Options
Expected term in years	6 years 1 month 6 days	6 years 1 month 6 days	6 years
Expected volatility	63.40%	62.30%	50.60%
Risk-free interest rate	1.00%	1.50%	2.30%
Dividend yield	0.00%	0.00%	0.00%
Weighted-average fair value at grant date	$ 1.84	$ 3.33	$ 5.49
Total stock-based compensation expense (in thousand)	$ 6,865	$ 9,424	$ 8,266

Stock-Based Compensation (Details Textual) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2012 USD ($) PurchasePeriod CompensationPlan $ / shares shares	Dec. 31, 2011 USD ($) $ / shares shares	Dec. 31, 2010 USD ($) shares	Jan. 31, 2013 shares
Stock Option Plans (Additional Textual) [Abstract]
Common stock were purchased \| shares	1,000,000	1,000,000	1,000,000,000
Stock Option Plans (Textual) [Abstract]
Percentage of fair market value at which stock can be purchased	85.00%
Purchase period of ESPP	6 months
Number of purchase periods \| PurchasePeriod	4
Number of equity compensation plans \| CompensationPlan	3
Aggregate intrinsic value	$ 1,700
Aggregate intrinsic value exercisable options	300
Total intrinsic value of options exercised	700	$ 11,000	$ 6,000
Aggregate intrinsic value outstanding	900
Unrecognized compensation costs	$ 19,400
Weighted average remaining contractual life	2 years 10 months 24 days
Options granted to non-employees	$ 100	$ 200	1,000
Weighted-average grant date fair value \| $ / shares	$ 3.13
Weighted average remaining contractual life for exercisable	6 years 6 months
Options Granted to Non-employees \| shares	60,000	12,750
Stock Option Plans [Member]
Stock Option Plans (Additional Textual) [Abstract]
Cash received from option exercises	$ 600	$ 4,300	$ 1,700
2010 Equity Incentive Plan[Member]
Stock Option Plans (Additional Textual) [Abstract]
Common stock reserved for issuance \| shares	6,500,000			2,800,000
Stock options granted	10 years
Stock Options Vest in period percentage	25.00%
Stock Options Vest in period	4 years
2010 Outside Director Equity Incentive Plan[Member]
Stock Option Plans (Additional Textual) [Abstract]
Common stock reserved for issuance \| shares	1,000,000			600,000
Stock options granted	10 years
Stock Options Vest in period percentage	33.00%
Employee Stock Purchase Plan [Member]
Stock Option Plans (Additional Textual) [Abstract]
Shares issued under the ESPP \| shares	400,000
Cash received from ESPP	$ 2,100	$ 3,400
Common stock were purchased \| shares	832,878	620,424	0
Minimum [Member] \| 2010 Outside Director Equity Incentive Plan[Member]
Stock Option Plans (Additional Textual) [Abstract]
Stock Options Vest in period	1 year
Maximum [Member] \| 2010 Outside Director Equity Incentive Plan[Member]
Stock Option Plans (Additional Textual) [Abstract]
Stock Options Vest in period	3 years
Non Employees [Member]
Stock Option Plans (Additional Textual) [Abstract]
Exercise price, upper range \| $ / shares		$ 13.50
Exercise price options to non employees \| $ / shares	$ 3.30

Net Loss Per Share (Details) - USD ($) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Numerator
Net loss	$ (94,465)	$ (109,388)	$ (140,166)
Denominator:
Weighted average shares of common stock outstanding	55,733,000	53,874,000	10,024,000
Less: Shares of common stock subject to repurchase			(86,000)
Weighted average shares used in computation of basic and diluted net loss per share	55,733	53,874	9,938
Basic and diluted net loss per share	$ (1.69)	$ (2.03)	$ (14.10)

- Definition

The portion of profit or loss for the period, net of income taxes, which is attributable to the parent.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Net Income
-URI http://asc.fasb.org/extlink&oid=6518256

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
-SubTopic 10
-Section 45
-Paragraph 28
-URI http://asc.fasb.org/extlink&oid=6943989&loc=d3e3602-108585

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.19)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 225
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SX 210.5-03.18)
-URI http://asc.fasb.org/extlink&oid=6880815&loc=d3e20235-122688

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 944
-SubTopic 225
-Section S99
-Paragraph 1
-Subparagraph (SX 210.7-04.22)
-URI http://asc.fasb.org/extlink&oid=6879464&loc=d3e573970-122913

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Other Comprehensive Income
-URI http://asc.fasb.org/extlink&oid=6519514

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 220
-SubTopic 10
-Section 45
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=20435746&loc=d3e565-108580

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph d
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 130
-Paragraph 10, 15
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 11: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph A7
-Appendix A

Reference 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 87-21
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 03
-Paragraph 19
-Article 5

Reference 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 51
-Paragraph 38
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 15: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 95
-Paragraph 28, 29, 30
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 16: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Paragraph 20
-Article 9

+ Details

- Definition

This element represents the weighted average total number of shares issued throughout the period including the first (beginning balance outstanding) and last (ending balance outstanding) day of the period before considering any reductions (for instance, shares held in treasury) to arrive at the weighted average number of shares outstanding. Weighted average relates to the portion of time within a reporting period that common shares have been issued and outstanding to the total time in that period. Such concept is used in determining the weighted average number of shares outstanding for purposes of calculating earnings per share (basic).

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 10
-URI http://asc.fasb.org/extlink&oid=7655603&loc=d3e1448-109256

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 45
-Paragraph 13
-URI http://asc.fasb.org/extlink&oid=7655603&loc=d3e2646-109256

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 10
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 40
-Subparagraph a
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Net Loss Per Share (Details 1) - shares shares in Thousands	12 Months Ended
Net Loss Per Share (Details 1) - shares shares in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Options outstanding [Member]
Anti-dilutive excluded from computation of diluted net loss per share
Stock excluded from the computation of diluted net loss per share	12,016	10,522	9,813
Common Stock subject to repurchase[Member]
Anti-dilutive excluded from computation of diluted net loss per share
Stock excluded from the computation of diluted net loss per share			169
Warrants to purchase common stock [Member]
Anti-dilutive excluded from computation of diluted net loss per share
Stock excluded from the computation of diluted net loss per share	10	10	10

- Definition

Securities (including those issuable pursuant to contingent stock agreements) that could potentially dilute basic earnings per share (EPS) or earnings per unit (EPU) in the future that were not included in the computation of diluted EPS or EPU because to do so would increase EPS or EPU amounts or decrease loss per share or unit amounts for the period presented.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Antidilution
-URI http://asc.fasb.org/extlink&oid=6505113

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Diluted Earnings Per Share
-URI http://asc.fasb.org/extlink&oid=6510752

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Glossary Contingent Stock Agreement
-URI http://asc.fasb.org/extlink&oid=6508534

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 260
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (c)
-URI http://asc.fasb.org/extlink&oid=6371337&loc=d3e3550-109257

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 40
-Subparagraph c
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 13, 14
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 07-4
-Paragraph 4
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 128
-Paragraph 171
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Segment and Geographic Information (Details Textual) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Segment and Geographic Information (Textual) [Abstract]
Revenue	$ 25,983	$ 33,863	$ 1,674
USA [Member]
Segment and Geographic Information (Textual) [Abstract]
Revenue	11,400	27,600	$ 1,700
Europe [Member]
Segment and Geographic Information (Textual) [Abstract]
Revenue	6,600	5,100
Asia [Member]
Segment and Geographic Information (Textual) [Abstract]
Revenue	$ 8,000	$ 1,200

Restructuring (Details) $ in Thousands	12 Months Ended
Restructuring (Details) $ in Thousands	Dec. 31, 2011 USD ($)
Summary of the Company's restructuring expense and accrued restructuring liability
Expense for Year Ended December 31, 2011	$ 4,939
Balance January 1, 2011
Accrued	4,939
Paid	(4,773)
Balance December 31, 2011	166
Salaries and Benefits [Member]
Summary of the Company's restructuring expense and accrued restructuring liability
Expense for Year Ended December 31, 2011	4,592
Balance January 1, 2011
Accrued	4,592
Paid	(4,426)
Balance December 31, 2011	166
Administrative [Member]
Summary of the Company's restructuring expense and accrued restructuring liability
Expense for Year Ended December 31, 2011	347
Balance January 1, 2011
Accrued	347
Paid	$ (347)

Restructuring (Details Textual) $ in Millions	1 Months Ended	12 Months Ended
Restructuring (Details Textual) $ in Millions	Sep. 30, 2011 Person	Dec. 31, 2012 USD ($)	Dec. 31, 2011 USD ($)
Restructuring (Additional Textual) [Abstract]
Restructuring consist of termination benefits		$ 4.9	$ 4.9
Accrued		0.0	0.0
Restructuring (Textual) [Abstract]
Workforce Reduction Number of Employees \| Person	130
Workforce Reduction, Percentage	28.00%
Research and development [Member]
Restructuring (Additional Textual) [Abstract]
Restructuring consist of termination benefits		3.5	3.5
Sales, General and Administrative Expenses [Member]
Restructuring (Additional Textual) [Abstract]
Restructuring consist of termination benefits		$ 1.4	$ 1.4

- Definition

Amount of any reversal and other adjustment made during the period to the amount of a previously accrued liability for a specified type of restructuring cost, excluding adjustments for costs incurred during the period, costs settled during the period, and foreign currency translation adjustments.

+ References + Details

- Definition

The charge against earnings in the period for known and estimated costs of termination benefits provided to current employees that are involuntarily terminated under a benefit arrangement associated with exit from or disposal of business activities or restructurings pursuant to a duly authorized plan, excluding costs or losses pertaining to an entity newly acquired in a business combination or a discontinued operation as defined by generally accepted accounting principles and costs associated with one-time termination benefits.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section 50
-Paragraph 1
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6394359&loc=d3e17939-110869

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 5.P.4(b))
-URI http://asc.fasb.org/extlink&oid=6394695&loc=d3e140904-122747

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 715
-SubTopic 20
-Section 50
-Paragraph 1
-Subparagraph (a)(10)
-URI http://asc.fasb.org/extlink&oid=21915506&loc=d3e1928-114920

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 420
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SAB TOPIC 5.P.3)
-URI http://asc.fasb.org/extlink&oid=6394695&loc=d3e140864-122747

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 230
-SubTopic 10
-Section 45
-Paragraph 28
-Subparagraph (b)
-URI http://asc.fasb.org/extlink&oid=6943989&loc=d3e3602-108585

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5-8
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Staff Accounting Bulletin (SAB)
-Number Topic 5
-Section P
-Subsection 3, 4

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 146
-Paragraph 8-13, 20
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS146-1
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 112
-Paragraph 7
-LegacyDoc This reference is SUPERSEDED by the Accounting Standards Codification effective for interim and annual periods ending after September 15, 2009. This reference is included to help users transition from the previous accounting hierarchy and will be removed from future versions of this taxonomy.

+ Details

Subsequent Event (Details) - Subsequent Event [Member]	12 Months Ended
Subsequent Event (Details) - Subsequent Event [Member]	Dec. 31, 2012 USD ($) shares	Feb. 05, 2013 USD ($) $ / EPU shares
Subsequent Event (Textual) [Abstract]
Facility Agreement period	7 years
Principal Early Repayments Maximum Requirement of Net Sales Amount	$ 41,000,000
Due amount of Facility principal balance	33.00%
Facility Due Dates	on each of the third, fourth and fifth anniversaries of the date of the Facility Agreement
Facility agreement exercisable limit \| shares	15,000,000
Percentage of net proceeds from out side financing or equity component	25.00%
Cash and cash equivalent minimum amount quarterly required	$ 2,000,000
Purchase shares of Common Stock \| shares		5,500,000
Common stock aggregate exercise price \| $ / EPU		2.63
Percentage of principal amount repaid	100.00%
Deerfield Promissory Notes [Member]
Subsequent Event (Textual) [Abstract]
Deerfield promissory notes aggregate principal amount		$ 20,500,000
Deerfield promissory notes simple interest	8.75%
facility fee	$ 500,000
Net proceeds of payable quarterly arrears	$ 20,000,000