10-Q/A

UNITED STATES

SECURITIES AND EXCHANGE COMMISSION

WASHINGTON, D.C. 20549

FORM 10-Q/A

(Mark One)

x	QUARTERLY REPORT PURSUANT TO SECTION 13 OR 15 (d) OF THE SECURITIES EXCHANGE ACT OF 1934 for the quarterly period ended March 31, 2013
OR
¨	TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 for the transition period from ___________ to _____________.

Commission File Number 000-23357

BIOANALYTICAL SYSTEMS, INC.

(Exact name of the registrant as specified in its charter)

INDIANA (State or other jurisdiction of incorporation or organization)	35-1345024 (I.R.S. Employer Identification No.)
2701 KENT AVENUE WEST LAFAYETTE, INDIANA (Address of principal executive offices)	47906 (Zip code)
(765) 463-4527 (Registrant's telephone number, including area code)

Indicate by check mark whether the registrant (1) has filed all reports required to be filed by Section 13 or 15(d) of the Securities Exchange Act of 1934 during the preceding 12 months (or for such shorter period that the registrant was required to file such reports), and (2) has been subject to such filing requirements for the past 90 days. YES x        NO ¨

Indicate by check mark whether the registrant has submitted electronically and posted on its corporate website, if any, every Interactive Data File required to be submitted and posted pursuant to Rule 405 of Regulation S-T (§232.405 of this chapter) during the preceding 12 months (or for such shorter period that the registrant was required to submit and post such files). YES x NO o

Indicate by check mark whether the registrant is a large accelerated filer, an accelerated filer, a non-accelerated filer or a smaller reporting company. See definitions of “large accelerated filer,” “accelerated filer,” and “smaller reporting company” in Rule 12b-2 of the Exchange Act. (Check one):

Large accelerated filer o   Accelerated filer o   Non-accelerated filer o   Smaller Reporting Company x

Indicate by check mark whether the registrant is a shell company (as defined in Rule 12b-2 of the Act). YES o NO x

As of May 10, 2013, 7,672,736 of the registrant's common shares were outstanding.

 TABLE OF CONTENTS

		Page
PART I	FINANCIAL INFORMATION
	Explanatory Note	2
Item 1	Condensed Consolidated Financial Statements (Unaudited):
	Condensed Consolidated Balance Sheets as of March 31, 2013 and September 30, 2012	3
	Condensed Consolidated Statements of Operations and Comprehensive Income (Loss) for the Three and Six Months Ended March 31, 2013 and 2012	4
	Condensed Consolidated Statements of Cash Flows for the Six Months Ended March 31, 2013 and 2012	5
	Notes to Condensed Consolidated Financial Statements	6
Item 2	Management’s Discussion and Analysis of Financial Condition and Results of Operations	15
Item 3	Quantitative and Qualitative Disclosures about Market Risk	27
Item 4	Controls and Procedures	27
PART II	OTHER INFORMATION
Item 1A	Risk Factors	28
Item 6	Exhibits	28
	Signatures	29

Explanatory Note

Bioanalytical Systems, Inc. (“we”, “us”, “our”, or the “Company”) is filing this Amended Quarterly Report on Form 10-Q/A (this “Amendment”) to amend our Quarterly Report on Form 10-Q for the quarter ended March 31, 2013, originally filed with the Securities and Exchange Commission (the “SEC”) on May 15, 2013 (the “Original Filing”). The Amendment restates our unaudited condensed consolidated financial statements and related disclosures for the three and six months ended March 31, 2012 and March 31, 2013.  This Amendment also amends certain other Items in the Original Filing, as listed in “Items Amended in this Amendment” below, as a result of the restatement. Details of the impact of this restatement are discussed below and in Note 2 to the accompanying unaudited condensed consolidated financial statements and in Management's Discussion and Analysis of Financial Condition and Results of Operations.

Restatement Background

In August 2013, we announced a delay in filing our Form 10-Q for the three and nine months ended June 30, 2013 until management resolved a complex accounting issue related to the accounting treatment for our outstanding warrants. In the same month, we announced that investors should no longer rely upon our previously issued consolidated financial statements and the related independent auditors’ reports for the fiscal years ended September 30, 2012 and September 30, 2011 or the quarterly financial statements for the first two quarters of fiscal 2013, or any earnings releases relating to these periods, because of errors in such financial statements.

As a result of the identification of such errors, we have undertaken a comprehensive review of our previously filed consolidated financial statements. We concluded that the warrants issued in connection with our public offering in May 2011 were incorrectly accounted for as equity and the fair value of those warrants should have been recorded as a liability. As a result, we have restated our previously reported consolidated financial statements for the years ended September 30, 2012 and 2011, as well as the condensed consolidated financial statements for the three and six months ended March 31, 2013. The restatement adjustments to the full fiscal years ended September 30, 2012 and 2011 are more fully described in Note 3 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012, which was filed on the date hereof.

Internal Control Consideration

Our management has determined that there was a control deficiency in our internal control over financial reporting that constitutes a material weakness and has concluded that our disclosure controls and procedures were not effective as of March 31, 2013 as a result of the issues that resulted in the restatement of our financial statements for the period and as discussed in Part I — Item 4 of this Amendment. A material weakness is a control deficiency, or combination of control deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of the annual or interim condensed consolidated financial statements will not be prevented or detected on a timely basis. For a discussion of management’s consideration of our disclosure controls and procedures, internal control over financial reporting and the material weakness identified, see Part I — Item 4 included in this Amendment.

Items Amended in This Amendment

For the convenience of the reader, this Amendment sets forth the Original Filing, in its entirety, as modified and superseded where necessary to reflect the restatement.  The following items in the Original Filing have been amended as a result of, and to reflect, the restatement:

• Part I – Item 1. Financial Statements;

• Part I – Item 2. Management’s Discussion and Analysis of Financial Condition and Results of Operations; and

• Part I– Item 4. Controls and Procedures.

In accordance with applicable SEC rules, this Amendment includes new certifications required under the Securities and Exchange Act of 1934, as amended (“Exchange Act"), dated as of the filing date of this Amendment.

We have not updated items in this Amendment to reflect events occurring after the Original Filing date, other than those associated with the restatement of our financial statements. 

2

BIOANALYTICAL SYSTEMS, INC.

CONDENSED CONSOLIDATED BALANCE SHEETS

(In thousands, except share amounts)

	March 31,   2013			September 30, 2012
	(Restated)			(Restated)
	(Unaudited)
Assets
Current assets:
Cash and cash equivalents	$	140		$	721
Accounts receivable
Trade, less allowances of $162 and $123 as of March 31, 2013 and September 30, 2012, respectively.		2,436			3,366
Unbilled revenues and other		1,136			921
Inventories		1,653			1,656
Refundable Income Taxes		2			—
Prepaid expenses		194			228
Total current assets		5,561			6,892
Property and equipment, net		17,736			18,628
Goodwill		1,383			1,383
Debt issue costs		59			18
Other assets		51			54
Total assets	$	24,790		$	26,975
Liabilities and shareholders’ equity
Current liabilities:
Accounts payable	$	3,659		$	3,934
Accrued expenses		1,420			2,067
Customer advances – deferred revenues		2,675			3,012
Income tax accruals		16			17
Revolving line of credit		813			1,444
Fair value of warrant liability		1,238			1,213
Current portion of capital lease obligation		260			330
Current portion of long-term debt		5,549			583
Total current liabilities		15,630			12,600
Capital lease obligation, less current portion		607			739
Long-term debt, less current portion		—			5,259
Commitments and contingencies
Shareholders’ equity:
Preferred shares, authorized 1,000,000 shares, no par value:
1,335 Series A shares at $1,000 stated value issued and outstanding at March 31, 2013 and at September 30, 2012		1,335			1,335
Common shares, no par value:
Authorized 19,000,000 shares; 7,671,364 issued and outstanding at March 31, 2013 and 7,638,738 at September 30, 2012		1,880			1,871
Additional paid-in capital		19,802			19,635
Accumulated deficit		(14,548	)		(14,493	)
Accumulated other comprehensive income		84			29
Total shareholders’ equity		8,553			8,377
Total liabilities and shareholders’ equity	$	24,790		$	26,975

The accompanying notes are an integral part of the condensed consolidated financial statements.

3

BIOANALYTICAL SYSTEMS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS

AND COMPREHENSIVE INCOME (LOSS)

(In thousands, except per share amounts)

(Unaudited)

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Service revenue	$	3,667		$	5,279		$	8,337		$	10,890
Product revenue		1,489			1,687			2,623			3,592
Total revenue		5,156			6,966			10,960			14,482
Cost of service revenue		3,230			5,066			6,612			10,322
Cost of product revenue		668			757			1,234			1,535
Total cost of revenue		3,898			5,823			7,846			11,857
Gross profit		1,258			1,143			3,114			2,625
Operating expenses:
Selling		292			996			662			1,994
Research and development		123			162			208			340
General and administrative		852			1,626			1,950			3,234
Total operating expenses		1,267			2,784			2,820			5,568
Restructuring charges		—			64			—			64
Operating income (loss)		(9	)		(1,705	)		294			(3,007	)
Interest expense		(163	)		(179	)		(329	)		(368	)
Change in fair value of warrant liability – (increase) decrease		(142	)		56			(25	)		—
Other income		3			—			5			—
Loss before income taxes		(311	)		(1,828	)		(55	)		(3,375	)
Income taxes		—			—			—			—
Net loss	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Other comprehensive income (loss):
Foreign currency translation adjustment		46			23			55			22
Comprehensive loss	$	(265	)	$	(1,805	)	$	—		$	(3,353	)
Basic net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)
Diluted loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)
Weighted common shares outstanding:
Basic		7,657			7,034			7,648			6,989
Diluted		7,657			7,034			7,648			6,989

The accompanying notes are an integral part of the condensed consolidated financial statements.

4

BIOANALYTICAL SYSTEMS, INC.

CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS

(In thousands)

(Unaudited)

	Six Months Ended March 31,
	2013			2012
	(Restated)			(Restated)
Operating activities:
Net loss	$	(55	)	$	(3,375	)
Adjustments to reconcile net income (loss) to net cash provided by operating activities:
Depreciation and amortization		908			1,145
Change in fair value of warrant liability - increase		25			—
Employee stock compensation expense		135			73
Provision for doubtful accounts		39			46
Loss (gain) on sale of property and equipment		(19	)		3
Changes in operating assets and liabilities:
Accounts receivable		676			495
Inventories		4			(218	)
Refundable income taxes		(3	)		(46	)
Prepaid expenses and other assets		(7	)		151
Accounts payable		(231	)		886
Accrued expenses		(647	)		372
Customer advances		(337	)		107
Net cash provided (used) by operating activities		488			(361	)
Investing activities:
Capital expenditures		(12	)		(817	)
Proceeds from sale of equipment		20			—
Net cash provided (used) by investing activities		8			(817	)
Financing activities:
Payments of long-term debt		(293	)		(378	)
Payments on revolving line of credit		(11,018	)		(14,680	)
Borrowings on revolving line of credit		10,387			14,434
Payments on capital lease obligations		(202	)		(311	)
Net cash used by financing activities		(1,126	)		(935	)
Effect of exchange rate changes		49			3
Net decrease in cash and cash equivalents		(581	)		(2,110	)
Cash and cash equivalents at beginning of period		721			2,963
Cash and cash equivalents at end of period	$	140		$	853
Supplemental disclosure of non-cash financing activities:
Preferred stock dividends paid in common shares	$	(40	)	$	(61	)

The accompanying notes are an integral part of the condensed consolidated financial statements.

5

BIOANALYTICAL SYSTEMS, INC.
NOTES TO CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

(Amounts in thousands except per share data or as otherwise indicated)

(Unaudited)

1. DESCRIPTION OF THE BUSINESS AND BASIS OF PRESENTATION

Bioanalytical Systems, Inc. and its subsidiaries (“We,” the “Company” or “BASi”) engage in contract laboratory research services and other services related to pharmaceutical development. We also manufacture scientific instruments for life sciences research, which we sell with related software for use in industrial, governmental and academic laboratories. Our customers are located throughout the world.

We have prepared the accompanying unaudited interim condensed consolidated financial statements pursuant to the rules and regulations of the Securities and Exchange Commission (“SEC”) regarding interim financial reporting. Accordingly, they do not include all of the information and footnotes required by generally accepted accounting principles (“GAAP”) and should be read in conjunction with our audited consolidated financial statements, and the notes thereto, for the year ended September 30, 2012. In the opinion of management, the condensed consolidated financial statements for the three and six months ended March 31, 2013 and 2012 include all adjustments which are necessary for a fair presentation of the results of the interim periods and of our financial position at March 31, 2013. The results of operations for the three and six months ended March 31, 2013 are not necessarily indicative of the results for the year ending September 30, 2013.

2. RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

In August 2013, we announced the delay in filing our Form 10-Q for the three and nine months ended June 30, 2013 until management resolved a complex accounting issue related to the accounting treatment for our outstanding warrants. In the same month, we announced that investors should no longer rely upon our previously issued consolidated financial statements and the independent auditors’ reports for the fiscal years ended September 30, 2012 and 2011 or the quarterly financial statements for the first two quarters of fiscal 2013, or any earnings releases relating to these periods, because of errors in such financial statements.

As a result of the identification of such errors, we have undertaken a comprehensive review of our previously filed consolidated financial statements. We concluded that the warrants issued in connection our public offering in May 2011 were incorrectly accounted for as equity and should have been recorded as a liability. As a result, we have restated our previously reported consolidated financial statements for the years ended September 30, 2012 and 2011 as well as the condensed consolidated financial statements for three and six months ended March 31, 2013. The restatement adjustments to the full fiscal years ended September 30, 2012 and 2011 are more fully described in Note 3 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012.

As of March 31, 2013 and September 30, 2012, respectively, the restatement adjustments resulted in a cumulative net decrease to total shareholders’ equity of $1,238 and $1,213. As a result of the adjustments, we reported an increase of $142 and $25 in previously reported net loss for the three and six months ended March 31, 2013, respectively, and a decrease of $56 to previously reported net loss for the three months ended March 31, 2012. The net effect on net income for the six months ended March 31, 2012 was zero. The changes in net income (loss) were a result of the changes in the fair value of the warrant liability that is now correctly recorded in other income (expense). Except as otherwise specified, all information presented in the accompanying condensed consolidated financial statements and the related notes are presented after inclusion of all such adjustments. There was no net effect on the consolidated statements of cash flows for the three and six months ended March 31, 2013 and 2012, respectively, as the change in the fair value of the warrant liability is a non-cash item.

6

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations and comprehensive income (loss) items for the three months ended March 31:

	2013									2012
	As Reported			Adjustment			Restated			As Reported			Adjustment		Restated
Total revenue	$	5,156		$	-		$	5,156		$	6,966				$	6,966
Total cost of revenue		3,898			-			3,898			5,823					5,823
Gross profit		1,258			-			1,258			1,143			-		1,143
Total operating expenses		1,267			-			1,267			2,784					2,784
Restructuring charges		-			-			-			64			-		64
Operating income (loss)		(9	)		-			(9	)		(1,705	)		-		(1,705	)
Interest expense		(163	)		-			(163	)		(179	)				(179	)
Change in fair value of warrant liability - (increase) decrease		-			(142	)		(142	)		-			56		56
Other income		3			-			3			-			-		-
Income (loss) before income taxes		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Income tax expense		-			-			-			-					-
Net income (loss)		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Other comprehensive income (loss):
Foreign currency translation adjustment		46			-			46			23			-		23
Comprehensive income (loss)	$	(123	)	$	(142	)	$	(265	)	$	(1,861	)	$	56	$	(1,805	)
Basic EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)
Diluted EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations items for the six months ended March 31:

	2013
	As Reported			Adjustment			Restated
Total revenue	$	10,960		$	-		$	10,960
Total cost of revenue		7,846			-			7,846
Gross profit		3,114			-			3,114
Total operating expenses		2,820			-			2,820
Restructuring charges		-			-			-
Operating income (loss)		294			-			294
Interest expense		(329	)		-			(329	)
Change in fair value of warrant liability - (increase) decrease		-			(25	)		(25	)
Other income		5			-			5
Income (loss) before income taxes		(30	)		(25	)		(55	)
Income tax expense		-			-			-
Net income (loss)		(30	)		(25	)		(55	)
Other comprehensive income (loss):
Foreign currency translation adjustment		55			-			55
Comprehensive income (loss)	$	25		$	(25	)	$	-
Basic EPS	$	-		$	(0.01	)	$	(0.01	)
Diluted EPS	$	-		$	(0.01	)	$	(0.01	)

7

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated balance sheet items as of March 31, 2013 and September 30, 2012:

	March 31, 2013									September 30, 2012
	As Reported			Adjustment			Restated			As Reported			Adjustment			Restated
Total assets	$	24,790		$	-		$	24,790		$	26,975					$	26,975
Total other current liabilities		14,392			-			14,392			11,387						11,387
Fair value of warrant liability		-			1,238			1,238			-			1,213			1,213
Total current liabilities		14,392			1,238			15,630			11,387			1,213			12,600
Other long-term debt		607			-			607			5,998						5,998
Total liabilities		14,999			1,238			16,237			17,385			1,213			18,598
Shareholders' equity:
Preferred Shares		1,335			-			1,335			1,335			-			1,335
Common Shares		1,880			-			1,880			1,871			-			1,871
Additional paid-in capital		20,618			(816	)		19,802			20,451			(816	)		19,635
Accumulated deficit		(14,126	)		(422	)		(14,548	)		(14,096	)		(397	)		(14,493	)
Accumulated other comprehensive income		84			-			84			29						29
Total shareholders' equity		9,791			(1,238	)		8,553			9,590			(1,213	)		8,377
Total liabilities and shareholders' equity	$	24,790		$	-		$	24,790		$	26,975		$	-		$	26,975

3. STOCK-BASED COMPENSATION

The 2008 Stock Option Plan (“the Plan”) is used to promote our long-term interests by providing a means of attracting and retaining officers, directors and key employees and aligning their interests with those of our shareholders. The Plan is described more fully in Note 10 in the Notes to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012. All options granted under the Plan had an exercise price equal to the market value of the underlying common shares on the date of grant. We expense the estimated fair value of stock options over the vesting periods of the grants. We recognize expense for awards subject to graded vesting using the straight-line attribution method, reduced for estimated forfeitures. Forfeitures are revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates and an adjustment is recognized at that time. The Compensation Committee may also issue non-qualified stock option grants with vesting periods different from the 2008 Plan. As of March 31, 2013, there are 125 shares outstanding that were granted outside of the Plan. The assumptions used are detailed in Note 10 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012. Stock based compensation expense for the three and six months ended March 31, 2013 was $61 and $135, respectively. Stock based compensation expense for the three and six months ended March 31, 2012 was $26 and $73, respectively.

A summary of our stock option activity for the six months ended March 31, 2013 is as follows (shares in thousands):

	Options (shares)			Weighted- Average Exercise Price		Weighted- Average Grant Date Fair Value
Outstanding - October 1, 2012		354		$	1.99	$	1.46
Exercised		(7	)		1.35		1.14
Granted		179			1.46		1.20
Terminated		(24	)		2.80		1.89
Outstanding - March 31, 2013		502		$	1.77	$	1.35

During the six months ended March 31, 2013, we granted options for 179 common shares under the Plan. The fair value of each option grant is estimated on the date of the grant. The weighted-average assumptions used to compute the fair value of these options were as follows:

8

Risk-free interest rate	1.00% - 1.95%
Dividend yield	0.00%
Expected volatility	93.55% - 93.71%
Expected life of the options (years)	8.0
Forfeitures	3.00%

4. INCOME (LOSS) PER SHARE

We compute basic income (loss) per share using the weighted average number of common shares outstanding.

The Company has three categories of dilutive potential common shares: the Series A preferred shares issued in May 2011 in connection with the registered direct offering, the Warrants issued in connection with the same offering in May 2011, and shares issuable upon exercise of options. We compute diluted earnings per share using the if-converted method for preferred stock and the treasury stock method for stock options and warrants. Shares issuable upon exercise of options were not considered in computing diluted earnings per share for the three and six months ended March 31, 2013 and 2012, respectively, because they were anti-dilutive. Warrants for 1,377 common shares and 668 common shares issuable upon conversion of preferred shares were not considered in computing diluted earnings per share for the three and six months ended March 31, 2013, because they were anti-dilutive. Warrants for 2,753 common shares and 1,044 common shares issuable upon conversion of preferred shares were not considered in computing diluted earnings per share for the three and six months ended March 31, 2012 because they were also anti-dilutive.

The following table reconciles our computation of basic income (loss) per share to diluted income (loss) per share:

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Basic net loss per share:
Net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Basic net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)
Diluted net loss per share:
Diluted net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Dilutive stock options/shares		—			—			—			—
Diluted weighted average common shares outstanding		7,657			7,034			7,648			6,989
Diluted net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)

9

5. INVENTORIES

Inventories consisted of the following:

	March 31,  2013			September 30, 2012
Raw materials	$	1,401		$	1,407
Work in progress		337			283
Finished goods		226			276
	$	1,964		$	1,966
Obsolescence reserve		(311	)		(310	)
	$	1,653		$	1,656

6. SEGMENT INFORMATION

We operate in two principal segments - research services and research products. Our Services segment provides research and development support on a contract basis directly to pharmaceutical companies. Our Products segment provides liquid chromatography, electrochemical and physiological monitoring products to pharmaceutical companies, universities, government research centers and medical research institutions. Our accounting policies in these segments are the same as those described in the summary of significant accounting policies found in Note 2 to Consolidated Financial Statements in our annual report on Form 10-K/A for the year ended September 30, 2012.

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Revenue:
Service	$	3,667		$	5,279		$	8,337		$	10,890
Product		1,489			1,687			2,623			3,592
	$	5,156		$	6,966		$	10,960		$	14,482
Operating income (loss):
Service	$	(365	)	$	(1,419	)	$	(150	)	$	(2,685	)
Product		356			(275	)		444			(311	)
Corporate		—			(11	)		—			(11	)
	$	(9	)	$	(1,705	)	$	294		$	(3,007	)
Interest expense		(163	)		(179	)		(329	)		(368	)
Change in fair value of warrant liability – (increase) decrease		(142	)		56			(25	)		—
Other income		3			—			5			—
Income (loss) before income taxes	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)

Restructuring costs of $53 and $11 are included in the operating losses for the three and six months ended March 31, 2012 for the Service and Corporate segments, respectively.

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7. INCOME TAXES

We use the asset and liability method of accounting for income taxes.  We recognize deferred tax assets and liabilities for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and operating loss and tax credit carryforwards. We measure deferred tax assets and liabilities using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. We recognize the effect on deferred tax assets and liabilities of a change in tax rates in income in the period that includes the enactment date. We record valuation allowances based on a determination of the expected realization of tax assets.

We recognize the tax benefit from an uncertain tax position only if it is more likely than not to be sustained upon examination based on the technical merits of the position. We measure the amount of the accrual for which an exposure exists as the largest amount of benefit determined on a cumulative probability basis that we believe is more likely than not to be realized upon ultimate settlement of the position.

At March 31, 2013 and September 30, 2012, we had a $16 liability for uncertain income tax positions. The difference between the federal statutory rate of 34% and our effective rate of 0% is due to changes in our evaluation allowance on our net deferred tax assets.

We record interest and penalties accrued in relation to uncertain income tax positions as a component of income tax expense. Any changes in the liability for uncertain tax positions would impact our effective tax rate. We do not expect the total amount of unrecognized tax benefits to significantly change in the next twelve months.

We file income tax returns in the U.S., several U.S. States, and the United Kingdom. We remain subject to examination by taxing authorities in the jurisdictions in which we have filed returns for years after 2008.

8. DEBT

Mortgages and note payable

We have a term loan from Regions Bank (“Regions”) aggregating approximately $5,549 at March 31, 2013 and $5,842 at September 30, 2012, which is secured by mortgages on our facilities in West Lafayette and Evansville, Indiana.

On November 29, 2010, we executed amendments on two loans with Regions. As part of the amendments, we agreed to a $500 principal payment on one of the loans and a $500 principal payment on the other loan in exchange for certain modifications to the financial covenants in the loan agreements described below. The principal payments were made on December 17, 2010 and February 11, 2011, respectively. Upon receipt of these two payments, Regions incorporated the two loans into a replacement note payable for $1,341 maturing on November 1, 2012. The replacement note payable bore interest at a per annum rate equal to the 30-day LIBOR plus 300 basis points (minimum of 4.5%) with monthly principal payments of approximately $14 plus interest. The replacement note payable was secured by real estate at our West Lafayette and Evansville, Indiana locations.

As part of the amendment, Regions also agreed to amend the loan covenants for the related debt to be more favorable to us. Regions requires us to maintain a fixed charge coverage ratio of not less than 1.25 to 1.00 and a total liabilities to tangible net worth ratio of not greater than 2.10 to 1.00. At March 31, 2013, on a restated basis, we were in compliance with the fixed charge coverage, but in breach of the total liabilities to tangible net worth ratios in the Regions agreements. On September 10, 2013, Regions waived compliance with the total liabilities to tangible net worth ratio for the current quarter. Failure to comply with those covenants in future quarters would be a default under the Regions loans, requiring us to negotiate with Regions regarding loan modifications or waivers. If we are unable to obtain such modifications or waivers, Regions could accelerate the maturity of the loans and cause a cross default with our other lender.

On November 9, 2012, we executed a sixth amendment with Regions which we further modified on December 21, 2012. In the sixth amendment, Regions agreed to extend the term loan and mortgage loan maturity dates to October 31, 2013. The unpaid principal on the notes was incorporated into a replacement note payable for $5,786 bearing interest at LIBOR plus 400 basis points (minimum of 6.0%) with monthly principal payments of approximately $47 plus interest. The replacement note payable is secured by real estate at our West Lafayette and Evansville, Indiana locations. At March 31, 2013, the replacement note payable had a balance of $5,549.

The Regions loan agreement contains cross-default provisions with the revolving line of credit with Entrepreneur Growth Capital LLC (“EGC”) described below.

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The replacement note payable with Regions matures in the first quarter of fiscal 2014. We intend to refinance the amounts in lieu of making balloon payments for the remaining principal balances or sell the building in West Lafayette, Indiana. On July 12, 2012, we listed for sale our 7.25 acres and 120,000 square foot facility at 2701 Kent Avenue, West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. The asking price was $12,500. We performed an impairment analysis on the building when we listed it for sale, but noted no impairment necessary. As of March 31, 2013, the net book value of the facility and land was $9,492.

We may be unsuccessful in renegotiating the terms of the debt or those terms may be unfavorable to us. For these reasons, if we are unsuccessful at refinancing our long-term debt, our operating results and financial condition could be adversely affected.

Revolving Line of Credit

We have a $3,000 revolving line of credit agreement (“Credit Agreement”) with EGC. The term of the Credit Agreement expires on January 31, 2014. If we terminate prior to the expiration of the term, then we are subject to an early termination fee equal to the minimum interest charge of $15 for each of the months remaining until expiration.

Borrowings under the Credit Agreement bear interest at an annual rate equal to Citibank’s Prime Rate plus five percent (5%), or 8.25% as of March 31, 2013, with minimum monthly interest of $15. Interest is paid monthly. The line of credit also carries an annual facilities fee of 2% and a 0.2% collateral monitoring fee. Borrowings under the Credit Agreement are secured by a blanket lien on our personal property, including certain eligible accounts receivable, inventory, and intellectual property assets, a second mortgage on our West Lafayette and Evansville real estate and all common stock of our U.S. subsidiaries and 65% of the common stock of our non-United States subsidiary. Borrowings are calculated based on 75% of eligible accounts receivable. Under the Credit Agreement, the Company has agreed to restrict advances to subsidiaries, limit additional indebtedness and capital expenditures and maintain a minimum tangible net worth of at least $8,500. Pursuant to the terms of the Credit Agreement, the line of credit will automatically renew on January 31, 2014 unless either party gives a 60-day notice of intent to terminate or withdraw.

On December 21, 2012, we negotiated an amendment to this Credit Agreement. The amendment reduced the minimum tangible net worth covenant requirement from $8,500 to $8,000, effective on January 1, 2013, and waived all non-compliances with this covenant through December 31, 2012. At March 31, 2013, on a restated basis, we were in breachof the minimum tangible net worth covenant requirement. Due to the reclassification of the Class A Warrants to a liability from equity as discussed in Note 2, we expect to be in breach of the tangible net worth covenant for our third fiscal quarter of 2013. On October 9, 2013, EGC waived compliance with the tangible net worth covenant for our current quarter and our expected breach for the third fiscal quarter of 2013.

The Credit Agreement also contains cross-default provisions with the Regions loan and any future EGC loans.

At March 31, 2013, we had available borrowing capacity of $1,330 on this line, of which $813 was outstanding. At September 30, 2012, we had available borrowing capacity of $1,927 on this line, of which $1,444 was outstanding.

9. RESTRUCTURING

In March 2012, we announced a plan to restructure our bioanalytical laboratory operations. We consolidated our laboratory in McMinnville, Oregon into our 120,000 square foot headquarters facility in West Lafayette, Indiana. This plan was implemented to reduce operating costs and strengthen our ability to meet clients’ needs by improving laboratory utilization. In the fourth fiscal quarter of 2012, we decided to initiate closure of our facility and bioanalytical laboratory in Warwickshire, United Kingdom after careful evaluation of its financial performance and analysis of our strategic alternatives. We will continue to sell our products globally while further consolidating delivery of our CRO services into our Indiana locations. As part of the overall evaluation of our business, personnel reductions in the Selling, R&D and General and Administrative functions were also implemented at both of our Indiana locations during the second half of fiscal 2012. In total, 74 employees were terminated as part of the restructuring activities in fiscal 2012.

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We have reserved for lease payments at the UK location as of the cease use date and have considered free rent, sublease rentals and the number of days it would take to restore the space to its original condition prior to our improvements. In the first fiscal quarter of 2013, we began amortizing into normal operating income, equally through the cease use date, the estimated rent income of $200 when the reserve was originally established. Based on these, we have $837 reserved for UK lease related costs.

The following table sets forth the rollforward of the restructuring activity for the six months ended March 31, 2013.

	Balance, September 30,  2012			Total Charges		Cash Payments			Other		Balance, March 31, 2013
One-time termination benefits	$	448		$	-	$	(448	)	$	-	$	-
Lease related costs		800			-		-			37		837
Equipment moving costs and method transfers		49			-		(49	)		-		-
Travel and relocation costs		4			-		(4	)		-		-
Receivable from sale of equipment		(93	)		-		-			61		(32	)
Other costs		197			-		(56	)		-		141
Total	$	1,405		$	-	$	(557	)	$	98	$	946

Other costs include legal and professional fees and other costs incurred in connection with transitioning services from sites being closed as well as costs incurred to remove improvements previously made to the UK facility. Other activity in the reserve rollforward primarily reflects a receivable for settlement of the capital lease in the UK.

10. FAIR VALUE OF FINANCIAL INSTRUMENTS

The carrying amounts for cash and cash equivalents, accounts receivable, inventories, prepaid expenses and other assets, accounts payable and other accruals approximate their fair values because of their nature and respective duration. The fair value of the revolving credit facility and certain long-term debt is equal to their carrying values due to the variable nature of their interest rates. Our long-term fixed rate debt was initiated in February 2011 and renewed on November 1, 2012.

We have Class A and B Warrants from the May 2011 offering that are measured at fair value on a recurring basis. We recorded these warrants as a liability determining the fair value at inception on May 11, 2011. Subsequent quarterly fair value measurements, using the Black Scholes model which is considered a level 2 measurement under ASC 820-10, are calculated with changes charged to the statement of operations and comprehensive income (loss) as other income (expense) labeled change in fair value of warrant liability. Class B Warrants expired in May 2012 and the liability was reduced to zero. The assumptions used to compute the fair value of the warrants at March 31, 2013 and September 30, 2012 were as follows:

	March 31, 2013			September 30, 2012
	Warrant A			Warrant A
Risk-free interest rate		0.39	%		0.41	%
Dividend yield		0.00	%		0.00	%
Volatility of the Company's common stock		92.69	%		117.30	%
Expected life of the options (years)		3.1			3.6
Fair value per unit	$	0.899		$	0.881

11. MANAGEMENT’S PLAN

Our long-term strategic objective is to maximize the Company’s intrinsic value per share.   However, in response to our financial performance through the second quarter of fiscal 2012, we began to operate the business in a manner designed to place more emphasis on cash flow generation. Thus, our short-term tactical objective is to maximize free cash flow from operating activities.

During the first half of fiscal 2013, revenues declined approximately 24.3%, but gross margin improved 18.6% from the first half of fiscal 2012. We reported a positive operating income for the first half of fiscal 2013. We also generated $488 in cash from operations and maintained strict controls on expenditures.

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We negotiated an amendment to our loans with Regions Bank, extending the maturity date to October 2013. Our line of credit with Entrepreneur Growth Capital LLC was renewed for another year. Further, we listed for sale our headquarters facility in West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. Proceeds from this transaction would be used to pay down our debt.

For the remainder of fiscal 2013, we will continue to assess the need for additional cost controls such as reducing non-essential expenses and monitoring our operations for efficiencies to further reduce our break-even point. For the remainder of fiscal 2013, we expect to see slow but continued improvement in the volume of new bookings with little improvement in pricing. We also expect improved gross profit margins from fiscal 2012 due to cost controls implemented and restructuring activities. We have debt and lease obligations of approximately $5.8 million due in the next twelve months, including $5.5 million for the Regions loan. Based on our expected revenue, the availability on our line of credit, the impact of the cost reductions implemented and restructuring activities during fiscal 2012, we project that we will have the liquidity required to meet our fiscal 2013 operations and debt obligations. If we are unable to refinance our debt or enter into a sale-leaseback for the building in West Lafayette, we may not have sufficient liquidity to meet our debt obligations coming due in October 2013 and be able to continue our business.

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ITEM 2 - MANAGEMENT'S DISCUSSION AND ANALYSIS OF FINANCIAL CONDITION AND RESULTS OF OPERATIONS

This report contains statements that constitute forward looking statements within the meaning of the Private Securities Litigation Reform Act of 1995. Those statements appear in a number of places in this Report and may include statements regarding our intent, belief or current expectations with respect to, but are not limited to (i) our strategic plans; (ii) trends in the demand for our products and services; (iii) trends in the industries that consume our products and services; (iv) our ability to develop new products and services; (v) our ability to make capital expenditures and finance operations; (vi) global economic conditions, especially as they impact our markets; (vii) our cash position; (viii) our ability to integrate a new sales and marketing team; (ix) our ability to refinance our outstanding indebtedness and (x) our expectations regarding the volume of new bookings, pricing, gross profit margins and liquidity. Readers are cautioned that any such forward-looking statements are not guarantees of future performance and involve risks and uncertainties. Actual results may differ materially from those in the forward looking statements as a result of various factors, many of which are beyond our control.

In addition, we have based these forward-looking statements on our current expectations and projections about future events. Although we believe that the assumptions on which the forward-looking statements contained herein are based are reasonable, actual events may differ from those assumptions, and as a result, the forward-looking statements based upon those assumptions may not accurately project future events. The following discussion and analysis should be read in conjunction with the unaudited condensed consolidated financial statements and notes thereto included or incorporated by reference elsewhere in this Report. In addition to the historical information contained herein, the discussions in this Report may contain forward-looking statements that may be affected by risks and uncertainties, including those discussed in Item 1A, Risk Factors contained in our annual report on Form 10-K for the fiscal year ended September 30, 2012. Our actual results could differ materially from those discussed in the forward-looking statements.

The following amounts are in thousands, unless otherwise indicated.

Restatement of Previously Issued Consolidated Financial Statements

This Amendment Form 10-Q/A (the “Amendment”) amends the Quarterly Report on Form 10-Q for the quarterly period ended March 31, 2013, originally filed with the SEC on May 15, 2013 (the “Original Filing”). Certain financial information presented in this Amendment reflects restated consolidated financial information for the three and six months ended March 31, 2013 and 2012.

In August 2013, we announced the delay in filing our Form 10-Q for the three and nine months ended June 30, 2013 until management resolved a complex accounting issue related to the accounting treatment for our outstanding warrants. In the same month, we announced that that investors should no longer rely upon our previously issued consolidated financial statements and the independent auditors’ reports for the fiscal years ended September 30, 2012 and 2011 or the quarterly financial statements for the first two quarters of fiscal 2013, or any earnings releases relating to these periods, because of errors in such financial statements. See Item 4, Controls and Procedures.

Following a comprehensive review of our previously filed financial statements, we concluded that the warrants issued in connection our public offering in May 2011 were incorrectly accounted for as equity. As a result, we have reclassified the fair value of the warrants from equity into a liability. Also, we have recalculated the fair value of the warrants at each quarterly reporting period subsequent to the offering with an entry to other income or expense and an offset to the liability. As a result, we have restated our previously reported consolidated financial statements for the years ended September 30, 2012 and 2011 as well as the condensed consolidated financial statements for three and six months ended March 31, 2013 and December 31, 2012, respectively. The restatement adjustments to the full fiscal years ended September 30, 2012 and 2011 are more fully described in Note 3 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012.

As of March 31, 2013 and September 30, 2012, respectively, the restatement adjustments resulted in a cumulative net decrease to total shareholders’ equity of $1,238 and $1,213. As a result of the adjustments, we reported an increase of $142 and $25 in previously reported net loss for the three and six months ended March 31, 2013, respectively, and a decrease of $56 to previously reported net loss for the three months ended March 31, 2012. The net effect on net income for the six months ended March 31, 2012 was zero. The changes in net income (loss) were a result of the changes in the fair value of the warrant liability that is now correctly recorded in other income (expense). Except as otherwise specified, all information presented in the accompanying condensed consolidated financial statements and the related notes are presented after inclusion of all such adjustments. There was no net effect on the consolidated statements of cash flows for the three and six months ended March 31, 2013 and 2012, respectively, as the change in the fair value of the warrant liability is a non-cash item. More detail can be found in Note 2, Restatement of Previously Issued Condensed Consolidated Financial Statements.

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General

We are an international contract research organization providing drug discovery and development services. Our clients and partners include pharmaceutical, biotechnology, academic and governmental organizations. We apply innovative technologies and products and a commitment to quality to help clients and partners accelerate the development of safe and effective therapeutics and maximize the returns on their research and development investments. We offer an efficient, variable-cost alternative to our clients' internal product development programs. Outsourcing development work to reduce overhead and speed drug approvals through the Food and Drug Administration ("FDA") is an established alternative to in-house development among pharmaceutical companies. We derive our revenues from sales of our research services and drug development tools, both of which are focused on determining drug safety and efficacy. The Company has been involved in the research of drugs to treat numerous therapeutic areas for over 35 years.

We support the preclinical and clinical development needs of researchers and clinicians for small molecule and large biomolecule drug candidates. We believe our scientists have the skills in analytical instrumentation development, chemistry, computer software development, physiology, medicine, analytical chemistry and toxicology to make the services and products we provide increasingly valuable to our current and potential clients. Our principal clients are scientists engaged in analytical chemistry, drug safety evaluation, clinical trials, drug metabolism studies, pharmacokinetics and basic research at many of the small start-up biotechnology companies and the largest global pharmaceutical companies.

Our business is largely dependent on the level of pharmaceutical and biotechnology companies' efforts in new drug discovery and approval. Our services segment is a direct beneficiary of these efforts, through outsourcing by these companies of research work. Our products segment is an indirect beneficiary of these efforts, as increased drug development leads to capital expansion, providing opportunities to sell the equipment we produce and the consumable supplies we provide that support our products.

Developments within the industries we serve have a direct, and sometimes material, impact on our operations. Currently, many large pharmaceutical companies have major "block-buster" drugs that are nearing the end of their patent protections. This puts significant pressure on these companies both to develop new drugs with large market appeal, and to re-evaluate their cost structures and the time-to-market of their products. Contract research organizations ("CRO's") have benefited from these developments, as the pharmaceutical industry has turned to out-sourcing to both reduce fixed costs and to increase the speed of research and data development necessary for new drug applications. The number of significant drugs that have reached or are nearing the end of their patent protection has also benefited the generic drug industry. Generic drug companies provide a significant source of new business for CROs as they develop, test and manufacture their generic compounds.

A significant portion of innovation in the pharmaceutical industry is now being driven by biotech and small, venture capital funded, drug development companies. Many of these companies are "single-molecule" entities, whose success depends on one innovative compound. While several of the biotech companies have reached the status of major pharmaceuticals, the industry is still characterized by smaller entities. These developmental companies generally do not have the resources to perform much of the research within their organizations, and are therefore dependent on the CRO industry for both their research and for guidance in preparing their FDA submissions. These companies have provided significant new opportunities for the CRO industry, including us. They do, however, provide challenges in selling, as they frequently have only one product in development, which causes CROs to be unable to develop a flow of projects from a single company. These companies may expend all their available funds and cease operations prior to fully developing a product. Additionally, the funding of these companies is subject to investment market fluctuations, which changes as the risk profiles and appetite of investors change.

Research services are capital intensive. The investment in equipment and facilities to serve our markets is substantial and continuing. While our physical facilities are adequate to meet market needs for the near term, rapid changes in automation, precision, speed and technologies necessitate a constant investment in equipment and software to meet market demands. We are also impacted by the heightened regulatory environment and the need to improve our business infrastructure to support our increasingly diverse operations, which will necessitate additional capital investment. Our ability to generate capital to reinvest in our capabilities, both through operations and financial transactions, is critical to our success. While we are currently committed to fully utilizing recent additions to capacity, sustained growth will require additional investment in future periods. Our financial position could limit our ability to make such investments.

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Patient Protection and Affordable Care Act

In March 2010, the Patient Protection and Affordable Care Act (the “Act”) was enacted by the U.S. Congress and signed into law by the President. The purpose of the legislation is to extend medical insurance coverage to a higher percentage of U.S. citizens. Many of the provisions in the Act have delayed effective dates over the next decade, and will require extensive regulatory guidance. Companies in our principal client industry, pharmaceuticals, will be required under the Act to provide additional discounts on medicines provided under Medicare and Medicaid to assist in the funding of the program; however, government estimates are that over 31 million additional citizens will eventually be covered by medical insurance as a result of the Act, which should expand the markets for their products. It is premature to accurately predict the impacts these and other competing forces will have on our basic client market, drug development. Additionally, the Act does not directly impact spiraling health care costs in the U.S., which could lead to additional legislation impacting our target markets in the future.

We maintain an optional health benefits package for all of our full-time employees, which is largely paid by our contributions with employees paying a portion of the cost, generally less than 20% of the total. Based on our current understanding of the Act, we do not anticipate significant changes to our programs or of their costs to the Company or our employees as a result of the Act.

We are exploring options in plan funding, delivery of benefits and employee wellness in our continuing effort to obtain maximum benefit for our health care expenditures, while maintaining quality programs for our employees. We do not expect these efforts to have a material financial impact on the Company.

Executive Overview

Our revenues are dependent on a relatively small number of industries and clients. As a result, we closely monitor the market for our services. In the first six months of fiscal 2013, we experienced a decline in the demand for our products and services as compared to the first six months of fiscal 2012, some of which can be explained by the closure of two bioanalytical laboratories in the second half of fiscal 2012. We believe in the fundamentals of the market and that it will rebound in future periods. For the remainder of fiscal 2013, we plan to focus on sales execution, operational excellence and building strategic partnerships with pharmaceutical and biotechnology companies, to differentiate our company and create value for our clients and shareholders.

We review various metrics to evaluate our financial performance, including revenue, margins and earnings. In the first six months of fiscal 2013, we had a 24.3% decline in revenues over the same period in fiscal 2012. Gross margin and operating income, however, increased in the current fiscal year due to lower costs of revenues of 33.8% and lower operating expenses of 49.4%. As a result, we reported operating income of $294 for the first half of fiscal 2013. The improved margins and earnings were due to the restructuring activities we completed in the second half of fiscal 2012 as well as dedication to cost monitoring. We consolidated our bioanlaytical laboratories into our headquarters in West Lafayette, Indiana, closing facilities in McMinnville, Oregon and the UK to reduce operating costs and strengthen our ability to meet clients’ needs by improving laboratory utilization. We also implemented personnel reductions and other cost cutting measures in Selling, R&D and General and Administrative functions. For a detailed discussion of our revenue, margins, earnings and other financial results for the three and six months ended March 31, 2013, see “Results of Operations” below.

As of March 31, 2013, we had $140 of cash and cash equivalents as compared to $721 of cash and cash equivalents at the end of fiscal 2012. In the first six months of 2013, we generated $488 in cash from operations partially due to the lower net loss we reported versus the first six months of 2012. Total capital expenditures declined to only $12 in fiscal 2013 from $817 in fiscal 2012, as we limited spending to only necessary expenditures. We negotiated an amendment on our loans with Regions Bank, extending the maturity date to October 2013. Our line of credit with Entrepreneur Growth Capital LLC was automatically renewed for another year. In fiscal 2012, we listed for sale our headquarters facility in West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. Further, we announced the launch of Culex® NxT, the latest generation of the Company’s proprietary in vivo automated sampling system, which we expect to begin shipping in the third quarter of fiscal 2013.

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We believe that the development of innovative new drugs is going through an evolution, evidenced by the significant reduction of expenditures on research and development at several major international pharmaceutical companies, accompanied by increases in outsourcing and investments in smaller start-up companies that are performing the early development work on new compounds. Many of these companies are funded by either venture capital or pharmaceutical investment, or both, and generally do not build internal staffs that possess the extensive scientific and regulatory capabilities to perform the various activities necessary to progress a drug candidate to the filing of an Investigative New Drug (“IND”) application with the FDA.

While continuing to maintain and develop our relationships with large pharmaceutical companies, we intend to aggressively promote our services to developing businesses, which will require us to expand our existing capabilities to provide services early in the drug development process, and to consult with clients on regulatory strategy and compliance leading to their FDA filings. We have recently launched our Enhanced Drug Discovery services as part of this strategy, utilizing our proprietary Culex® technology to provide early experiments in our laboratories that previously would have been conducted in the sponsor’s facilities. As we move forward, we must balance the demands of the large pharmaceutical companies with the personal touch needed by smaller biotechnology companies to develop a competitive advantage. We intend to accomplish this through the use of and expanding upon our existing project management skills, strategic partnerships and relationship management.

We are focused on improving our cash flow from operations in fiscal 2013 to reduce our reliance on our line of credit. If we are unable to increase cash flow from operations in fiscal 2013, we may not have sufficient liquidity to continue our business.

Critical Accounting Policies

"Management's Discussion and Analysis of Financial Condition and Results of Operations" and "Liquidity and Capital Resources" discuss the unaudited condensed consolidated financial statements of the Company, which have been prepared in accordance with accounting principles generally accepted in the United States. Preparation of these financial statements requires management to make judgments and estimates that affect the reported amounts of assets, liabilities, revenues and expenses, and the disclosures of contingent assets and liabilities. Certain significant accounting policies applied in the preparation of the financial statements require management to make difficult, subjective or complex judgments, and are considered critical accounting policies. We have identified the following areas as critical accounting policies.

Revenue Recognition

The majority of our service contracts involve the processing of bioanalytical samples for pharmaceutical companies. These contracts generally provide for a fixed fee for each assay method developed or sample processed and revenue is recognized under the specific performance method of accounting. Under the specific performance method, revenue and related direct costs are recognized when services are performed. Other service contracts generally consist of preclinical studies for pharmaceutical companies. Service revenue is recognized under the proportional performance method of accounting. Losses on contracts are provided in the period in which the loss becomes determinable. Revisions in profit estimates are reflected on a cumulative basis in the period in which such revisions become known. The establishment of contract prices and total contract costs involves estimates made by the Company at the inception of the contract period. These estimates could change during the term of the contract which could impact the revenue and costs reported in the consolidated financial statements. Projected losses on contracts are provided for in their entirety when known. Revisions to estimates have not been material. Service contract fees received upon acceptance are deferred and classified within customer advances, until earned. Unbilled revenues represent revenues earned under contracts in advance of billings.

Product revenue from sales of equipment not requiring installation, testing or training is recognized upon shipment to customers. One product includes internally developed software and requires installation, testing and training, which occur concurrently. Revenue from these sales is recognized upon completion of the installation, testing and training when the services are bundled with the equipment sale.

Long-Lived Assets, Including Goodwill

Long-lived assets, such as property and equipment, and purchased intangibles subject to amortization, are reviewed for impairment whenever events or changes in circumstances indicate that the carrying amount of an asset may not be recoverable. Recoverability of assets to be held and used is measured by a comparison of the carrying amount of an asset to estimated undiscounted future cash flows expected to be generated by the asset. If the carrying amount of an asset exceeds its estimated future cash flows, an impairment charge is recognized by the amount by which the carrying amount of the asset exceeds the fair value of the asset.

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We carry goodwill at cost. Other intangible assets with definite lives are stated at cost and are amortized on a straight-line basis over their estimated useful lives. All intangible assets acquired that are obtained through contractual or legal right, or are capable of being separately sold, transferred, licensed, rented, or exchanged, are recognized as an asset apart from goodwill. Goodwill is not amortized.

Goodwill is tested annually for impairment and more frequently if events and circumstances indicate that the asset might be impaired. First, we can assess qualitative factors in determining whether it is more likely than not that the fair value of a reporting unit is less than its carrying amount. Then, we follow a two-step quantitative process. In the first step, we compare the fair value of each reporting unit, as computed primarily by present value cash flow calculations, to its book carrying value, including goodwill. We do not believe that market value is indicative of the true fair value of the Company mainly due to average daily trading volumes of less than 1%. If the fair value exceeds the carrying value, no further work is required and no impairment loss is recognized. If the carrying value exceeds the fair value, the goodwill of the reporting unit is potentially impaired and we would then complete step 2 in order to measure the impairment loss. In step 2, the implied fair value is compared to the carrying amount of the goodwill. If the implied fair value of goodwill is less than the carrying value of goodwill, we would recognize an impairment loss equal to the difference. The implied fair value is calculated by allocating the fair value of the reporting unit (as determined in step 1) to all of its assets and liabilities (including unrecognized intangible assets) and any excess in fair value that is not assigned to the assets and liabilities is the implied fair value of goodwill.

The discount rate, gross margin and sales growth rates are the two material assumptions utilized in our calculations of the present value cash flows used to estimate the fair value of the reporting units when performing the annual goodwill impairment test. Our reporting units with goodwill at March 31, 2013 are Vetronics, which is included in our Products segment, bioanalytical services and preclinical services located in Evansville, Indiana, which are both included in our Services segment, based on the discrete financial information available which is reviewed by management. We utilize a cash flow approach in estimating the fair value of the reporting units, where the discount rate reflects a weighted average cost of capital rate. The cash flow model used to derive fair value is sensitive to the discount rate and sales growth assumptions used.

Considerable management judgment is necessary to evaluate the impact of operating and macroeconomic changes and to estimate future cash flows. Assumptions used in our impairment evaluations, such as forecasted sales growth rates and our cost of capital or discount rate, are based on the best available market information. Changes in these estimates or a continued decline in general economic conditions could change our conclusion regarding an impairment of goodwill and potentially result in a non-cash impairment loss in a future period. The assumptions used in our impairment testing could be adversely affected by certain of the risks discussed in “Risk Factors” in Item 1A of our 10-K for the fiscal year ended September 30, 2012. There have been no significant events since the timing of our impairment tests that have triggered additional impairment testing.

At March 31, 2013, remaining recorded goodwill was $1,383.

Stock-Based Compensation

We recognize the cost resulting from all share-based payment transactions in our financial statements using a fair-value-based method. We measure compensation cost for all share-based awards based on estimated fair values and recognize compensation over the vesting period for awards.. We recognized stock based compensation related to stock options of $61 and $135 for the three and six months ended March 31, 2013, respectively. We recognized an expense of $26 and $73 for the three and six months ended March 31, 2012, respectively.

We use the binomial option valuation model to determine the grant date fair value. The determination of fair value is affected by our stock price as well as assumptions regarding subjective and complex variables such as expected employee exercise behavior and our expected stock price volatility over the term of the award. Generally, our assumptions are based on historical information and judgment is required to determine if historical trends may be indicators of future outcomes. We estimated the following key assumptions for the binomial valuation calculation:

• Risk-free interest rate. The risk-free interest rate is based on U.S. Treasury yields in effect at the time of grant for the expected term of the option.

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• Expected volatility. We use our historical stock price volatility on our common stock for our expected volatility assumption.

• Expected term. The expected term represents the weighted-average period the stock options are expected to remain outstanding. The expected term is determined based on historical exercise behavior, post-vesting termination patterns, options outstanding and future expected exercise behavior.

• Expected dividends. We assumed that we will pay no dividends.

Employee stock-based compensation expense recognized in the first three and six months of fiscal 2013 and 2012 was calculated based on awards ultimately expected to vest and has been reduced for estimated forfeitures. Forfeitures are revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates and an adjustment will be recognized at that time.

Changes to our underlying stock price, our assumptions used in the binomial option valuation calculation and our forfeiture rate as well as future grants of equity could significantly impact compensation expense to be recognized in fiscal 2013 and future periods.

Income Taxes

As described in Note 7 to the condensed consolidated financial statements, we use the asset and liability method of accounting for income taxes.  We recognize deferred tax assets and liabilities for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and operating loss and tax credit carryforwards. We measure deferred tax assets and liabilities using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. We recognize the effect on deferred tax assets and liabilities of a change in tax rates in income in the period that includes the enactment date. We record valuation allowances based on a determination of the expected realization of tax assets.

We recognize the tax benefit from an uncertain tax position only if it is more likely than not to be sustained upon examination based on the technical merits of the position. We measure the amount of the accrual for which an exposure exists as the largest amount of benefit determined on a cumulative probability basis that we believe is more likely than not to be realized upon ultimate settlement of the position.

We record interest and penalties accrued in relation to uncertain income tax positions as a component of income tax expense. Any changes in the accrued liability for uncertain tax positions would impact our effective tax rate. Over the next twelve months we do not anticipate changes to the carrying value of our reserve.  Interest and penalties are included in the reserve.

As of March 31, 2013 and September 30, 2012, we had a $16 liability for uncertain income tax positions, respectively.

We file income tax returns in the U.S., several U.S. states, and the foreign jurisdiction of the United Kingdom. We remain subject to examination by taxing authorities in the jurisdictions in which we have filed returns for years after 2008.

We have an accumulated net deficit in our UK subsidiary. Consequently, United States deferred tax assets on such earnings have not been recorded. Also, a valuation allowance was established in fiscal 2009 against the U.S. deferred income tax balance. We had previously recorded a valuation allowance on the UK subsidiary deferred income tax balance.

Inventories

Inventories are stated at the lower of cost or market using the first-in, first-out (FIFO) cost method of accounting. We evaluate inventories on a regular basis to identify inventory on hand that may be obsolete or in excess of current and future projected market demand. For inventory deemed to be obsolete, we provide a reserve for this inventory. Inventory that is in excess of current and projected use is reduced by an allowance to a level that approximates the estimate of future demand.

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Results of Operations

The following table summarizes the condensed consolidated statement of operations as a percentage of total revenues:

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Service revenue		71.1	%		75.8	%		76.1	%		75.2	%
Product revenue		28.9			24.2			23.9			24.8
Total revenue		100.0			100.0			100.0			100.0
Cost of service revenue (a)		88.1			96.0			79.3			94.8
Cost of product revenue (a)		44.9			44.9			47.1			42.7
Total cost of revenue		75.6			83.6			71.6			81.9
Gross profit		24.4			16.4			28.4			18.1
Total operating expenses		24.6			40.0			25.7			38.4
Restructuring expenses		—			0.9			—			0.4
Operating income (loss)		(0.2	)		(24.5	)		2.7			(20.7	)
Other expense		5.9			1.8			3.2			2.5
Income (loss) before income taxes		(6.1	)		(26.3	)		(0.5	)		(23.2	)
Income taxes		—			—			—			—
Net income (loss)		(6.1	)%		(26.3	)%		(0.5	)%		(23.2	)%

(a) Percentage of service and product revenues, respectively

Three Months Ended March 31, 2013 Compared to Three Months Ended March 31, 2012

Service and Product Revenues

Revenues for the fiscal quarter ended March 31, 2013 decreased 26.0% to $5,156 compared to $6,966 for the same period last year.

Our Service revenue decreased 30.5% to $3,667 in the current quarter compared to $5,279 for the prior year period. The consolidation of the McMinnville, Oregon laboratory into the West Lafayette location as well as the closure of the UK facility, both in fiscal 2012, contributed to the decline in bioanalytical analysis revenues in the current fiscal quarter as well as a lower number of samples to assay. Pharmaceutical analysis and toxicology revenues in our second fiscal quarter of 2013 were negatively impacted by study delays by clients.

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	Three Months Ended March 31,
	2013		2012		Change			%
Bioanalytical analysis	$	1,633	$	2,780	$	(1,147	)		-41.3	%
Toxicology		1,457		1,748		(291	)		-16.6	%
Other laboratory services		577		751		(174	)		-23.2	%

Sales in our Products segment decreased 11.7% in the current fiscal quarter from $1,687 to $1,489 when compared to the same period in the prior fiscal year. The majority of the decrease stems from lower sales of our mature analytical products as well as our Culex automated in vivo sampling systems over the same period in the prior fiscal year.

	Three Months Ended March 31,
	2013		2012		Change			%
Culex®, in-vivo sampling systems	$	628	$	772	$	(144	)		-18.7	%
Analytical instruments		612		776		(164	)		-21.1	%
Other instruments		249		139		110			79.1	%

Cost of Revenues

Cost of revenues for the current quarter was $3,898 or 75.6% of revenue, compared to $5,823, or 83.6% of revenue for the prior year period.

Cost of Service revenue as a percentage of Service revenue decreased to 88.1% in the current quarter from 96.0% in the comparable period last year. The principal cause of this decrease was due to the restructuring activities in the second half of fiscal 2012 that reduced our fixed cost base as well as strict spend monitoring.

Costs of Products revenue as a percentage of Product revenue in the current quarter remained at 44.9% from the comparable prior year period.

Operating Expenses

Selling expenses for the three months ended March 31, 2013 decreased 70.7% to $292 from $996 for the comparable period last year. This decrease stems from restructuring activities in the prior year as well as reductions in commissions, travel and marketing expenses in the current quarter.

Research and development expenses for the second quarter of fiscal 2013 decreased 24.1% over the comparable period last year to $123 from $162. The decrease was primarily due to restructuring activities in the prior year and reduced spending on consulting services in the current quarter.

General and administrative expenses for the current quarter decreased 47.6% to $852 from $1,626 for the comparable prior year period. The principal reasons for the decrease were lower salaries, benefits and rent expenses due to restructuring activities in fiscal 2012, as well as lower travel and consulting fees in the current quarter as we monitored spend closely.

Other Income (Expense)

Other expense for the current fiscal quarter increased to $302 from $123 for the same quarter of the prior fiscal year.The primary reason for the increase is the increase in the fair value of the warrant liability offset slightly by lower lease interest in fiscal 2013 due to maturities.

Income Taxes

Our effective tax rate for the quarters ended March 31, 2013 and 2012 was 0.0%. No net benefits have been provided on taxable losses in the current fiscal year. We continue to maintain a full valuation allowance on our U.S. and UK subsidiary deferred income tax balances.

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Six Months Ended March 31, 2013 Compared to Six Months Ended March 31, 2012

Service and Product Revenues

Revenues for the six months ended March 31, 2013 decreased 24.3% to $10,960 compared to $14,482 for the same period last year.

Our Service revenue decreased 23.4% to $8,337 in the first six months of fiscal 2013 compared to $10,890 for the prior year period. The consolidation of the McMinnville, Oregon laboratory into the West Lafayette location as well as the closure of the UK facility, both in fiscal 2012, contributed to the decline in bioanalytical analysis revenues in the current fiscal quarter as well as a lower number of samples to assay. Pharmaceutical analysis and toxicology revenues in our second fiscal quarter of 2013 were negatively impacted by study delays by clients.

	Six Months Ended March 31,
	2013		2012		Change			%
Bioanalytical analysis	$	3,934	$	5,636	$	(1,702	)		-30.2	%
Toxicology		3,353		3,666		(313	)		-8.5	%
Other laboratory services		1,050		1,588		(538	)		-33.9	%

Sales in our Products segment declined 27.0% in the first six months of fiscal 2013 from $3,592 to $2,623 when compared to the same period in the prior year. The majority of the decline stems from lower sales of our Culex®, in-vivo sampling systems over the same period of the prior fiscal year primarily due to the delayed launch of Culex Nxt. The following table shows more detail for our Product revenue.

	Six Months Ended March 31,
	2013		2012		Change			%
Culex®, in-vivo sampling systems	$	1,000	$	1,943	$	(943	)		-48.5	%
Analytical instruments		1,187		1,301		(114	)		-8.8	%
Other instruments		436		348		88			25.3	%

Cost of Revenues

Cost of revenues for the first six months of fiscal 2013 was $7,846 or 71.6% of revenue, compared to $11,857, or 81.9% of revenue, for the comparable period in the prior year.

Cost of Service revenue as a percentage of Service revenue decreased to 79.3% in the first six months of fiscal 2013 from 94.8% in the comparable period last year. The principal cause of this decrease was due to the restructuring activities in the second half of fiscal 2012 that reduced our fixed cost base as well as strict spend monitoring.

Cost of Product revenue as a percentage of Product revenue in the six months ending March 31, 2013 increased to 47.1% from 42.7% in the comparable period in the prior year. This increase is mainly due to a change in the mix of products sold in the current fiscal year.

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Operating Expenses

Selling expenses for the six months ended March 31, 2013 decreased 66.8% to $662 from $1,994 for the comparable period last year. This decrease stems from restructuring activities in the prior year as well as reductions in commissions, travel, marketing and consulting expenses in the current fiscal year.

Research and development expenses for the first half of fiscal 2013 decreased 38.8% from the comparable period of the prior year to $208 from $340. The decrease was primarily due to restructuring activities in the prior year and reduced spending on consulting services in the current fiscal year.

General and administrative expenses for the first six months of fiscal 2013 decreased 39.7% to $1,950 from $3,234 for the comparable period in the prior year. The principal reasons for the decrease were lower salaries, benefits and rent expenses due to restructuring activities in fiscal 2012, as well as lower travel and consulting fees in the current fiscal year as we monitored spend closely.

Other Income (Expense)

Other expense for the first six months of fiscal 2013 decreased to $349 from $368 for the same period of the prior year.The primary reasons for the decrease are lower lease interest in fiscal 2013 due to maturities offset slightly by an increase in the fair value of the warrant liability.

Income Taxes

Our effective tax rate for the six months ended March 31, 2013 and 2012 was 0.0%. No net benefits have been provided on taxable losses in the current fiscal year. We continue to maintain a full valuation allowance on our U.S. and UK subsidiary deferred income tax balances.

Restructuring Activities

In March 2012, we announced a plan to restructure our bioanalytical laboratory operations. We consolidated our laboratory in McMinnville, Oregon into our 120,000 square foot headquarters facility in West Lafayette, Indiana. This plan was implemented to reduce operating costs and strengthen our ability to meet clients’ needs by improving laboratory utilization. In the fourth quarter of fiscal 2012, we decided to initiate closure of our facility and bioanalytical laboratory in Warwickshire, United Kingdom after careful evaluation of its financial performance and analysis of our strategic alternatives. We will continue to sell our products globally while further consolidating delivery of our CRO services into our Indiana locations. As part of the overall evaluation of our business, personnel reductions in the Selling, R&D and General and Administrative functions were also implemented at both of our Indiana locations during the second half of fiscal 2012. In total, 74 employees were terminated as part of the restructuring activities in fiscal 2012.

We have reserved for lease payments at the UK location as of the cease use date and have considered free rent, sublease rentals and the number of days it would take to restore the space to its original condition prior to our improvements. In the first quarter of fiscal 2013, we began amortizing into normal operating income, equally through the cease use date, the estimated rent income of $200 when the reserve was originally established. Based on these, we have $837 reserved for UK lease related costs.

The following table sets forth the rollforward of the restructuring activity for the six months ended March 31, 2013.

	Balance, September 30, 2012			Total Charges		Cash Payments			Other		Balance, March 31,  2013
One-time termination benefits	$	448		$	-	$	(448	)	$	-	$	-
Lease related costs		800			-		-			37		837
Equipment moving costs and method transfers		49			-		(49	)		-		-
Travel and relocation costs		4			-		(4	)		-		-
Receivable from sale of equipment		(93	)		-		-			61		(32	)
Other costs		197			-		(56	)		-		141
Total	$	1,405		$	-	$	(557	)	$	98	$	946

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Other costs include legal and professional fees and other costs incurred in connection with transitioning services from sites being closed as well as costs incurred to remove improvements previously made to the UK facility. Other activity in the reserve rollforward primarily reflects a receivable for settlement of the capital lease in the UK.

Liquidity and Capital Resources

Comparative Cash Flow Analysis

At March 31, 2013, we had cash and cash equivalents of $140, compared to $721 at September 30, 2012.

Net cash provided by operating activities was $488 for the six months ended March 31, 2013 compared to $361 cash used for the six months ended March 31, 2012. The increase in cash provided by operating activities in the current fiscal year partially results from the lower operating loss in the current period versus the prior year period. Other contributing factors to our cash from operations were noncash charges of $908 for depreciation and amortization and a net decrease in accounts receivable of $676, offset slightly by cash paid during the current year for restructuring activities of $557, a net decrease in accounts payable of $231 and customer advances of $337. Included in operating activities for the first six months of fiscal 2012 are an operating loss for the period, plus non-cash charges of $1,145 for depreciation and amortization, a reduction in accounts receivable of $495 and an increase in accounts payable of $886 and accrued expenses of $372. The impact on operating cash flow of other changes in working capital was not material.

Investing activities provided $8 in the first half of fiscal 2013 as compared to $817 used in the first half of fiscal 2012. In the first half of fiscal 2013, net proceeds received from the sale of equipment provided $20 offset slightly by capital expenditures of $12. The decline in capital spending is related to our freeze on non-essential capital expenditures and cost controls implemented in the second half of fiscal 2012.

Financing activities used $1,126 in the first six months of fiscal 2013 as compared to $935 used for the first six months of fiscal 2012. The main use of cash in the first half of fiscal 2013 was for long-term debt and capital lease payments of $495 as well as net payments on our line of credit of $631. In the first half of fiscal 2012, we had long-term debt and capital lease payments of $689, as well as net payments on our line of credit of $246.

Capital Resources

We have a term loan from Regions Bank (“Regions”) aggregating approximately $5,549 at March 31, 2013, which is secured by mortgages on our facilities in West Lafayette and Evansville, Indiana and a $3,000 line of credit with Entrepreneur Growth Capital LLC (EGC). The EGC line of credit is subject to availability limitations that may substantially reduce or eliminate our borrowing capacity at any time.

On November 9, 2012, we executed a sixth amendment with Regions which we further modified on December 21, 2012. In the sixth amendment, Regions agreed to extend the term loan and mortgage loan maturity dates to October 31, 2013. The unpaid principal on the notes was incorporated into a replacement note payable for $5,786 bearing interest at LIBOR plus 400 basis points (minimum of 6.0%) with monthly principal payments of approximately $47 plus interest. The replacement note payable is secured by real estate at our West Lafayette and Evansville, Indiana locations. At March 31, 2013, the replacement note payable had a balance of $5,549 at March 31, 2013 and $5,842 at September 30, 2012.

Regions requires us to maintain a fixed charge coverage ratio of not less than 1.25 to 1.00 and a total liabilities to tangible net worth ratio of not greater than 2.10 to 1.00. At March 31, 2013, on a restated basis, we were in compliance with the fixed charge coverage, but in breach of the total liabilities to tangible net worth ratios in the Regions agreements. On September 10, 2013, Regions waived compliance with the total liabilities to tangible net worth ratio for the current quarter. Failure to comply with those covenants in future quarters would be a default under the Regions loans, requiring us to negotiate with Regions regarding loan modifications or waivers. If we are unable to obtain such modifications or waivers, Regions could accelerate the maturity of the loans and cause a cross default with our other lender.

The Regions loan agreements both contain cross-default provisions with each other and with the revolving line of credit with Entrepreneur Growth Capital LLC (“EGC”) described below.

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The replacement note payable with Regions matures in the first quarter of fiscal 2014. We intend to refinance the amounts in lieu of making balloon payments for the remaining principal balances or sell the building in West Lafayette, Indiana. On July 12, 2012, we listed for sale our 7.25 acres and 120,000 square foot facility at 2701 Kent Avenue, West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. The asking price was $12,500. We performed an impairment analysis on the building when we listed it for sale, but noted no impairment necessary. As of March 31, 2013, the net book value of the facility and land was $9,492.

We may be unsuccessful in renegotiating the terms of the debt or those terms may be unfavorable to us. For these reasons, if we are unsuccessful at refinancing our long-term debt, our operating results and financial condition could be adversely affected and we may not have sufficient liquidity to meet our debt obligations coming due in October 2013 and be able to continue our business.

Revolving Line of Credit

We have a $3,000 revolving line of credit agreement (“Credit Agreement”) with EGC. The term of the Credit Agreement expires on January 31, 2014. If we terminate prior to the expiration of the term, then we are subject to an early termination fee equal to the minimum interest charges of $15 for each of the months remaining until expiration.

Borrowings under the Credit Agreement bear interest at an annual rate equal to Citibank’s Prime Rate plus five percent (5%), or 8.25% as of March 31, 2013, with minimum monthly interest of $15. Interest is paid monthly. The line of credit also carries an annual facilities fee of 2% and a 0.2% collateral monitoring fee. Borrowings under the Credit Agreement are secured by a blanket lien on our personal property, including certain eligible accounts receivable, inventory, and intellectual property assets, a second mortgage on our West Lafayette and Evansville real estate and all common stock of our U.S. subsidiaries and 65% of the common stock of our non-United States subsidiary. Borrowings are calculated based on 75% of eligible accounts receivable. Under the Credit Agreement, the Company has agreed to restrict advances to subsidiaries, limit additional indebtedness and capital expenditures and maintain a minimum tangible net worth of at least $8,500. Pursuant to the terms of the Credit Agreement, the line of credit will automatically renew on January 31, 2014 unless either party gives a 60-day notice of intent to terminate or withdraw.

On December 21, 2012, we negotiated an amendment to this Credit Agreement. The amendment reduced the minimum tangible net worth covenant requirement from $8,500 to $8,000, effective on January 1, 2013. At March 31, 2013, on a restated basis, we were in breach of the minimum tangible net worth covenant requirement. Due to the reclassification of the Class A Warrants to a liability from equity as discussed in Note 2, we expect to be in breach of the tangible net worth covenant for our third fiscal quarter of 2013. On October 9, 2013, EGC waived compliance with the tangible net worth covenant for our current quarter and our expected breach for the third fiscal quarter of 2013. The Credit Agreement also contains cross-default provisions with the Regions loan and any future EGC loans.

Based on our current business activities and cash on hand, we expect to borrow on our revolving credit facility in fiscal 2013 to finance working capital. To conserve cash, we instituted a freeze on non-essential capital expenditures. As of March 31, 2013, we had $1,330 of total borrowing capacity with the line of credit, of which $813 was outstanding, and $140 of cash on hand. This compares to a borrowing capacity of $1,927 and $1,444 outstanding at September 30, 2012. The decline in the borrowing capacity for our first six months is due to the decline in revenues, which lowers our receivables balance.

For the remainder of fiscal 2013, we will continue to assess the need for additional cost controls such as reducing non-essential expenses and monitoring our operations for efficiencies to further reduce our break-even point. For the remainder of fiscal 2013, we expect to see slow but continued improvement in the volume of new bookings with little improvement in pricing. We also expect improved gross profit margins from fiscal 2012 due to cost controls implemented and restructuring activities. We have debt and lease obligations of approximately $1.3 million in fiscal 2013. Based on our expected revenue, the availability on our line of credit, the impact of the cost reductions implemented and restructuring activities during fiscal 2012, we project that we will have the liquidity required to meet our fiscal 2013 operations and debt obligations.

Should operations materially fail to meet our expectations for the coming fiscal year, we may not be able to comply with all of our debt covenants, requiring that we obtain a waiver at that time. If that situation arises, we will be required to negotiate with our lenders again to obtain loan modifications or waivers as described above. We cannot predict whether our lenders will provide those waivers, if required, what the terms of any such waivers might be or what impact any such waivers will have on our liquidity, financial condition or results of operations.

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ITEM 3 – QUANTITATIVE AND QUALITATIVE DISCLOSURES ABOUT MARKET RISK

A smaller reporting company is not required to provide the information required by this Item 3.

ITEM 4 - CONTROLS AND PROCEDURES

In the evaluation of disclosure controls and procedures included in our Original Report on Form 10-Q for the quarter ended March 31, 2013, the Company disclosed that under the supervision and with the participation of our Principal Executive Officer and Principal Financial Officer, concluded that our disclosure controls and procedures were effective to provide reasonable assurance of achieving the desired control objectives. As a result of the issues that resulted in the restatement of our financial statements for the period, the Company's Principal Executive Officer and Principal Financial Officer subsequently concluded that the Company’s disclosure controls and procedures were not effective as of March 31, 2013 for the reasons discussed in the section below entitled, Remediation Plan.

Remediation Plan

Our management is responsible for establishing and maintaining adequate internal control over financial reporting. Under the supervision and with the participation of our management, including our Principal Executive Officer and Principal Financial Officer, we conducted an evaluation of the effectiveness of our internal control over financial reporting based on the framework in Internal Control—Integrated Framework issued by the Committee of Sponsoring Organizations of the Treadway Commission.

After the filing of the Original Filing, Management identified material weaknesses in the proper accounting treatment of the warrants issued in connection with the May 2011 public offering. Based on these material weaknesses, management determined that the Company's internal control over financial reporting was not effective for the three months ended March 31, 2013. A material weakness is a control deficiency, or combination of control deficiencies, in internal control over financial reporting such that there is a reasonable possibility that a material misstatement of the annual or interim financial statements will not be prevented or detected on a timely basis.

In May 2011, we sold units of convertible preferred shares and warrants in a public offering which raised new capital for the Company. We erroneously recorded the warrants as equity instead of a liability. This error caused other calculations related to the offering, such as the beneficial conversion feature and deemed dividend, to be misstated. Further, other income from the change in the fair value of warrant liability was misstated because we did not correctly record the fair value of the warrants at each reporting period. Based on the erroneous recordation of the warrants as equity instead of a liability, we have restated our previously issued condensed consolidated financial statements for the fiscal years ending September 30, 2011 and September 30, 2012 and for the first two quarters of fiscal 2013.

As a corrective action, we intend to seek the counsel of other experts in accounting before discussions with our auditors on future unusual and non-recurring transactions.

Changes in Internal Controls

There were no changes in our internal control over financial reporting, as defined in Rules 13a-15(f) and 15d-15(f) under the Exchange Act, during the first six months of fiscal 2013 that have materially affected or are reasonably likely to materially affect our internal control over financial reporting.

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PART II

ITEM 1A - RISK FACTORS

You should carefully consider the risks described in our Annual Report on Form 10-K/A for the year ended September 30, 2012, including those under the heading “Risk Factors” appearing in Item 1A of Part I of the Form 10-K/A and other information contained in this Quarterly Report before investing in our securities. Realization of any of these risks could have a material adverse effect on our business, financial condition, cash flows and results of operations.

ITEM 6 - EXHIBITS

(a) Exhibits:

See Exhibit Index.

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SIGNATURES

Pursuant to the requirements of the Securities Exchange Act of 1934, the Registrant has duly caused this report to be signed on its behalf by the undersigned thereunto duly authorized:

	BIOANALYTICAL SYSTEMS, INC.
	(Registrant)
Date:   October 11, 2013	By:  /s/   Jacqueline M. Lemke
	Jacqueline M. Lemke
	President and Chief Executive Officer and Vice President of Finance and Chief Financial Officer

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EXHIBIT INDEX

Number		Description of Exhibits
(10)	10.1	Employee Incentive Stock Option Agreement between Jacqueline M. Lemke and Bioanalytical Systems, Inc., dated February 7, 2013 (incorporated by reference to Exhibit 10.1 for Form 10-Q filed May 15, 2013).
	10.2	Amended and Restated Employment Agreement between Jacqueline M. Lemke and Bioanalytical Systems, Inc. effective February 7, 2013 (incorporated by reference to Exhibit 10.2 for Form 10-Q filed May 15, 2013).
	10.3	Waiver letter from Regions Bank dated September 10, 2013 (incorporated by reference to Exhibit 10.25 for Form 10-K/A filed October 11, 2013).
	10.4	Waiver letter from EGC dated October 9, 2013 (incorporated by reference to Exhibit 10.26 for Form 10-K/A filed October 11, 2013).
(31)	31.1	Certification of Chief Executive Officer and Chief Financial Officer (filed herewith).
(32)	32.1	Written Statement of Chief Executive Officer and Chief Financial Officer Pursuant to Section 906 of the Sarbanes-Oxley Act of 2002 (18 U.S.C. Section 1350) (filed herewith)..
	101	XBRL data file (filed herewith).

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EX-31.1

CERTIFICATIONS

I, Jacqueline M. Lemke, President and Chief Executive Officer, Vice President of Finance and Chief Financial Officer, certify that:

1. I have reviewed this report on Form 10-Q/A of Bioanalytical Systems, Inc.;

2. Based on my knowledge, this report does not contain any untrue statement of a material fact or omit to state a material fact necessary to make the statements made, in light of the circumstances under which such statements were made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financial information included in this report, fairly present in all material respects the financial condition, results of operations and cash flows of the registrant as of, and for, the periods presented in this report;

4. The registrant's other certifying officer(s) and I are responsible for establishing and maintaining disclosure controls and procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal control over financial reporting (as defined in Exchange Act Rules 13a-15(f) and 15d-15(f)) for the registrant and have:

a. Designed such disclosure controls and procedures, or caused such disclosure controls and procedures to be designed under our supervision, to ensure that material information relating to the registrant, including its consolidated subsidiaries, is made known to us by others within those entities, particularly during the period in which this report is being prepared;

b. Designed such internal control over financial reporting, or caused such internal control over financial reporting to be designed under our supervision, to provide reasonable assurance regarding the reliability of financial reporting and the preparation of financial statements for external purposes in accordance with generally accepted accounting principles;

c. Evaluated the effectiveness of the registrant's disclosure controls and procedures and presented in this report our conclusions about the effectiveness of the disclosure controls and procedures, as of the end of the period covered by this report based on such evaluation; and

d. Disclosed in this report any change in the registrant's internal control over financial reporting that occurred during the registrant's most recent fiscal quarter (the registrant's fourth fiscal quarter in the case of an annual report) that has materially affected, or is reasonably likely to materially affect, the registrant's internal control over financial reporting.

5. The registrant's other certifying officer(s) and I have disclosed, based on our most recent evaluation of internal control over financial reporting, to the registrant's auditors and the audit committee of the registrant's board of directors (or persons performing the equivalent functions);

a. All significant deficiencies and material weaknesses in the design or operation of internal control over financial reporting which are reasonably likely to adversely affect the registrant's ability to record, process, summarize and report financial information; and

b. Any fraud, whether or not material, that involves management or other employees who have a significant role in the registrant's internal control over financial reporting.

	/s/ Jacqueline M. Lemke
	Jacqueline M. Lemke
Date:  October 11, 2013	President and Chief Executive Officer,
	Vice President of Finance and Chief Financial Officer

EX-32.1

Certifications of Chief Executive Officer and Chief Financial Officer

Pursuant to Section 906

Of the Sarbanes-Oxley Act of 2002 (18 U.S.C. Section 1350)

The undersigned, the President and Chief Executive Officer, Vice President of Finance and Chief Financial Officer of Bioanalytical Systems Inc. (the “Company”), hereby certifies that, to the best of her knowledge:

(a)	the Form 10-Q/A QuarterlyReport of the Company for the three and six months ended March 31, 2013 filed with the Securities and Exchange Commission (the “Report”) fully complies with the requirements of Section 13(a) or 15(d) of the Securities Exchange Act of 1934; and
(b)	the information contained in the Report fairly presents, in all material respects, the financial condition and results of operations of the Company.

By:  /s/  Jacqueline M. Lemke

Jacqueline M. Lemke

President and  Chief Executive Officer, Vice President of

Finance and Chief Financial Officer

Date:   October 11, 2013

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RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Tables)

6 Months Ended

Mar. 31, 2013

RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS [Abstract]

Schedule of Effects of Restatement Adjustments

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations and comprehensive income (loss) items for the three months ended March 31:

	2013									2012
	As Reported			Adjustment			Restated			As Reported			Adjustment		Restated
Total revenue	$	5,156		$	-		$	5,156		$	6,966				$	6,966
Total cost of revenue		3,898			-			3,898			5,823					5,823
Gross profit		1,258			-			1,258			1,143			-		1,143
Total operating expenses		1,267			-			1,267			2,784					2,784
Restructuring charges		-			-			-			64			-		64
Operating income (loss)		(9	)		-			(9	)		(1,705	)		-		(1,705	)
Interest expense		(163	)		-			(163	)		(179	)				(179	)
Change in fair value of warrant liability - (increase) decrease		-			(142	)		(142	)		-			56		56
Other income		3			-			3			-			-		-
Income (loss) before income taxes		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Income tax expense		-			-			-			-					-
Net income (loss)		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Other comprehensive income (loss):
Foreign currency translation adjustment		46			-			46			23			-		23
Comprehensive income (loss)	$	(123	)	$	(142	)	$	(265	)	$	(1,861	)	$	56	$	(1,805	)
Basic EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)
Diluted EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations items for the six months ended March 31:

	2013
	As Reported			Adjustment			Restated
Total revenue	$	10,960		$	-		$	10,960
Total cost of revenue		7,846			-			7,846
Gross profit		3,114			-			3,114
Total operating expenses		2,820			-			2,820
Restructuring charges		-			-			-
Operating income (loss)		294			-			294
Interest expense		(329	)		-			(329	)
Change in fair value of warrant liability - (increase) decrease		-			(25	)		(25	)
Other income		5			-			5
Income (loss) before income taxes		(30	)		(25	)		(55	)
Income tax expense		-			-			-
Net income (loss)		(30	)		(25	)		(55	)
Other comprehensive income (loss):
Foreign currency translation adjustment		55			-			55
Comprehensive income (loss)	$	25		$	(25	)	$	-
Basic EPS	$	-		$	(0.01	)	$	(0.01	)
Diluted EPS	$	-		$	(0.01	)	$	(0.01	)

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated balance sheet items as of March 31, 2013 and September 30, 2012:

	March 31, 2013									September 30, 2012
	As Reported			Adjustment			Restated			As Reported			Adjustment			Restated
Total assets	$	24,790		$	-		$	24,790		$	26,975					$	26,975
Total other current liabilities		14,392			-			14,392			11,387						11,387
Fair value of warrant liability		-			1,238			1,238			-			1,213			1,213
Total current liabilities		14,392			1,238			15,630			11,387			1,213			12,600
Other long-term debt		607			-			607			5,998						5,998
Total liabilities		14,999			1,238			16,237			17,385			1,213			18,598
Shareholders' equity:
Preferred Shares		1,335			-			1,335			1,335			-			1,335
Common Shares		1,880			-			1,880			1,871			-			1,871
Additional paid-in capital		20,618			(816	)		19,802			20,451			(816	)		19,635
Accumulated deficit		(14,126	)		(422	)		(14,548	)		(14,096	)		(397	)		(14,493	)
Accumulated other comprehensive income		84			-			84			29						29
Total shareholders' equity		9,791			(1,238	)		8,553			9,590			(1,213	)		8,377
Total liabilities and shareholders' equity	$	24,790		$	-		$	24,790		$	26,975		$	-		$	26,975

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CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
CONDENSED CONSOLIDATED STATEMENTS OF OPERATIONS AND COMPREHENSIVE INCOME (LOSS) [Abstract]
Service revenue	$ 3,667	$ 5,279	$ 8,337	$ 10,890
Product revenue	1,489	1,687	2,623	3,592
Total revenue	5,156	6,966	10,960	14,482
Cost of service revenue	3,230	5,066	6,612	10,322
Cost of product revenue	668	757	1,234	1,535
Total cost of revenue	3,898	5,823	7,846	11,857
Gross profit	1,258	1,143	3,114	2,625
Operating expenses:
Selling	292	996	662	1,994
Research and development	123	162	208	340
General and administrative	852	1,626	1,950	3,234
Total operating expenses	1,267	2,784	2,820	5,568
Restructuring charges		64		64
Operating income (loss)	(9)	(1,705)	294	(3,007)
Interest expense	(163)	(179)	(329)	(368)
Change in fair value of warrant liability - (increase) decrease	(142)	56	(25)
Other income	3		5
Loss before income taxes	(311)	(1,828)	(55)	(3,375)
Income tax expense
Net loss	(311)	(1,828)	(55)	(3,375)
Other comprehensive income (loss):
Foreign currency translation adjustment	46	23	55	22
Comprehensive loss	$ (265)	$ (1,805)		$ (3,353)
Basic net loss per share	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)
Diluted loss per share	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)
Weighted common shares outstanding:
Basic	7,657	7,034	7,648	6,989
Diluted	7,657	7,034	7,648	6,989

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INVENTORIES

6 Months Ended

Mar. 31, 2013

INVENTORIES [Abstract]

INVENTORIES

5. INVENTORIES

Inventories consisted of the following:

	March 31,  2013			September 30, 2012
Raw materials	$	1,401		$	1,407
Work in progress		337			283
Finished goods		226			276
	$	1,964		$	1,966
Obsolescence reserve		(311	)		(310	)
	$	1,653		$	1,656

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RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Statements of Operations) (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Total revenue	$ 5,156	$ 6,966	$ 10,960	$ 14,482
Total cost of revenue	3,898	5,823	7,846	11,857
Gross profit	1,258	1,143	3,114	2,625
Total operating expenses	1,267	2,784	2,820	5,568
Restructuring charges		64		64
Operating income (loss)	(9)	(1,705)	294	(3,007)
Interest expense	(163)	(179)	(329)	(368)
Change in fair value of warrant liability - (increase) decrease	(142)	56	(25)
Other income	3		5
Loss before income taxes	(311)	(1,828)	(55)	(3,375)
Income tax expense
Net loss	(311)	(1,828)	(55)	(3,375)
Other comprehensive income (loss):
Foreign currency translation adjustment	46	23	55	22
Comprehensive loss	(265)	(1,805)		(3,353)
Basic EPS	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)
Diluted EPS	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)
As Reported [Member]
Total revenue	5,156	6,966	10,960
Total cost of revenue	3,898	5,823	7,846
Gross profit	1,258	1,143	3,114
Total operating expenses	1,267	2,784	2,820
Restructuring charges		64
Operating income (loss)	(9)	(1,705)	294
Interest expense	(163)	(179)	(329)
Change in fair value of warrant liability - (increase) decrease
Other income	3		5
Loss before income taxes	(169)	(1,884)	(30)
Income tax expense
Net loss	(169)	(1,884)	(30)
Other comprehensive income (loss):
Foreign currency translation adjustment	46	23	55
Comprehensive loss	(123)	(1,861)	25
Basic EPS	$ 0.02	$ (0.27)
Diluted EPS	$ (0.02)	$ (0.27)
Adjustment [Member]
Total revenue
Total cost of revenue
Gross profit
Total operating expenses
Restructuring charges
Operating income (loss)
Interest expense
Change in fair value of warrant liability - (increase) decrease	(142)	56	(25)
Other income
Loss before income taxes	(142)	56	(25)
Income tax expense
Net loss	(142)	56	(25)
Other comprehensive income (loss):
Foreign currency translation adjustment
Comprehensive loss	$ (142)	$ 56	$ (25)
Basic EPS	$ (0.02)	$ 0.01	$ (0.01)
Diluted EPS	$ (0.02)	$ 0.01	$ (0.01)

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STOCK-BASED COMPENSATION (Tables)

6 Months Ended

Mar. 31, 2013

STOCK-BASED COMPENSATION [Abstract]

Summary of Stock Option Activity

A summary of our stock option activity for the six months ended March 31, 2013 is as follows (shares in thousands):

	Options (shares)			Weighted- Average Exercise Price		Weighted- Average Grant Date Fair Value
Outstanding - October 1, 2012		354		$	1.99	$	1.46
Exercised		(7	)		1.35		1.14
Granted		179			1.46		1.20
Terminated		(24	)		2.80		1.89
Outstanding - March 31, 2013		502		$	1.77	$	1.35

Fair Value Assumptions

During the six months ended March 31, 2013, we granted options for 179 common shares under the Plan. The fair value of each option grant is estimated on the date of the grant. The weighted-average assumptions used to compute the fair value of these options were as follows:

Risk-free interest rate	1.00% - 1.95%
Dividend yield	0.00%
Expected volatility	93.55% - 93.71%
Expected life of the options (years)	8.0
Forfeitures	3.00%

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MANAGEMENT'S PLAN (Details) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Sep. 30, 2012
MANAGEMENT'S PLAN [Abstract]
Revenue decline to previous period, percentage	24.30%
Gross margin improvement to prior period, percentage	18.60%
Cash generated from operations	$ 488	$ (361)
Long-term debt and capital lease obligations, current	5,800
Current portion of long-term debt	$ 5,549		$ 583

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STOCK-BASED COMPENSATION (Summary of Stock Option Activity) (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	6 Months Ended
	Mar. 31, 2013
Options (shares)
Outstanding - October 1, 2012	354
Exercised	(7)
Granted	179
Terminated	(24)
Outstanding - March 31, 2013	502
Weighted-Average Exercise Price
Outstanding - October 1, 2012	$ 1.99
Exercised	$ 1.35
Granted	$ 1.46
Terminated	$ 2.80
Outstanding - March 31, 2013	$ 1.77
Weighted-Average Grant Date Fair Value
Outstanding - October 1, 2012	$ 1.46
Exercised	$ 1.14
Granted	$ 1.20
Terminated	$ 1.89
Outstanding - March 31, 2013	$ 1.35

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STOCK-BASED COMPENSATION (Narrative) (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012	Sep. 30, 2012
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Employee stock compensation expense	$ 61	$ 26	$ 135	$ 73
Shares outstanding	502		502		354
Options granted			179
Non-qualified Plan [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Shares outstanding	125		125

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DEBT (Details) (USD $) In Thousands, unless otherwise specified		6 Months Ended		6 Months Ended				6 Months Ended			6 Months Ended
	Mar. 31, 2013 acre sqft	Mar. 31, 2013 Revolving Line of Credit [Member]	Mar. 31, 2013 Revolving Line of Credit [Member] Original Covenant Terms [Member]	Mar. 31, 2013 Revolving Line of Credit [Member] Minimum [Member]	Mar. 31, 2013 Amended Revolving Line of Credit [Member]	Mar. 31, 2013 Notes Payable to Regions Bank [Member]	Sep. 30, 2012 Notes Payable to Regions Bank [Member]	Mar. 31, 2013 Replacement Note Payable [Member]	Dec. 17, 2010 Note Payable, Maturing December 18, 2010 [Member]	Dec. 17, 2010 Mortgage Payable, Maturing February 11, 2011[Member]	Mar. 31, 2013 Second Replacement Note Payable [Member]
Debt Instrument [Line Items]
Long-term debt						$ 5,549	$ 5,842				$ 5,549
Debt instrument, maturity date		Jan. 31, 2014						Nov. 01, 2012			Oct. 31, 2013
Debt instrument, frequency of periodic payments								monthly			monthly
Debt instrument, principal payment								14			47
Debt instrument, one-time principal payment									500	500
Debt instrument, face amount								1,341			5,786
Debt instrument, variable interest reference rate		Citibank's Prime Rate						LIBOR			LIBOR
Debt instrument, basis spread on variable rate		5.00%						3.00%			4.00%
Debt instrument, minimum interest rate								4.50%			6.00%
Fixed charge coverage ratio								1.25
Total liabilities to tangible net worth ratio								2.1
Debt instrument, effective interest rate		8.25%
Line of credit, maximum borrowing capacity		3,000
Line of credit, frequency of periodic payments		monthly
Line of credit, periodic interest payments				15
Line of credit, frequency of facilities fee payments		annually
Line of credit, facilities fee, percentage		2.00%
Line of credit, collateral monitoring fee, percentage		0.20%
Line of credit, collateral		Borrowings under the Credit Agreement are secured by a blanket lien on our personal property, including certain eligible accounts receivable, inventory, and intellectual property assets, and a second mortgage on our West Lafayette and Evansville real estate and all common stock of our U.S. subsidiaries and 65% of the common stock of our non-United States subsidiary.
Line of credit, borrowings, based on eligible accounts receivable, percentage		75.00%
Minimum net worth convenant requirement		8,500	8,000
Line of credit, current borrowing capacity		1,330			1,927
Line of credit, amount outstanding		813			1,444
Acres of land	7.25
Acres of headquarters facility	120,000
Net book value of facility and land	9,492
Asking price	$ 12,500

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INVENTORIES (Details) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Sep. 30, 2012
INVENTORIES [Abstract]
Raw materials	$ 1,401	$ 1,407
Work in process	337	283
Finished goods	226	276
Gross inventories	1,964	1,966
Obsolescence reserve	(311)	(310)
Inventories	$ 1,653	$ 1,656

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RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS (Balance Sheet) (Details) (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Sep. 30, 2012
Total assets	$ 24,790	$ 26,975
Total other current liabilities	14,392	11,387
Fair value of warrant liability	1,238	1,213
Total current liabilities	15,630	12,600
Other long-term debt	607	5,998
Total liabilities	16,237	18,598
Shareholders' equity:
Preferred Shares	1,335	1,335
Common Shares	1,880	1,871
Additional paid-in capital	19,802	19,635
Accumulated deficit	(14,548)	(14,493)
Accumulated other comprehensive income	84	29
Total shareholders' equity	8,553	8,377
Total liabilities and shareholders' equity	24,790	26,975
As Reported [Member]
Total assets	24,790	26,975
Total other current liabilities	14,392	11,387
Fair value of warrant liability
Total current liabilities	14,392	11,387
Other long-term debt	607	5,998
Total liabilities	14,999	17,385
Shareholders' equity:
Preferred Shares	1,335	1,335
Common Shares	1,880	1,871
Additional paid-in capital	20,618	20,451
Accumulated deficit	(14,126)	(14,096)
Accumulated other comprehensive income	84	29
Total shareholders' equity	9,791	9,590
Total liabilities and shareholders' equity	24,790	26,975
Adjustment [Member]
Total assets
Total other current liabilities
Fair value of warrant liability	1,238	1,213
Total current liabilities	1,238	1,213
Other long-term debt
Total liabilities	1,238	1,213
Shareholders' equity:
Preferred Shares
Common Shares
Additional paid-in capital	(816)	(816)
Accumulated deficit	(422)	(397)
Accumulated other comprehensive income
Total shareholders' equity	(1,238)	(1,213)
Total liabilities and shareholders' equity

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DESCRIPTION OF THE BUSINESS

6 Months Ended

Mar. 31, 2013

DESCRIPTION OF THE BUSINESS [Abstract]

DESCRIPTION OF THE BUSINESS

1. DESCRIPTION OF THE BUSINESS AND BASIS OF PRESENTATION

Bioanalytical Systems, Inc. and its subsidiaries ("We," the "Company" or "BASi") engage in contract laboratory research services and other services related to pharmaceutical development. We also manufacture scientific instruments for life sciences research, which we sell with related software for use in industrial, governmental and academic laboratories. Our customers are located throughout the world.

We have prepared the accompanying unaudited interim condensed consolidated financial statements pursuant to the rules and regulations of the Securities and Exchange Commission ("SEC") regarding interim financial reporting. Accordingly, they do not include all of the information and footnotes required by generally accepted accounting principles ("GAAP") and should be read in conjunction with our audited consolidated financial statements, and the notes thereto, for the year ended September 30, 2012. In the opinion of management, the condensed consolidated financial statements for the three and six months ended March 31, 2013 and 2012 include all adjustments which are necessary for a fair presentation of the results of the interim periods and of our financial position at March 31, 2013. The results of operations for the three and six months ended March 31, 2013 are not necessarily indicative of the results for the year ending September 30, 2013.

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STOCK-BASED COMPENSATION

6 Months Ended

Mar. 31, 2013

STOCK-BASED COMPENSATION [Abstract]

STOCK-BASED COMPENSATON

3. STOCK-BASED COMPENSATION

The 2008 Stock Option Plan ("the Plan") is used to promote our long-term interests by providing a means of attracting and retaining officers, directors and key employees and aligning their interests with those of our shareholders. The Plan is described more fully in Note 10 in the Notes to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012. All options granted under the Plan had an exercise price equal to the market value of the underlying common shares on the date of grant. We expense the estimated fair value of stock options over the vesting periods of the grants. We recognize expense for awards subject to graded vesting using the straight-line attribution method, reduced for estimated forfeitures. Forfeitures are revised, if necessary, in subsequent periods if actual forfeitures differ from those estimates and an adjustment is recognized at that time. The Compensation Committee may also issue non-qualified stock option grants with vesting periods different from the 2008 Plan. As of March 31, 2013, there are 125 shares outstanding that were granted outside of the Plan. The assumptions used are detailed in Note 10 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012. Stock based compensation expense for the three and six months ended March 31, 2013 was $61 and $135, respectively. Stock based compensation expense for the three and six months ended March 31, 2012 was $26 and $73, respectively.

A summary of our stock option activity for the six months ended March 31, 2013 is as follows (shares in thousands):

	Options (shares)			Weighted- Average Exercise Price		Weighted- Average Grant Date Fair Value
Outstanding - October 1, 2012		354		$	1.99	$	1.46
Exercised		(7	)		1.35		1.14
Granted		179			1.46		1.20
Terminated		(24	)		2.80		1.89
Outstanding - March 31, 2013		502		$	1.77	$	1.35

During the six months ended March 31, 2013, we granted options for 179 common shares under the Plan. The fair value of each option grant is estimated on the date of the grant. The weighted-average assumptions used to compute the fair value of these options were as follows:

Risk-free interest rate	1.00% - 1.95%
Dividend yield	0.00%
Expected volatility	93.55% - 93.71%
Expected life of the options (years)	8.0
Forfeitures	3.00%

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SEGMENT INFORMATION

6 Months Ended

Mar. 31, 2013

SEGMENT INFORMATION [Abstract]

SEGMENT INFORMATION

6. SEGMENT INFORMATION

We operate in two principal segments - research services and research products. Our Services segment provides research and development support on a contract basis directly to pharmaceutical companies. Our Products segment provides liquid chromatography, electrochemical and physiological monitoring products to pharmaceutical companies, universities, government research centers and medical research institutions. Our accounting policies in these segments are the same as those described in the summary of significant accounting policies found in Note 2 to Consolidated Financial Statements in our annual report on Form 10-K/A for the year ended September 30, 2012.

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Revenue:
Service	$	3,667		$	5,279		$	8,337		$	10,890
Product		1,489			1,687			2,623			3,592
	$	5,156		$	6,966		$	10,960		$	14,482
Operating income (loss):
Service	$	(365	)	$	(1,419	)	$	(150	)	$	(2,685	)
Product		356			(275	)		444			(311	)
Corporate		-			(11	)		-			(11	)
	$	(9	)	$	(1,705	)	$	294		$	(3,007	)
Interest expense		(163	)		(179	)		(329	)		(368	)
Change in fair value of warrant liability - (increase) decrease		(142	)		56			(25	)		-
Other income		3			-			5			-
Income (loss) before income taxes	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)

Restructuring costs of $53 and $11 are included in the operating losses for the three and six months ended March 31, 2012 for the Service and Corporate segments, respectively.

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INCOME (LOSS) PER SHARE

6 Months Ended

Mar. 31, 2013

INCOME (LOSS) PER SHARE [Abstract]

INCOME (LOSS) PER SHARE

4. INCOME (LOSS) PER SHARE

We compute basic income (loss) per share using the weighted average number of common shares outstanding.

The Company has three categories of dilutive potential common shares: the Series A preferred shares issued in May 2011 in connection with the registered direct offering, the Warrants issued in connection with the same offering in May 2011, and shares issuable upon exercise of options. We compute diluted earnings per share using the if-converted method for preferred stock and the treasury stock method for stock options and warrants. Shares issuable upon exercise of options were not considered in computing diluted earnings per share for the three and six months ended March 31, 2013 and 2012, respectively, because they were anti-dilutive. Warrants for 1,377 common shares and 668 common shares issuable upon conversion of preferred shares were not considered in computing diluted earnings per share for the three and six months ended March 31, 2013, because they were anti-dilutive. Warrants for 2,753 common shares and 1,044 common shares issuable upon conversion of preferred shares were not considered in computing diluted earnings per share for the three and six months ended March 31, 2012 because they were also anti-dilutive.

The following table reconciles our computation of basic income (loss) per share to diluted income (loss) per share:

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Basic net loss per share:
Net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Basic net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)
Diluted net loss per share:
Diluted net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Dilutive stock options/shares		-			-			-			-
Diluted weighted average common shares outstanding		7,657			7,034			7,648			6,989
Diluted net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)

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STOCK-BASED COMPENSATION (Fair Value Assumptions) (Details) (Stock Options [Member])	3 Months Ended
	Mar. 31, 2013
Stock Options [Member]
Share-based Compensation Arrangement by Share-based Payment Award [Line Items]
Risk-free interest rate, minimum	1.00%
Risk-free interest rate, maximum	1.95%
Dividend yield	0.00%
Expected volatility, minimum	93.55%
Expected volitility, maximum	93.71%
Expected life of the options (years)	8 years
Forfeitures	3.00%

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SEGMENT INFORMATION (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Segment Reporting Information [Line Items]
Revenue:	$ 5,156	$ 6,966	$ 10,960	$ 14,482
Operating income (loss):	(9)	(1,705)	294	(3,007)
Interest expense	(163)	(179)	(329)	(368)
Change in fair value of warrant liability - (increase) decrease	(142)	56	(25)
Other income	3		5
Loss before income taxes	(311)	(1,828)	(55)	(3,375)
Restructuring charges		64		64
Service [Member]
Segment Reporting Information [Line Items]
Revenue:	3,667	5,279	8,337	10,890
Operating income (loss):	(365)	(1,419)	(150)	(2,685)
Restructuring charges		53		53
Product [Member]
Segment Reporting Information [Line Items]
Revenue:	1,489	1,687	2,623	3,592
Operating income (loss):	356	(275)	444	(311)
Corporate [Member]
Segment Reporting Information [Line Items]
Operating income (loss):		(11)		(11)
Restructuring charges		$ 11		$ 11

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FAIR VALUE OF FINANCIAL INSTRUMENTS (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified				6 Months Ended	12 Months Ended
	Mar. 31, 2013	Sep. 30, 2012	May 31, 2012 Class B Warrant [Member]	Mar. 31, 2013 Derivative Financial Instruments, Liabilities [Member] Class A Warrant [Member]	Sep. 30, 2012 Derivative Financial Instruments, Liabilities [Member] Class A Warrant [Member]
Fair Value Measurements, Recurring and Nonrecurring, Valuation Techniques [Line Items]
Risk-free interest rate				0.39%	0.41%
Dividend yield				0.00%	0.00%
Volatility of the Company's common stock				92.69%	117.30%
Expected life of the options				3 years 1 month 6 days	3 years 7 months 6 days
Fair value per unit				$ 0.899	$ 0.881
Fair value of warrant liability	$ 1,238	$ 1,213	$ 0

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CONDENSED CONSOLIDATED BALANCE SHEETS (Parenthetical) (USD $) In Thousands, except Share data, unless otherwise specified	Mar. 31, 2013	Sep. 30, 2012
Allowance for doubtful accounts	$ 162	$ 123
Common stock, no par value
Common stock, shares authorized	19,000,000	19,000,000
Common stock, shares issued	7,671,364	7,638,738
Common stock, shares outstanding	7,671,364	7,638,738
Series A Preferred Stock [Member]
Preferred stock, shares authorized	1,000,000	1,000,000
Preferred stock, no par value
Preferred stock, shares issued	1,335	1,335
Preferred stock, shares outstanding	1,335	1,335
Preferred stock, stated value per share	$ 1,000	$ 1,000

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RESTRUCTURING

6 Months Ended

Mar. 31, 2013

RESTRUCTURING [Abstract]

RESTRUCTURING

9. RESTRUCTURING

In March 2012, we announced a plan to restructure our bioanalytical laboratory operations. We consolidated our laboratory in McMinnville, Oregon into our 120,000 square foot headquarters facility in West Lafayette, Indiana. This plan was implemented to reduce operating costs and strengthen our ability to meet clients' needs by improving laboratory utilization. In the fourth fiscal quarter of 2012, we decided to initiate closure of our facility and bioanalytical laboratory in Warwickshire, United Kingdom after careful evaluation of its financial performance and analysis of our strategic alternatives. We will continue to sell our products globally while further consolidating delivery of our CRO services into our Indiana locations. As part of the overall evaluation of our business, personnel reductions in the Selling, R&D and General and Administrative functions were also implemented at both of our Indiana locations during the second half of fiscal 2012. In total, 74 employees were terminated as part of the restructuring activities in fiscal 2012.

We have reserved for lease payments at the UK location as of the cease use date and have considered free rent, sublease rentals and the number of days it would take to restore the space to its original condition prior to our improvements. In the first fiscal quarter of 2013, we began amortizing into normal operating income, equally through the cease use date, the estimated rent income of $200 when the reserve was originally established. Based on these, we have $837 reserved for UK lease related costs.

The following table sets forth the rollforward of the restructuring activity for the six months ended March 31, 2013.

	Balance, September 30,  2012			Total Charges		Cash Payments			Other		Balance, March 31, 2013
One-time termination benefits	$	448		$	-	$	(448	)	$	-	$	-
Lease related costs		800			-		-			37		837
Equipment moving costs and method transfers		49			-		(49	)		-		-
Travel and relocation costs		4			-		(4	)		-		-
Receivable from sale of equipment		(93	)		-		-			61		(32	)
Other costs		197			-		(56	)		-		141
Total	$	1,405		$	-	$	(557	)	$	98	$	946

Other costs include legal and professional fees and other costs incurred in connection with transitioning services from sites being closed as well as costs incurred to remove improvements previously made to the UK facility. Other activity in the reserve rollforward primarily reflects a receivable for settlement of the capital lease in the UK.

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CONDENSED CONSOLIDATED STATEMENTS OF CASH FLOWS (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012
Operating activities:
Net loss	$ (55)	$ (3,375)
Adjustments to reconcile net income (loss) to net cash (used) provided by operating activities:
Depreciation and amortization	908	1,145
Change in fair value of warrant liability - increase (decrease)	25
Employee stock compensation expense	135	73
Provision for doubtful accounts	39	46
Loss (gain) on sale of property and equipment	(19)	3
Changes in operating assets and liabilities:
Accounts receivable	676	495
Inventories	4	(218)
Refundable income taxes	(3)	(46)
Prepaid expenses and other assets	(7)	151
Accounts payable	(231)	886
Accrued expenses	(647)	372
Customer advances	(337)	107
Net cash provided (used) by operating activities	488	(361)
Investing activities:
Capital expenditures	(12)	(817)
Proceeds from sale of equipment	20
Net cash provided (used) by investing activities	8	(817)
Financing activities:
Payments of long-term debt	(293)	(378)
Payments on revolving line of credit	(11,018)	(14,680)
Borrowings on revolving line of credit	10,387	14,434
Payments on capital lease obligations	(202)	(311)
Net cash used by financing activities	(1,126)	(935)
Effect of exchange rate changes	49	3
Net decrease in cash and cash equivalents	(581)	(2,110)
Cash and cash equivalents at beginning of period	721	2,963
Cash and cash equivalents at end of period	140	853
Supplemental disclosure of non-cash financing activities:
Preferred stock dividends paid in common shares	$ (40)	$ (61)

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CONDENSED CONSOLIDATED BALANCE SHEETS (USD $) In Thousands, unless otherwise specified	Mar. 31, 2013	Sep. 30, 2012
Current assets:
Cash and cash equivalents	$ 140	$ 721
Accounts receivable
Trade, less allowances of $162 and $123 as of March 31, 2013 and September 30, 2012, respectively.	2,436	3,366
Unbilled revenues and other	1,136	921
Inventories	1,653	1,656
Refundable Income Taxes	2
Prepaid expenses	194	228
Total current assets	5,561	6,892
Property and equipment, net	17,736	18,628
Goodwill	1,383	1,383
Debt issue costs	59	18
Other assets	51	54
Total assets	24,790	26,975
Current liabilities:
Accounts payable	3,659	3,934
Accrued expenses	1,420	2,067
Customer advances - deferred revenues	2,675	3,012
Income tax accruals	16	17
Revolving line of credit	813	1,444
Fair value of warrant liability	1,238	1,213
Current portion of capital lease obligation	260	330
Current portion of long-term debt	5,549	583
Total current liabilities	15,630	12,600
Capital lease obligation, less current portion	607	739
Long-term debt, less current portion		5,259
Commitments and contingencies
Shareholders' equity:
Preferred shares, authorized 1,000,000 shares, no par value: 1,335 Series A shares at $1,000 stated value issued and outstanding at March 31, 2013 and at September 30, 2012	1,335	1,335
Common shares, no par value: Authorized 19,000,000 shares; 7,671,364 issued and outstanding at March 31, 2013 and 7,638,738 at September 30, 2012	1,880	1,871
Additional paid-in capital	19,802	19,635
Accumulated deficit	(14,548)	(14,493)
Accumulated other comprehensive income	84	29
Total shareholders' equity	8,553	8,377
Total liabilities and shareholders' equity	24,790	26,975
Series A Preferred Stock [Member]
Shareholders' equity:
Preferred shares, authorized 1,000,000 shares, no par value: 1,335 Series A shares at $1,000 stated value issued and outstanding at March 31, 2013 and at September 30, 2012	$ 1,335	$ 1,335

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INCOME (LOSS) PER SHARE (Narrative) (Details) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Warrant [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive shares not considered in computing diluted earnings per share	1,377	2,753	1,377	2,753
Common Stock [Member]
Antidilutive Securities Excluded from Computation of Earnings Per Share [Line Items]
Antidilutive shares not considered in computing diluted earnings per share	668	1,044	668	1,044

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FAIR VALUE OF FINANCIAL INSTRUMENTS (Tables)

6 Months Ended

Mar. 31, 2013

FAIR VALUE OF FINANCIAL INSTRUMENTS [Abstract]

Summary of Assumptions Used to Compute Fair Value of Warrants

The assumptions used to compute the fair value of the warrants at March 31, 2013 and September 30, 2012 were as follows:

	March 31, 2013			September 30, 2012
	Warrant A			Warrant A
Risk-free interest rate		0.39	%		0.41	%
Dividend yield		0.00	%		0.00	%
Volatility of the Company's common stock		92.69	%		117.30	%
Expected life of the options (years)		3.1			3.6
Fair value per unit	$	0.899		$	0.881

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RESTRUCTURING (Narrative) (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended
	Dec. 31, 2012	Mar. 31, 2013 sqft	Sep. 30, 2012
Restructuring Cost and Reserve [Line Items]
Acres of headquarters facility		120,000
Rent income	$ 200
Restructuring reserve		946	1,405
Lease Related Costs [Member]
Restructuring Cost and Reserve [Line Items]
Restructuring reserve		$ 837	$ 800

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RESTRUCTURING (Summary of Restructuring Activity) (Details) (USD $) In Thousands, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Restructuring Cost and Reserve [Line Items]
Balance			$ 1,405
Total Charges		64		64
Cash Payments			(557)
Other			98
Balance	946		946
One-time Termination Benefits [Member]
Restructuring Cost and Reserve [Line Items]
Balance			448
Total Charges
Cash Payments			(448)
Other
Balance
Lease Related Costs [Member]
Restructuring Cost and Reserve [Line Items]
Balance			800
Total Charges
Cash Payments
Other			37
Balance	837		837
Equipment Moving Costs And Method Transfers [Member]
Restructuring Cost and Reserve [Line Items]
Balance			49
Total Charges
Cash Payments			(49)
Other
Balance
Travel and Relocation Costs [Member]
Restructuring Cost and Reserve [Line Items]
Balance			4
Total Charges
Cash Payments			(4)
Other
Balance
Receivable from sale of equipment [Member]
Restructuring Cost and Reserve [Line Items]
Balance			(93)
Total Charges
Cash Payments
Other			61
Balance	(32)		(32)
Other Costs [Member]
Restructuring Cost and Reserve [Line Items]
Balance			197
Total Charges
Cash Payments			(56)
Other
Balance	$ 141		$ 141

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DEBT

6 Months Ended

Mar. 31, 2013

DEBT [Abstract]

DEBT

8. DEBT

Mortgages and note payable

We have a term loan from Regions Bank ("Regions") aggregating approximately $5,549 at March 31, 2013 and $5,842 at September 30, 2012, which is secured by mortgages on our facilities in West Lafayette and Evansville, Indiana.

On November 29, 2010, we executed amendments on two loans with Regions. As part of the amendments, we agreed to a $500 principal payment on one of the loans and a $500 principal payment on the other loan in exchange for certain modifications to the financial covenants in the loan agreements described below. The principal payments were made on December 17, 2010 and February 11, 2011, respectively. Upon receipt of these two payments, Regions incorporated the two loans into a replacement note payable for $1,341 maturing on November 1, 2012. The replacement note payable bore interest at a per annum rate equal to the 30-day LIBOR plus 300 basis points (minimum of 4.5%) with monthly principal payments of approximately $14 plus interest. The replacement note payable was secured by real estate at our West Lafayette and Evansville, Indiana locations.

As part of the amendment, Regions also agreed to amend the loan covenants for the related debt to be more favorable to us. Regions requires us to maintain a fixed charge coverage ratio of not less than 1.25 to 1.00 and a total liabilities to tangible net worth ratio of not greater than 2.10 to 1.00. At March 31, 2013, on a restated basis, we were in compliance with the fixed charge coverage, but in breach of the total liabilities to tangible net worth ratios in the Regions agreements. On September 10, 2013, Regions waived compliance with the total liabilities to tangible net worth ratio for the current quarter. Failure to comply with those covenants in future quarters would be a default under the Regions loans, requiring us to negotiate with Regions regarding loan modifications or waivers. If we are unable to obtain such modifications or waivers, Regions could accelerate the maturity of the loans and cause a cross default with our other lender.

On November 9, 2012, we executed a sixth amendment with Regions which we further modified on December 21, 2012. In the sixth amendment, Regions agreed to extend the term loan and mortgage loan maturity dates to October 31, 2013. The unpaid principal on the notes was incorporated into a replacement note payable for $5,786 bearing interest at LIBOR plus 400 basis points (minimum of 6.0%) with monthly principal payments of approximately $47 plus interest. The replacement note payable is secured by real estate at our West Lafayette and Evansville, Indiana locations. At March 31, 2013, the replacement note payable had a balance of $5,549.

The Regions loan agreement contains cross-default provisions with the revolving line of credit with Entrepreneur Growth Capital LLC ("EGC") described below.

The replacement note payable with Regions matures in the first quarter of fiscal 2014. We intend to refinance the amounts in lieu of making balloon payments for the remaining principal balances or sell the building in West Lafayette, Indiana. On July 12, 2012, we listed for sale our 7.25 acres and 120,000 square foot facility at 2701 Kent Avenue, West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. The asking price was $12,500. We performed an impairment analysis on the building when we listed it for sale, but noted no impairment necessary. As of March 31, 2013, the net book value of the facility and land was $9,492.

We may be unsuccessful in renegotiating the terms of the debt or those terms may be unfavorable to us. For these reasons, if we are unsuccessful at refinancing our long-term debt, our operating results and financial condition could be adversely affected.

Revolving Line of Credit

We have a $3,000 revolving line of credit agreement ("Credit Agreement") with EGC. The term of the Credit Agreement expires on January 31, 2014. If we terminate prior to the expiration of the term, then we are subject to an early termination fee equal to the minimum interest charge of $15 for each of the months remaining until expiration.

Borrowings under the Credit Agreement bear interest at an annual rate equal to Citibank's Prime Rate plus five percent (5%), or 8.25% as of March 31, 2013, with minimum monthly interest of $15. Interest is paid monthly. The line of credit also carries an annual facilities fee of 2% and a 0.2% collateral monitoring fee. Borrowings under the Credit Agreement are secured by a blanket lien on our personal property, including certain eligible accounts receivable, inventory, and intellectual property assets, a second mortgage on our West Lafayette and Evansville real estate and all common stock of our U.S. subsidiaries and 65% of the common stock of our non-United States subsidiary. Borrowings are calculated based on 75% of eligible accounts receivable. Under the Credit Agreement, the Company has agreed to restrict advances to subsidiaries, limit additional indebtedness and capital expenditures and maintain a minimum tangible net worth of at least $8,500. Pursuant to the terms of the Credit Agreement, the line of credit will automatically renew on January 31, 2014 unless either party gives a 60-day notice of intent to terminate or withdraw.

On December 21, 2012, we negotiated an amendment to this Credit Agreement. The amendment reduced the minimum tangible net worth covenant requirement from $8,500 to $8,000, effective on January 1, 2013, and waived all non-compliances with this covenant through December 31, 2012. At March 31, 2013, on a restated basis, we were in breachof the minimum tangible net worth covenant requirement. Due to the reclassification of the Class A Warrants to a liability from equity as discussed in Note 2, we expect to be in breach of the tangible net worth covenant for our third fiscal quarter of 2013. On October 9, 2013, EGC waived compliance with the tangible net worth covenant for our current quarter and our expected breach for the third fiscal quarter of 2013.

The Credit Agreement also contains cross-default provisions with the Regions loan and any future EGC loans.

At March 31, 2013, we had available borrowing capacity of $1,330 on this line, of which $813 was outstanding. At September 30, 2012, we had available borrowing capacity of $1,927 on this line, of which $1,444 was outstanding.

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INCOME (LOSS) PER SHARE (Reconciliation of Computation of Basic Income or Loss Per Share to Diluted Income or Loss Per Share) (Details) (USD $) In Thousands, except Per Share data, unless otherwise specified	3 Months Ended		6 Months Ended
	Mar. 31, 2013	Mar. 31, 2012	Mar. 31, 2013	Mar. 31, 2012
Basic net loss per share:
Net loss applicable to common shareholders	$ (311)	$ (1,828)	$ (55)	$ (3,375)
Weighted average common shares outstanding	7,657	7,034	7,648	6,989
Basic net loss per share	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)
Diluted net loss per share:
Diluted net loss applicable to common shareholders	$ (311)	$ (1,828)	$ (55)	$ (3,375)
Weighted average common shares outstanding	7,657	7,034	7,648	6,989
Plus: Incremental shares from assumed conversions
Dilutive stock options/shares
Diluted weighted average common shares outstanding	7,657	7,034	7,648	6,989
Diluted loss per share	$ (0.04)	$ (0.26)	$ (0.01)	$ (0.48)

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MANAGEMENT'S PLAN

6 Months Ended

Mar. 31, 2013

MANAGEMENT'S PLAN [Abstract]

MANAGEMENT'S PLAN

11. MANAGEMENT'S PLAN

Our long-term strategic objective is to maximize the Company's intrinsic value per share.   However, in response to our financial performance through the second quarter of fiscal 2012, we began to operate the business in a manner designed to place more emphasis on cash flow generation. Thus, our short-term tactical objective is to maximize free cash flow from operating activities.

During the first half of fiscal 2013, revenues declined approximately 24.3%, but gross margin improved 18.6% from the first half of fiscal 2012. We reported a positive operating income for the first half of fiscal 2013. We also generated $488 in cash from operations and maintained strict controls on expenditures.

We negotiated an amendment to our loans with Regions Bank, extending the maturity date to October 2013. Our line of credit with Entrepreneur Growth Capital LLC was renewed for another year. Further, we listed for sale our headquarters facility in West Lafayette, Indiana with the intent to leaseback 80% of that square footage in which to continue our laboratory and manufacturing operations. Proceeds from this transaction would be used to pay down our debt.

For the remainder of fiscal 2013, we will continue to assess the need for additional cost controls such as reducing non-essential expenses and monitoring our operations for efficiencies to further reduce our break-even point. For the remainder of fiscal 2013, we expect to see slow but continued improvement in the volume of new bookings with little improvement in pricing. We also expect improved gross profit margins from fiscal 2012 due to cost controls implemented and restructuring activities. We have debt and lease obligations of approximately $5.8 million due in the next twelve months, including $5.5 million for the Regions loan. Based on our expected revenue, the availability on our line of credit, the impact of the cost reductions implemented and restructuring activities during fiscal 2012, we project that we will have the liquidity required to meet our fiscal 2013 operations and debt obligations. If we are unable to refinance our debt or enter into a sale-leaseback for the building in West Lafayette, we may not have sufficient liquidity to meet our debt obligations coming due in October 2013 and be able to continue our business.

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INCOME TAXES

6 Months Ended

Mar. 31, 2013

INCOME TAXES [Abstract]

INCOME TAXES

7. INCOME TAXES

We use the asset and liability method of accounting for income taxes.  We recognize deferred tax assets and liabilities for the future tax consequences attributable to differences between the financial statement carrying amounts of existing assets and liabilities and their respective tax bases and operating loss and tax credit carryforwards. We measure deferred tax assets and liabilities using enacted tax rates expected to apply to taxable income in the years in which those temporary differences are expected to be recovered or settled. We recognize the effect on deferred tax assets and liabilities of a change in tax rates in income in the period that includes the enactment date. We record valuation allowances based on a determination of the expected realization of tax assets.

We recognize the tax benefit from an uncertain tax position only if it is more likely than not to be sustained upon examination based on the technical merits of the position. We measure the amount of the accrual for which an exposure exists as the largest amount of benefit determined on a cumulative probability basis that we believe is more likely than not to be realized upon ultimate settlement of the position.

At March 31, 2013 and September 30, 2012, we had a $16 liability for uncertain income tax positions. The difference between the federal statutory rate of 34% and our effective rate of 0% is due to changes in our evaluation allowance on our net deferred tax assets.

We record interest and penalties accrued in relation to uncertain income tax positions as a component of income tax expense. Any changes in the liability for uncertain tax positions would impact our effective tax rate. We do not expect the total amount of unrecognized tax benefits to significantly change in the next twelve months.

We file income tax returns in the U.S., several U.S. States, and the United Kingdom. We remain subject to examination by taxing authorities in the jurisdictions in which we have filed returns for years after 2008.

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RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

6 Months Ended

Mar. 31, 2013

RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS [Abstract]

RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

2. RESTATEMENT OF PREVIOUSLY ISSUED CONDENSED CONSOLIDATED FINANCIAL STATEMENTS

In August 2013, we announced the delay in filing our Form 10-Q for the three and nine months ended June 30, 2013 until management resolved a complex accounting issue related to the accounting treatment for our outstanding warrants. In the same month, we announced that investors should no longer rely upon our previously issued consolidated financial statements and the independent auditors' reports for the fiscal years ended September 30, 2012 and 2011 or the quarterly financial statements for the first two quarters of fiscal 2013, or any earnings releases relating to these periods, because of errors in such financial statements.

As a result of the identification of such errors, we have undertaken a comprehensive review of our previously filed consolidated financial statements. We concluded that the warrants issued in connection our public offering in May 2011 were incorrectly accounted for as equity and should have been recorded as a liability. As a result, we have restated our previously reported consolidated financial statements for the years ended September 30, 2012 and 2011 as well as the condensed consolidated financial statements for three and six months ended March 31, 2013. The restatement adjustments to the full fiscal years ended September 30, 2012 and 2011 are more fully described in Note 3 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012.

As of March 31, 2013 and September 30, 2012, respectively, the restatement adjustments resulted in a cumulative net decrease to total shareholders' equity of $1,238 and $1,213. As a result of the adjustments, we reported an increase of $142 and $25 in previously reported net loss for the three and six months ended March 31, 2013, respectively, and a decrease of $56 to previously reported net loss for the three months ended March 31, 2012. The net effect on net income for the six months ended March 31, 2012 was zero. The changes in net income (loss) were a result of the changes in the fair value of the warrant liability that is now correctly recorded in other income (expense). Except as otherwise specified, all information presented in the accompanying condensed consolidated financial statements and the related notes are presented after inclusion of all such adjustments. There was no net effect on the consolidated statements of cash flows for the three and six months ended March 31, 2013 and 2012, respectively, as the change in the fair value of the warrant liability is a non-cash item.

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations and comprehensive income (loss) items for the three months ended March 31:

	2013									2012
	As Reported			Adjustment			Restated			As Reported			Adjustment		Restated
Total revenue	$	5,156		$	-		$	5,156		$	6,966				$	6,966
Total cost of revenue		3,898			-			3,898			5,823					5,823
Gross profit		1,258			-			1,258			1,143			-		1,143
Total operating expenses		1,267			-			1,267			2,784					2,784
Restructuring charges		-			-			-			64			-		64
Operating income (loss)		(9	)		-			(9	)		(1,705	)		-		(1,705	)
Interest expense		(163	)		-			(163	)		(179	)				(179	)
Change in fair value of warrant liability - (increase) decrease		-			(142	)		(142	)		-			56		56
Other income		3			-			3			-			-		-
Income (loss) before income taxes		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Income tax expense		-			-			-			-					-
Net income (loss)		(169	)		(142	)		(311	)		(1,884	)		56		(1,828	)
Other comprehensive income (loss):
Foreign currency translation adjustment		46			-			46			23			-		23
Comprehensive income (loss)	$	(123	)	$	(142	)	$	(265	)	$	(1,861	)	$	56	$	(1,805	)
Basic EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)
Diluted EPS	$	(0.02	)	$	(0.02	)	$	(0.04	)	$	(0.27	)	$	0.01	$	(0.26	)

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated statements of operations items for the six months ended March 31:

	2013
	As Reported			Adjustment			Restated
Total revenue	$	10,960		$	-		$	10,960
Total cost of revenue		7,846			-			7,846
Gross profit		3,114			-			3,114
Total operating expenses		2,820			-			2,820
Restructuring charges		-			-			-
Operating income (loss)		294			-			294
Interest expense		(329	)		-			(329	)
Change in fair value of warrant liability - (increase) decrease		-			(25	)		(25	)
Other income		5			-			5
Income (loss) before income taxes		(30	)		(25	)		(55	)
Income tax expense		-			-			-
Net income (loss)		(30	)		(25	)		(55	)
Other comprehensive income (loss):
Foreign currency translation adjustment		55			-			55
Comprehensive income (loss)	$	25		$	(25	)	$	-
Basic EPS	$	-		$	(0.01	)	$	(0.01	)
Diluted EPS	$	-		$	(0.01	)	$	(0.01	)

The following table summarizes the effects of the restatement adjustments, previously discussed, on the consolidated balance sheet items as of March 31, 2013 and September 30, 2012:

	March 31, 2013									September 30, 2012
	As Reported			Adjustment			Restated			As Reported			Adjustment			Restated
Total assets	$	24,790		$	-		$	24,790		$	26,975					$	26,975
Total other current liabilities		14,392			-			14,392			11,387						11,387
Fair value of warrant liability		-			1,238			1,238			-			1,213			1,213
Total current liabilities		14,392			1,238			15,630			11,387			1,213			12,600
Other long-term debt		607			-			607			5,998						5,998
Total liabilities		14,999			1,238			16,237			17,385			1,213			18,598
Shareholders' equity:
Preferred Shares		1,335			-			1,335			1,335			-			1,335
Common Shares		1,880			-			1,880			1,871			-			1,871
Additional paid-in capital		20,618			(816	)		19,802			20,451			(816	)		19,635
Accumulated deficit		(14,126	)		(422	)		(14,548	)		(14,096	)		(397	)		(14,493	)
Accumulated other comprehensive income		84			-			84			29						29
Total shareholders' equity		9,791			(1,238	)		8,553			9,590			(1,213	)		8,377
Total liabilities and shareholders' equity	$	24,790		$	-		$	24,790		$	26,975		$	-		$	26,975

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INCOME TAXES (Details) (USD $) In Thousands, unless otherwise specified	6 Months Ended
	Mar. 31, 2013	Sep. 30, 2012
INCOME TAXES [Abstract]
Liability for other uncertain income tax positions	$ 16	$ 16
Statutory federal income tax rate	34.00%
Effective income tax rate	0.00%

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INCOME (LOSS) PER SHARE (Tables)

6 Months Ended

Mar. 31, 2013

INCOME (LOSS) PER SHARE [Abstract]

Reconciliation of Computation of Basic Loss Per Share to Diluted Net Loss Per Share

The following table reconciles our computation of basic income (loss) per share to diluted income (loss) per share:

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Basic net loss per share:
Net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Basic net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)
Diluted net loss per share:
Diluted net loss applicable to common shareholders	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)
Weighted average common shares outstanding		7,657			7,034			7,648			6,989
Dilutive stock options/shares		-			-			-			-
Diluted weighted average common shares outstanding		7,657			7,034			7,648			6,989
Diluted net loss per share	$	(0.04	)	$	(0.26	)	$	(0.01	)	$	(0.48	)

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FAIR VALUE OF FINANCIAL INSTRUMENTS

6 Months Ended

Mar. 31, 2013

FAIR VALUE OF FINANCIAL INSTRUMENTS [Abstract]

FAIR VALUE OF FINANCIAL INSTRUMENTS

10. FAIR VALUE OF FINANCIAL INSTRUMENTS

The carrying amounts for cash and cash equivalents, accounts receivable, inventories, prepaid expenses and other assets, accounts payable and other accruals approximate their fair values because of their nature and respective duration. The fair value of the revolving credit facility and certain long-term debt is equal to their carrying values due to the variable nature of their interest rates. Our long-term fixed rate debt was initiated in February 2011 and renewed on November 1, 2012.

We have Class A and B Warrants from the May 2011 offering that are measured at fair value on a recurring basis. We recorded these warrants as a liability determining the fair value at inception on May 11, 2011. Subsequent quarterly fair value measurements, using the Black Scholes model which is considered a level 2 measurement under ASC 820-10, are calculated with changes charged to the statement of operations and comprehensive income (loss) as other income (expense) labeled change in fair value of warrant liability. Class B Warrants expired in May 2012 and the liability was reduced to zero. The assumptions used to compute the fair value of the warrants at March 31, 2013 and September 30, 2012 were as follows:

	March 31, 2013			September 30, 2012
	Warrant A			Warrant A
Risk-free interest rate		0.39	%		0.41	%
Dividend yield		0.00	%		0.00	%
Volatility of the Company's common stock		92.69	%		117.30	%
Expected life of the options (years)		3.1			3.6
Fair value per unit	$	0.899		$	0.881

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RESTRUCTURING (Tables)

6 Months Ended

Mar. 31, 2013

RESTRUCTURING [Abstract]

Summary of Restructuring Activity

The following table sets forth the rollforward of the restructuring activity for the six months ended March 31, 2013.

	Balance, September 30,  2012			Total Charges		Cash Payments			Other		Balance, March 31, 2013
One-time termination benefits	$	448		$	-	$	(448	)	$	-	$	-
Lease related costs		800			-		-			37		837
Equipment moving costs and method transfers		49			-		(49	)		-		-
Travel and relocation costs		4			-		(4	)		-		-
Receivable from sale of equipment		(93	)		-		-			61		(32	)
Other costs		197			-		(56	)		-		141
Total	$	1,405		$	-	$	(557	)	$	98	$	946

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INVENTORIES (Tables)

6 Months Ended

Mar. 31, 2013

INVENTORIES [Abstract]

Summary of Inventories

Inventories consisted of the following:

	March 31,  2013			September 30, 2012
Raw materials	$	1,401		$	1,407
Work in progress		337			283
Finished goods		226			276
	$	1,964		$	1,966
Obsolescence reserve		(311	)		(310	)
	$	1,653		$	1,656

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Document and Entity Information

6 Months Ended

Mar. 31, 2013

May 10, 2013

Document And Entity Information [Abstract]

Document Type

10-Q

Amendment Flag

true

Document Period End Date

Mar. 31, 2013

Document Fiscal Year Focus

2013

Document Fiscal Period Focus

Q2

Trading Symbol

BASI

Entity Registrant Name

BIOANALYTICAL SYSTEMS INC

Entity Central Index Key

0000720154

Current Fiscal Year End Date

--09-30

Entity Filer Category

Smaller Reporting Company

Entity Common Stock, Shares Outstanding

7,672,736

Amendment Description

Explanatory Note

Bioanalytical Systems, Inc. ("we", "us", "our", or the "Company") is filing this Amended Quarterly Report on Form 10-Q/A (this "Amendment") to amend our Quarterly Report on Form 10-Q for the quarter ended March 31, 2013, originally filed with the Securities and Exchange Commission (the "SEC") on May 15, 2013 (the "Original Filing"). The Amendment restates our unaudited condensed consolidated financial statements and related disclosures for the three and six months ended March 31, 2012 and March 31, 2013.  This Amendment also amends certain other Items in the Original Filing, as listed in "Items Amended in this Amendment" below, as a result of the restatement. Details of the impact of this restatement are discussed below and in Note 2 to the accompanying unaudited condensed consolidated financial statements and in Management's Discussion and Analysis of Financial Condition and Results of Operations.

Restatement Background

In August 2013, we announced a delay in filing our Form 10-Q for the three and nine months ended June 30, 2013 until management resolved a complex accounting issue related to the accounting treatment for our outstanding warrants. In the same month, we announced that investors should no longer rely upon our previously issued consolidated financial statements and the related independent auditors' reports for the fiscal years ended September 30, 2012 and September 30, 2011 or the quarterly financial statements for the first two quarters of fiscal 2013, or any earnings releases relating to these periods, because of errors in such financial statements.

As a result of the identification of such errors, we have undertaken a comprehensive review of our previously filed consolidated financial statements. We concluded that the warrants issued in connection with our public offering in May 2011 were incorrectly accounted for as equity and the fair value of those warrants should have been recorded as a liability. As a result, we have restated our previously reported consolidated financial statements for the years ended September 30, 2012 and 2011, as well as the condensed consolidated financial statements for the three and six months ended March 31, 2013. The restatement adjustments to the full fiscal years ended September 30, 2012 and 2011 are more fully described in Note 3 to the Consolidated Financial Statements in our Form 10-K/A for the year ended September 30, 2012, which was filed on the date hereof.

Internal Control Consideration

Our management has determined that there was a control deficiency in our internal control over financial reporting that constitutes a material weakness and has concluded that our disclosure controls and procedures were not effective as of March 31, 2013 as a result of the issues that resulted in the restatement of our financial statements for the period and as discussed in Part I - Item 4 of this Amendment. A material weakness is a control deficiency, or combination of control deficiencies, in internal control over financial reporting, such that there is a reasonable possibility that a material misstatement of the annual or interim condensed consolidated financial statements will not be prevented or detected on a timely basis. For a discussion of management's consideration of our disclosure controls and procedures, internal control over financial reporting and the material weakness identified, see Part I - Item 4 included in this Amendment.

Items Amended in This Amendment

For the convenience of the reader, this Amendment sets forth the Original Filing, in its entirety, as modified and superseded where necessary to reflect the restatement.  The following items in the Original Filing have been amended as a result of, and to reflect, the restatement:

• Part I - Item 1. Financial Statements;

• Part I - Item 2. Management's Discussion and Analysis of Financial Condition and Results of Operations; and

• Part I- Item 4. Controls and Procedures.

In accordance with applicable SEC rules, this Amendment includes new certifications required under the Securities and Exchange Act of 1934, as amended ("Exchange Act"), dated as of the filing date of this Amendment.

We have not updated items in this Amendment to reflect events occurring after the Original Filing date, other than those associated with the restatement of our financial statements. 

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SEGMENT INFORMATION (Tables)

6 Months Ended

Mar. 31, 2013

SEGMENT INFORMATION [Abstract]

Opertaing Segments

Our accounting policies in these segments are the same as those described in the summary of significant accounting policies found in Note 2 to Consolidated Financial Statements in our annual report on Form 10-K/A for the year ended September 30, 2012.

	Three Months Ended March 31,						Six Months Ended March 31,
	2013			2012			2013			2012
	(Restated)			(Restated)			(Restated)			(Restated)
Revenue:
Service	$	3,667		$	5,279		$	8,337		$	10,890
Product		1,489			1,687			2,623			3,592
	$	5,156		$	6,966		$	10,960		$	14,482
Operating income (loss):
Service	$	(365	)	$	(1,419	)	$	(150	)	$	(2,685	)
Product		356			(275	)		444			(311	)
Corporate		-			(11	)		-			(11	)
	$	(9	)	$	(1,705	)	$	294		$	(3,007	)
Interest expense		(163	)		(179	)		(329	)		(368	)
Change in fair value of warrant liability - (increase) decrease		(142	)		56			(25	)		-
Other income		3			-			5			-
Income (loss) before income taxes	$	(311	)	$	(1,828	)	$	(55	)	$	(3,375	)