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Document and Entity Information - shares	3 Months Ended
Document and Entity Information - shares	Mar. 31, 2013	Apr. 30, 2013
Document and Entity Information [Abstract]
Entity Registrant Name	PACIFIC BIOSCIENCES OF CALIFORNIA, INC.
Entity Central Index Key	0001299130
Document Type	10-Q
Document Period End Date	Mar. 31, 2013
Amendment Flag	false
Document Fiscal Year Focus	2013
Document Fiscal Period Focus	Q1
Current Fiscal Year End Date	--12-31
Entity Filer Category	Accelerated Filer
Entity Common Stock, Shares Outstanding		60,823,575

Condensed Consolidated Balance Sheets (Unaudited) - USD ($) $ in Thousands	Mar. 31, 2013	Dec. 31, 2012
Current assets
Cash and cash equivalents	$ 53,038	$ 46,540
Investments	59,267	54,040
Accounts receivable	2,009	2,822
Inventory, net	10,597	9,592
Prepaid expenses and other current assets	1,570	2,006
Total current assets	126,481	115,000
Property and equipment, net	12,779	14,329
Other long-term assets	514	354
Total assets	139,774	129,683
Current liabilities
Accounts payable	3,011	2,988
Accrued expenses and other current liabilities	7,425	8,204
Deferred revenue, current	2,961	3,378
Facility financing obligation, current	182	173
Total current liabilities	13,579	14,743
Deferred revenue, non-current	794	800
Deferred rent and other long-term liabilities	1,895	2,145
Notes payable, non-current	12,851
Financing derivative	999
Facility financing obligation, non-current	2,565	2,613
Total liabilities	32,683	20,301
Stockholders' equity
Convertible Preferred Stock, $0.001 par value: Authorized 50,000 shares; No shares issued or outstanding at March 31, 2013 and December 31, 2012
Common Stock and additional paid-in-capital, $0.001 par value: Authorized 1,000,000 shares; Issued and outstanding 60,824 shares at March 31, 2013 and 56,170 shares at December 31, 2012	664,204	645,372
Accumulated other comprehensive income	11	30
Accumulated deficit	(557,124)	(536,020)
Total stockholders' equity	107,091	109,382
Total liabilities and stockholders' equity	$ 139,774	$ 129,683

Condensed Consolidated Balance Sheets (Parenthetical) (Unaudited) - $ / shares	Mar. 31, 2013	Dec. 31, 2012
Condensed 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	60,824	56,170
Common Stock, shares outstanding	60,824	56,170

Condensed Consolidated Statements of Operations and Comprehensive Loss (Unaudited) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Revenue:
Product revenue	$ 3,833	$ 8,715
Service and other revenue	1,475	1,053
Grant revenue	270	270
Total revenue	5,578	10,038
Cost of Revenue:
Cost of product revenue	3,200	8,607
Cost of service and other revenue	1,448	1,583
Total cost of revenue	4,648	10,190
Gross profit (loss)	930	(152)
Operating Expense:
Research and development	11,983	12,073
Sales, general and administrative	9,554	15,285
Total operating expense	21,537	27,358
Operating loss	(20,607)	(27,510)
Other income (expense), net	(497)	(70)
Net loss	(21,104)	(27,580)
Other comprehensive income (loss):
Unrealized gain (loss) on investments	(19)	78
Comprehensive loss	$ (21,123)	$ (27,502)
Net loss per share:
Basic and diluted net loss per share	$ (0.37)	$ (0.50)
Shares used in computing basic and diluted net loss per share	57,372	55,201

Condensed Consolidated Statements of Cash Flows (Unaudited) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Cash flows from operating activities
Net loss	$ (21,104)	$ (27,580)
Adjustments to reconcile net loss to net cash used in operating activities
Depreciation	1,493	1,629
Stock-based compensation	2,746	2,187
Other items	121	53
Changes in assets and liabilities
Accounts receivable	813	3,052
Inventory	(607)	3,094
Prepaid expenses and other assets	431	245
Accounts payable	22	(492)
Accrued expenses and other current liabilities	(779)	1,220
Deferred revenue	(423)	(489)
Lease incentives and other long-term liabilities	(288)	(257)
Net cash used in operating activities	(17,575)	(17,338)
Cash flows from investing activities
Purchase of property and equipment	(297)	(274)
Purchase of investments	(42,466)	(20,137)
Sales of investments		3,500
Maturities of investments	37,180	29,889
Net cash provided by (used in) investing activities	(5,583)	12,978
Cash flows from financing activities
Proceeds from issuance of common stock, net of issuance costs	9,890	1,755
Proceeds from issuance of debt facility, net of issuance costs	19,766
Net cash provided by financing activities	29,656	1,755
Net increase (decrease) in cash and cash equivalents	6,498	(2,605)
Cash and cash equivalents at beginning of period	46,540	58,865
Cash and cash equivalents at end of period	53,038	56,260
Supplemental disclosure of non-cash investing and financing activities
Inventory transferred to (from) property and equipment	$ (398)	$ 602

Overview

3 Months Ended

Mar. 31, 2013

Overview/Balance Sheet Components [Abstract]

Overview

1. Overview

Pacific Biosciences of California, Inc., (“Pacific Biosciences”, the “Company”, “we”, “us”) has commercialized the PacBio RS High Resolution Genetic Analyzer and the recently launched the PacBio RS II Sequencing System to help scientists solve genetically complex problems. Based on our novel Single Molecule, Real-Time (SMRT) technology, our products enable scientists to increase their understanding of biological systems through targeted sequencing and insight into genetic variations.

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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-Publisher AICPA
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-Number 94-6
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+ Details

Summary of Significant Accounting Policies

3 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies [Abstract]

Summary of Significant Accounting Policies

2. Summary of Significant Accounting Policies

Basis of Presentation

In the opinion of management, the accompanying unaudited Condensed Consolidated Financial Statements (“financial statements”) of Pacific Biosciences of California, Inc. and its wholly-owned subsidiaries have been prepared on a consistent basis with the December 31, 2012 audited Consolidated Financial Statements and include all adjustments, consisting of only normal recurring adjustments, necessary to fairly state the information set forth herein. Certain prior year amounts in the financial statements and notes thereto have been reclassified to conform to the current year’s presentation. The financial statements have been prepared in accordance with the rules and regulations of the Securities and Exchange Commission (“SEC”), and, therefore, omit certain information and footnote disclosures necessary to present the statements in accordance with U.S. generally accepted accounting principles (“GAAP”). These financial statements should be read in conjunction with the audited Consolidated Financial Statements and Notes thereto included in the Company’s Annual Report on Form 10-K for the fiscal year ended December 31, 2012, which was filed on March 15, 2013. The results of operations for the first three months of fiscal 2013 are not necessarily indicative of the results to be expected for the entire fiscal year or any future periods.

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

Assets and Liabilities measured at fair value on a recurring basis

The following table sets forth the fair value of our financial assets and liabilities that were measured on a recurring basis as of March 31, 2013 and December 31, 2012, respectively:


(in thousands)	March 31, 2013								December 31, 2012
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	17,995	$	—	$	—	$	17,995	$	11,847	$	—	$	—	$	11,847
Commercial paper		—		35,043		—		35,043		—		34,693		—		34,693

Total cash and cash equivalents		17,995		35,043		—		53,038		11,847		34,693		—		46,540

Investments:
Commercial paper		—		45,919		—		45,919		—		28,866		—		28,866
Corporate debt securities		—		8,230		—		8,230		—		13,203		—		13,203
Asset backed securities		—		615		—		615		—		955		—		955
Certificates of deposits		—		—		—		—		—		2,008		—		2,008
U.S. government and agency securities		—		4,503		—		4,503		—		9,008		—		9,008

Total investments		—		59,267		—		59,267		—		54,040		—		54,040

Total assets measured at fair value	$	17,995	$	94,310	$	—	$	112,305	$	11,847	$	88,733	$	—	$	100,580

Liabilities
Financing derivative	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

Total liabilities measured at fair value	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

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.

During the three month periods ended March 31, 2013 and 2012, realized gains and losses on the sale of investments were immaterial and there were no impairments of our investments.

The fair value of the Financing Derivative resulting from the debt facility entered into during the first quarter of 2013 was determined using Level 3 inputs, or significant unobservable inputs. Refer to Note 7. Debt Facility for the detailed description and valuation approach. The following table provides the changes in the fair value of the Financial Derivative during the quarter ended March 31, 2013 (in thousands):


Financial Derivative	Amount
Balance as of December 31, 2012	$	—
Value at issuance		(967	)
Loss on change in fair value of Financing Derivative		(32	)

Balance as of March 31, 2013	$	(999	)

For the three-month period ended March 31, 2013 there were no assets or liabilities transferred between Level 1, Level 2, Level 3 reported at fair value on a recurring basis and valuation techniques did not change compared to the prior quarter.

Financial Assets and Liabilities not measured at fair value on a recurring basis

The carrying amount of our 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. The carrying value of the Deerfield notes is believed to approximate fair value as there have been no significant changes to the underlying assumptions or forecasted future cash flows since the notes were issued on February 5, 2013. Refer to Note 7. Debt Facility for the detailed description and valuation approach.

Net Loss Per Share

The following table presents the computation of basic and diluted net loss per share:


	Three-Months Ended March 31,
(in thousands, except per share amounts)	2013			2012
Net loss per share
Numerator:
Net loss	$	(21,104	)	$	(27,580	)

Denominator:
Weighted average shares of common stock outstanding - basic and diluted		57,372			55,201

Basic and diluted net loss per share	$	(0.37	)	$	(0.50	)

The following were excluded from the computation of diluted net loss per share for the periods presented because including them would have had an anti-dilutive effect:


	As of March 31,
(in thousands)	2013		2012
Options outstanding		13,741		12,457
Warrants to purchase common stock		5,504		10

Recent Accounting Pronouncements

Effective January 1, 2013 we adopted the accounting guidance which requires an entity to provide information about amounts reclassified out of accumulated other comprehensive income by component. The amounts were not material to our financial statements in the periods presented.

Cash, Cash Equivalents and Investments

3 Months Ended

Mar. 31, 2013

Cash, Cash Equivalents and Investments [Abstract]

Cash, Cash Equivalents and Investments

3. Cash, Cash Equivalents and Investments

The following table summarizes our investments as of March 31, 2013 and December 31, 2012 (in thousands):


	As of March 31, 2013
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	17,995	$	—	$	—		$	17,995
Commercial paper		35,041		2		—			35,043

Total cash and cash equivalents		53,036		2		—			53,038

Investments:
Commercial paper		45,915		6		(2	)		45,919
Corporate debt securities		8,228		3		(1	)		8,230
Asset backed securities		615		—		—			615
U.S. government and agency securities		4,501		2		—			4,503

Total investments		59,259		11		(3	)		59,267

Total cash, cash equivalents and investments	$	112,295	$	13	$	(3	)	$	112,305


	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

The estimated fair value of marketable debt securities (corporate debt securities, asset backed securities, U.S. government and agency securities, and commercial paper) as of March 31, 2013, by contractual maturity, are as follows:


(in thousands)	Fair Value
Due in one year or less	$	93,695
Due after one year through 3 years		615

Total investments in debt securities	$	94,310

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

Balance Sheet Components

3 Months Ended

Mar. 31, 2013

Overview/Balance Sheet Components [Abstract]

Balance Sheet Components

4. Balance Sheet Components

As of March 31, 2013 and December 31, 2012 our inventory, net, consisted of the following components:


(in thousands)	March 31, 2013		December 31, 2012
Purchased materials, net	$	3,250	$	3,823
Work in process, net		6,773		3,494
Finished goods, net		574		2,275

Inventory, net	$	10,597	$	9,592

As of March 31, 2013 and December 31, 2012, our accrued expenses and other current liabilities consisted of the following:


(in thousands)	March 31, 2013		December 31, 2012
Salaries and benefits	$	3,426	$	4,660
Legal and professional services		1,696		1,093
Customer deposits		48		685
Short-term portion of deferred rent		964		941
Other		1,291		825

Accrued expenses and other current liabilities	$	7,425	$	8,204

Contingencies

3 Months Ended

Mar. 31, 2013

Contingencies [Abstract]

Contingencies

5. 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 March 31, 2013, 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. After an October 11, 2012 hearing, the District Court on April 15, 2013 granted the defendants’ motion to dismiss the amended complaint. The District Court’s order granted the plaintiffs leave to amend within sixty days of the date of the order.

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. After considering the relevant case law and the potential hurdles to successfully proceeding with the Burlingame action, the plaintiff agreed to dismiss the litigation in its entirety. Accordingly, by stipulation of the parties, the Burlingame action was voluntarily dismissed without prejudice on April 11, 2013, which dismissal was ordered by the District Court on April 12, 2013.

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 above, 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, as amended and restated. 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 IPO 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 terms of these indemnification agreements are 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 March 31, 2013.

- Definition

The entire disclosure for loss and gain contingencies. Describes any existing condition, situation, or set of circumstances involving uncertainty as of the balance sheet date (or prior to issuance of the financial statements) as to a probable or reasonably possible loss incurred by an entity that will ultimately be resolved when one or more future events occur or fail to occur, and typically discloses the amount of loss recorded or a range of possible loss, or an assertion that no reasonable estimate can be made.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 6
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Reference 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Interpretation (FIN)
-Number 14
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Reference 11: 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

3 Months Ended

Mar. 31, 2013

Litigation Settlements [Abstract]

Litigation Settlements

6. 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 us 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. We 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 minimus. 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.

Debt Facility

3 Months Ended

Mar. 31, 2013

Debt Facility [Abstract]

Debt Facility

7. Debt Facility

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 Agreement has a maximum term of seven years from inception; however provides for the early repayment of principal in the event we have net sales (as defined in the Facility Agreement) of less than $41.0 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, options, warrants or other securities convertible or exchangeable for shares of our 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 15.0 million 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. As of March 31, 2013, approximately 3.9 million shares of common stock have been sold through our “at-the-market” offering program.

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 Notes 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.

Financing Derivative

A number of features embedded in the Notes to the Facility Agreement required accounting for as a derivative, including the indemnification of certain withholding taxes and the acceleration of debt upon (a) a qualified financing, (b) an Event of Default, (c) a Major Transaction, and (d) the exercise of the Warrant via offset to debt principal. These features represent a single derivative (the “Financing Derivative”) that was bifurcated from the debt instrument and accounted for as a liability at fair value, with changes in fair value between reporting periods recorded in other income (expense), net. The fair value of the Financing Derivative on February 5, 2013 and March 31, 2013, was $1.0 million.

The value of the Financing Derivative was determined by comparing the difference between the fair value of the Notes with and without the Financing Derivative by calculating the respective present values from future cash flows using a 20.8% weighted average market yield.

Warrants

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 per share 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.

The Warrants are classified within additional paid in capital and reported at their grant date fair value on February 5, 2013, of $6.4 million. The fair value of the Warrants was estimated using the Black-Scholes model using the following assumptions:


Expected term	7 years
Expected volatility	50	%
Risk-free interest rate	1.4	%
Dividend yield	—

Notes

The Notes and Warrants were initially recorded at a value of $14.1 million and $6.4 million, respectively, based upon the relative fair value allocation of the $20.5 million proceeds. Additionally, facility fees and other issuance costs were allocated based on the relative fair value of the Facility and the Warrants. The amount allocated to the Notes was then reduced by the $1.0 million fair value of the Financing Derivative, such that the Financing Derivative was recorded at its absolute fair value. As a result, the carrying value of the Notes at the inception of the debt was $12.8 million resulting in an original issue discount of $7.7 million. The discount will be accreted to the $20.5 million face value of the Notes over the expected maturity period of seven years using the effective interest method, with an effective interest rate of 20.6%.

The following amounts comprise expenses related to the facility included in other income (expense), net for the quarter ended March 31, 2013 (in thousands):


Cash interest expense at 8.75%	$	(270	)
Non-cash amortization of Original Issue Discount		(87	)
Amortization of debt issuance costs		(2	)

Interest Expense					(359	)
Loss on financing derivative					(32	)

Other income (expense), net				$	(391	)

- Definition

The entire disclosure for information about short-term and long-term debt arrangements, which includes amounts of borrowings under each line of credit, note payable, commercial paper issue, bonds indenture, debenture issue, own-share lending arrangements and any other contractual agreement to repay funds, and about the underlying arrangements, rationale for a classification as long-term, including repayment terms, interest rates, collateral provided, restrictions on use of assets and activities, whether or not in compliance with debt covenants, and other matters important to users of the financial statements, such as the effects of refinancing and noncompliance with debt covenants.

+ References + Details

Stockholders' Equity

3 Months Ended

Mar. 31, 2013

Stockholders' Equity [Abstract]

Stockholders' Equity

8. Stockholders’ Equity

Stock Offering

During 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 $150.0 million of our common stock, warrants or debt securities. On May 1, 2012, the registration statement was declared effective by the SEC, which allows 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 pay Cantor a commission equal to 3.0% 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. We commenced selling shares on February 7, 2013 and as of March 31, 2013, we have sold 3.9 million shares of our common stock, resulting in net proceeds of $8.7 million. The shares were issued at an average price of $2.34 per share of common stock.

- 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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-Name Accounting Standards Codification
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-URI http://asc.fasb.org/extlink&oid=6228006&loc=d3e74512-122707

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Reference 11: http://www.xbrl.org/2003/role/presentationRef
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-Name Accounting Standards Codification
-Glossary Preferred Stock
-URI http://asc.fasb.org/extlink&oid=6521494

Reference 12: http://www.xbrl.org/2003/role/presentationRef
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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
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 5
-Paragraph 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 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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-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 29, 30, 31
-Article 5

Reference 19: http://www.xbrl.org/2003/role/presentationRef
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-Name Staff Accounting Bulletin (SAB)
-Number Topic 4
-Section E

Reference 20: http://www.xbrl.org/2003/role/presentationRef
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-Name Regulation S-X (SX)
-Number 210
-Section 08
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Reference 21: http://www.xbrl.org/2003/role/presentationRef
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Reference 22: 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 23: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 04
-Article 3

+ Details

Stock Option Plans

3 Months Ended

Mar. 31, 2013

Stock Option Plans [Abstract]

Stock Option Plans

9. Stock Option Plans

As of March 31, 2013, 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 (the “ESPP”).

As of March 31, 2013, 786,255 shares of our common stock remain reserved for issuance under our ESPP. Our ESPP permits eligible employees to purchase common stock at a discount through payroll deductions during defined offering periods. Each offering period generally consists of four purchase periods, each purchase period being 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. Shares issued under the ESPP totaled 733,111 and 428,604 shares during the three-month periods ended March 31, 2013 and 2012, respectively. We estimate the value of the employee stock purchase rights on the grant date using the Black-Scholes option pricing model.

The following table summarizes stock option activity for all stock option plans (in thousands, except per share amounts):


	Shares available for grant			Common Stock Options Outstanding
	Shares available for grant			Number of shares			Exercise price		Weighted average exercise price
Balances, December 31, 2012		2,872			12,016		$	0.20 – 16.00	$	5.37
Additional shares reserved		3,370
Options granted		(1,840	)		1,840			2.18 – 2.78		2.23
Options exercised		—			(1	)		2.52 – 2.52		2.52
Options canceled		114			(114	)		1.16 – 16.00		5.56

Balances, March 31, 2013		4,516			13,741		$	0.20 – 16.00	$	4.95

Stock-based Compensation

Total stock-based compensation expense for employee stock options and stock purchases under the ESPP, consists of the following (in thousands):


	Three-Month Periods Ended March 31,
	2013		2012
Cost of revenue	$	136	$	166
Research and development		1,217		1,133
Sales, general and administrative		1,393		888

Total stock-based compensation expense	$	2,746	$	2,187

We estimated the fair value of employee stock options using the Black-Scholes option pricing model. The fair value of employee stock options is being amortized on a straight-line basis over the requisite service period of the awards.

The fair values of the common stock underlying stock options granted through the date of our IPO, 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 was no public market for our common stock, our board of directors 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 was determined by our board of directors until such time as our common stock was publicly traded. Our common stock became publicly listed upon our IPO from which time options granted are issued with an exercise price equal to the closing price on the date of grant.

The fair value of employee stock options was estimated using the following weighted average assumptions:


	Three-Month Periods Ended March 31,
	2013			2012
Expected term		6.1 years			6.1 years
Expected volatility		65	%		65	%
Risk-free interest rate		1.1	%		1.1	%
Dividend yield		—			—

Expected term — Expected term represents the period that our stock-based awards are expected to be outstanding. Our assumptions about the expected term have been on our historic cancellation and exercise experience and trends as well as our expectations for future periods.

Expected volatility — 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 terms of the options.

Risk-free interest rate — The risk-free interest rate is based on the U.S. Treasury yield curve in effect at the time of grant for zero coupon U.S. Treasury notes with maturities approximately equal to the option’s expected term.

Expected dividend yield — We have never paid dividends and do not expect to pay dividends in the foreseeable future.

Expected forfeiture rate —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.

- 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

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 40
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6418621&loc=d3e17540-113929

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-Name Accounting Standards Codification
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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

Summary of Significant Accounting Policies (Policies)

3 Months Ended

Mar. 31, 2013

Summary of Significant Accounting Policies [Abstract]

Basis of Presentation

Basis of Presentation

Use of Estimates

Use of Estimates

Fair Value of Financial Instruments

Fair Value of Financial Instruments

Assets and Liabilities measured at fair value on a recurring basis

The following table sets forth the fair value of our financial assets and liabilities that were measured on a recurring basis as of March 31, 2013 and December 31, 2012, respectively:


(in thousands)	March 31, 2013								December 31, 2012
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	17,995	$	—	$	—	$	17,995	$	11,847	$	—	$	—	$	11,847
Commercial paper		—		35,043		—		35,043		—		34,693		—		34,693

Total cash and cash equivalents		17,995		35,043		—		53,038		11,847		34,693		—		46,540

Investments:
Commercial paper		—		45,919		—		45,919		—		28,866		—		28,866
Corporate debt securities		—		8,230		—		8,230		—		13,203		—		13,203
Asset backed securities		—		615		—		615		—		955		—		955
Certificates of deposits		—		—		—		—		—		2,008		—		2,008
U.S. government and agency securities		—		4,503		—		4,503		—		9,008		—		9,008

Total investments		—		59,267		—		59,267		—		54,040		—		54,040

Total assets measured at fair value	$	17,995	$	94,310	$	—	$	112,305	$	11,847	$	88,733	$	—	$	100,580

Liabilities
Financing derivative	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

Total liabilities measured at fair value	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

Net Loss Per Share

Net Loss Per Share

The following table presents the computation of basic and diluted net loss per share:


	Three-Months Ended March 31,
(in thousands, except per share amounts)	2013			2012
Net loss per share
Numerator:
Net loss	$	(21,104	)	$	(27,580	)

Denominator:
Weighted average shares of common stock outstanding - basic and diluted		57,372			55,201

Basic and diluted net loss per share	$	(0.37	)	$	(0.50	)

The following were excluded from the computation of diluted net loss per share for the periods presented because including them would have had an anti-dilutive effect:


	As of March 31,
(in thousands)	2013		2012
Options outstanding		13,741		12,457
Warrants to purchase common stock		5,504		10

Recent Accounting Pronouncements

Recent Accounting Pronouncements

- Definition

Disclosure of accounting policy for computing basic and diluted earnings or loss per share for each class of common stock and participating security. Addresses all significant policy factors, including any antidilutive items that have been excluded from the computation and takes into account stock dividends, splits and reverse splits that occur after the balance sheet date of the latest reporting period but before the issuance of the financial statements.

+ References + Details

Summary of Significant Accounting Policies (Tables)

3 Months Ended

Mar. 31, 2013

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 and liabilities that were measured on a recurring basis as of March 31, 2013 and December 31, 2012, respectively:


(in thousands)	March 31, 2013								December 31, 2012
	Level 1		Level 2		Level 3		Total		Level 1		Level 2		Level 3		Total
Assets
Cash and cash equivalents:
Cash and money market funds	$	17,995	$	—	$	—	$	17,995	$	11,847	$	—	$	—	$	11,847
Commercial paper		—		35,043		—		35,043		—		34,693		—		34,693

Total cash and cash equivalents		17,995		35,043		—		53,038		11,847		34,693		—		46,540

Investments:
Commercial paper		—		45,919		—		45,919		—		28,866		—		28,866
Corporate debt securities		—		8,230		—		8,230		—		13,203		—		13,203
Asset backed securities		—		615		—		615		—		955		—		955
Certificates of deposits		—		—		—		—		—		2,008		—		2,008
U.S. government and agency securities		—		4,503		—		4,503		—		9,008		—		9,008

Total investments		—		59,267		—		59,267		—		54,040		—		54,040

Total assets measured at fair value	$	17,995	$	94,310	$	—	$	112,305	$	11,847	$	88,733	$	—	$	100,580

Liabilities
Financing derivative	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

Total liabilities measured at fair value	$	—	$	—	$	999	$	999	$	—	$	—	$	—	$	—

Changes in the fair value of the Financial Derivative

The following table provides the changes in the fair value of the Financial Derivative during the quarter ended March 31, 2013 (in thousands):


Financial Derivative	Amount
Balance as of December 31, 2012	$	—
Value at issuance		(967	)
Loss on change in fair value of Financing Derivative		(32	)

Balance as of March 31, 2013	$	(999	)

Computation of basic and diluted net loss per share

The following table presents the computation of basic and diluted net loss per share:


	Three-Months Ended March 31,
(in thousands, except per share amounts)	2013			2012
Net loss per share
Numerator:
Net loss	$	(21,104	)	$	(27,580	)

Denominator:
Weighted average shares of common stock outstanding - basic and diluted		57,372			55,201

Basic and diluted net loss per share	$	(0.37	)	$	(0.50	)

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

The following were excluded from the computation of diluted net loss per share for the periods presented because including them would have had an anti-dilutive effect:


	As of March 31,
(in thousands)	2013		2012
Options outstanding		13,741		12,457
Warrants to purchase common stock		5,504		10

- 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

Cash, Cash Equivalents and Investments (Tables)

3 Months Ended

Mar. 31, 2013

Cash, Cash Equivalents and Investments [Abstract]

Summary of cash and cash equivalents and investments

The following table summarizes our investments as of March 31, 2013 and December 31, 2012 (in thousands):


	As of March 31, 2013
	Amortized Cost		Gross unrealized gains		Gross unrealized losses			Fair Value
Cash and cash equivalents:
Cash and money market funds	$	17,995	$	—	$	—		$	17,995
Commercial paper		35,041		2		—			35,043

Total cash and cash equivalents		53,036		2		—			53,038

Investments:
Commercial paper		45,915		6		(2	)		45,919
Corporate debt securities		8,228		3		(1	)		8,230
Asset backed securities		615		—		—			615
U.S. government and agency securities		4,501		2		—			4,503

Total investments		59,259		11		(3	)		59,267

Total cash, cash equivalents and investments	$	112,295	$	13	$	(3	)	$	112,305


	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

Estimated fair value of marketable debt securities


(in thousands)	Fair Value
Due in one year or less	$	93,695
Due after one year through 3 years		615

Total investments in debt securities	$	94,310

Balance Sheet Components (Tables)

3 Months Ended

Mar. 31, 2013

Overview/Balance Sheet Components [Abstract]

Components of inventory

As of March 31, 2013 and December 31, 2012 our inventory, net, consisted of the following components:


(in thousands)	March 31, 2013		December 31, 2012
Purchased materials, net	$	3,250	$	3,823
Work in process, net		6,773		3,494
Finished goods, net		574		2,275

Inventory, net	$	10,597	$	9,592

Schedule of accrued expenses and other current liabilities

As of March 31, 2013 and December 31, 2012, our accrued expenses and other current liabilities consisted of the following:


(in thousands)	March 31, 2013		December 31, 2012
Salaries and benefits	$	3,426	$	4,660
Legal and professional services		1,696		1,093
Customer deposits		48		685
Short-term portion of deferred rent		964		941
Other		1,291		825

Accrued expenses and other current liabilities	$	7,425	$	8,204

Debt Facility (Tables)

3 Months Ended

Mar. 31, 2013

Debt Facility [Abstract]

Fair value of warrants

The fair value of the Warrants was estimated using the Black-Scholes model using the following assumptions:


Expected term	7 years
Expected volatility	50	%
Risk-free interest rate	1.4	%
Dividend yield	—

Components of expenses related to the facility included in other income (expense), net

The following amounts comprise expenses related to the facility included in other income (expense), net for the quarter ended March 31, 2013 (in thousands):


Cash interest expense at 8.75%	$	(270	)
Non-cash amortization of Original Issue Discount		(87	)
Amortization of debt issuance costs		(2	)

Interest Expense					(359	)
Loss on financing derivative					(32	)

Other income (expense), net				$	(391	)

Stock Option Plans (Tables)

3 Months Ended

Mar. 31, 2013

Stock Option Plans [Abstract]

Summary of Stock Option Activity

The following table summarizes stock option activity for all stock option plans (in thousands, except per share amounts):


	Shares available for grant			Common Stock Options Outstanding
	Shares available for grant			Number of shares			Exercise price		Weighted average exercise price
Balances, December 31, 2012		2,872			12,016		$	0.20 – 16.00	$	5.37
Additional shares reserved		3,370
Options granted		(1,840	)		1,840			2.18 – 2.78		2.23
Options exercised		—			(1	)		2.52 – 2.52		2.52
Options canceled		114			(114	)		1.16 – 16.00		5.56

Balances, March 31, 2013		4,516			13,741		$	0.20 – 16.00	$	4.95

Schedule of Stock-Based Compensation Expense

Total stock-based compensation expense for employee stock options and stock purchases under the ESPP, consists of the following (in thousands):


	Three-Month Periods Ended March 31,
	2013		2012
Cost of revenue	$	136	$	166
Research and development		1,217		1,133
Sales, general and administrative		1,393		888

Total stock-based compensation expense	$	2,746	$	2,187

Schedule of Fair Value of Employee Stock Options

The fair value of employee stock options was estimated using the following weighted average assumptions:


	Three-Month Periods Ended March 31,
	2013			2012
Expected term		6.1 years			6.1 years
Expected volatility		65	%		65	%
Risk-free interest rate		1.1	%		1.1	%
Dividend yield		—			—

Summary of Significant Accounting Policies (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Dec. 31, 2012
Assets
Total assets measured at fair value	$ 112,305	$ 100,580
Liabilities
Total liabilities measured at fair value	999
Financing derivative [Member]
Liabilities
Total liabilities measured at fair value	999
Cash and cash equivalents [Member]
Assets
Total cash and cash equivalents	53,038	46,540
Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total cash and cash equivalents	17,995	11,847
Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total cash and cash equivalents	35,043	34,693
Investments [Member]
Assets
Total investments	59,267	54,040
Investments [Member] \| Commercial paper [Member]
Assets
Total investments	45,919	28,866
Investments [Member] \| Corporate debt securities [Member]
Assets
Total investments	8,230	13,203
Investments [Member] \| Asset backed securities [Member]
Assets
Total investments	615	955
Investments [Member] \| Certificates of deposits [Member]
Assets
Total investments		2,008
Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total investments	4,503	9,008
Level 1 [Member]
Assets
Total assets measured at fair value	17,995	11,487
Liabilities
Total liabilities measured at fair value
Level 1 [Member] \| Financing derivative [Member]
Liabilities
Total liabilities measured at fair value
Level 1 [Member] \| Cash and cash equivalents [Member]
Assets
Total cash and cash equivalents	17,995	11,847
Level 1 [Member] \| Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total cash and cash equivalents	17,995	11,847
Level 1 [Member] \| Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total cash and cash equivalents
Level 1 [Member] \| Investments [Member]
Assets
Total investments
Level 1 [Member] \| Investments [Member] \| Commercial paper [Member]
Assets
Total investments
Level 1 [Member] \| Investments [Member] \| Corporate debt securities [Member]
Assets
Total investments
Level 1 [Member] \| Investments [Member] \| Asset backed securities [Member]
Assets
Total investments
Level 1 [Member] \| Investments [Member] \| Certificates of deposits [Member]
Assets
Total investments
Level 1 [Member] \| Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total investments
Level 2 [Member]
Assets
Total assets measured at fair value	94,310	88,733
Liabilities
Total liabilities measured at fair value
Level 2 [Member] \| Financing derivative [Member]
Liabilities
Total liabilities measured at fair value
Level 2 [Member] \| Cash and cash equivalents [Member]
Assets
Total cash and cash equivalents	35,043	34,693
Level 2 [Member] \| Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total cash and cash equivalents
Level 2 [Member] \| Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total cash and cash equivalents	35,043	34,693
Level 2 [Member] \| Investments [Member]
Assets
Total investments	59,267	54,040
Level 2 [Member] \| Investments [Member] \| Commercial paper [Member]
Assets
Total investments	45,919	28,866
Level 2 [Member] \| Investments [Member] \| Corporate debt securities [Member]
Assets
Total investments	8,230	13,203
Level 2 [Member] \| Investments [Member] \| Asset backed securities [Member]
Assets
Total investments	615	955
Level 2 [Member] \| Investments [Member] \| Certificates of deposits [Member]
Assets
Total investments		2,008
Level 2 [Member] \| Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total investments	4,503	9,008
Level 3 [Member]
Assets
Total assets measured at fair value
Liabilities
Total liabilities measured at fair value	999
Level 3 [Member] \| Financing derivative [Member]
Liabilities
Total liabilities measured at fair value	999
Level 3 [Member] \| Cash and cash equivalents [Member]
Assets
Total cash and cash equivalents
Level 3 [Member] \| Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Assets
Total cash and cash equivalents
Level 3 [Member] \| Cash and cash equivalents [Member] \| Commercial paper [Member]
Assets
Total cash and cash equivalents
Level 3 [Member] \| Investments [Member]
Assets
Total investments
Total assets measured at fair value
Level 3 [Member] \| Investments [Member] \| Commercial paper [Member]
Assets
Total investments
Level 3 [Member] \| Investments [Member] \| Corporate debt securities [Member]
Assets
Total investments
Level 3 [Member] \| Investments [Member] \| Asset backed securities [Member]
Assets
Total investments
Level 3 [Member] \| Investments [Member] \| Certificates of deposits [Member]
Assets
Total investments
Level 3 [Member] \| Investments [Member] \| U.S. government and agency securities [Member]
Assets
Total investments

Summary of Significant Accounting Policies (Details 1) $ in Thousands	3 Months Ended
	Mar. 31, 2013 USD ($)
Financial Derivative
Beginning Balance
Value at issuance	(967)
Loss on change in fair value of Financing Derivative	(32)
Ending Balance	$ (999)

Summary of Significant Accounting Policies (Details 2) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Numerator
Net loss	$ (21,104)	$ (27,580)
Denominator:
Weighted average shares of common stock outstanding - basic and diluted	57,372	55,201
Basic and diluted net loss per share	$ (0.37)	$ (0.50)

- 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

Summary of Significant Accounting Policies (Details 3) - shares shares in Thousands	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
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	13,741	12,457
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	5,504	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

Summary of Significant Accounting Policies (Details Textual) - USD ($) $ in Thousands	3 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Summary of Significant Accounting Policies (Textual) [Abstract]
Impairment charges on investments	$ 0	$ 0
Fair value assets liabilities transfer between levels	$ 0

Cash, Cash Equivalents and Investments (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Dec. 31, 2012
Summary of cash and cash equivalents and investments
Amortized Cost	$ 112,295	$ 100,550
Gross unrealized gains	13	30
Gross unrealized losses	(3)
Fair Value	112,305	100,580
Cash and cash equivalents [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	53,036	46,537
Gross unrealized gains	2	3
Gross unrealized losses
Fair Value	53,038	46,540
Cash and cash equivalents [Member] \| Cash and money market funds [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	17,995	11,847
Gross unrealized gains
Gross unrealized losses
Fair Value	17,995	11,847
Cash and cash equivalents [Member] \| Commercial paper [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	35,041	34,690
Gross unrealized gains	2	3
Gross unrealized losses
Fair Value	35,043	34,693
Investments [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	59,259	54,013
Gross unrealized gains	11	27
Gross unrealized losses	(3)
Fair Value	59,267	54,040
Investments [Member] \| Commercial Paper [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	45,915	28,859
Gross unrealized gains	6	7
Gross unrealized losses	(2)
Fair Value	45,919	28,866
Investments [Member] \| Corporate debt securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	8,228	13,190
Gross unrealized gains	3	13
Gross unrealized losses	(1)
Fair Value	8,230	13,203
Investments [Member] \| Asset backed securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	615	954
Gross unrealized gains		1
Gross unrealized losses
Fair Value	615	955
Investments [Member] \| Certificates of deposits [Member]
Summary of cash and cash equivalents and investments
Amortized Cost		2,005
Gross unrealized gains		3
Gross unrealized losses
Fair Value		2,008
Investments [Member] \| U.S. government and agency securities [Member]
Summary of cash and cash equivalents and investments
Amortized Cost	4,501	9,005
Gross unrealized gains	2	3
Gross unrealized losses
Fair Value	$ 4,503	$ 9,008

Cash, Cash Equivalents and Investments (Details1) $ in Thousands	Mar. 31, 2013 USD ($)
Estimated fair value of marketable debt securities
Total investments in debt securities	$ 94,310
Due in one year or less [Member]
Estimated fair value of marketable debt securities
Total investments in debt securities	93,695
Due after one year through 3 years [Member]
Estimated fair value of marketable debt securities
Total investments in debt securities	$ 615

Balance Sheet Components (Details) - USD ($) $ in Thousands	Mar. 31, 2013	Dec. 31, 2012
Components of inventory
Purchased materials, net	$ 3,250	$ 3,823
Work in process, net	6,773	3,494
Finished goods, net	574	2,275
Inventory, net	$ 10,597	$ 9,592

Balance Sheet Components (Details 1) - USD ($) $ in Thousands	Mar. 31, 2013	Dec. 31, 2012
Schedule of accrued expenses and other current liabilities
Salaries and benefits	$ 3,426	$ 4,660
Legal and professional services	1,696	1,093
Customer deposits	48	685
Short-term portion of deferred rent	964	941
Other	1,291	825
Accrued expenses and other current liabilities	$ 7,425	$ 8,204

- 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

Contingencies (Details) $ in Thousands	3 Months Ended
Contingencies (Details) $ in Thousands	Mar. 31, 2013 USD ($) Claims
Contingencies (Textual) [Abstract]
Additional liability associated with indemnification obligations \| $	$ 0
Court's order granted plaintiffs leave	60 days
Number of putative class action \| Claims	3

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

Debt Facility (Details)	3 Months Ended
Debt Facility (Details)	Mar. 31, 2013
Fair value of the warrants
Expected term	7 years
Expected volatility	50.00%
Risk-free interest rate	1.40%
Dividend yield

Debt Facility (Details 1) - USD ($) $ in Thousands	3 Months Ended
Debt Facility (Details 1) - USD ($) $ in Thousands	Mar. 31, 2013	Mar. 31, 2012
Components of expenses related to the facility included in other income (expense), net
Cash interest expense at 8.75%	$ (270)
Non-cash amortization of Original Issue Discount	(87)
Amortization of debt issuance costs	(2)
Interest Expense	(359)
Loss on financing derivative	(32)
Other income (expense), net	$ (497)	$ (70)

Debt Facility (Details Textual)	3 Months Ended
Debt Facility (Details Textual)	Mar. 31, 2013 USD ($) $ / EPU shares	Feb. 05, 2013 USD ($)	Dec. 31, 2012 USD ($)
Line of Credit Facility [Line Items]
Deerfield promissory notes aggregate principal amount		$ 14,100,000
Facility Agreement (Textual) [Abstract]
Purchase shares of Common Stock \| shares	5,500,000
Common stock aggregate exercise price \| $ / EPU	2.63
Facility Agreement period	7 years
Principal Early Repayments Maximum Requirement of Net Sales Amount	$ 41,000,000
Facility Due Dates	on each of the third, fourth and fifth anniversaries of the date of the Facility Agreement.
Percentage of net proceeds from out side financing or equity component	25.00%
Facility agreement exercisable limit \| shares	15,000,000
Shares issued \| shares	3,900,000
Percentage of principal amount repaid	100.00%
Cash and cash equivalent minimum amount quarterly required	$ 2,000,000
Notes recorded	12,851,000	12,800,000
Additional discount allocated to the warrants	$ 7,700,000
Effective interest rate	20.60%
Fair value of the warrants		6,400,000
Expected maturity period	7 years
Fair value of the Financing Derivative	$ (999,000)	1,000,000
Allocation of notes calculated on a relative fair value basis	$ 20,500,000
Weighted average market yield of derivative	20.80%
Principal amount of notes		$ 14,100,000
Deerfield Promissory Notes [Member]
Line of Credit Facility [Line Items]
Deerfield promissory notes aggregate principal amount	$ 20,500,000
Deerfield promissory notes simple interest	8.75%
Facility fee	$ 20,000,000
Net proceeds of payable quarterly arrears	500,000
Facility Agreement (Textual) [Abstract]
Principal amount of notes	$ 20,500,000

Stockholders' Equity (Details) - USD ($)	1 Months Ended	2 Months Ended	3 Months Ended
Stockholders' Equity (Details) - USD ($)	Apr. 30, 2012	Mar. 31, 2013	Mar. 31, 2013	Mar. 31, 2012	Dec. 31, 2012	Oct. 05, 2012
Stockholders Equity (Additional Textual) [Abstract]
Common stock offering price Cantor shares		$ 664,204,000	$ 664,204,000		$ 645,372,000
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
Convertible Preferred Stock, shares authorized		50,000	50,000		50,000
Preferred stock shares par value		$ 0.001	$ 0.001		$ 0.001
Preferred stock issued
Preferred stock outstanding
Common stock, warrants or debt securities	$ 150,000,000
Commission to Cantor			3.00%
Shares issued			3,900,000
Proceeds from issuance of common stock		$ 8,700,000	$ 9,890,000	$ 1,755,000
Average common stock price per share			$ 2.34
Cantor [Member]
Stockholders Equity (Additional Textual) [Abstract]
Common stock offering price Cantor shares						$ 30,000,000
Legal expenses incurred by Cantor			$ 50,000

Stock Option Plans (Details) - $ / shares shares in Thousands	3 Months Ended	12 Months Ended
	Mar. 31, 2013	Dec. 31, 2012
Reconciliation of Outstanding and Exercisable Stock Options
Balances, December, 31, 2012 , shares available for grant	2,872
Additional shares reserved, Shares available for grant	3,370
Options granted, Shares available for grant	(1,840)
Options cancelled, Shares available for grant	114
Balances, March, 31, 2013 , shares available for grant	4,516	2,872
Balances, December, 31, 2012 , Number of shares	12,016
Options granted, Number of shares	1,840
Options exercised, Number of shares	(1)
Options cancelled, Number of shares	(114)
Balances, March, 31, 2013 , Number of shares	13,741	12,016
Balances, December, 31, 2012 , Weighted average exercise price per share	$ 5.37
Options granted, Weighted average exercise price per share	2.23
Options exercised, Weighted average exercise price per share	2.52
Options cancelled, Weighted average exercise price per share	5.56
Balances, March, 31, 2013 , Weighted average exercise price per share	4.95	$ 5.37
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
3.01 - 4.79 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	2.18
Exercise price, upper range	2.78
0.20 - 3.86 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	2.52
Exercise price, upper range	2.52
1.96 - 16.00 [Member]
Reconciliation of Outstanding and Exercisable Stock Options
Exercise price, lower range	1.16
Exercise price, upper range	$ 16.00

Stock Option Plans (Details 1) - USD ($) $ in Thousands	3 Months Ended
Stock Option Plans (Details 1) - USD ($) $ in Thousands	Mar. 31, 2013	Mar. 31, 2012
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	$ 2,746	$ 2,187
Cost of revenue [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	136	166
Research and development [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	1,217	1,133
Sales, General and Administrative Expenses [Member]
Schedule Of Stock-Based Compensation Expense
Stock-based compensation	$ 1,393	$ 888

Stock Option Plans (Details 2)	3 Months Ended
Stock Option Plans (Details 2)	Mar. 31, 2013	Mar. 31, 2012
Schedule of Fair Value of Employee Stock Options
Expected term	6 years 1 month 6 days	6 years 1 month 6 days
Expected volatility	65.00%	65.00%
Risk-free interest rate	1.10%	1.10%
Dividend yield

Stock Option Plans (Details Textual)	3 Months Ended
Stock Option Plans (Details Textual)	Mar. 31, 2013 PurchasePeriod CompensationPlan shares	Mar. 31, 2012 shares
Stock Options Plans (Textual) [Abstract]
Number of equity compensation plans \| CompensationPlan	3
Common stock reserved for issuance	786,255
Number of purchase periods \| PurchasePeriod	4
Purchase period of ESPP	6 months
Percentage of fair market value at which stock can be purchased	85.00%
Shares issued under the ESPP	733,111	428,604

- Definition

Number of shares issued during the period as a result of an employee stock purchase plan.

+ References + Details