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Document and Entity Information - USD ($)	12 Months Ended
Document and Entity Information - USD ($)	Dec. 31, 2012	Jan. 31, 2013	Jun. 30, 2012
Document and Entity Information [Abstract]
Entity Registrant Name	BIOCRYST PHARMACEUTICALS INC
Entity Central Index Key	0000882796
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			$ 197,330,676
Entity Common Stock, Shares Outstanding		50,928,144

Consolidated Balance Sheets - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
ASSETS
Cash and cash equivalents	$ 20,891	$ 16,444
Restricted cash	308	625
Investments	14,708	25,274
Receivables	4,562	5,831
Interest reserve		1,742
Inventory		263
Prepaid expenses and other current assets	1,097	378
Deferred collaboration expense	412	2,301
Total current assets	41,978	52,858
Investments	1,151	15,382
Furniture and equipment, net	583	1,098
Deferred collaboration expense	5,033	5,437
Other assets	8,694	7,433
Total assets	57,439	82,208
LIABILITIES AND STOCKHOLDERS' EQUITY
Accounts payable	3,974	2,497
Accrued expenses	9,860	12,616
Interest payable	1,998	1,400
Deferred collaboration revenue	1,392	9,786
Total current liabilities	17,224	26,299
Deferred collaboration revenue	5,920	7,103
Foreign currency derivative	4,749	4,000
Non-recourse notes payable	30,000	30,000
Stockholders' equity:
Preferred stock, $0.001 par value; shares authorized - 5,000; no shares outstanding
Common stock, $0.01 par value; shares authorized - 95,000; shares issued and outstanding - 50,893 in 2012 and 45,662 in 2011	509	457
Additional paid-in capital	391,611	367,829
Accumulated other comprehensive income	27	40
Accumulated deficit	(392,601)	(353,520)
Total stockholders' (deficit) equity	(454)	14,806
Total liabilities and stockholders' equity	$ 57,439	$ 82,208

Consolidated Balance Sheets (Parenthetical) - $ / shares shares in Thousands	Dec. 31, 2012	Dec. 31, 2011
Consolidated Balance Sheets [Abstract]
Preferred stock, par value	$ 0.001	$ 0.001
Preferred stock, shares authorized	5,000	5,000
Preferred stock, shares outstanding
Common stock, par value	$ 0.01	$ 0.01
Common stock, shares authorized	95,000	95,000
Common stock, shares issued	50,893	45,662
Common stock, shares outstanding	50,893	45,662

Consolidated Statements of Comprehensive Loss - USD ($) shares in Thousands, $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Revenues
Royalty revenue	$ 3,317
Product sales			$ 325
Collaborative and other research and development	22,976	$ 19,643	62,056
Total revenues	26,293	19,643	62,381
Expenses
Cost of products sold			86
Research and development	51,464	57,249	83,900
General and administrative	6,826	11,981	11,718
Royalty	132
Restructuring	1,759		1,034
Total operating expenses	60,181	69,230	96,738
Loss from operations	(33,888)	(49,587)	(34,357)
Interest and other income	222	413	504
Interest expense	(4,666)	(3,774)
Loss on foreign currency derivative	(749)	(4,000)
Net loss	$ (39,081)	$ (56,948)	$ (33,853)
Basic and diluted net loss per common share	$ (0.79)	$ (1.26)	$ (0.76)
Weighted average shares outstanding	49,474	45,144	44,564
Unrealized loss on available for sale investments	$ (13)	$ (65)	$ 131
Comprehensive Loss	$ (39,094)	$ (57,013)	$ (33,722)

Consolidated Statements of Cash Flows - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Operating activities:
Net loss	$ (39,081)	$ (56,948)	$ (33,853)
Adjustments to reconcile net loss to net cash used in operating activities:
Depreciation, amortization, and impairment	628	886	2,267
Stock-based compensation expense	4,167	4,772	6,302
Amortization of debt issuance costs	439	356
Change in fair value of foreign currency derivative	749	4,000
Changes in operating assets and liabilities:
Receivables from collaborations	1,269	24,396	3,495
Inventory	263	635	5,383
Prepaid expenses and other assets	(623)	626	51
Deferred collaboration expense	2,301	1,309	(220)
Accounts payable and accrued expenses	2,068	(10,731)	(9,483)
Deferred collaboration revenue	(9,577)	(1,552)	(2,497)
Net cash used in operating activities;	(37,397)	(32,251)	(28,555)
Investing activities:
Acquisitions of furniture and equipment	(113)	(55)	(325)
Change in restricted cash	317
Purchases of investments	(16,153)	(45,500)	(55,909)
Sales and maturities of investments	40,833	56,873	56,455
Net cash provided by investing activities:	24,884	11,318	221
Financing activities:
Sale of common stock, net	17,805	1,027
Exercise of stock options	534	278	553
Employee stock purchase plan sales	321	300	283
Purchases of treasury stock		(61)	(5)
Issuance of non-recourse notes payable, net		25,691
Payment of foreign currency derivative collateral	(1,700)	(3,480)
Net cash provided by financing activities:	16,960	23,755	831
Increase (decrease) in cash and cash equivalents	4,447	2,822	(27,503)
Cash and cash equivalents at beginning of year	16,444	13,622	41,125
Cash and cash equivalents at end of year	$ 20,891	$ 16,444	$ 13,622

Consolidated Statements of Stockholders' Equity - USD ($) $ in Thousands	Total	Common Stock	Additional Paid-In Capital	Accumulated Other Comprehensive (Loss) Income	Accumulated Deficit
Beginning Balance at Dec. 31, 2009	$ 86,266	$ 439	$ 348,572	$ (26)	$ (262,719)
Net loss	(33,853)				(33,853)
Other Comprehensive Income (Loss)	131			131
Comprehensive loss	(33,722)
Exercise of stock options, 240, 184, 348 shares, net for the year 2010, 2011 and 2012 respectively	552	2	550
Employee stock purchase plan sales, 51, 94, 110 shares for the year 2010, 2011 and 2012 respectively	283	1	282
Issuance of common stock, 761, 437, 4774 shares, net for the year 2010, 2011 and 2012 respectively	5,827	8	5,819
Purchases of treasury stock, 1 and 12, shares for the year 2010 and 2011 respectively	(5)		(5)
Stock-based compensation expense	6,302		6,302
Ending Balance at Dec. 31, 2010	65,503	450	361,520	105	(296,572)
Net loss	(56,948)				(56,948)
Other Comprehensive Income (Loss)	(65)			(65)
Comprehensive loss	(57,013)
Exercise of stock options, 240, 184, 348 shares, net for the year 2010, 2011 and 2012 respectively	278	2	276
Employee stock purchase plan sales, 51, 94, 110 shares for the year 2010, 2011 and 2012 respectively	300	1	299
Issuance of common stock, 761, 437, 4774 shares, net for the year 2010, 2011 and 2012 respectively	1,027	4	1,023
Purchases of treasury stock, 1 and 12, shares for the year 2010 and 2011 respectively	(61)		(61)
Stock-based compensation expense	4,772		4,772
Ending Balance at Dec. 31, 2011	14,806	457	367,829	40	(353,520)
Net loss	(39,081)				(39,081)
Other Comprehensive Income (Loss)	(13)			(13)
Comprehensive loss	(39,094)
Exercise of stock options, 240, 184, 348 shares, net for the year 2010, 2011 and 2012 respectively	539	3	536
Employee stock purchase plan sales, 51, 94, 110 shares for the year 2010, 2011 and 2012 respectively	321	1	320
Issuance of common stock, 761, 437, 4774 shares, net for the year 2010, 2011 and 2012 respectively	18,807	48	18,759
Stock-based compensation expense	4,167		4,167
Ending Balance at Dec. 31, 2012	$ (454)	$ 509	$ 391,611	$ 27	$ (392,601)

- Definition

This element represents the amount of recognized equity-based compensation during the period, that is, the amount recognized as expense in the income statement (or as asset if compensation is capitalized). Alternate captions include the words "stock-based compensation".

+ References

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+ Details

- Definition

The change in equity [net assets] of a business enterprise during a period from transactions and other events and circumstances from non-owner sources which are attributable to the reporting entity. It includes all changes in equity during a period except those resulting from investments by owners and distributions to owners, but excludes any and all transactions which are directly or indirectly attributable to that ownership interest in subsidiary equity which is not attributable to the parent.

+ References + Details

- Definition

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

+ References

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+ Details

Consolidated Statements of Stockholders' Equity (Parenthetical) - shares shares in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Exercise of stock options	348	184	240
Employee stock purchase plan sales, shares	110	94	51
Sale of common stock, shares	4,774	437	761
Purchases of treasury stock, shares		12	1
Common Stock
Exercise of stock options	348	184	240
Employee stock purchase plan sales, shares	110	94	51
Sale of common stock, shares	4,774	437	761
Additional Paid-In Capital
Exercise of stock options	348	184	240
Employee stock purchase plan sales, shares	110	94	51
Sale of common stock, shares	4,774	437	761
Purchases of treasury stock, shares		12	1

- Definition

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

+ References + Details

Significant Accounting Policies

12 Months Ended

Dec. 31, 2012

Significant Accounting Policies [Abstract]

Significant Accounting Policies

Note 1 — Significant Accounting Policies

The Company

BioCryst Pharmaceuticals, Inc. (the “Company”) is a biotechnology company that designs, optimizes and develops novel drugs that block key enzymes involved in the pathogenesis of diseases related to therapeutic areas with unmet medical needs aligned with its capabilities and expertise. The Company was incorporated in Delaware in 1986 and its headquarters is located in Durham, North Carolina. The Company integrates the disciplines of biology, crystallography, medicinal chemistry and computer modeling to discover and develop small molecule pharmaceuticals through the process known as structure-guided drug design. BioCryst has incurred losses and negative cash flows from operations since inception.

The Company has undergone two recent restructurings. In the fourth quarter of 2012, it implemented a restructuring plan to significantly reduce its cost structure in response to setbacks in its developmental programs. In the fourth quarter of 2010, it implemented a restructuring plan to consolidate its core facilities and move its headquarters to Durham, North Carolina. Based on its current operating plans, the Company expects it has sufficient liquidity, with its existing cash and investments of $37,058, to continue its planned operations into the second quarter of 2014. The Company’s liquidity needs, and ability to address those needs, will largely be determined by the success of its product candidates and key development and regulatory events in the future. In order to continue its operations substantially beyond mid-2014 it will need to: (1) successfully secure or increase U.S. Government funding of its programs; (2) out-license rights to certain of its product candidates, pursuant to which the Company would receive cash milestones; (3) raise additional capital through equity or debt financings or from other sources; (4) obtain product candidate regulatory approvals, which would generate revenue and cash flow; (5) reduce spending on one or more research and development programs; and/or (6) restructure operations. The Company will continue to incur operating losses and negative cash flows until revenues reach a level sufficient to support ongoing operations.

Basis of Presentation

Beginning in March 2011, the consolidated financial statements include the accounts of the Company and its wholly-owned subsidiary, JPR Royalty Sub LLC (“Royalty Sub”). Royalty Sub was formed in connection with a $30,000 financing transaction the Company completed on March 9, 2011. See Note 3, Royalty Monetization, for a further description of this transaction. All intercompany transactions and balances have been eliminated.

The Company’s financial statements became consolidated beginning in March 2011 with the creation of Royalty Sub, and have been prepared in accordance with accounting principles generally accepted in the United States. Such financial statements reflect all adjustments that are, in management’s opinion, necessary to present fairly, in all material respects, the Company’s financial position, results of operations, and cash flows. There were no adjustments other than normal recurring adjustments.

Reclassifications

During the second quarter of 2012, the Company changed its classification of facilities costs and other costs directly related to its laboratory facility in Birmingham, Alabama from general and administrative expense to research and development expense. This change resulted in $351 of expenses being reclassified from general and administrative expense to research and development expense in 2011. This reclassification had no effect on previously reported operating expenses or net loss amounts.

Cash and Cash Equivalents

The Company generally considers cash equivalents to be all cash held in commercial checking accounts, money market accounts or investments in debt instruments with maturities of three months or less at the time of purchase. The carrying value of cash and cash equivalents approximates fair value due to the short-term nature of these items.

Restricted Cash

Restricted cash as of December 31, 2012 includes $300 ($625 as of December 31, 2011) that the Company is required to maintain in an interest bearing money market account to serve as collateral for a corporate credit card program. The remaining $8 in restricted cash for December 31, 2012 relates to royalty receipts paid by Shionogi & Co. Ltd. (“Shionogi”) designated for interest on the PhaRMA Notes (see in Note 3).

Investments

The Company invests in high credit quality investments in accordance with its investment policy, which is designed to minimize the possibility of loss. The objective of the Company’s investment policy is to ensure the safety and preservation of invested funds, as well as maintaining liquidity sufficient to meet cash flow requirements. The Company places its excess cash with high credit quality financial institutions, commercial companies, and government agencies in order to limit the amount of its credit exposure. Per its policy, the Company is able to invest in marketable debt securities that may consist of U.S. government and government agency securities, money market and mutual fund investments, municipal and corporate notes and bonds, commercial paper and asset or mortgage-backed securities, among others. The Company’s investment policy requires it to purchase high-quality marketable securities with a maximum individual maturity of three years and requires an average portfolio maturity of no more than 18 months. Some of the securities the Company invests in may have market risk. This means that a change in prevailing interest rates may cause the principal amount of the investment to fluctuate. To minimize this risk, the Company schedules its investments with maturities that coincide with expected cash flow needs, thus avoiding the need to redeem an investment prior to its maturity date. Accordingly, the Company does not believe it has a material exposure to interest rate risk arising from its investments. Generally, the Company’s investments are not collateralized. The Company has not realized any significant losses from its investments.

The Company classifies all of its investments as available-for-sale. Unrealized gains and losses on investments are recognized in comprehensive income/(loss), unless an unrealized loss is considered to be other than temporary, in which case the unrealized loss is charged to operations. The Company periodically reviews its investments for other than temporary declines in fair value below cost basis and whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. The Company believes the individual unrealized losses represent temporary declines primarily resulting from interest rate changes. Realized gains and losses are reflected in interest and other income in the Consolidated Statements of Comprehensive Loss and are determined using the specific identification method with transactions recorded on a settlement date basis. Investments with original maturities at date of purchase beyond three months and which mature at or less than 12 months from the balance sheet date are classified as current. Investments with a maturity beyond 12 months from the balance sheet date are classified as long-term. At December 31, 2012, the Company believes that the costs of its investments are recoverable in all material respects.

The following tables summarize the fair value of the Company’s investments by type. The estimated fair value of the Company’s fixed income investments are classified as Level 2 in the fair value hierarchy as defined in U.S. GAAP with the exception of U.S. Treasury securities, which are classified as Level 1. These valuations are based on observable direct and indirect inputs, primarily quoted prices of similar, but not identical, instruments in active markets or quoted prices for identical or similar instruments in markets that are not active. These fair values are obtained from independent pricing services which utilize Level 2 inputs.


	December 31, 2012
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized		Estimated
	Cost		Interest		Gains		Losses		Fair Value
U.S. Treasury securities	$	999	$	2	$	2	$	—	$	1,003
Obligations of U.S. government and its agencies		3,505		6		2		—		3,513
Corporate debt securities		4,035		22		6		—		4,063
Commercial paper		1,695		—		1		—		1,696
Municipal obligations		5,541		27		16		—		5,584

Total investments	$	15,775	$	57	$	27	$	—	$	15,859


	December 31, 2011
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,998	$	2	$	14	$	—		$	2,014
Obligations of U.S. government and its agencies		5,000		10		—		—			5,010
Corporate debt securities		10,924		80		15		(9	)		11,010
Commercial paper		10,939		—		2		(1	)		10,940
Asset-backed securities		611		—		—		—			611
Certificate of deposit		801		1		—		—			802
Municipal obligations		10,182		68		21		(2	)		10,269

Total investments	$	40,455	$	161	$	52	$	(12	)	$	40,656

The following table summarizes the scheduled maturity for the Company’s investments at December 31, 2012 and 2011.


	2012		2011
Maturing in one year or less	$	14,708	$	25,274
Maturing after one year through two years		1,151		14,628
Maturing after two years		—		754

Total investments	$	15,859	$	40,656

Receivables

Receivables are recorded for amounts due to the Company related to reimbursable research and development costs from the U.S. Department of Health and Human Services or royalty receivables from Shionogi & Co. Ltd. These receivables are evaluated to determine if any reserve or allowance should be established at each reporting date. At December 31, 2012 and 2011, the Company had the following receivables.


	December 31, 2012
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	150	$	3,888	$	4,038
Shionogi & Co. Ltd.		524		—		524

Total receivables	$	674	$	3,888	$	4,562


	December 31, 2011
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	1,146	$	4,683	$	5,829
Shionogi & Co. Ltd.		2		—		2

Total receivables	$	1,148	$	4,683	$	5,831

Monthly invoices are submitted to the U.S. Department of Health and Human Services Biomedical Advanced Research and Development Authority (“BARDA/HHS”) related to reimbursable research and development costs. The Company is also entitled to monthly reimbursement of indirect costs based on rates stipulated in the underlying contract. The Company’s calculations of its indirect cost rates are subject to audit by the federal government.

Inventory

At December 31, 2012 and 2011, the Company’s inventory consisted of peramivir finished goods inventory and supplies for the manufacture of peramivir. Inventory is stated at the lower of cost, determined under the first-in, first-out (“FIFO”) method, or market. The Company expenses costs related to the production of inventories as research and development expenses in the period incurred until such time it is believed that future economic benefit is expected to be recognized, which generally is reliant upon receipt of regulatory approval. Upon regulatory approval, the Company capitalizes subsequent costs related to the production of inventories.

During 2011, based on the annual variability of influenza, which impacts potential clinical and commercial demand and timing for peramivir administration, as well as the costs to store and maintain supplies, the Company decided for economic reasons to reduce its supplies inventory. During the fourth quarter of 2012, in connection with the termination of the peramivir Phase 3 301 clinical trial, the Company decided to reserve the remaining balance of its supplies inventory for the manufacture of peramivir.

The Company’s inventory consisted of the following:


	As of December 31,
	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods and supplies		(4,243	)		(4,615	)

Net inventories	$	—		$	263

Furniture and Equipment

Furniture and equipment are recorded at cost. Depreciation is computed using the straight-line method with estimated useful lives of five and seven years. Laboratory equipment, office equipment, and software are depreciated over a life of five years. Furniture and fixtures are depreciated over a life of seven years. Leasehold improvements are amortized over their estimated useful lives or the remaining lease term, whichever is less.

In accordance with generally accepted accounting principles, the Company periodically reviews its furniture and equipment for impairment when events or changes in circumstances indicate that the carrying amount of such assets may not be recoverable. Determination of recoverability is based on an estimate of undiscounted future cash flows resulting from the use of the asset and its eventual disposition. In the event that such cash flows are not expected to be sufficient to recover the carrying amount of the assets, the assets are written down to their estimated fair values. Furniture and equipment to be disposed of are reported at the lower of carrying amount or fair value less cost to sell.

Patents and Licenses

The Company seeks patent protection on all internally developed processes and products. All patent related costs are expensed to research development expenses when incurred as recoverability of such expenditures is uncertain.

Accrued Expenses

The Company generally enters into contractual agreements with third-party vendors who provide research and development, manufacturing, and other services in the ordinary course of business. Some of these contracts are subject to milestone-based invoicing and services are completed over an extended period of time. The Company records liabilities under these contractual commitments when it determines an obligation has been incurred, regardless of the timing of the invoice. This process involves reviewing open contracts and purchase orders, communicating with applicable Company personnel to identify services that have been performed on its behalf and estimating the level of service performed and the associated cost incurred for the service when the Company has not yet been invoiced or otherwise notified of actual cost. The majority of service providers invoice the Company monthly in arrears for services performed. The Company makes estimates of accrued expenses as of each balance sheet date in its financial statements based on the facts and circumstances. The Company periodically confirms the accuracy of its estimates with the service providers and makes adjustments if necessary. Examples of estimated accrued expenses include:

•

fees paid to Clinical Research Organizations (“CROs”) in connection with preclinical and toxicology studies and clinical trials;

•

fees paid to investigative sites in connection with clinical trials;

•

fees paid to contract manufacturers in connection with the production of our raw materials, drug substance and drug products; and

•

professional fees.

The Company bases its expenses related to clinical trials on its estimates of the services received and efforts expended pursuant to contracts with multiple research institutions and clinical research organizations that conduct and manage clinical trials on the Company’s behalf. The financial terms of these agreements are subject to negotiation, vary from contract to contract and may result in uneven payment flows. Payments under some of these contracts depend on factors such as the successful enrollment of patients and the completion of clinical trial milestones. In accruing service fees, the Company estimates the time period over which services will be performed and the level of effort expended in each period. If the actual timing of the performance of services or the level of effort varies from the estimate, the Company will adjust the accrual accordingly. Accrued expenses as of December 31, 2012 and 2011 included $6,573 and $8,622, respectively, of research and development costs.

Income Taxes

The liability method is used in the Company’s accounting for income taxes. Under this method, deferred tax assets and liabilities are determined based on differences between financial reporting and tax bases of assets and liabilities and are measured using the enacted tax rates and laws that are expected to be in effect when the differences are expected to reverse.

Accumulated Other Comprehensive (Loss) Income

Accumulated other comprehensive (loss) income is comprised of unrealized gains and losses on investments available-for-sale and is disclosed as a separate component of stockholders’ equity.

Revenue Recognition

The Company recognizes revenues from collaborative and other research and development arrangements and product sales. Revenue is realized or realizable and earned when all of the following criteria are met: (i) persuasive evidence of an arrangement exists; (ii) delivery has occurred or services have been rendered; (iii) the seller’s price to the buyer is fixed or determinable; and (iv) collectability is reasonably assured.

Collaborative and Other Research and Development Arrangements and Royalties

Revenue from license fees, royalty payments, event payments, and research and development fees are recognized as revenue when the earnings process is complete and the Company has no further continuing performance obligations or the Company has completed the performance obligations under the terms of the agreement. Fees received under licensing agreements that are related to future performance are deferred and recognized over an estimated period determined by management based on the terms of the agreement and the products licensed. In the event a license agreement contains multiple deliverables, the Company evaluates whether the deliverables are separate or combined units of accounting. Revisions to revenue or profit estimates as a result of changes in the estimated revenue period are recognized prospectively.

Under certain of our license agreements, the Company receives royalty payments based upon our licensees’ net sales of covered products. Generally, under these agreements, the Company receives royalty reports from our licensees approximately one quarter in arrears, that is, generally in the second month of the quarter after the licensee has sold the royalty-bearing product. The Company recognizes royalty revenues when it can reliably estimate such amounts and collectability is reasonably assured.

Royalty revenue paid by Shionogi on their product sales is subject to returns. Prior to the third quarter of 2012, the Company did not have sufficient historical experience to reasonably estimate product returns and therefore could not reasonably record the underlying revenue. As of the end of the second quarter of 2012, the Company deferred recognition of all RAPIACTA ^® royalty revenue from Shionogi sales in 2011 and the first six months of 2012. During the third quarter of 2012, and after the completion of the 2011/2012 flu season in Japan, the Company obtained sufficient historical information to reasonably estimate product returns and recognized royalty revenue of $2,848, net of an allowance for estimated returns. During the fourth quarter of 2012, the Company recognized royalty revenue of $469, for a total of $3,317 in 2012. Prospectively, the Company expects to have sufficient information to recognize royalty revenue on a quarterly basis, net of an allowance for estimated returns.

Reimbursements received for direct out-of-pocket expenses related to research and development costs are recorded as revenue in the Consolidated Statements of Comprehensive Loss rather than as a reduction in expenses. Event payments are recognized as revenue upon the achievement of specified events if (1) the event is substantive in nature and the achievement of the event was not reasonably assured at the inception of the agreement and (2) the fees are non-refundable and non-creditable. Any event payments received prior to satisfying these criteria are recorded as deferred revenue. Under the Company’s contract with BARDA/HHS, revenue is recognized as reimbursable direct and indirect costs are incurred.

Product Sales

Sales are recognized when there is persuasive evidence that an arrangement exists, title has passed, the price was fixed and determinable, and collectability is reasonably assured. Product sales are recognized net of estimated allowances, discounts, sales returns, chargebacks and rebates. Product sales recognized during 2010 were not subject to a contractual right of return.

The Company recorded the following revenues for the years ended December 31:


	2012		2011		2010
Royalty revenue	$	3,317	$	—	$	—
Product sales:
NT Pharma Limited (Hong Kong)		—		—		250
Other		—		—		75

Total product sales		—		—		325
Collaborative and other research and development revenues:
U.S. Department of Health and Human Services		14,026		17,099		42,530
Shionogi (Japan)		1,184		1,181		15,933
Mundipharma (United Kingdom)		7,766		1,277		1,860
Grants (United States)		—		86		978
Other		—		—		755

Total collaborative and other research and development revenues		22,976		19,643		62,056

Total revenues	$	26,293	$	19,643	$	62,381

Research and Development Expenses

The Company’s research and development costs are charged to expense when incurred. Research and development expenses include all direct and indirect development costs related to the development of the Company’s portfolio of product candidates. Advance payments for goods or services that will be used or rendered for future research and development activities are deferred and capitalized. Such amounts are recognized as expense when the related goods are delivered or the related services are performed. Research and development expenses include, among other items, personnel costs, including salaries and benefits, manufacturing costs, clinical, regulatory, and toxicology services performed by CROs, materials and supplies, and overhead allocations consisting of various administrative and facilities related costs. Most of the Company’s manufacturing and clinical and preclinical studies are performed by third-party CROs. Costs for studies performed by CROs are accrued by the Company over the service periods specified in the contracts and estimates are adjusted, if required, based upon the Company’s on-going review of the level of services actually performed.

Additionally, the Company has license agreements with third parties, such as Albert Einstein College of Medicine of Yeshiva University (“AECOM”), Industrial Research, Ltd. (“IRL”), and the University of Alabama at Birmingham (“UAB”), which requires fees related to sublicense agreements or maintenance fees. The Company expenses sublicense payments as incurred unless they are related to revenues that have been deferred, in which case the expenses are deferred and recognized over the related revenue recognition period. The Company expenses maintenance payments as incurred.

Deferred collaboration expenses represent sub-license payments, paid to the Company’s academic partners upon receipt of consideration from various commercial partners, and other consideration paid to our academic partners for modification to existing license agreements. These deferred expenses would not have been incurred without receipt of such payments or modifications from the Company’s commercial partners and are being expensed in proportion to the related revenue being recognized. The Company believes that this accounting treatment appropriately matches expenses with the associated revenue.

Stock-Based Compensation

All share-based payments, including grants of stock option awards and restricted stock awards, are recognized in the Company’s Consolidated Statements of Comprehensive Loss based on their fair values. The fair value of stock option awards is estimated using the Black-Scholes option pricing model. The fair value of restricted stock awards is based on the grant date closing price of the common stock. Stock-based compensation cost is recognized as expense on a straight-line basis over the requisite service period of the award.

Interest Expense and Deferred Financing Costs

Interest expense for the years ended December 31, 2012 and 2011 was $4,666 and $3,774, respectively, and relates to the issuance of the PhaRMA Notes. Costs directly associated with the issuance of the PhaRMA Notes have been capitalized and are included in other non-current assets on the Consolidated Balance Sheets. These costs are being amortized to interest expense over the term of the PhaRMA Notes using the effective interest rate method. Amortization of deferred financing costs included in interest expense for the years ended December 31, 2012 and 2011 was $439 and $356, respectively.

Currency Hedge Agreement

In connection with the issuance by Royalty Sub of the PhaRMA Notes, the Company entered into a Currency Hedge Agreement to hedge certain risks associated with changes in the value of the Japanese yen relative to the U.S. dollar. The Currency Hedge Agreement does not qualify for hedge accounting treatment; therefore mark to market adjustments are recognized in the Company’s Consolidated Statements of Comprehensive Loss. Cumulative mark to market adjustments for the years ended December 31, 2012 and 2011 resulted in a loss of $749 and $4,000, respectively. Mark to market adjustments are determined by a third party pricing model which uses quoted prices in markets that are not actively traded and for which significant inputs are observable directly or indirectly, representing Level 2 in the fair value hierarchy as defined by generally accepted accounting principles. The Company is also required to post collateral in connection with the mark to market adjustments based on defined thresholds. As of December 31, 2012 and 2011, $5,180 and $3,480 of hedge collateral was posted under the agreement, respectively.

Restructuring Activities

During the fourth quarter of 2012, the Company announced a restructuring plan in response to setbacks in its development programs. For example, the Company terminated its 301 peramivir Phase 3 clinical trial and will conduct meetings and discussions with government and regulatory agencies to determine the future of the program. Also, the Company withdrew its BCX5191 Investigational New Drug application due to regulatory concerns. The Company ultimately terminated the BXC5191 program and does not intend to pursue future development. The restructuring plan was implemented to significantly reduce the Company’s cost structure and scale the organization appropriately for its current portfolio and operations. In connection with this plan, the Company recognized restructuring costs of $1,759, consisting of one-time termination benefits and charges related to vacant office space.

During the fourth quarter of 2010, the Company announced a restructuring plan to consolidate core facilities and outsource non-core activities. In connection with this plan, the Company recognized approximately $302 in one-time termination benefits, of which approximately $144 was expensed in 2010 and the remaining balance was expensed in 2011. The Company also recognized approximately $890 in accelerated depreciation during the fourth quarter of 2010 for fixed assets no longer used by the Company.

The following table sets forth activity in the restructuring liability for the years ended December 31, 2012, 2011 and 2010.


	Employee separation costs			Facilities related charges		Total
Balance at December 31, 2009	$	—		$	—	$	—
Accruals		158			—		158
Payments		—			—		—

Balance at December 31, 2010		158			—		158
Payments		(158	)		—		(158	)

Balance at December 31, 2011		—			—		—
Accruals		1,662			97		1,759
Payments		(58	)		—		(58	)

Balance at December 31, 2012	$	1,604		$	97	$	1,701

Net Loss Per Share

Net loss per share is based upon the weighted average number of common shares outstanding during the period. Diluted loss per share is equivalent to basic net loss per share for all periods presented herein because common equivalent shares from unexercised stock options, outstanding warrants, and common shares expected to be issued under the Company’s employee stock purchase plan were anti-dilutive. The calculation of diluted earnings per share for the years ended December 31, 2012, 2011, and 2010 does not include 6,172, 5,681, and 4,043, respectively, of potential common shares, as their impact would be anti-dilutive.

Use of Estimates

The preparation of financial statements in conformity with accounting principles generally accepted in the United States (“U.S. GAAP”) requires the Company to make estimates and assumptions that affect the amounts reported in the financial statements. Actual results could differ from those estimates.

Concentration of Market Risk

The Company’s primary source of revenue that has an underlying cash flow stream is reimbursement of peramivir development expenses, which was earned under the cost-plus-fixed-fee contract with BARDA/HHS. The Company relies on BARDA/HHS to reimburse predominantly all of the development costs for its peramivir program. Accordingly, reimbursement of these expenses represents a significant portion of the Company’s collaborative and other research and development revenues. The completion or termination of this program/collaboration could negatively impact the Company’s future Consolidated Statements of Comprehensive Loss and Cash Flows. In addition, the Company also recognizes royalty revenue from the net sales of RAPIACTA ; however, the underlying cash flow from these royalty payments goes directly to pay the interest, and then the principal, on the Company’s non-recourse notes payable. Payment of the interest and the ultimate repayment of principal of these notes will be entirely funded by future royalty payments derived from net sales of RAPIACTA. The Company’s drug development activities are performed by a limited group of third party vendors. If any of these vendors were unable to perform their services, this could significantly impact the Company’s ability to complete its drug development activities.

Credit Risk

Cash equivalents and investments are financial instruments which potentially subject the Company to concentration of risk to the extent recorded on the Consolidated Balance Sheets. The Company deposits excess cash with major financial institutions in the United States. Balances may exceed the amount of insurance provided on such deposits. The Company believes it has established guidelines for investment of its excess cash relative to diversification and maturities that maintain safety and liquidity. To minimize the exposure due to adverse shifts in interest rates, the Company maintains a portfolio of investments with an average maturity of approximately 24 months or less. This majority of the Company’s receivables are due from BARDA/HHS, for which there is no assumed credit risk.

Furniture and Equipment

12 Months Ended

Dec. 31, 2012

Furniture and Equipment [Abstract]

Furniture and Equipment

Note 2 — Furniture and Equipment

Furniture and equipment consisted of the following at December 31:


	2012			2011
Furniture and fixtures	$	596		$	596
Office equipment		1,486			1,500
Software		1,421			1,409
Laboratory equipment		6,050			6,033
Leased equipment		63			63
Leasehold improvements		5,316			5,267

		14,932			14,868
Less accumulated depreciation and amortization		(14,349	)		(13,770	)

Furniture and equipment, net	$	583		$	1,098

Depreciation and amortization expense for the years ended December 31, 2012, 2011 and 2010 was $628, $886 and $2,267, respectively.

- Definition

The entire disclosure for long-lived, physical assets that are used in the normal conduct of business to produce goods and services and not intended for resale. Examples include land, buildings, machinery and equipment, and other types of furniture and equipment including, but not limited to, office equipment, furniture and fixtures, and computer equipment and software. This disclosure may include property plant and equipment accounting policies and methodology, a schedule of property, plant and equipment gross, additions, deletions, transfers and other changes, depreciation, depletion and amortization expense, net, accumulated depreciation, depletion and amortization expense and useful lives, income statement disclosures, assets held for sale and public utility disclosures.

+ References + Details

Royalty Monetization

12 Months Ended

Dec. 31, 2012

Royalty Monetization [Abstract]

Royalty Monetization

Note 3— Royalty Monetization

Overview

On March 9, 2011, the Company completed a $30,000 financing transaction to monetize certain future royalty and milestone payments under the Shionogi Agreement, pursuant to which Shionogi licensed from the Company the rights to market RAPIACTA in Japan and, if approved for commercial sale, Taiwan. The Company received net proceeds of $22,691 from the transaction after transaction costs of $4,309 and the establishment of a $3,000 interest reserve account by Royalty Sub, available to help cover interest shortfalls in the future. All of the interest reserve account has been fully utilized through payment of the September 2012 interest payment. As of December 31, 2012, approximately $572 of interest due at September 1, 2012 is in arrears.

As part of the transaction, the Company entered into a purchase and sale agreement dated as of March 9, 2011 with Royalty Sub, whereby the Company transferred to Royalty Sub, among other things, (i) its rights to receive certain royalty and milestone payments from Shionogi arising under the Shionogi Agreement, and (ii) the right to receive payments under a Japanese yen/US dollar foreign currency hedge arrangement (as further described below, the “Currency Hedge Agreement”) put into place by the Company in connection with the transaction. Royalty payments will be paid by Shionogi in Japanese yen and milestone payments will paid in U.S. dollars. The Company’s collaboration with Shionogi was not impacted as a result of this transaction.

Non-Recourse Notes Payable

On March 9, 2011, Royalty Sub completed a private placement to institutional investors of $30,000 in aggregate principal amount of its PhaRMA Senior Secured 14.0% Notes due 2020 (the “PhaRMA Notes”). The PhaRMA Notes were issued by Royalty Sub under an Indenture, dated as of March 9, 2011 (the “Indenture”), by and between Royalty Sub and U.S. Bank National Association, as Trustee. Principal and interest on the PhaRMA Notes issued are payable from, and are secured by, the rights to royalty and milestone payments under the Shionogi Agreement transferred by the Company to Royalty Sub and payments, if any, made to Royalty Sub under the Currency Hedge Agreement. The PhaRMA Notes bear interest at 14% per annum, payable annually in arrears on September 1^st of each year, beginning on September 1, 2011 (the “Payment Date”). The Company remains entitled to receive any royalties and milestone payments related to sales of peramivir by Shionogi following repayment of the PhaRMA Notes.

Royalty Sub’s obligations to pay principal and interest on the PhaRMA Notes are obligations solely of Royalty Sub and are without recourse to any other person, including the Company, except to the extent of the Company’s pledge of its equity interests in Royalty Sub in support of the PhaRMA Notes. The Company may, but is not obligated to, make capital contributions to a capital account that may be used to redeem, or on up to one occasion pay any interest shortfall on, the PhaRMA Notes.

Prorated interest expense for the first Payment Date covering the period March 9, 2011 through the September 1, 2011 totaled $2,018. Payment of such interest was made through $760 in royalty payments collected from Shionogi and a $1,258 draw-down from the interest reserve account. Interest expense for the second Payment Date in September 2012 totaled $4,200. Partial payment of this amount was paid in September 2012 totaling $3,628, consisting of royalty payments collected from Shionogi of $1,886 and the remaining balance of the interest reserve account of $1,742. This payment resulted in an interest shortfall of $572 from the total interest amount due and payable of $4,200. As stipulated under the PhaRMA Notes Indenture, if the amounts available for payment on any Payment Date are insufficient to pay all of the interest due on a Payment Date, unless sufficient capital is contributed to Royalty Sub by the Company as permitted under the Indenture or the interest reserve account is available to make such payment, the shortfall in interest will accrue interest at the interest rate applicable to the PhaRMA Notes compounded annually. Accordingly, commencing in September 2012, the Company began accruing interest at 14% per annum on the interest shortfall of $572. Under the terms of the Indenture, Royalty Sub’s inability to pay the full amount of interest payable in September 2012 did not constitute an event of default under the PhaRMA Notes unless Royalty Sub fails to pay such unpaid interest, plus interest thereon, on or prior to the next succeeding Payment Date for the PhaRMA Notes, which is September 1, 2013.

The Indenture does not contain any financial covenants. The Indenture includes customary representations and warranties of Royalty Sub, affirmative and negative covenants of Royalty Sub, Events of Default and related remedies, and provisions regarding the duties of the Trustee, indemnification of the Trustee, and other matters typical for indentures used in structured financings of this type.

As of December 31, 2012, the aggregate fair value of the PhaRMA Notes approximates its carrying value of $30,000. The estimated fair value of the PhaRMA Notes is classified as Level 2 in the fair value hierarchy as defined in U.S. GAAP.

Beginning on March 9, 2012, the PhaRMA Notes became redeemable by Royalty Sub. Accordingly, the PhaRMA Notes will be redeemable at the option of Royalty Sub at any time at a redemption price equal to the percentage of the outstanding principal balance of the PhaRMA Notes being redeemed specified below for the period in which the redemption occurs, plus accrued and unpaid interest through the redemption date on the PhaRMA Notes being redeemed.


	Redemption
Payment Dates (Between Indicated Dates)	Percentage
From and including March 9, 2012 to and including March 8, 2013		107.0	%
From and including March 9, 2013 to and including March 8, 2014		103.5	%
From and including March 9, 2014 and thereafter		100.0	%

Foreign Currency Hedge

In connection with the issuance by Royalty Sub of the PhaRMA Notes, the Company entered into a Currency Hedge Agreement to hedge certain risks associated with changes in the value of the Japanese yen relative to the U.S. dollar. Under the Currency Hedge Agreement, the Company has the right to purchase dollars and sell yen at a rate of 100 yen per dollar for which the Company may be required to pay a premium in each year from 2014 through 2020, provided the Currency Hedge Agreement remains in effect. A payment of $1,950 will be required if, on May 18 of the relevant year, the U.S. dollar is worth 100 yen or less as determined in accordance with the Currency Hedge Agreement.

The Currency Hedge Agreement does not qualify for hedge accounting treatment; therefore mark to market adjustments are recognized in the Company’s Consolidated Statement of Comprehensive Loss. Cumulative mark to market adjustments in 2012 and 2011 resulted in a loss of $749 and $4,000, respectively. The Company is also required to post collateral in connection with the mark to market adjustments based on defined thresholds. As of December 31, 2012 and 2011, $5,180 and $3,480 respectively, were posted under the Currency Hedge Agreement. The Company will not be required at any time to post collateral exceeding the maximum premium payments remaining payable under the Currency Hedge Agreement. Subject to certain obligations the Company has in connection with the PhaRMA Notes, the Company has the right to terminate the Currency Hedge Agreement with respect to the 2016 through 2020 period by giving notice to the counterparty prior to May 18, 2014 and payment of a $1,950 termination fee. If the Company terminates the hedge agreement with respect to currency hedges for 2016 through 2020, the maximum obligation under the currency hedge is $5,850, including the $1,950 termination fee.

Lease Obligations and Other Contingencies

12 Months Ended

Dec. 31, 2012

Lease Obligations and Other Contingencies [Abstract]

Lease Obligations and Other Contingencies

Note 4 — Lease Obligations and Other Contingencies

The Company has the following minimum payments under operating lease obligations that existed at December 31, 2012:


2013	$	1,012
2014		1,049
2015		370

Total minimum payments	$	2,431

The obligations in the preceding table are primarily related to the Company’s leases for buildings in Birmingham, Alabama and Durham, North Carolina. The lease for the building in Alabama expires June 30, 2015 and has an option to renew an additional five years at the current market rate on the date of termination. The lease for the building in Durham, North Carolina expires December 31, 2014. Rent expense for operating leases was $629, $714, and $771 in 2012, 2011, and 2010, respectively.

- 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
-Publisher FASB
-Name Accounting Standards Codification
-Topic 460
-SubTopic 10
-Section 50
-Paragraph 8
-URI http://asc.fasb.org/extlink&oid=6398077&loc=d3e12565-110249

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 450
-SubTopic 20
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6952336&loc=d3e14435-108349

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.25)
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 440
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6394976&loc=d3e25287-109308

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

Stockholders' Equity

12 Months Ended

Dec. 31, 2012

Stockholders' Equity [Abstract]

Stockholders' Equity

Note 5 — Stockholders’ Equity

In June 2011, the Company entered into an At Market Issuance Sales Agreement (the “ATM Agreement”) with McNicoll, Lewis & Vlak (“MLV”) pursuant to which the Company may issue and sell $70,000 in shares of its common stock at current market prices under a Form S-3 registration statement with MLV acting as the sales agent. Subject to the terms and conditions of the ATM Agreement, MLV will use commercially reasonable efforts to sell the Company’s common stock from time to time, based upon the Company’s instruction, including any price, time or size limits or other customary parameters or conditions the Company may impose. The Company will pay MLV an aggregate commission rate of 2% or 3% of the gross proceeds of the sales price per share of any common stock sold under the ATM Agreement depending on the number of shares sold. On June 28, 2011, the Company filed a Registration Statement on Form S-3, which became effective on July 13, 2011, for the issuance and sale of up to $70,000 of equity or other securities. During 2011, the Company sold an aggregate of 437 shares of common stock at an average per share price of $2.65 for net proceeds of $1,027. During 2012, the Company sold an aggregate of 4,516 shares of common stock at an average per share price of $4.08 pursuant to the ATM Agreement for net proceeds of $17,805.

On March 15, 2012, the Company issued 193 shares of restricted common stock in lieu of a cash payment to employees as payment for their annual incentive award earned in 2011. The number of shares issued was based on the total value of the annual incentive earned in 2011 of $1,542, less $535 in withholding taxes paid in cash on the employees’ behalf, divided by the closing common stock price on March 15, 2012 of $5.23 per share.

In May 2010, the Company entered into an amendment to the License Agreement dated June 27, 2000, as subsequently amended (the “License Agreement”), by and among the Company and AECOM and IRL (the “Licensors”). The amendment further amended the License Agreement through which the Company obtained worldwide exclusive rights to develop and ultimately distribute any product candidates that might arise from research on a series of PNP inhibitors, including forodesine and ulodesine. Under the terms of the amendment, the Licensors agreed to accept a reduction of one-half in the percentage of future payments received from third-party sub licensees of the licensed PNP inhibitors that must be paid to the Licensors. This reduction does not apply to (i) any milestone payments the Company may receive in the future under its license agreement dated February 1, 2006 with Mundipharma International Holdings Limited (“Mundipharma”) and (ii) royalties received from the Company’s sub licensees in connection with the sale of licensed products, for which the original payment rate will remain in effect. The rate of royalty payments to the Licensors based on net sales of any resulting product made by the Company remains unchanged.

In consideration for the modifications to the license agreement, the Company issued to the Licensors shares of its common stock with an aggregate value of $5,827 and paid the Licensors $90 in cash. The Company deferred the value of this consideration and is amortizing to research and development expense through September 2027, which is the date of expiration of the last-to-expire patent related to this agreement. Additionally, at the Company’s sole option and subject to certain agreed upon conditions, any future non-royalty payments due to be paid by the Company to the Licensors under the License Agreement may be made either in cash, in shares of its common stock, or in a combination of cash and shares.

Stock-Based Compensation

12 Months Ended

Dec. 31, 2012

Stock-Based Compensation [Abstract]

Stock-Based Compensation

Note 6 — Stock-Based Compensation

Stock Incentive Plan

As of December 31, 2012, the Company had two stock-based employee compensation plans, the Stock Incentive Plan (“Incentive Plan”) and the Employee Stock Purchase Plan (“ESPP”), both which were amended and restated in March 2012 and approved by the Company’s stockholders in May 2012. During 2007, the Company made an inducement grant outside of the Incentive Plan and ESPP to recruit a new employee to a key position within the Company. Stock-based compensation expense of $4,167 ($4,010 of expense related to the Incentive Plan, $157 of expense related to the ESPP) was recognized during 2012, while $4,772 ($4,589 of expense related to the Incentive Plan, $146 of expense related to the ESPP and $37 of expense related to the inducement grant) was recognized during 2011, and $6,302 ($5,961 of expense related to the Incentive Plan, $192 of expense related to the ESPP, and $149 of expense related to the inducement grant) was recognized during 2010.

Under the Incentive Plan, the Company may grant stock option awards and restricted stock awards to its employees, directors, and consultants. Stock option awards are granted with an exercise price equal to the market price of the Company’s stock at the date of grant. Prior to March 1, 2011, stock option awards granted to employees generally vest 25% after one year and monthly thereafter on a pro rata basis over the next three years until fully vested after four years. Commencing in March 2011, stock option awards granted to employees generally vest 25% after each year until fully vested after four years. Stock option awards granted to non-employee directors of the Company generally vest over one year. Predominantly all stock option awards have contractual terms of 10 years. The vesting exercise provisions of all awards granted under the Incentive Plan are subject to acceleration in the event of certain stockholder-approved transactions, or upon the occurrence of a change in control as defined in the Incentive Plan. Under the Incentive Plan, the Company also grants shares of restricted common stock to employees that generally vest 25% after each year until fully vested after four years.

Related activity under the Incentive Plan is as follows:


							Weighted
							Average
	Awards			Options			Exercise
	Available			Outstanding			Price
Balance December 31, 2009		1,773			5,827		$	6.58
Plan amendment		1,300			—			—
Stock option awards granted		(1,550	)		1,550			6.68
Stock option awards exercised		—			(240	)		2.30
Stock option awards cancelled		335			(335	)		8.42

Balance December 31, 2010		1,858			6,802			6.66
Plan amendment		1,600			—			—
Restricted stock awards granted		(211	)		—			—
Restricted stock awards cancelled		8			—			—
Stock option awards granted		(1,830	)		1,830			3.97
Stock option awards exercised		—			(190	)		1.57
Stock option awards cancelled		584			(584	)		5.99

Balance December 31, 2011		2,009			7,858			6.21
Plan amendment		1,700			—			—
Restricted stock awards granted		(415	)		—			—
Restricted stock awards cancelled		86			—			—
Stock option awards granted		(1,617	)		1,617			4.65
Stock option awards exercised		—			(350	)		1.58
Stock option awards cancelled		1,052			(1,052	)		6.26

Balance December 31, 2012		2,815			8,073		$	6.09

For stock option awards granted under the Incentive Plan during 2012, 2011 and 2010, the fair value was estimated on the date of grant using a Black-Scholes option pricing model and the assumptions noted in the table below. The weighted average grant date fair value of these awards granted during 2012, 2011 and 2010 was $3.24, $2.64, and $4.65, respectively. The fair value of the stock option awards is amortized to expense over the vesting periods using a straight-line expense attribution method. The following explanations describe the assumptions used by the Company to value the stock option awards granted during 2012, 2011, and 2010. The expected life is based on the average of the assumption that all outstanding stock option awards will be exercised at full vesting and the assumption that all outstanding stock option awards will be exercised at the midpoint of the current date (if already vested) or at full vesting (if not yet vested) and the full contractual term. For 2011 and 2010, the expected volatility represents an average of the implied volatility on the Company’s publicly traded options, the volatility over the most recent period corresponding with the expected life, and the Company’s long-term reversion volatility. For 2012, the expected volatility represents the volatility over the most recent period corresponding with the expected life. The Company has assumed no expected dividend yield, as dividends have never been paid to stock or option holders and will not be for the foreseeable future. The weighted average risk-free interest rate is the implied yield currently available on zero-coupon government issues with a remaining term equal to the expected term.

Weighted Average Assumptions for Stock Option Awards Granted under the Incentive Plan


	2012			2011			2010
Expected Life		5.4			5.5			5.5
Expected Volatility		87	%		80	%		89	%
Expected Dividend Yield		0.0	%		0.0	%		0.0	%
Risk-Free Interest Rate		0.9	%		2.2	%		2.4	%

The total intrinsic value of stock option awards exercised under the Incentive Plan was $877 during 2012, $374 during 2011, $1,169 and during 2010. The intrinsic value represents the total proceeds (fair market value at the date of exercise, less the exercise price, times the number of stock option awards exercised) received by all individuals who exercised stock option awards during the period.

The following table summarizes, at December 31, 2012, by price range: (1) for stock option awards outstanding under the Incentive Plan, the number of stock option awards outstanding, their weighted average remaining life and their weighted average exercise price; and (2) for stock option awards exercisable under the Plan, the number of stock option awards exercisable and their weighted average exercise price:


	Outstanding						Exercisable
			Weighted		Weighted				Weighted
			Average		Average				Average
			Remaining		Exercise				Exercise
Range	Number		Life		Price		Number		Price
$0 to 3		1,024		5.4	$	1.55		943	$	1.50
3 to 6		3,510		7.3		4.19		1,448		3.88
6 to 9		2,082		4.6		7.37		1,829		7.46
9 to 12		640		3.7		11.36		640		11.36
12 to 15		811		3.4		12.54		798		12.54
15 to 18		4		3.0		15.45		4		15.45
18 to 21		2		0.2		18.99		2		18.99

$0 to 21		8,073		5.7	$	6.09		5,664	$	6.72

The weighted average remaining contractual life of stock option awards exercisable under the Incentive Plan at December 31, 2012 was 5.7 years.

The aggregate intrinsic value of stock option awards outstanding and exercisable under the Incentive Plan at December 31, 2012 was $163. The aggregate intrinsic value represents the value (the period’s closing market price, less the exercise price, times the number of in-the-money stock option awards) that would have been received by all stock option award holders under the Incentive Plan had they exercised their stock option awards at the end of the year.

The total fair value of the stock option awards vested under the Incentive Plan was $3,373 during 2012, $4,775 during 2011, and $4,441 during 2010.

As of December 31, 2012, the number of stock option awards vested and expected to vest under the Incentive Plan is 7,535. The weighted average exercise price of these stock option awards is $6.18 and their weighted average remaining contractual life is 6.1 years.

The following table summarizes the changes in the number and weighted-average grant-date fair value of non-vested stock option awards during 2012:


	Non-Vested Stock Option Awards			Weighted Average Grant-Date Fair Value
Balance December 31, 2011		2,733			3.04
Stock option awards granted		1,617			3.24
Stock option awards vested		(1,196	)		2.82
Stock option awards forfeited		(746	)		3.28

Balance December 31, 2012		2,408			3.18

As of December 31, 2012, there was approximately $6,272 of total unrecognized compensation cost related to non-vested employee stock option awards and restricted stock awards granted by the Company. That cost is expected to be recognized as follows: $2,959 in 2013, $2,010 in 2014, $1,148 in 2015, and $155 in 2016.

Employee Stock Purchase Plan

The Company has reserved a total of 975 shares of common stock to be purchased under the ESPP, of which 177 shares remain available for purchase at December 31, 2012. Eligible employees may authorize up to 15% of their salary to purchase common stock at the lower of 85% of the beginning or 85% of the ending price during six-month purchase intervals. No more than 3 shares may be purchased by any one employee at the six-month purchase dates and no employee may purchase stock having a fair market value at the commencement date of $25 or more in any one calendar year.

There were 110, 94, and 51 shares of common stock purchased under the ESPP in 2012, 2011, and 2010, respectively, at a weighted average price per share of $2.93, $3.21, and $5.50, respectively. Expense of $157, $146, and $192, related to the ESPP was recognized during 2012, 2011, and 2010, respectively. Compensation expense for shares purchased under the ESPP related to the purchase discount and the “look-back” option were determined using a Black-Scholes option pricing model. The weighted average grant date fair values of shares granted under the ESPP during 2012, 2011, and 2010, were $1.48, $1.33, and $2.76, respectively.

- 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

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5070-113901

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 1
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5047-113901

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 718
-SubTopic 10
-Section 50
-Paragraph 4
-URI http://asc.fasb.org/extlink&oid=6415400&loc=d3e5444-113901

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

Income Taxes

12 Months Ended

Dec. 31, 2012

Income Taxes [Abstract]

Income Taxes

Note 7 — Income Taxes

The Company has incurred net losses since inception and, consequently, has not recorded any U.S. federal and state income tax expense or benefit. The differences between the Company’s effective tax rate and the statutory tax rate in 2012, 2011, and 2010 are as follows:


	2012			2011			2010
Income tax benefit at federal statutory rate (35%)	$	(13,678	)	$	(19,932	)	$	(11,457	)
State and local income taxes net of federal tax benefit		(1,470	)		(2,503	)		(1,092	)
Permanent items		754			890			1,753
Rate change		1,147			(2,500	)		5,178
Expiration of attribute carryforwards		5,135			2,884			5,343
Research and development tax credits		829			(2,108	)		(5,359	)
Other		281			731			253
Change in valuation allowance		7,002			22,538			5,381

Income tax expense	$	—		$	—		$	—

The Company recognizes the impact of a tax position in its financial statements if it is more likely than not that the position will be sustained on audit based on the technical merits of the position. The Company has concluded that it has two uncertain tax positions pertaining to its research and development and orphan drug credit carryforwards. The Company has established these credits based on information and calculations it believes are appropriate and the best estimate of the underlying credit. Any future changes to the Company’s unrecognized tax benefits would be offset by an adjustment to the valuation allowance and there would be no impact on the Company’s financial statements.

Additionally, utilization of the Company’s net operating loss carryforwards could be subject to a substantial annual limitation due to ownership change limitations as described in Section 382 of the Internal Revenue Code and similar state provisions. The Company has performed an analysis as of December 31, 2012, and has determined that it has incurred changes in control as defined under Section 382. These ownership changes may limit the amount of net operating losses that can be utilized annually to offset future taxable income and tax.

Significant components of the Company’s deferred tax assets and liabilities are as follows:


	2012			2011
Deferred tax assets:
Net federal and state operating losses	$	108,498		$	97,054
Research and Development credits		36,142			38,119
Fixed assets		1,185			1,265
Reserve for inventories		1,654			1,827
Deferred revenue		2,645			5,801
Stock-based compensation		6,474			5,915
Foreign currency derivative		1,851			1,584
Other		539			422

Total deferred tax assets		158,989			151,987
Valuation allowance		(158,989	)		(151,987	)

Total deferred tax liabilities		—			—

Net deferred tax assets	$	—		$	—

The majority of the Company’s deferred tax assets relate to net operating loss and research and development carryforwards that can only be realized if the Company is profitable in future periods. It is uncertain whether the Company will realize any tax benefit related to these carryforwards. Accordingly, the Company has provided a full valuation allowance against the net deferred tax assets due to uncertainties as to their ultimate realization. The valuation allowance will remain at the full amount of the deferred tax assets until it is more likely than not that the related tax benefits will be realized. The Company’s valuation allowance increased by $7,002 in 2012, $22,538 in 2011, and $5,381 in 2010.

As of December 31, 2012, the Company had federal operating loss carryforwards of $277,298, state operating loss carryforwards of $311,643, and research and development credit carryforwards of $36,142, which will expire at various dates from 2013 through 2032.

The Company’s federal and state operating loss carryforwards include $4,901 of excess tax benefits related to a deduction from the exercise of stock options. The tax benefit of these deductions has not been recognized in deferred tax assets. If utilized, the benefits from these deductions will be recorded as adjustments to income tax expense and additional paid-in capital.

Tax years 2009-2011 remain open to examination by the major taxing jurisdictions to which the Company is subject. Additionally, years prior to 2009 are also open to examination to the extent of loss and credit carryforwards from those years. The Company recognizes interest and penalties accrued related to unrecognized tax benefits as components of its income tax provision. However, there were no provisions or accruals for interest and penalties in 2012, 2011, and 2010.

The American Taxpayer Relief Act of 2012 (the “Act”) was signed in to law on January 2, 2013. The Act retroactively restored several expired business tax provisions, including the research and development credit. Because a change in tax law is accounted for in the period of enactment, the retroactive effect of the Act on the Company’s research and development business credit carryforward will be recorded in 2013 for 2012 activities. The deferred tax asset related to general business credits will also be adjusted in 2013 due to this retroactive treatment. The Company will record a full valuation allowance to offset this potential benefit.

- 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

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.(h))
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e23780-122690

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32559-109319

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 15
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32718-109319

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32639-109319

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 740
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6907707&loc=d3e32537-109319

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 136, 172
-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 Regulation S-X (SX)
-Number 210
-Section 08
-Paragraph h
-Article 4

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 109
-Paragraph 43, 44, 45, 46, 47, 48, 49
-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

Employee 401(k) Plan

12 Months Ended

Dec. 31, 2012

Employee 401(k) Plan [Abstract]

Employee 401(k) Plan

Note 8 — Employee 401(k) Plan

In January 1991, the Company adopted an employee retirement plan (“401(k) Plan”) under Section 401(k) of the Internal Revenue Code covering all employees. Employee contributions may be made to the 401(k) Plan up to limits established by the Internal Revenue Service. Company matching contributions may be made at the discretion of the Board of Directors. The Company made matching contributions of $418, $391, and $434, in 2012, 2011, and 2010, respectively.

- Definition

The entire disclosure for pension and other postretirement benefits.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 715
-URI http://asc.fasb.org/topic&trid=2235017

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Implementation Guide (Q and A)
-Number FAS88
-Paragraph 63
-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 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5
-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 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 106
-Paragraph 518
-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 132R
-Paragraph 5
-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 Emerging Issues Task Force (EITF)
-Number 03-2
-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.

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 87
-Paragraph 264
-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 132R
-Paragraph 5
-Subparagraph q
-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 132R
-Paragraph 5
-Subparagraph h
-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 132R
-Paragraph 8
-Subparagraph m
-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 FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 132R
-Paragraph 5, 6, 7, 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 12: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 158
-Paragraph 7, 21, 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 13: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS106-2
-Paragraph 20, 21, 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 14: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Principles Board Opinion (APB)
-Number 30
-Paragraph 26
-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

Collaborative and Other Research and Development Contracts

12 Months Ended

Dec. 31, 2012

Collaborative and Other Research and Development Contracts [Abstract]

Collaborative and Other Research and Development Contracts

Note 9 — Collaborative and Other Research and Development Contracts

U.S. Department of Health and Human Services (“BARDA/HHS”). In January 2007, the U.S. Department of Health and Human Services (“BARDA/HHS”) awarded the Company a $102,661, four-year contract for the advanced development of peramivir for the treatment of influenza. During 2009, peramivir clinical development shifted to focus on intravenous delivery and the treatment of hospitalized patients. To support this focus, a September 2009 contract modification was awarded to extend the intravenous (“i.v.”) peramivir program by 12 months and to increase funding by $77,191. On February 24, 2011, the Company announced that BARDA/HHS had awarded it a $55,000 contract modification, intended to fund completion of the Phase 3 development of i.v. peramivir for the treatment of patients hospitalized with influenza. This contract modification brings the total award from BARDA/HHS to $234,852 and extends the contract term by 24 months through December 31, 2013, providing funding through completion of Phase 3 and to support the filing of a new drug application (“NDA”) to seek regulatory approval for i.v. peramivir in the U.S.

On November 7, 2012, the Company announced the completion of the planned interim analysis of the peramivir Phase 3 clinical trial in patients admitted to the hospital with influenza. The difference between peramivir and control groups for the primary endpoint was small and the recalculated sample size was greater than the predefined futility boundary of 320 subjects.

Based on the DMC recommendation that the study be discontinued, the Company suspended enrollment of patients in, and subsequently terminated, the clinical trial. The Company has completed a full analysis of the clinical trial, and the future of the program will be determined following discussions between the Company, BARDA/HHS and the Food and Drug Administration (“FDA”).

The contract with BARDA/HHS is a cost-plus-fixed-fee contract. That is, the Company is entitled to receive reimbursement for all costs incurred in accordance with the contract provisions that are related to the development of peramivir plus a fixed fee, or profit. BARDA/HHS will make periodic assessments of progress and the continuation of the contract is based on the Company’s performance, the timeliness and quality of deliverables, and other factors. The government has rights under certain contract clauses to terminate this contract. The contract is terminable by the government at any time for breach or without cause.

Shionogi & Co., Ltd. (“Shionogi”). In March 2007, the Company entered into an exclusive license agreement with Shionogi to develop and commercialize peramivir in Japan for the treatment of seasonal and potentially life-threatening human influenza. Under the terms of the agreement, Shionogi obtained rights to injectable formulations of peramivir in Japan. The Company developed peramivir under a license from UAB and will owe sublicense payments to them on any future milestone payments and/or royalties received by the Company from Shionogi. In October 2008, the Company and Shionogi amended the license agreement to expand the territory covered by the agreement to include Taiwan and to provide rights for Shionogi to perform a Phase 3 clinical trial in Hong Kong. Shionogi has commercially launched peramivir under the commercial name RAPIACTA in Japan.

Green Cross Corporation (“Green Cross”). In June 2006, the Company entered into an agreement with Green Cross to develop and commercialize peramivir in Korea. Under the terms of the agreement, Green Cross will be responsible for all development, regulatory, and commercialization costs in Korea. The Company received a one-time license fee of $250. The license also provides that the Company will share in profits resulting from the sale of peramivir in Korea, including the sale of peramivir to the Korean government for stockpiling purposes. Furthermore, Green Cross will pay the Company a premium over its cost to supply peramivir for development and any future marketing of peramivir products in Korea.

Mundipharma International Holdings Limited (“Mundipharma”). In February 2006, the Company entered into an exclusive, royalty bearing right and license agreement with Mundipharma for the development and commercialization of forodesine, a Purine Nucleoside Phosphorylase (“PNP”) inhibitor, for use in oncology (the “Original Agreement”). Under the terms of the Original Agreement, Mundipharma obtained rights to forodesine in markets across Europe, Asia, and Australasia in exchange for a $10,000 up-front payment.

The Company deferred revenue recognition of the $10,000 up-front payment that was received from Mundipharma in February 2006 because the Company was involved in the continued development of forodesine. Amortization of this revenue commenced in February 2006 and was initially scheduled to end in October 2017, which is the date of expiration for the last-to-expire patent covered by the agreement. The Company also deferred revenue recognition of a $5,000 payment received from Mundipharma in connection with the initiation of a clinical trial in 2007. Amortization of this deferred revenue commenced in 2007 and was initially scheduled to end in October 2017. Under its agreement with AECOM/IRL, the Company paid sublicense payments related to these upfront cash payments received from Mundipharma. Expense recognition of these sublicense payments was deferred and recognized under the same term as the related deferred revenue.

On November 11, 2011, the Company entered into the Amended and Restated License and Development Agreement (the “Amended and Restated Agreement”) with Mundipharma, amending and restating the Original Agreement. Under the terms of the Amended and Restated Agreement, Mundipharma obtained worldwide rights to forodesine. Commencing on November 11, 2011, Mundipharma controls the development and commercialization of forodesine and assumes all future development and commercialization costs. The Amended and Restated Agreement provides for the possibility of future event payments totaling $15,000 for achieving specified regulatory events for certain indications and tiered royalties ranging from mid to high single-digit percentages of net product sales in each country where forodesine is sold by Mundipharma. These royalties are subject to downward adjustments based on the then-existing patent coverage and/or the availability of generic compounds in each country.

The Amended and Restated Agreement is a multiple element arrangement for accounting purposes, in which the Company is required to deliver to Mundipharma both the worldwide rights to forodesine in the field of oncology and the transfer of product data and know-how to permit Mundipharma to develop and commercialize forodesine (the “Knowledge Transfer”). The Company accounted for these elements as a combined unit of accounting as they do not have stand-alone value to Mundipharma. The worldwide license rights were granted to Mundipharma on November 11, 2011 and the Knowledge Transfer was completed during the first quarter of 2012. Completion of the Knowledge Transfer concludes the Company’s obligations under the Amended and Restated Agreement and resulted in the recognition of the unamortized deferred revenue and expense of $7,766 and $1,864, respectively, in the Consolidated Statements of Comprehensive Loss for the year ended December 31, 2012.

Albert Einstein College of Medicine of Yeshiva University and Industrial Research, Ltd. (“AECOM” and “IRL” respectively). In June 2000, the Company licensed a series of potent inhibitors of PNP from AECOM and IRL, (collectively, the “Licensors”). The lead product candidates from this collaboration are forodesine and ulodesine. The Company has obtained worldwide exclusive rights to develop and ultimately distribute these, or any other, product candidates that might arise from research on these inhibitors. The Company has the option to expand the Agreement to include other inventions in the field made by the investigators or employees of the Licensors. The Company agreed to use commercially reasonable efforts to develop these drugs. In addition, the Company has agreed to pay certain milestone payments for each licensed product (which range in the aggregate from $1,400 to almost $4,000 per indication) for future development of these inhibitors, single digit royalties on net sales of any resulting product made by the Company, and to share approximately one quarter of future payments received from other third-party partners, if any. In addition, the Company has agreed to pay annual license fees, which can range from $150 to $500, that are creditable against actual royalties and other payments due to the Licensors. This agreement may be terminated by the Company at any time by giving 60 days advance notice or in the event of material uncured breach by the Licensors.

In May 2010, the Company amended the licensee agreement through which the Company obtained worldwide exclusive rights to develop and ultimately distribute any product candidates that might arise from research on a series of PNP inhibitors, including forodesine and ulodesine. Under the terms of the amendment, the Licensors agreed to accept a reduction of one-half in the percentage of future payments received from third-party sub licensees of the licensed PNP inhibitors that must be paid to the Licensors. This reduction does not apply to (i) any milestone payments the Company may receive in the future under its license agreement dated February 1, 2006 with Mundipharma and (ii) royalties received from its sub licensees in connection with the sale of licensed products, for which the original payment rate will remain in effect. The rate of royalty payments to the Licensors based on net sales of any resulting product made by the Company remains unchanged.

In consideration for these modifications in 2010, the Company issued to the Licensors shares of its common stock with an aggregate value of $5,911 and paid the Licensors $90 in cash. Additionally, at the Company’s sole option and subject to certain agreed upon conditions, any future non-royalty payments due to be paid by it to the Licensors under the license agreement may be made either in cash, in shares of its common stock, or in a combination of cash and shares.

On November 17, 2011, the Company further amended its agreements with the Licensors whereby the Licensors agreed to accept a reduction of one-half in the percentage of Net Proceeds (as defined) received by the Company under its Amended and Restated Agreement with Mundipharma that will be paid to AECOM/IRL.

On June 19, 2012, the Company further amended our agreements with AECOM/IRL whereby the parties clarified the definition of the field with respect to PNP inhibition and AECOM/IRL agreed to exclusive worldwide license of BCX4430 to BioCryst for any antiviral use.

At its sole option and subject to certain agreed upon conditions, any future non-royalty payments due to be paid by the Company to AECOM/IRL under the license agreement may be made either in cash, in shares of the Company’s common stock, or in a combination of cash and shares.

The University of Alabama at Birmingham (“UAB”). The Company currently has agreements with UAB for influenza neuraminidase and complement inhibitors. Under the terms of these agreements, UAB performed specific research for the Company in return for research payments and license fees. UAB has granted the Company certain rights to any discoveries in these areas resulting from research developed by UAB or jointly developed with the Company. The Company has agreed to pay single digit royalties on sales of any resulting product and to share in future payments received from other third-party partners. The Company has completed the research under the UAB agreements. These two agreements have initial 25-year terms, are automatically renewable for five-year terms throughout the life of the last patent and are terminable by the Company upon three months notice and by UAB under certain circumstances. Upon termination both parties shall cease using the other parties’ proprietary and confidential information and materials, the parties shall jointly own joint inventions and UAB shall resume full ownership of all UAB licensed products. There is currently no activity between the Company and UAB on these agreements, but when the Company licenses this technology, such as in the case of the Shionogi and Green Cross agreements, or commercializes products related to these programs, the Company will owe sublicense fees or royalties on amounts it receives.

Quarterly Financial Information (Unaudited)

12 Months Ended

Dec. 31, 2012

Quarterly Financial Information (Unaudited) [Abstract]

Quarterly Financial Information (Unaudited)

Note 10 — Quarterly Financial Information (Unaudited)


	First			Second			Third			Fourth
2012 Quarters
Revenues	$	12,221		$	4,210		$	5,761		$	4,101
Net Loss		(6,052	)		(12,276	)		(9,700	)		(11,053	)
Basic and diluted net loss per share		(0.13	)		(0.25	)		(0.19	)		(0.22	)
2011 Quarters
Revenues	$	5,435		$	3,735		$	5,249		$	5,224
Net loss		(13,027	)		(16,271	)		(14,459	)		(13,192	)
Basic and diluted net loss per share		(0.29	)		(0.36	)		(0.32	)		(0.29	)

- Definition

The entire disclosure for the quarterly financial data in the annual financial statements. The disclosure may include a tabular presentation of financial information for each fiscal quarter for the current and previous year, including revenues, gross profit, income or loss before extraordinary items and earnings per share data. It also includes an indication if the information in the note is unaudited, comments on the aggregate effect of year-end adjustments, and an explanation of matters or transactions that affect comparability or are pertinent to an understanding of the information furnished.

+ References + Details

Recent Accounting Pronouncements

12 Months Ended

Dec. 31, 2012

Recent Accounting Pronouncements [Abstract]

Recent Accounting Pronouncements

Note 11 — Recent Accounting Pronouncements

In May 2011, the Financial Accounting Standards Board (the “FASB”) issued Accounting Standards Update (“ASU”) 2011-04, “Fair Value Measurement (Topic 820): Amendments to Achieve Common Fair Value Measurements and Disclosure Requirement in U.S. GAAP and IFRS.” This ASU modifies the existing standards to include disclosure of all transfers between Level 1 and Level 2 asset and liability fair value categories. In addition, the ASU provides guidance on measuring the fair value of financial instruments managed within a portfolio and the application of premiums and discounts on fair value measurements. The ASU requires additional disclosure for Level 3 measurements regarding the sensitivity of fair value to changes in unobservable inputs and any interrelationships between those inputs. This guidance is effective for interim and annual periods beginning after December 15, 2011, with early adoption prohibited. The Company adopted this ASU in the first quarter of 2012.

In June 2011, the FASB issued ASU 2011-05, “Comprehensive Income (Topic 220): Presentation of Comprehensive Income.” This ASU eliminates the current option to report other comprehensive income and its components in the statement of changes in equity. Under this new ASU, an entity can elect to present items of net income, other comprehensive income and total comprehensive income in one continuous statement or in two separate, but consecutive statements. This guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. Early adoption is permitted, but retrospective application is required. The Company adopted this ASU in the first quarter of 2012.

In December 2011, the FASB issued ASU 2011-12, “Comprehensive Income (Topic 220): Deferral of the Effective Date for Amendments to the Presentation of Reclassifications of Items Out of Accumulated Other Comprehensive Income in Accounting Standards Update No. 2011-05.” This ASU defers the requirement in ASU 2011-05 to present reclassification adjustments for each component of accumulated other comprehensive income in both net income and other comprehensive income on the face of the financial statements. This ASU does not affect the requirement to present items of net income, and other comprehensive income and total comprehensive income in one continuous statement or in two separate, but consecutive statements. This guidance is effective for fiscal years, and interim periods within those years, beginning after December 15, 2011. Early adoption is permitted, but retrospective application is required. The Company adopted this ASU in the first quarter of 2012.

- Definition

The entire disclosure for reporting accounting changes and error corrections. It includes the conveyance of information necessary for a user of the Company's financial information to understand all aspects and required disclosure information concerning all changes and error corrections reported in the Company's financial statements for the period.

+ References + Details

Significant Accounting Policies (Policies)

12 Months Ended

Dec. 31, 2012

Significant Accounting Policies [Abstract]

The Company

The Company

Basis of Presentation

Basis of Presentation

Reclassifications

Reclassifications

Cash and Cash Equivalents

Cash and Cash Equivalents

Restricted Cash

Restricted Cash

Investments

Investments


	December 31, 2012
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized		Estimated
	Cost		Interest		Gains		Losses		Fair Value
U.S. Treasury securities	$	999	$	2	$	2	$	—	$	1,003
Obligations of U.S. government and its agencies		3,505		6		2		—		3,513
Corporate debt securities		4,035		22		6		—		4,063
Commercial paper		1,695		—		1		—		1,696
Municipal obligations		5,541		27		16		—		5,584

Total investments	$	15,775	$	57	$	27	$	—	$	15,859


	December 31, 2011
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,998	$	2	$	14	$	—		$	2,014
Obligations of U.S. government and its agencies		5,000		10		—		—			5,010
Corporate debt securities		10,924		80		15		(9	)		11,010
Commercial paper		10,939		—		2		(1	)		10,940
Asset-backed securities		611		—		—		—			611
Certificate of deposit		801		1		—		—			802
Municipal obligations		10,182		68		21		(2	)		10,269

Total investments	$	40,455	$	161	$	52	$	(12	)	$	40,656

The following table summarizes the scheduled maturity for the Company’s investments at December 31, 2012 and 2011.


	2012		2011
Maturing in one year or less	$	14,708	$	25,274
Maturing after one year through two years		1,151		14,628
Maturing after two years		—		754

Total investments	$	15,859	$	40,656

Receivables

Receivables


	December 31, 2012
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	150	$	3,888	$	4,038
Shionogi & Co. Ltd.		524		—		524

Total receivables	$	674	$	3,888	$	4,562


	December 31, 2011
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	1,146	$	4,683	$	5,829
Shionogi & Co. Ltd.		2		—		2

Total receivables	$	1,148	$	4,683	$	5,831

Inventory

Inventory

The Company’s inventory consisted of the following:


	As of December 31,
	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods and supplies		(4,243	)		(4,615	)

Net inventories	$	—		$	263

Furniture and Equipment

Furniture and Equipment

Patents and Licenses

Patents and Licenses

Accrued Expenses

Accrued Expenses

•

fees paid to Clinical Research Organizations (“CROs”) in connection with preclinical and toxicology studies and clinical trials;

•

fees paid to investigative sites in connection with clinical trials;

•

fees paid to contract manufacturers in connection with the production of our raw materials, drug substance and drug products; and

•

professional fees.

Income Taxes

Income Taxes

Accumulated Other Comprehensive (Loss) Income

Accumulated Other Comprehensive (Loss) Income

Accumulated other comprehensive (loss) income is comprised of unrealized gains and losses on investments available-for-sale and is disclosed as a separate component of stockholders’ equity.

Revenue Recognition

Revenue Recognition

Collaborative and Other Research and Development Arrangements and Royalties

Collaborative and Other Research and Development arrangements and Royalties

Product Sales

Product Sales

Research and Development Expenses

Research and Development Expenses

Stock-Based Compensation

Stock-Based Compensation

Interest Expense and Deferred Financing Costs

Interest Expense and Deferred Financing Costs

Currency Hedge Agreement

Currency Hedge Agreement

Restructuring Activities

Restructuring Activities

The following table sets forth activity in the restructuring liability for the years ended December 31, 2012, 2011 and 2010.


	Employee separation costs			Facilities related charges		Total
Balance at December 31, 2009	$	—		$	—	$	—
Accruals		158			—		158
Payments		—			—		—

Balance at December 31, 2010		158			—		158
Payments		(158	)		—		(158	)

Balance at December 31, 2011		—			—		—
Accruals		1,662			97		1,759
Payments		(58	)		—		(58	)

Balance at December 31, 2012	$	1,604		$	97	$	1,701

Net Loss Per Share

Net Loss Per Share

Use of Estimates

Use of Estimates

Concentration of Market Risk

Concentration of Market Risk

Credit Risk

Credit Risk

Significant Accounting Policies (Tables)

12 Months Ended

Dec. 31, 2012

Significant Accounting Policies [Abstract]

Fair value of the Company's investments by type

The following tables summarize the fair value of the Company’s investments by type.


	December 31, 2012
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized		Estimated
	Cost		Interest		Gains		Losses		Fair Value
U.S. Treasury securities	$	999	$	2	$	2	$	—	$	1,003
Obligations of U.S. government and its agencies		3,505		6		2		—		3,513
Corporate debt securities		4,035		22		6		—		4,063
Commercial paper		1,695		—		1		—		1,696
Municipal obligations		5,541		27		16		—		5,584

Total investments	$	15,775	$	57	$	27	$	—	$	15,859


	December 31, 2011
					Gross		Gross
	Amortized		Accrued		Unrealized		Unrealized			Estimated
	Cost		Interest		Gains		Losses			Fair Value
U.S. Treasury securities	$	1,998	$	2	$	14	$	—		$	2,014
Obligations of U.S. government and its agencies		5,000		10		—		—			5,010
Corporate debt securities		10,924		80		15		(9	)		11,010
Commercial paper		10,939		—		2		(1	)		10,940
Asset-backed securities		611		—		—		—			611
Certificate of deposit		801		1		—		—			802
Municipal obligations		10,182		68		21		(2	)		10,269

Total investments	$	40,455	$	161	$	52	$	(12	)	$	40,656

Scheduled maturity for the Company's investments

The following table summarizes the scheduled maturity for the Company’s investments at December 31, 2012 and 2011.


	2012		2011
Maturing in one year or less	$	14,708	$	25,274
Maturing after one year through two years		1,151		14,628
Maturing after two years		—		754

Total investments	$	15,859	$	40,656

Summary of receivables

At December 31, 2012 and 2011, the Company had the following receivables.


	December 31, 2012
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	150	$	3,888	$	4,038
Shionogi & Co. Ltd.		524		—		524

Total receivables	$	674	$	3,888	$	4,562


	December 31, 2011
	Billed		Unbilled		Total
U.S. Department of Health and Human Services	$	1,146	$	4,683	$	5,829
Shionogi & Co. Ltd.		2		—		2

Total receivables	$	1,148	$	4,683	$	5,831

Components of inventories

The Company’s inventory consisted of the following:


	As of December 31,
	2012			2011
Supplies	$	263		$	898
Finished goods		3,980			3,980
Reserve for finished goods and supplies		(4,243	)		(4,615	)

Net inventories	$	—		$	263

Summary of revenues

The Company recorded the following revenues for the years ended December 31:


	2012		2011		2010
Royalty revenue	$	3,317	$	—	$	—
Product sales:
NT Pharma Limited (Hong Kong)		—		—		250
Other		—		—		75

Total product sales		—		—		325
Collaborative and other research and development revenues:
U.S. Department of Health and Human Services		14,026		17,099		42,530
Shionogi (Japan)		1,184		1,181		15,933
Mundipharma (United Kingdom)		7,766		1,277		1,860
Grants (United States)		—		86		978
Other		—		—		755

Total collaborative and other research and development revenues		22,976		19,643		62,056

Total revenues	$	26,293	$	19,643	$	62,381

Activity in the restructuring liability

The following table sets forth activity in the restructuring liability for the years ended December 31, 2012, 2011 and 2010.


	Employee separation costs			Facilities related charges		Total
Balance at December 31, 2009	$	—		$	—	$	—
Accruals		158			—		158
Payments		—			—		—

Balance at December 31, 2010		158			—		158
Payments		(158	)		—		(158	)

Balance at December 31, 2011		—			—		—
Accruals		1,662			97		1,759
Payments		(58	)		—		(58	)

Balance at December 31, 2012	$	1,604		$	97	$	1,701

- Definition

Tabular disclosure of available-for-sale securities which includes, but is not limited to, changes in the cost basis and fair value, fair value and gross unrealized gain (loss), fair values by type of security, contractual maturity and classification, amortized cost basis, contracts to acquire securities to be accounted for as available-for-sale, debt maturities, transfers to trading, change in net unrealized holding gain (loss) net of tax, continuous unrealized loss position fair value, aggregate losses qualitative disclosures, other than temporary impairment (OTTI) losses or other disclosures related to available for sale securities.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62557-112803

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 7
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27337-111563

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27198-111563

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 942
-SubTopic 320
-Section 50
-Paragraph 3
-URI http://asc.fasb.org/extlink&oid=6957658&loc=d3e62586-112803

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27161-111563

Reference 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 9
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27357-111563

Reference 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 320
-SubTopic 10
-Section 50
-Paragraph 6
-URI http://asc.fasb.org/extlink&oid=6872113&loc=d3e27290-111563

Reference 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Statement of Financial Accounting Standard (FAS)
-Number 115
-Paragraph 19, 20, 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 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name FASB Staff Position (FSP)
-Number FAS115-1/124-1
-Paragraph 17
-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 10: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Emerging Issues Task Force (EITF)
-Number 03-1
-Paragraph 21
-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.

+ Details

Furniture and Equipment (Tables)

12 Months Ended

Dec. 31, 2012

Furniture and Equipment [Abstract]

Furniture and equipment component

Furniture and equipment consisted of the following at December 31:


	2012			2011
Furniture and fixtures	$	596		$	596
Office equipment		1,486			1,500
Software		1,421			1,409
Laboratory equipment		6,050			6,033
Leased equipment		63			63
Leasehold improvements		5,316			5,267

		14,932			14,868
Less accumulated depreciation and amortization		(14,349	)		(13,770	)

Furniture and equipment, net	$	583		$	1,098

Royalty Monetization (Tables)

12 Months Ended

Dec. 31, 2012

Royalty Monetization [Abstract]

Schedule of redemption percentage of notes


	Redemption
Payment Dates (Between Indicated Dates)	Percentage
From and including March 9, 2012 to and including March 8, 2013		107.0	%
From and including March 9, 2013 to and including March 8, 2014		103.5	%
From and including March 9, 2014 and thereafter		100.0	%

Lease Obligations and Other Contingencies (Tables)

12 Months Ended

Dec. 31, 2012

Lease Obligations and Other Contingencies [Abstract]

Minimum payments under operating lease obligations

The Company has the following minimum payments under operating lease obligations that existed at December 31, 2012:


2013	$	1,012
2014		1,049
2015		370

Total minimum payments	$	2,431

Stock-Based Compensation (Tables)

12 Months Ended

Dec. 31, 2012

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Changes in the number and weighted-average grant-date fair value of non-vested stock option awards

Related activity under the Incentive Plan is as follows:


							Weighted
							Average
	Awards			Options			Exercise
	Available			Outstanding			Price
Balance December 31, 2009		1,773			5,827		$	6.58
Plan amendment		1,300			—			—
Stock option awards granted		(1,550	)		1,550			6.68
Stock option awards exercised		—			(240	)		2.30
Stock option awards cancelled		335			(335	)		8.42

Balance December 31, 2010		1,858			6,802			6.66
Plan amendment		1,600			—			—
Restricted stock awards granted		(211	)		—			—
Restricted stock awards cancelled		8			—			—
Stock option awards granted		(1,830	)		1,830			3.97
Stock option awards exercised		—			(190	)		1.57
Stock option awards cancelled		584			(584	)		5.99

Balance December 31, 2011		2,009			7,858			6.21
Plan amendment		1,700			—			—
Restricted stock awards granted		(415	)		—			—
Restricted stock awards cancelled		86			—			—
Stock option awards granted		(1,617	)		1,617			4.65
Stock option awards exercised		—			(350	)		1.58
Stock option awards cancelled		1,052			(1,052	)		6.26

Balance December 31, 2012		2,815			8,073		$	6.09

Related activity under the Incentive Plan is as follows:


							Weighted
							Average
	Awards			Options			Exercise
	Available			Outstanding			Price
Balance December 31, 2009		1,773			5,827		$	6.58
Plan amendment		1,300			—			—
Stock option awards granted		(1,550	)		1,550			6.68
Stock option awards exercised		—			(240	)		2.30
Stock option awards cancelled		335			(335	)		8.42

Balance December 31, 2010		1,858			6,802			6.66
Plan amendment		1,600			—			—
Restricted stock awards granted		(211	)		—			—
Restricted stock awards cancelled		8			—			—
Stock option awards granted		(1,830	)		1,830			3.97
Stock option awards exercised		—			(190	)		1.57
Stock option awards cancelled		584			(584	)		5.99

Balance December 31, 2011		2,009			7,858			6.21
Plan amendment		1,700			—			—
Restricted stock awards granted		(415	)		—			—
Restricted stock awards cancelled		86			—			—
Stock option awards granted		(1,617	)		1,617			4.65
Stock option awards exercised		—			(350	)		1.58
Stock option awards cancelled		1,052			(1,052	)		6.26

Balance December 31, 2012		2,815			8,073		$	6.09

Weighted Average Assumptions for Stock Option Awards Granted to Employees and Directors under the Incentive Plan

Weighted Average Assumptions for Stock Option Awards Granted under the Incentive Plan


	2012			2011			2010
Expected Life		5.4			5.5			5.5
Expected Volatility		87	%		80	%		89	%
Expected Dividend Yield		0.0	%		0.0	%		0.0	%
Risk-Free Interest Rate		0.9	%		2.2	%		2.4	%

Stock-Based Compensation price range information


	Outstanding						Exercisable
			Weighted		Weighted				Weighted
			Average		Average				Average
			Remaining		Exercise				Exercise
Range	Number		Life		Price		Number		Price
$0 to 3		1,024		5.4	$	1.55		943	$	1.50
3 to 6		3,510		7.3		4.19		1,448		3.88
6 to 9		2,082		4.6		7.37		1,829		7.46
9 to 12		640		3.7		11.36		640		11.36
12 to 15		811		3.4		12.54		798		12.54
15 to 18		4		3.0		15.45		4		15.45
18 to 21		2		0.2		18.99		2		18.99

$0 to 21		8,073		5.7	$	6.09		5,664	$	6.72

Non Vested Award [Member]

Share-based Compensation Arrangement by Share-based Payment Award [Line Items]

Changes in the number and weighted-average grant-date fair value of non-vested stock option awards

The following table summarizes the changes in the number and weighted-average grant-date fair value of non-vested stock option awards during 2012:


	Non-Vested Stock Option Awards			Weighted Average Grant-Date Fair Value
Balance December 31, 2011		2,733			3.04
Stock option awards granted		1,617			3.24
Stock option awards vested		(1,196	)		2.82
Stock option awards forfeited		(746	)		3.28

Balance December 31, 2012		2,408			3.18

The following table summarizes the changes in the number and weighted-average grant-date fair value of non-vested stock option awards during 2012:


	Non-Vested Stock Option Awards			Weighted Average Grant-Date Fair Value
Balance December 31, 2011		2,733			3.04
Stock option awards granted		1,617			3.24
Stock option awards vested		(1,196	)		2.82
Stock option awards forfeited		(746	)		3.28

Balance December 31, 2012		2,408			3.18

Income Taxes (Tables)

12 Months Ended

Dec. 31, 2012

Income Taxes [Abstract]

Differences between the Company's effective tax rate and the statutory tax rate

The differences between the Company’s effective tax rate and the statutory tax rate in 2012, 2011, and 2010 are as follows:


	2012			2011			2010
Income tax benefit at federal statutory rate (35%)	$	(13,678	)	$	(19,932	)	$	(11,457	)
State and local income taxes net of federal tax benefit		(1,470	)		(2,503	)		(1,092	)
Permanent items		754			890			1,753
Rate change		1,147			(2,500	)		5,178
Expiration of attribute carryforwards		5,135			2,884			5,343
Research and development tax credits		829			(2,108	)		(5,359	)
Other		281			731			253
Change in valuation allowance		7,002			22,538			5,381

Income tax expense	$	—		$	—		$	—

Components of deferred tax assets and liabilities

Significant components of the Company’s deferred tax assets and liabilities are as follows:


	2012			2011
Deferred tax assets:
Net federal and state operating losses	$	108,498		$	97,054
Research and Development credits		36,142			38,119
Fixed assets		1,185			1,265
Reserve for inventories		1,654			1,827
Deferred revenue		2,645			5,801
Stock-based compensation		6,474			5,915
Foreign currency derivative		1,851			1,584
Other		539			422

Total deferred tax assets		158,989			151,987
Valuation allowance		(158,989	)		(151,987	)

Total deferred tax liabilities		—			—

Net deferred tax assets	$	—		$	—

Quarterly Financial Information (Unaudited) (Tables)

12 Months Ended

Dec. 31, 2012

Quarterly Financial Information (Unaudited) [Abstract]

Summary of Quarterly Financial Information


	First			Second			Third			Fourth
2012 Quarters
Revenues	$	12,221		$	4,210		$	5,761		$	4,101
Net Loss		(6,052	)		(12,276	)		(9,700	)		(11,053	)
Basic and diluted net loss per share		(0.13	)		(0.25	)		(0.19	)		(0.22	)
2011 Quarters
Revenues	$	5,435		$	3,735		$	5,249		$	5,224
Net loss		(13,027	)		(16,271	)		(14,459	)		(13,192	)
Basic and diluted net loss per share		(0.29	)		(0.36	)		(0.32	)		(0.29	)

Significant Accounting Policies (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Fair value of the Company's investments by type
Amortized Cost	$ 15,775	$ 40,455
Accrued Interest	57	161
Gross Unrealized Gains	27	52
Gross Unrealized Losses		(12)
Estimated Fair Value	15,859	40,656
U.S. Treasury securities [Member]
Fair value of the Company's investments by type
Gross Unrealized Losses
Obligations of U.S. government and its agencies [Member]
Fair value of the Company's investments by type
Gross Unrealized Losses
Level 2 [Member] \| U.S. Treasury securities [Member]
Fair value of the Company's investments by type
Amortized Cost	999	1,998
Accrued Interest	2	2
Gross Unrealized Gains	2	14
Gross Unrealized Losses
Estimated Fair Value	1,003	2,014
Level 2 [Member] \| Obligations of U.S. government and its agencies [Member]
Fair value of the Company's investments by type
Amortized Cost	3,505	5,000
Accrued Interest	6	10
Gross Unrealized Gains	2
Gross Unrealized Losses
Estimated Fair Value	3,513	5,010
Level 2 [Member] \| Corporate debt securities [Member]
Fair value of the Company's investments by type
Amortized Cost	4,035	10,924
Accrued Interest	22	80
Gross Unrealized Gains	6	15
Gross Unrealized Losses		(9)
Estimated Fair Value	4,063	11,010
Level 2 [Member] \| Commercial paper [Member]
Fair value of the Company's investments by type
Amortized Cost	1,695	10,939
Accrued Interest
Gross Unrealized Gains	1	2
Gross Unrealized Losses		(1)
Estimated Fair Value	1,696	10,940
Level 2 [Member] \| Asset-backed securities [Member]
Fair value of the Company's investments by type
Amortized Cost		611
Accrued Interest
Gross Unrealized Gains
Gross Unrealized Losses
Estimated Fair Value		611
Level 2 [Member] \| Certificate of deposit [Member]
Fair value of the Company's investments by type
Amortized Cost		801
Accrued Interest		1
Gross Unrealized Gains
Gross Unrealized Losses
Estimated Fair Value		802
Level 2 [Member] \| Municipal obligations [Member]
Fair value of the Company's investments by type
Amortized Cost	5,541	10,182
Accrued Interest	27	68
Gross Unrealized Gains	16	21
Gross Unrealized Losses		(2)
Estimated Fair Value	$ 5,584	$ 10,269

Significant Accounting Policies (Details 1) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Scheduled maturity for the Company's investments
Maturing in one year or less	$ 14,708	$ 25,274
Maturing after one year through two years	1,151	14,628
Maturing after two years		754
Total investments	$ 15,859	$ 40,656

- Definition

This element represents the portion of the balance sheet assertion valued at fair value by the entity whether such amount is presented as a separate caption or as a parenthetical disclosure. Additionally, this element may be used in connection with the fair value disclosures required in the footnote disclosures to the financial statements. The element may be used in both the balance sheet and disclosure in the same submission. This item represents Available-for-sale Securities which consist of all investments in certain debt and equity securities neither classified as trading or held-to-maturity securities. A debt security represents a creditor relationship with an enterprise. Debt securities include, among other items, US Treasury securities, US government securities, municipal securities, corporate bonds, convertible debt, commercial paper, and all securitized debt instruments. An equity security represents an ownership interest in an enterprise or the right to acquire or dispose of an ownership interest in an enterprise at fixed or determinable prices. Equity securities include, among other things, common stock, certain preferred stock, warrant rights, call options, and put options, but do not include convertible debt. An entity may opt to provide the reader with additional narrative text to better understand the nature of investments in debt and equity securities which are categorized as Available-for-sale.

+ References + Details

Significant Accounting Policies (Details 2) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Summary of receivables
Total receivables	$ 4,562	$ 5,831
U.S. Department of Health and Human Services [Member]
Summary of receivables
Total receivables	4,038	5,829
Shionogi & Co. Ltd. [Member]
Summary of receivables
Total receivables	524	2
Billed [Member]
Summary of receivables
Total receivables	674	1,148
Billed [Member] \| U.S. Department of Health and Human Services [Member]
Summary of receivables
Total receivables	150	1,146
Billed [Member] \| Shionogi & Co. Ltd. [Member]
Summary of receivables
Total receivables	524	2
Unbilled [Member]
Summary of receivables
Total receivables	3,888	4,683
Unbilled [Member] \| U.S. Department of Health and Human Services [Member]
Summary of receivables
Total receivables	3,888	4,683
Unbilled [Member] \| Shionogi & Co. Ltd. [Member]
Summary of receivables
Total receivables

Significant Accounting Policies (Details 3) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Components of inventories
Supplies	$ 263	$ 898
Finished goods	3,980	3,980
Reserve for finished goods and supplies	(4,243)	(4,615)
Net inventories		$ 263

- Definition

The amount of the valuation account as of the balance sheet date which reduces the carrying amount of inventory to net realizable value; takes into consideration such factors as market value, excessive quantities based on expected sales, technological obsolescence, and shrinkage. May also provide for estimated product returns or price concessions pertaining to product cost.

+ References

Reference 1: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 330
-SubTopic 10
-Section S99
-Paragraph 2
-Subparagraph (SAB TOPIC 5.BB)
-URI http://asc.fasb.org/extlink&oid=6386940&loc=d3e100047-122729

Reference 2: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 210
-SubTopic 10
-Section S99
-Paragraph 1
-Subparagraph (SX 210.5-02.6(a))
-URI http://asc.fasb.org/extlink&oid=6877327&loc=d3e13212-122682

Reference 3: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 235
-SubTopic 10
-Section S99
-Paragraph 4
-Subparagraph (SX 210.12-09)
-URI http://asc.fasb.org/extlink&oid=6881521&loc=d3e24092-122690

Reference 4: http://www.xbrl.org/2003/role/presentationRef
-Publisher FASB
-Name Accounting Standards Codification
-Topic 330
-SubTopic 10
-Section 35
-Paragraph 2
-URI http://asc.fasb.org/extlink&oid=6386567&loc=d3e3927-108312

Reference 5: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Paragraph 14
-Chapter 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 6: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Paragraph 8, 9, 14
-Chapter 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 7: http://www.xbrl.org/2003/role/presentationRef
-Publisher AICPA
-Name Accounting Research Bulletin (ARB)
-Number 43
-Section A
-Paragraph 9
-Chapter 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 8: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 09
-Article 12

Reference 9: http://www.xbrl.org/2003/role/presentationRef
-Publisher SEC
-Name Regulation S-X (SX)
-Number 210
-Section 02
-Paragraph 6
-Subparagraph a
-Article 5

+ Details

Significant Accounting Policies (Details 4) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Summary of revenues
Royalty revenue	$ 3,317
Product sales:
Product sales			$ 325
Collaborative and other research and development revenues:
Collaborative and other research and development	22,976	$ 19,643	62,056
Total revenues	26,293	19,643	62,381
U.S. Department of Health and Human Services [Member]
Collaborative and other research and development revenues:
Collaborative and other research and development	14,026	17,099	42,530
Shionogi (Japan) [Member]
Collaborative and other research and development revenues:
Collaborative and other research and development	1,184	1,181	15,933
NT Pharma Limited (Hong Kong) [Member]
Product sales:
Product sales			250
Mundipharma (United Kingdom) [Member]
Collaborative and other research and development revenues:
Collaborative and other research and development	$ 7,766	1,277	1,860
Grants (United States) [Member]
Collaborative and other research and development revenues:
Collaborative and other research and development		$ 86	978
Other [Member]
Product sales:
Product sales			75
Collaborative and other research and development revenues:
Collaborative and other research and development			$ 755

Significant Accounting Policies (Details 5) - USD ($) $ in Thousands	3 Months Ended	12 Months Ended
	Dec. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Activity in the restructuring liability
Beginning Balance			$ 158
Restructuring	$ 302	1,759		1,034
Payments		(58)	(158)
Ending Balance	158	1,701		158
Employee Severance [Member]
Activity in the restructuring liability
Beginning Balance			158
Restructuring		1,662		158
Payments		(58)	(158)
Ending Balance	158	1,604		158
Facility Closing [Member]
Activity in the restructuring liability
Beginning Balance
Restructuring		97
Payments
Ending Balance		$ 97

Significant Accounting Policies (Details Textual) - USD ($) shares in Thousands, $ in Thousands	3 Months Ended			12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Dec. 31, 2010	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Mar. 09, 2011
Significant Accounting Policies (Textual) [Abstract]
Restricted cash	$ 308			$ 308	$ 625
Unrealized gain (loss) on marketable securities available-for-sale				(13)	(65)	$ 131
Royalty receipts paid				3,317
Significant Accounting Policies (Additional Textual) [Abstract]
Cash and Investments	37,058			37,058
Expenses reclassified from general and administrative expense to research and development expense					351
Accrued expenses	6,573			6,573	8,622
Interest expenses				4,666	3,774
Amortization of deferred financing costs				439
Cumulative mark-to-market adjustments - loss				749	4,000
Hedge collateral under the agreement	5,180			5,180	$ 3,480
General and administrative expense, restructuring charges			$ 302	$ 1,759		$ 1,034
Accelerated depreciation			$ 890
Antidilutive effect of shares issued under employee Stock Purchase Plan				6,172	5,681	4,043
Average maturity for portfolio investments				24 months
Amortization of deferred financing costs				$ 439	$ 356
Property plant and equipment depreciation methods description				Depreciation is computed using the straight-line method with estimated useful lives of five and seven years.
Leasehold improvement amortization description				Leasehold improvements are amortized over their estimated useful lives or the remaining lease term, whichever is less
Money Market Funds [Member]
Significant Accounting Policies (Textual) [Abstract]
Restricted cash	300			$ 300
Laboratory equipment [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				5 years
Office Equipment [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				5 years
Software [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				5 years
Furniture and Fixtures [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				7 years
Maximum [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				7 years
Maturity period for high-quality marketable securities				3 years
Average portfolio maturity period for high-quality marketable securities				18 months
Maturity period of investments				12 months
Maturity of investments				3 months
Minimum [Member]
Significant Accounting Policies (Textual) [Abstract]
Estimated useful lives				5 years
Maturity period of investments				3 months
JPR Royalty Sub LLC [Member]
Significant Accounting Policies (Textual) [Abstract]
Proceeds from non-recourse notes							$ 30,000
Shionogi (Japan) [Member] \| Royalty Receivable [Member]
Significant Accounting Policies (Textual) [Abstract]
Restricted cash	8			$ 8
RAPIACTA [Member]
Significant Accounting Policies (Textual) [Abstract]
Royalty payments received	$ 469	$ 2,848		$ 3,317

Furniture and Equipment (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Furniture and equipment component
Property, Plant and Equipment, Gross	$ 14,932	$ 14,868
Less accumulated depreciation and amortization	(14,349)	(13,770)
Furniture and equipment, net	583	1,098
Furniture and Fixtures [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	596	596
Office Equipment [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	1,486	1,500
Software [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	1,421	1,409
Laboratory equipment [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	6,050	6,033
Leased equipment [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	63	63
Leasehold improvements [Member]
Furniture and equipment component
Property, Plant and Equipment, Gross	$ 5,316	$ 5,267

Furniture and Equipment (Details Textual) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Furniture and Equipment (Textual) [Abstract]
Depreciation and amortization expense	$ 628	$ 886	$ 2,267

Royalty Monetization (Details)	12 Months Ended
Royalty Monetization (Details)	Dec. 31, 2012
Accrued and unpaid interest through the redemption date
From and including March 9, 2012 to and including March 8, 2013	107.00%
From and including March 9, 2013 to and including March 8, 2014	103.50%
From and including March 9, 2014 and thereafter	100.00%

Royalty Monetization (Details Textual) $ in Thousands	3 Months Ended		12 Months Ended
Royalty Monetization (Details Textual) $ in Thousands	Sep. 30, 2011 USD ($)	Mar. 31, 2011	Dec. 31, 2012 JPY (¥) Rate	Dec. 31, 2012 USD ($) Rate	Dec. 31, 2011 USD ($)	Sep. 01, 2012 USD ($)	Sep. 01, 2011 USD ($)	Mar. 09, 2011 USD ($)
Royalty Monetization (Textual) [Abstract]
Interest Due				$ 1,998	$ 1,400		$ 4,200
Prorated interest				4,200	2,018
Interest Paid From Royalty Collected				3,628	760
Interest Paid From Interest Reserve Account				1,886	1,258
Royalty Monetization (Additional Textual) [Abstract]
Interest reserve account				1,742
Interest payments				$ 132
Yen rate per dollar \| Rate			100	100
Payment of premium				$ 1,950
Change in fair value of foreign currency derivative				749	4,000
Termination fee				1,950
Currency Hedge Agreement				5,180	$ 3,480
Termination maximum obligation				$ 5,850
Pharma Notes Interest payment date of first payment		Sep. 01, 2011
Interest shortfall amount	$ 572
Currency hedge premium payable period range one			2014	2014
Currency hedge premium payable period range two			2020	2020
Currency hedge agreement termination period range one			2016	2016
Currency hedge agreement termination period range two			2020	2020
Minimum currency value required for payment of premium on specified date \| ¥			¥ 100
JPR Royalty Sub LLC [Member]
Royalty Monetization (Textual) [Abstract]
Proceeds from non-recourse notes								$ 30,000
Net proceeds from transaction				$ 22,691
Transaction costs				4,309
Establishment costs				3,000
Interest Due						$ 572
PhaRMA Notes [Member]
Royalty Monetization (Textual) [Abstract]
Aggregate principal amount								$ 30,000
Aggregate fair value of PhaRMA Notes				$ 30,000
Percentage of interest on notes secured								14.00%

Lease Obligations and Other Contingencies (Details) $ in Thousands	Dec. 31, 2012 USD ($)
Minimum payments under operating lease obligations
2013	$ 1,012
2014	1,049
2015	370
Total minimum payments	$ 2,431

Lease Obligations and Other Contingencies (Details Textual) - USD ($) $ in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Lease Obligations and Other Contingencies (Textual) [Abstract]
Rent expense for operating lease	$ 629	$ 714	$ 771
Building at North Carolina [Member]
Lease Obligations and Other Contingencies (Textual) [Abstract]
Expiry date of building lease in Alabama	Dec. 31, 2014
Building at Alabama [Member]
Lease Obligations and Other Contingencies (Textual) [Abstract]
Lease Extension Period	5 years
Expiry date of building lease in Alabama	Jun. 30, 2015

Stockholders' Equity (Details) - USD ($) $ / shares in Units, shares in Thousands, $ in Thousands	1 Months Ended	12 Months Ended
	Jun. 30, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010	Mar. 15, 2012
Stockholders' Equity (Textual) [Abstract]
Selling of company aggregate shares of common stock		50,893	45,662
Consideration for Modification of License Agreement to licensors paid in Shares Value		$ 18,807	$ 1,027	$ 5,827
Common stock Share issued		4,774	437	761
Series B Preferred stock, par value		$ 0.001	$ 0.001
Authorized shares		5,000	5,000
Preferred Stock purchase price
Authorized shares		95,000	95,000
Stockholders' Equity (Additional Textual) [Abstract]
Issue of common stock	$ 70,000	$ 509	$ 457
Common stock were issued and sales at market price		$ 70,000
Average price per share		$ 4.08	$ 2.65
Net proceeds under the agreement		$ 17,805	$ 1,027
Incentive earned		1,542
Taxes paid		$ 535
Common stock price					$ 5.23
Sales [Member]
Stockholders' Equity (Textual) [Abstract]
Selling of company aggregate shares of common stock		4,516	437
Restricted Common Stock [Member]
Stockholders' Equity (Textual) [Abstract]
Restricted common stock in shares		193
Maximum [Member]
Stockholders' Equity (Textual) [Abstract]
Commission rate	3.00%
Minimum [Member]
Stockholders' Equity (Textual) [Abstract]
Commission rate	2.00%
License Agreement [Member]
Stockholders' Equity (Textual) [Abstract]
Consideration for Modification of License Agreement to licensors paid in Shares Value		$ 5,827
Consideration for Modification of License Agreement to licensors paid in Cash		$ 90
Expiry Date of Market Issuance Sales Agreement		2027-09

Stock-Based Compensation (Details) - $ / shares shares in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Summary of related activity under Incentive Plan
Awards Available, Beginning balance	2,009	1,858	1,773
Plan amendment, Awards Available	1,700	1,600	1,300
Restricted stock awards granted, Awards Available	(415)	(211)
Restricted stock awards cancelled, Awards Available	86	8
Stock option awards granted, Awards Available	(1,617)	(1,830)	(1,550)
Stock option awards cancelled, Awards Available	1,052	584	335
Awards Available, Ending balance	2,815	2,009	1,858
Beginning balance, options	7,858	6,802	5,827
Stock option awards granted, Options Outstanding	1,617	1,830	1,550
Stock option awards exercised, Options Outstanding	(348)	(184)	(240)
Stock option awards forfeited/cancelled, Options Outstanding	(1,052)	(584)	(335)
Ending balance, options	8,073	7,858	6,802
Weighted Average Exercise Price, Beginning balance	$ 6.21	$ 6.66	$ 6.58
Stock option awards granted, Weighted Average Exercise Price	4.65	3.97	6.68
Stock option awards exercised, Weighted Average Exercise Price	1.58	1.57	2.30
Stock option awards cancelled, Weighted Average Exercise Price	6.26	5.99	8.42
Weighted Average Exercise Price, Ending balance	$ 6.09	$ 6.21	$ 6.66

Stock-Based Compensation (Details 1)	12 Months Ended
Stock-Based Compensation (Details 1)	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Weighted Average Assumptions for Stock Option Awards Granted under the Incentive Plan
Expected Life	5 years 4 months 24 days	5 years 6 months	5 years 6 months
Expected Volatility	87.00%	80.00%	89.00%
Expected Dividend Yield	0.00%	0.00%	0.00%
Risk-Free Interest Rate	0.90%	2.20%	2.40%

Stock-Based Compensation (Details 2) shares in Thousands	12 Months Ended
Stock-Based Compensation (Details 2) shares in Thousands	Dec. 31, 2012 $ / shares shares
Stock-Based Compensation price range information
Number of outstanding options \| shares	8,073
Weighted average remaining life, Outstanding options	5 years 8 months 12 days
Weighted average exercise price, Outstanding options	$ 6.09
Number of exercisable options \| shares	5,664
Weighted average exercise price, Exercisable options	$ 6.72
$0 to $3 [Member]
Stock-Based Compensation price range information
Lower limit	0
Upper limit	$ 3
Number of outstanding options \| shares	1,024
Weighted average remaining life, Outstanding options	5 years 4 months 24 days
Weighted average exercise price, Outstanding options	$ 1.55
Number of exercisable options \| shares	943
Weighted average exercise price, Exercisable options	$ 1.50
$3 to $6 [Member]
Stock-Based Compensation price range information
Lower limit	3
Upper limit	$ 6
Number of outstanding options \| shares	3,510
Weighted average remaining life, Outstanding options	7 years 3 months 18 days
Weighted average exercise price, Outstanding options	$ 4.19
Number of exercisable options \| shares	1,448
Weighted average exercise price, Exercisable options	$ 3.88
$6 to $9 [Member]
Stock-Based Compensation price range information
Lower limit	6
Upper limit	$ 9
Number of outstanding options \| shares	2,082
Weighted average remaining life, Outstanding options	4 years 7 months 6 days
Weighted average exercise price, Outstanding options	$ 7.37
Number of exercisable options \| shares	1,829
Weighted average exercise price, Exercisable options	$ 7.46
$9 to $12 [Member]
Stock-Based Compensation price range information
Lower limit	9
Upper limit	$ 12
Number of outstanding options \| shares	640
Weighted average remaining life, Outstanding options	3 years 8 months 12 days
Weighted average exercise price, Outstanding options	$ 11.36
Number of exercisable options \| shares	640
Weighted average exercise price, Exercisable options	$ 11.36
$12 to $15 [Member]
Stock-Based Compensation price range information
Lower limit	12
Upper limit	$ 15
Number of outstanding options \| shares	811
Weighted average remaining life, Outstanding options	3 years 4 months 24 days
Weighted average exercise price, Outstanding options	$ 12.54
Number of exercisable options \| shares	798
Weighted average exercise price, Exercisable options	$ 12.54
$15 to $18 [Member]
Stock-Based Compensation price range information
Lower limit	15
Upper limit	$ 18
Number of outstanding options \| shares	4
Weighted average remaining life, Outstanding options	3 years
Weighted average exercise price, Outstanding options	$ 15.45
Number of exercisable options \| shares	4
Weighted average exercise price, Exercisable options	$ 15.45
$18 to $21 [Member]
Stock-Based Compensation price range information
Lower limit	18
Upper limit	$ 21
Number of outstanding options \| shares	2
Weighted average remaining life, Outstanding options	2 months 12 days
Weighted average exercise price, Outstanding options	$ 18.99
Number of exercisable options \| shares	2
Weighted average exercise price, Exercisable options	$ 18.99
$0 to $21 [Member]
Stock-Based Compensation price range information
Lower limit	0
Upper limit	$ 21

Stock-Based Compensation (Details 3) - $ / shares shares in Thousands	12 Months Ended
	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Changes in the number and weighted-average grant-date fair value of non-vested stock option awards
Beginning balance, options	7,858	6,802	5,827
Weighted Average Exercise Price, Beginning balance	$ 6.21	$ 6.66	$ 6.58
Stock option awards granted, options	1,617	1,830	1,550
Stock option awards granted, Weighted Average Grant-Date Fair Value	$ 4.65	$ 3.97	$ 6.68
Stock option awards forfeited/cancelled, Options Outstanding	(1,052)	(584)	(335)
Stock option awards forfeited, Weighted Average Grant-Date Fair Value	$ 6.26	$ 5.99	$ 8.42
Ending balance, options	8,073	7,858	6,802
Weighted Average Exercise Price, Ending balance	$ 6.09	$ 6.21	$ 6.66
Non Vested Options [Member]
Changes in the number and weighted-average grant-date fair value of non-vested stock option awards
Beginning balance, options	2,733
Weighted Average Exercise Price, Beginning balance	$ 3.04
Stock option awards granted, options	1,617
Stock option awards granted, Weighted Average Grant-Date Fair Value	$ 3.24
Stock option awards vested, options	1,196
Stock option awards vested, Weighted Average Grant-Date Fair Value	$ 2.82
Stock option awards forfeited/cancelled, Options Outstanding	(746)
Stock option awards forfeited, Weighted Average Grant-Date Fair Value	$ 3.28
Ending balance, options	2,408	2,733
Weighted Average Exercise Price, Ending balance	$ 3.18	$ 3.04

Stock-Based Compensation (Details Textual) $ / shares in Units, $ in Thousands	12 Months Ended
	Dec. 31, 2012 USD ($) Plan $ / shares shares	Dec. 31, 2011 USD ($) $ / shares shares	Dec. 31, 2010 USD ($) $ / shares shares	Dec. 31, 2009 shares
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 4,167	$ 4,772	$ 6,302
Stock option contractual terms	10 years
Grant date fair value per share \| $ / shares	$ 3.24	$ 2.64	$ 4.65
Number of restricted stock awards granted under incentive plan \| shares	415,000	211,000
Remaining common stock shares \| shares	2,815,000	2,009,000	1,858,000	1,773,000
Common stock purchased under ESPP \| shares	110,000	94,000	51,000
Stock option awards granted, options \| shares	1,617,000	1,830,000	1,550,000
Share Based Compensation (Additional Textual) [Abstract]
Stock option vesting period	4 years
Stock option granting period after granted	1 year
Vesting period after grant date	4 years
Stock option granted to non employee directors	1 year
Unrecognized compensation cost	$ 6,272
Restricted Common stock Fully vested period	4 years
Restricted Common stock vested Percentage	25.00%
Recognized cost, 2013	$ 2,959
Recognized cost, 2014	2,010
Recognized cost, 2015	1,148
Recognized cost, 2016	$ 155
Number of stock based Compensation Plan \| Plan	2
Incentive Plan [Member]
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 4,010	$ 4,589	$ 5,961
Stock option awards granted in percentage	25.00%	25.00%
Intrinsic value of stock options exercised under Incentive Plan	$ 877	$ 374	1,169
Weighted average contractual life of stock option awards exercisable under incentive plan	5 years 8 months 12 days
Aggregate intrinsic value of stock option Exercisable under stock incentive plan	$ 163
Fair value of stock option awards vested under Incentive Plan	$ 3,373	4,775	4,441
Number of stock option awards vested and expected to vest \| shares	7,535,000
Weighted average exercise price of stock option awards \| $ / shares	$ 6.18
Weighted average remaining contractual life	6 years 1 month 6 days
ESPP [Member]
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense	$ 157	$ 146	$ 192
Weighted average grant date fair value per share under ESPP \| $ / shares	$ 1.48	$ 1.33	$ 2.76
Common stock shares reserved \| shares	975,000
Remaining common stock shares \| shares	177,000
Percentage of salary to purchase common stock	15.00%
Percentage of common stock shares Beginning	85.00%
Percentage of common stock shares Ending	85.00%
Purchase of common stock shares \| shares	3
Maximum number of shares per employee amount \| $ / shares	$ 25
Common stock purchased under ESPP \| shares	110,000	94,000	51,000
Weighted average exercise price of stock issued under ESPP \| $ / shares	$ 2.93	$ 3.21	$ 5.50
Compensation expense related to ESPP	$ 157	$ 146	$ 192
Inducement grant [Member]
Stock-Based Compensation (Textual) [Abstract]
Stock-based compensation expense		$ 37	$ 149

Income Taxes (Details) - USD ($) $ in Thousands	12 Months Ended
Income Taxes (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Differences between the Company's effective tax rate and the statutory tax rate
Income tax benefit at federal statutory rate (35%)	$ (13,678)	$ (19,932)	$ (11,457)
State and local income taxes net of federal tax benefit	(1,470)	(2,503)	(1,092)
Permanent items	754	890	1,753
Rate change	1,147	(2,500)	5,178
Expiration of attribute carryforwards	5,135	2,884	5,343
Research and development tax credits	829	(2,108)	(5,359)
Other	281	731	253
Change in valuation allowance	7,002	22,538	5,381
Income tax expense

Income Taxes (Details 1) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011
Deferred tax assets:
Net federal and state operating losses	$ 108,498	$ 97,054
Research and Development credits	36,142	38,119
Fixed assets	1,185	1,265
Reserve for inventories	1,654	1,827
Deferred revenue	2,645	5,801
Stock-based compensation	6,474	5,915
Foreign currency derivative	1,851	1,584
Other	539	422
Total deferred tax assets	158,989	151,987
Valuation allowance	(158,989)	(151,987)
Total deferred tax liabilities
Net deferred tax assets

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
Income Taxes (Additional Textual) [Abstract]
Income tax benefit at federal statutory rate	35.00%
Unrecognized tax benefits	$ 0
Accruals for interest and penalties related to unrecognized tax benefit	0	$ 0	$ 0
Federal and state operating loss carryforwards include excess tax benefit from the exercise of stock options	$ 4,901
Operating loss carry forwards expiration starting year	2013
Operating loss carry forwards expiration ending year	2032
Change in valuation allowance	$ 7,002	$ 22,538	$ 5,381
Maximum [Member]
Income Taxes (Textual) [Abstract]
Tax year open to examination	2011
Minimum [Member]
Income Taxes (Textual) [Abstract]
Tax year open to examination	2009
Research [Member]
Income Taxes (Textual) [Abstract]
Research and Development tax credit carry forward	$ 36,142
State [Member]
Income Taxes (Textual) [Abstract]
Operating loss carryforwards	311,643
Domestic [Member]
Income Taxes (Textual) [Abstract]
Operating loss carryforwards	$ 277,298

Employee 401(k) Plan (Details) - USD ($) $ in Thousands	12 Months Ended
Employee 401(k) Plan (Details) - USD ($) $ in Thousands	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Employee 401(k) Plan (Textual) [Abstract]
Matching contributions plan	$ 418	$ 391	$ 434

Collaborative and Other Research and Development Contracts (Details) $ in Thousands	1 Months Ended								12 Months Ended
	Nov. 30, 2012 Sample	Feb. 28, 2011 USD ($)	May 31, 2010 USD ($)	Sep. 30, 2009 USD ($)	Jan. 31, 2007 USD ($)	Jun. 30, 2006 USD ($)	Feb. 28, 2006 USD ($)	Jun. 30, 2000 USD ($)	Dec. 31, 2012 USD ($) Agreement	Nov. 11, 2011 USD ($)
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Royalty reduction percentage of net proceeds									0.50%
U.S. Department of Health and Human Services [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Collaborative agreement contract value					$ 102,661
Collaborative agreement period of agreement					4 years
Collaborative agreement additional contract period				12 months
Collaborative agreement additional contract value		$ 55,000		$ 77,191
Collaborative agreement adjusted contract value									$ 234,852
Collaborative agreement planned interim analysis sample size \| Sample	320
Contract term									24 months
Green Cross Corporation [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
License fee received						$ 250
Mundipharma International Holdings Limited [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Up-front payment receivable amount							$ 10,000
Deferred revenue up-front payment receivable							10,000
Deferred revenue initiation of clinic trail payment received							$ 5,000
Potential milestone payments receivable										$ 15,000
Unamortized deferred revenue, related to Amended and Restated Agreement									$ 7,766
Unamortized deferred expenses, related to Amended and Restated Agreement									$ 1,864
AECOM and IRL [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Advance notice period for termination of agreement								60 days
Milestone payment minimum								$ 1,400
Milestone payment maximum								4,000
Annual license fees minimum								150
Annual license fees maximum								$ 500
Stock issued during period value for modification of license agreement			$ 5,911
Payments for modification of license agreement			$ 90
UAB [Member]
Collaborative and Other Research and Development Contracts (Textual) [Abstract]
Period of agreement			25 years
Number of agreements \| Agreement									2
Renewable period of agreement			5 years

Quarterly Financial Information (Unaudited) (Details) - USD ($) $ / shares in Units, $ in Thousands	3 Months Ended								12 Months Ended
	Dec. 31, 2012	Sep. 30, 2012	Jun. 30, 2012	Mar. 31, 2012	Dec. 31, 2011	Sep. 30, 2011	Jun. 30, 2011	Mar. 31, 2011	Dec. 31, 2012	Dec. 31, 2011	Dec. 31, 2010
Summary of Quarterly Financial Information
Revenues	$ 4,101	$ 5,761	$ 4,210	$ 12,221	$ 5,224	$ 5,249	$ 3,735	$ 5,435	$ 26,293	$ 19,643	$ 62,381
Net loss	$ (11,053)	$ (9,700)	$ (12,276)	$ (6,052)	$ (13,192)	$ (14,459)	$ (16,271)	$ (13,027)	$ (39,081)	$ (56,948)	$ (33,853)
Basic and diluted net loss per share	$ (0.22)	$ (0.19)	$ (0.25)	$ (0.13)	$ (0.29)	$ (0.32)	$ (0.36)	$ (0.29)	$ (0.79)	$ (1.26)	$ (0.76)

- Definition

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

+ References

+ Details