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PLA 2.1 Manual - PLA 3.0 – Software for Biostatistical Analysis

1. F test Non significance of difference of models parallelism F test for the non significance of the difference of models unrestricted minus restricted The significance level defines the sensitivity higher values less sensitive The test passes if F lt F critical After pressing Add a list of 33 different tests is offered to be added to your assay Using Filter you can easily find the tests you are looking for You can add multiple tests at once Note You can add any test to any object regardless wether this test is available when the calculation is carried out Our recommendation is to define tests at the assay level and bind the test of the objects to the assay level using the Inherit Properties feature As always in PLA the test are only carried out when they are activily defined at the standard or the preparation or bound the assay level via the Inherit Properties feature 16 May 2013 Page 85 of 193 i PLA 2 1 Select Test Class Filter Select the items to copy to your assay F test Significance of regression wj F test Lack of fit linearity Wj F test Non signiticance of difference of models parallelism wj F test Non signiticance of quadratic term linearity separate ANOVA required wj F test Significance of Slope wj Additional test Sum of squares non linearity linearity rae Equivalence test Difference of slopes HEH Equivalence test Difference of lower asyroi
2. sample Preparation 1 Ratio of slopes Sample Preparation 2 0 Graph Type 0 Dose Response Graph Equivalence Margins Display Options Show Legend Show Grid Regression Lines Restricted Model U Mean Line Data Yalues Include Statistical Outliers Include Technical Outliers lt ISG Error Bars 1 0 c E Bor amp Whisker Plot Irvert 3 Anis Showy Asis Origin Y Axis Transformation Linear Preliminary Preparation Results Sample Preparation Test Results Sample suitability J Overall test result ao ae Assay suitability Estim Potency Ratio and Confidence Interval 0 546 Confidence Interval 0 501 0 595 Potency A atio E Saveimage Recalculate Close You can see the confidence interval falls entirely between the goalposts Therefor the parallelism test is passed Close the Assay Explorer After we have finalized our initial analysis we now start the final computation 6 8 Final Computation and Reporting For the final computation we select the assay or any child of the assay in the navigator Then we start Calculate amp Report from the file menu the navigators context menu or from the toolbar 16 May 2013 Page 130 of 193 Bia PLA 2 1 Iculat te Assays and Create Reports
3. o PLA 2 1 PLA 2 1 User Manual Stegmann Systems Raiffeisenstr 2 C1 C2 63110 Rodgau Germany Phone 49 6106 77010 0 Fax 49 6106 77010 29 support bioassay de www bioassay de 16 May 2013 Page 1 of 193 Table of Contents 1 Introduction 1 1 Statistical Features 1 2 Test Features 1 3 Data Management and Reporting Features 1 4 GxP Features 1 5 21 CFR Part 11 2 Overview of the Manuals 2 1 PLA User 2 2 PLA Administrator 2 3 IT Administration and Validation 3 Getting Support 3 1 Website 3 2 E Mail 3 3 Phone 3 4 Fax 4 Getting Started 4 1 Parallel Line and Parallel Logistic Assays 4 1 1 Parallel Logistic Assay 4 Parameter Fit 4 1 2 Parallel Line Model Linear Regression with selection of active region 4 2 Installation of PLA 2 1 4 2 1 PLA 2 0 Coexistence 4 2 2 CD ROM Version of PLA 2 1 4 2 3 Download Version of PLA 2 1 4 2 4 PLA 2 1 Upgrade 4 2 5 Accept the Terms of License 4 2 6 Select Destination Folder 4 2 7 Start the Installation 4 3 Software Licensing Attachment of the Software Licensing Module Hardlock 4 3 1 Software Licensing 4 3 2 Attachment of the Software License Module Hardlock 4 4 Basic Database Management 4 4 1 File Based Database 4 4 2 Database Server Based Databases 4 5 Basic Concepts of PLA 2 1 4 5 1 Database Storage Concepts 4 5 2 Object Types and Hierarchy 4 5 3 Inheritance of Object Properties 4 6 Basics of PLA 2 1 Mathematical Features 4 6 1 Doses and Potencies 4 6 2 Assigned
4. 2 1 PLA User A PLA User uses PLA to define and calculate assays based on the settings a PLA administrator defined for the database in use The most relevant sources of information are PLA 2 1 User Guide Sj Learn the principles of PLA and its efficient use PLA 2 1 My First Assay with PLA Sj Follow a systematic guide to define and analyze a simple assay PLA 2 1 Reference Sj Find reference information for mathematical and technical options of PLA PLA 2 0 Tutorial Videos L Some Flash Videos for common tasks within PLA Online Help only 2 2 PLA Administrator The PLA Administrator is responsible for setting up an already installed PLA for a workgroup He defines user accounts and the global settings for the assay analysis PLA Administrator is a role inside PLA PLA 2 1 Administration Guide oe Find information concerning the PLA Administration PLA 2 1 Validation Guide Sj Find out how to validate PLA using the PLA Validation Package 16 May 2013 Page 11 of 193 es i PLA 2 1 2 3 IT Administration and Validation The IT administration is responsible for installing PLA in your environment and set up central database services PLA 2 1 IT Administration Guide So Find information for the IT administration of PLA PLA 2 1 Validation Guide L Find out how to validate PLA using the PLA Validation Package 16 May 2013 Page 12 of 193 3 Getting Support PLA 2 1 There are several ways to get support Do not hesitat
5. If you are currently using PLA 1 2 or PLA 2 0 the following notes may be relevant for you 10 1 No Interaction of PLA 1 2 PLA 2 0 and PLA 2 1 You may install and use PLA 1 2 PLA 2 0 and PLA 2 1 on the same computer system without any restrictions All versions do not influence or interact with each other You may install and un install them in any order PLA Database Migration While the software does not interact you have to be aware of database migration warnings If you open a PLA 2 0 database with PLA 2 1 PLA 2 1 asks for the permission to migrate the database If it is migrated PLA 2 0 has no longer access to the migrated database 10 2 Data Migration for PLA 1 2 If you want to migrate your data from PLA 1 2 you have to export them in PLA 1 2 and then import the corresponding data file in PLA 2 1 10 3 PLA 2 0 PLA 2 1 Licensing If you have purchased PLA 2 1 you are free to use PLA 2 0 on the same computer too 16 May 2013 Page 187 of 193 PLA 2 1 11 Stegmann Systems GmbH Stegmann Systems formerly known as Stegmann Systemberatung has been founded 1996 It is located in near Frankfurt Main in Germany Stegmann Systems GmbH Raiffeisenstr 2 C1 C2 63110 Rodgau Germany Phone 49 0 6106 77010 0 Fax 49 0 6106 77010 29 E Mail support bioassay de Website www bioassay de 16 May 2013 Page 188 of 193 o PLA 2 1 12 System Requirements Your computer needs to meet the system req
6. 0 592 vF ti EL reperanan Confidence Interval 04933 0698 E Saveimage Recalculate The assay now passes all hypothesis tests and the visual inspection displays a solution in accordance to our expectations The Potency ratio is calculated as 0 54 with a confidence interval of 0 485 to 0 602 Now lets switch to full curve fitting with the 5 parameter method and lets have how this solution is calculated 16 May 2013 Page 127 of 193 PLA 2 1 6 6 Switching the Regression Model to 5 Parameter Logistic The 5 parameter logistic functions is used very often nowadays since it allows to take the full curve into account and due to fifth parameter it is able to fit asymmetric dose response relationships Since we have activated the inheritance property on the analysis page we open the assay and go to analysis page Select 5 parameter logistic curve fit as the model Then save the assay Start the Assay Explorer with Check from the toolbar x7 Data Explorer Check Online Example amp z Graph Type Dose Response Graph Equivalence Margins Display Options 0 650 Show Legend Show Grid 0 600 Regression Lines Restricted Model F Mean Line 0 550 Data Values F Include Statistical Outliers 0 200 Include Technical Outliers a 0 450 Error Bars 1 0 0 S E Bor amp Whisker Plat yr 0 400 lnvert 8 Axis Showy Axis Origin _ 0 350 Y Ass T
7. Analysis A _ Documentation Configuration EE Inherit Properties PO errr errr rity Wise range properties of the assay object Upen Assay Definitions Dann snEL seuss ee sues autnavene suse ee eae suse Gy a a Geers Linear Range Configuration Full Range Analysis Options We now have to select the analysis options We want to start with the parallel line method We select the analysis of the editor and select the following Model parallel line method Significance of Regression and Linearity 98 Inherit the Analysis Properties Yes 16 May 2013 Page 120 of 193 i PLA 2 1 Configuration Audit Trall Inherit Properties J use analysis properties of the assay object Upen Assay Definitions Response Adjustment no adjustment default 0 Response Transformation no transformation Outher Detection No Outlier Test Contamination a 0 1 recursive testing x n o Testin Z Regression Model amp ANOVA 4 parameter logistic curve full curve Fit 4 Invert potency ratio fired value T AN OYA based on residual error lack of fit pure error Confidence Interval for Potency Estimation Fiducial limit of potency estimation 2 Muse Fleller s Theorem EC50 Calculation parallel line model Method Calculate 50 Response by Do not calculate This object Once we have set these options save the object from the file menu or the tool
8. Press Download License Keys if you have an internet connection or type in the license keys you have received with your license 16 May 2013 Page 152 of 193 Se gt gt gt TO PLA 2 1 Note The License Keys match the hardlock id If your License Keys are marked as invalid check that your hardlock id matches the keys 16 May 2013 Page 153 of 193 PLA 2 1 9 Reference The reference section is divided into two parts e User Interface Reference Get information on the dialogs of PLA e System Message Reference What to do when a message raises 9 1 Technical Reference 9 1 1 Account Management Dialogue The Account Management dialog allows you to create new user accounts and to modify or delete existing ones 8 Account Menngenert hl z ee ee S ee hl ee a ACCOU nt Management a lelet jeer 1 J im Se i r Defined Accounts Settings for account n al Account Hame Account Password Retype password change password at next login This account i member of the following group Deactivated Users Standard U zers System Inspectors System Administrators Administrator can create accounts and modify GLPYSOP Settings Modify Delete Cancel Close Defined Accounts A list of existent accounts Selecting an account allows you to delete or modify it 16 May 2013 Page 154 of 193 PLA 2 1 Add Create a new account Modify Modify the selected
9. Softmas Pro soe 4ow 5e Wavelength 2 4da Softmas Pro sisal Soe Wavelength 1 2 4da Import in Progress Please select the file you want to import Fress Select File to choose the import file 2 Select Import File YAPLA 2 1 Example PEF Select File Results of Initial Analysis Selected File YAPLA 2 15E sample PEF Selected Format FLA 2 x Enhanced Format Analyzing the input file Please wait complete Input file contains 40 valid objects If the analysis is successful the Next gt button gets activated Our sample shows 40 valid objects If the selected file format requires a PLA Import Module to be executed it will start automatically You will see an result code of the external Import Module Press Next gt to view the objects to be imported The Object Import Tree The PLA Import Wizard now displays the Import Tree 16 May 2013 Page 60 of 193 Select Input File Choose Destination Control and Summary Ar a Include Import in Progress E Gidd Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Assay 2 Assay 3 Assay 4 Assay D Assay 6 Assay r Assay g Assay 9 Please choose or create the destination where the imported data will be saved Fress Fe to rename objects You may use these yarables in object names U User 0 D ate 7 T ime F Filename On this page you have several options e Include and Exclude parts of the tree by selecting an object and pressing
10. fa PLA 2 1 InstallShield Wizard License Agreement Please read the following license agreement carefully Software Licensing Agreement All products sold by Stegmann Systems GmbH or companies associated therewith including demonstration sets hardware media and manuals hereinafter referred to collectively as Product as well as all future orders shall be subject to the following provisions If you do not accept these provisions please return the product to us within seven 7 days of having purchased or received the Product We will 7 I accept the terms in the license agreement I do not accept the terms in the license agreemen InstallShield Once you select accept the terms in the license agreement the Next gt button is enabled Select Next gt to proceed 16 May 2013 Page 17 of 193 Se gt lt PLA 2 1 4 2 6 Select Destination Folder By default PLA is installed in the Program Files folder of your computer system This screen allows you to select a different destination folder ie PLA 2 1 InstallShield Wizard Destination Folder Click Next to install to this folder or cick Change to install to a different folder Install PLA 2 1 to pa C Program Files x86 Stegmann Systems PLA 2 14 InstallShield Press Next gt to continue 16 May 2013 Page 18 of 193 PLA 2 1 4 2 7 Start the Installation ie PLA 2 1
11. Assumed Potency 4 6 3 Model Response Transformation and Outlier Detection 4 6 4 Analysis of Variance ANOVA 16 May 2013 PLA 2 1 O CO CO OO 11 11 11 12 13 13 13 13 13 14 14 14 15 16 16 16 16 16 17 18 19 21 21 22 22 24 24 25 25 25 26 27 27 28 28 30 Page 2 of 193 4 7 4 6 5 Configuration Optimization The PLA 2 1 Test System 4 7 1 Difference Tests 4 7 2 Similiarity Tests 4 7 3 Additional Tests 4 7 4 Test Scopes Levels and Severity 5 User Guide 5 1 5 2 5 3 5 4 5 5 6 1 6 2 6 3 6 4 6 5 6 6 6 7 6 8 Connect to PLA 5 1 1 Log in to PLA 5 1 2 Screen Layout The Objects of PLA 5 2 1 Managing Objects 5 2 2 Editing Objects 5 2 3 Inheritance Templates and the Apply Function 5 2 4 Import and Export Object Properties 5 3 1 General Properties 5 3 2 Dose Properties 5 3 3 Data Properties 5 3 4 Analysis Properties 5 3 5 Test Properties 5 3 6 Configuration Properties 5 3 7 Documentation Properties 5 3 8 GxP Settings Analyze Assays 5 4 1 Explore your Assay 5 4 2 Combination of Assay Results 5 4 3 Calculate amp Report Advanced Topics 5 5 1 Electronic Signatures 5 5 2 Secure Transfer of Data and Objects 5 5 3 Audit Trail 5 5 4 Test System My First Assay with PLA The Sample Data for the Tutorial Hierarchy of Objects Data Input 6 3 1 Create the Project 6 3 2 Create The Assay 6 3 3 Create The Standard Object 6 3 4 Create The Preparation
12. I paa LLL Saveimage Recalculate Close As expected the hypothesis regarding the validity of assay fail We have selected Full Range for the configuration which is a bad choice for this assay With the Assay Explorer you cannot manipulate data So take the chance and try all options of the dialog We should now try to optimize our configuration to achieve a valid parallel line assay 6 5 Optimizing the Configuration In a sigmoid example it is necessary to thoroughly select the valid dose response regions for the assay You can do this by selecting a fixed range on the configuration page of each object But you can also let PLA do 16 May 2013 Page 124 of 193 PLA 2 1 the work for you If you decide to try the automatic optimization you should nevertheless thoroughly check results We will try the following PLA should search for a maximal region in the assay that fulfills the hypothesis criteria The 50 response of the assay should be included The optimized solution should have identical number of points treatments for both Standard and Preparation So we go to the Configuration page of the assay since we activated the inheritance option If we didn t the next steps have to executed on the standard and the preparation Now we select the options as follows 16 May 2013 Page 125 of 193 eal PLA 2 1 Inherit Properties Use range properties of the assay object Open Assay Definitions Linear Range Confi
13. InstallShield Wizard Ready to Install the Program The wizard is ready to begin installation Click Install to begin the installation If you want to review or change any of your installation settings dick Back Click Cancel to exit the wizard InstallShield Click Install to start the installation procedure The setup program starts the installation sequence 16 May 2013 Page 19 of 193 PLA 2 1 Installing PLA 2 1 The program features you selected are being installed Please wait while the InstallShield Wizard installs PLA 2 1 This may take several minutes Status wm InstallShield lt Back Next gt The InstallShield Wizard has successfully installed PLA 2 1 Click Finish to exit the wizard l Cancel 16 May 2013 Page 20 of 193 eo gt gt gt TO PLA 2 1 If you have received a Software License Module Hardlock dongle with your retail package attach it to your system PLA is completely installed now Where to go from here e Basic Database Management e Basic Concepts of PLA 2 1 4 3 Software Licensing Attachment of the Software Licensing Module Hardlock 4 3 1 Software Licensing PLA 2 1 can be run in three different modes e Trial Mode e Seat License Mode e Network Concurrent Use License Mode Trial Mode When you download PLA 2 1 for
14. Object Sample Parallel Line Assays Sample Parallel Line Assays Sample Parallel Line Assays Sample Parallel Line Assays Sample Parallel Line Assays Standard Sample Parallel Line Assays Standard Sample Parallel Line Assays Sample Parallel Line Assays Sample Parallel Line Assays Sample Parallel Line Assays 2 Sample Farallel Line Assays Sample Farallel Line Assays Sample Farallel Line Assays Standard Samole Parallel Line 4ssave Old Yalue 2013 04 29 10 43 44 0 0 0 Figure Audit Trail Inspection from the system menu 16 May 2013 gt Assay 9 gt Sample gt Assay 9 gt Sample gt Assay 9 gt Sample gt Assay 9 gt Sample gt Assay 9 gt gt Assay 9 gt gt Assay 9 gt Assay 9 gt Assay 6 gt Sample gt Assay Oo gt Sample gt Assay 8 gt Sample gt Assay 8 gt Sample gt Assay 5 gt gt Assay O gt Operator fork PLA Administrator 1 PLA Administrator PLA Administrator 1 PLA Administrator 1 PLA Administrator 7 PLA Administrator 1 PLA Administrator 1 PLA Administrator 1 PLA Administrator 1 PLA Administrator 7 PLA Administrator 1 PLA Administrator 1 PLA Administrator 7 PLA Administrator 1 7 F New Value 2013 04 29 11 27 02 g5 g5 g5 Page 105 of 193 a PLA 2 1 sviin e Audit Trail H Timestamp ction Operator Workstation ID 104 29 04 2013 11 26 56 OBJECT_SIGN
15. Project Sample Project as the object type Once the object is created we will set the initial parameters of the objects Three groups of information have to be set 1 The Assay Dimension 2 The Configuration Optimzation Option 3 The Analysis Options Assay Dimension The standard and the preparation both have twelve treatments dilution steps and three replicates Now open the assay if not already open and move to the data page Configuration Documentation G F Audit Trall Doses Data Analysis Tests General Dimension and Dilution Scale Number of treatments dilution steps 12 allowed 2 25 Number of replicates 7 allowed 1 25 Dilution scale Lin Z twofold series x Set the number of treatments and the number of replicates Configuration Optimization We will start with the Full Range option set This leads to the inclusion of all data points in the computation Select the Configuration page and set the optimization method to Full Range General Doses Data Analysis Tests Configuration Documentation GF Audit Trail Inherit Properties fuse range properties of the assay object Upen Assay Definitions Linear Range Configuration Full Range 16 May 2013 Page 119 of 193 4 PLA 2 1 For easier maintenance in the case we want to switch this method we decide to switch on the Inheritance Property General Doses
16. the analysis of variance considers the regression model and deviations from the regression model as sources of variation The lack of fit gets part of the error term so there is no separate test of linearity with this approach This approach is available with one or more replicates Hypothesis tests based on separate ANOVAs This method was the old approach of PLA 1 2 It has been set to deprecated in PLA 2 0 and it has been removed from PLA 2 1 The old method was based on an inhomogeneuos ANOVA for the parallelism Bound to the old Hypothesis tests based on separate ANOVAs what to do If you still want to use the method you can do the following 1 Switch to ANOVA based on Residual Error 2 Add the F Test for deviations of Parallelism to your preparations or on the assay level 16 May 2013 Page 30 of 193 h PLA 2 1 3 Add the F Test for the significance of the slope to all elements of your assay 4 Add the F Test for the insignificance of the quadratic term to all elements of your assay The only difference of this configuration is the use of a homogenious ANOVA for parallelism Q Note a homogeneuos ANOVA is corrected by the mean of the response values making the ANOVA independent to a shift in the response data The ANOVA looses one degree of freedom in comparison to the inhomogeneuos ANOVA 4 6 5 Configuration Optimization The configuration of an assay in terms of PLA is the selection of individual treatments o
17. 09 2005 11 06 19 Last modified PLA Administrator at 08 05 2006 15 52 47 Parent Object Examples from Literature 21 CFR part 11 Electronic Signatures Doubleclick for details R No signatures have been applied yet Remove Figure Screen Layout of the General Properties 5 3 2 Dose Properties Dose properties describe the way an standard or preparation is prepared for analysis They allow the definition of raw material or stock solution potencies If defined PLA calculates the potency factors for these potencies Property Description Raw Material Raw Material 16 May 2013 Page 78 of 193 Assigned Assumed Potency Amount Solvent Volume Assume identical potency of standard and preparation Stock Solution Stock Solution Assigned Assumed Potency Assume identical potency of standard and preparation Pre Dilution Pre Dilution Pre Dilution Factor Additional Pre Dilution Factor Include Pre Dilution Factor in potency ratio estimation 16 May 2013 PLA 2 1 A raw material bulk substance potency will be given The calculation results will contain a potency estimation for the raw material The potency of the raw material given as a number and the numerator of the units E g if the potency is 5 IU ug type in 5 and IU The denominator has to be given in the amount units The amount of raw material used In the above example the amount has to be given in ug The volume in which the used amoun
18. 1 For an existing assay Activate the Inherit Properties on the assay level then use apply to apply the setting to every child object Test Level A test is defined either as an assay suitablity test or as a sample suitability test A sample suitability test fails the current potency calculation of a single preparation The test result of all other calculations within the single assay is not influenced A assay suitability test fails all preparations in a single assay Additional test Max number of outliers Margin 0 2 Sample Suitability Test Test Scope 1 Assay Suitability Test Test Severity tabi Test Passed Message default Test Failed Message default Example Consider an assay consisting of two preparations Consider Preparation A is passing the test itself while Preparation B is failing the test The overall result of both tests is given in the next table Test setup as Overall Result of Overall Result of Assay 1 Assay1 Preparation A Preparation B Test passed Test failed Sample Suitability Test PASSED FAILED Assay Suitability Test FAILED FAILED Test Scope Every test has a scope The scope is necessary to allow the test definition on the project or assay level even for sophisticated setups You can mark a preparation object of your assay as an assay control 16 May 2013 Page 111 of 193 Name Value Additional test Max number of outliers Margin g Test Level 2 Sample Suitabili
19. 1 e Severity While the calculation of a parallel line or parallel logistic assay does not require tests for the estimation of the potency it is strongly recommended to add validity criteria to your assay definition PLA 2 1 has 32 different tests available that can be used to assure the validity of your system The tests have to be thourougly choosen In the test setup you compose the different tests to your individual test setup Note not all of the tests may be available to your system The availabity depends on the choosen regression model and the dimension of your system Due to the inheritance architecture of PLA you are always free to add any test to your system regardless wether they are available or not How to develop equivalence margins There are several approaches to develop equivalence margins PLA 2 1 is fitted with a special report for Microsoft Excel tm which allows to calculate historical assay data The report calculates equivalence margins for a set of given assays You can use the variation of the different candidate margins to get a guess which equivalence margins might be fit to match your needs A major advantage of the system is to mix tests of the classical difference testing and the newer approach of similarity testing to one single test scenario allowing this scenaria to match the aceptance criteria of the European Pharmacopoeia and the US Pharmacopoeia 4 7 1 Difference Tests Difference Tests are performe
20. 127 1 256 0 111 0 133 0 127 1 512 0 119 0 128 0 11 1 1024 0 118 0 12 0 136 1 2048 0 131 0 128 0 129 This is a graphics of our exemplary data 0 700 0 600 0 500 Response 0 400 0 300 g Y7fEO4 45576 0353 3126 02 1 77E 01 1 00E00 Dose Preparation Standard The assay has a strong lower asymptote a highly significant area and it seems to close in an upper 16 May 2013 Page 116 of 193 PLA 2 1 asymptote This is not to easy to be analyzed We would prefer to analyze the data as a parallel line assay but we will have a look at the 5 parameter logistic too 6 2 Hierarchy of Objects For this assay to be analyzed with PLA we need the following structure of objects A parent project which serves as a container for any number of assays Sample Project An assay object representing the full assay Assay A standard for the settings of the standard Standard A preparation for the data whose potency is of interest Preparation In the user manual it is stated that the inheritance is a major tool in PLA to setup assays as easy as possible In this tutorial we will make use of this starting at the assay level If we had to analyze many assays of this type we could use the properties of the project to have defaults for all objects To reach best efficiency we will create the project without defining anything Then we will add an assay and define our initial properties The last step is the creation of the stan
21. 180 of 193 nal PLA 2 1 Enter your city into this field Zip code Enter the corresponding zip code here State Region Enter your state or region here Country Enter your country here E mail Enter your e mail address here Phone Enter your or your company s phone number here Fax Enter your or your company s fax number here Keep me informed about PLA and your other bioassay products by email Enable this option if you want to receive latest information about PLA and other bioassay products of Stegmann Systems Privacy statement A statement explaining to you that your data will not be made available to any third party Submit online Submit your registration online PLA transmits the data entered above to the Stegmann Systems user database Note This feature requires an internet connection Generate file PLA generates a file which you can print fax or send via Mail Never ask again Closes this dialog PLA won t ask you again for registration However you can open this dialog again by clicking the Click to edit hyperlink on the Login Dialog Close Closes this dialog You will be asked again to register upon next startup 9 1 17 Session amp Lock Management This dialog allows you to manage all active sessions of a PLA database and their corresponding locks 16 May 2013 Page 181 of 193 Daal PLA 2 1 Session Username 5 N Login Timestamp keep Alive Timestamp PLA Administrator 15367176 WPB
22. 2 CD ROM Version of PLA 2 1 Insert the disc into your CD ROM drive PLA 2 1 Setup should be executed automatically If you have disabled the auto run feature please start setup exe by using the Windows Explorer or by selecting Run from your Start menu The program to be executed is lt DriveLetterofCDDrive gt setup exe e g D setup exe 4 2 3 Download Version of PLA 2 1 Please download the most current version of PLA from our website at www bioassay de and run the downloaded installation file e g PLA 2 1 Setup build 600 exe The PLA Setup routine initializes Q Note There may be a security warning of your computer system when you try to execute a downloaded program 4 2 4 PLA 2 1 Upgrade If you already had installed a previous version of PLA 2 1 the old version has to be un installed first PLA Setup automatically recognizes the old version and you will receive the following warning message 16 May 2013 Page 16 of 193 i PLA 2 1 1 PLA Upgrade Warning Version 2 1 0 0600 of PLA ts already installed P You must uninstall the existing version before installing version 2 1 0 0600 of PLA Do you want to automatically uninstall the existing version of PLA now Note the Yes and No answers are localized Select Yes to uninstall the old version No data will be lost 4 2 5 Accept the Terms of License The next step is the acceptance of the Terms of License This is required to proceed with the installation of PLA
23. 4 1 PLA Databases 8 4 2 PLA Database Maintenance 8 4 3 Distribution of Connection Profiles Using Registry Settings PLA License Management 8 5 1 Retail Mode 9 Reference 9 1 Technical Reference 9 1 1 Account Management Dialogue 9 1 2 Action Menu 9 1 3 Apply 9 1 4 System Audit Trail 9 1 5 Change your Password 9 1 6 Context Menu 9 1 7 Create Object 9 1 8 Database Manager 9 1 9 Database Manager Connect 9 1 10 File Menu 9 1 11 Help Menu 16 May 2013 PLA 2 1 132 132 132 132 133 133 133 133 134 137 137 138 140 140 140 142 143 143 144 144 144 145 145 145 145 146 146 146 146 146 151 151 151 154 154 154 155 156 158 159 160 161 163 164 166 168 Page 4 of 193 9 1 12 License Management 9 1 13 Login 9 1 14 Options 9 1 15 Product Information 9 1 16 Register Your Copy of PLA 9 1 17 Session amp Lock Management 9 1 18 System Menu 9 1 19 System Locked 9 1 20 Validation Menu 9 1 21 Window Menu 10 PLA 2 1 vs PLA 2 0 vs PLA 1 2 10 1 No Interaction of PLA 1 2 PLA 2 0 and PLA 2 1 10 2 Data Migration for PLA 1 2 10 3 PLA 2 0 PLA 2 1 Licensing 11 Stegmann Systems GmbH 12 System Requirements 13 Copyright 14 Licensing Agreement 15 Revision History 15 1 PLA 2 1 build 600 16 May 2013 PLA 2 1 169 170 172 178 179 181 183 184 185 185 187 187 187 187 188 189 190 191 193 193 Page 5 of 193 oo T ae o These pages contain the PLA 2 1 documentation and other
24. Assay 5 Assay B Assay f Assay A Assay 9 Dixon Test no adjustment default Response Transformation no transhormation Outher Detection F a cli Sample Parallel Logistics Assays Contamination o 0 2 recursive testing xtnto Testn 2 linear regression parallel line model Invert potency ratio fixed value ANOVA based on pure error separation Confidence Interval for Potency Estimation Fiducial limit of potency estimation 95 0 use Fieller s Theorem EC50 Calculation parallel line model Method Calculate 50 Response by Do not calculate This object a Outlier testing iz activated You need at least 3 replicates for outlier testing E include hidden items E refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator 16 May 2013 Page 56 of 193 oe gt gt gt TO PLA 2 1 5 2 4 Import and Export PLAs External Data Formats The Import Export methods of PLA directly support three file formats PLA Secure Format PSF The PLA Secure Format is the preferred external data format of PLA The format is digitally signed by PLA s internal PKI This prevents the format from any manipulation and thus allows to securely transfer even electronic signatures from one PLA installation to another The digital signature of a PSF file is checked on every import If the signature is invalid the PSF is not imported PLA External Format PEF The PLA Ext
25. Object A First Look Optimizing the Configuration Switching the Regression Model to 5 Parameter Logistic What About Equivalence Testing Final Computation and Reporting 16 May 2013 PLA 2 1 31 31 32 32 34 34 36 37 37 38 40 40 46 50 57 76 71 78 80 81 84 87 88 90 93 93 97 99 101 101 102 103 107 115 115 117 117 117 119 121 122 123 124 128 129 130 Page 3 of 193 oe gt gt gt TO 7 Validation Guide 7 1 7 2 7 3 74 7 5 What is included in the package Principles of Validation 7 2 1 Validation of Each System 7 2 2 Cryptographically Secured Reference Data 7 2 3 Recommendation for your 0 OO Procedures Installation Qualification 7 3 1 The Installation Qualification Process 7 3 2 Performing the Installation Qualification Operational Qualification 7 4 1 The Operational Qualification Process 7 4 2 Performing the Operational Qualification Performance Qualification 7 5 1 The Performance Qualification Process 7 5 2 Preparing the Performance Qualification 7 5 3 Performing the Performance Qualification 8 IT Administration Guide 8 1 8 2 8 3 8 4 8 5 Description of PLA for IT Professionals PLA Setup Basics 8 2 1 PLA is Microsoft Windows Compliant 8 2 2 Customizable Directories of PLA 8 2 3 Other Directories of Interest 8 2 4 Hardlock Installation Security Basics 8 3 1 User Account Security 8 3 2 Data Integrity 8 3 3 Database Security Database Guide 8
26. are displayed on the summary page for final control When you are ready press Finish to start the Importation 16 May 2013 Page 62 of 193 Summary Select Input File Summary of operation Please check with care YAPLA 2 15E sample PEF Choose Destination Control and Summary Import file Import in Progress Creation cheme The following objects will be imported Please check the settings you made on the previous pages You can start the import by selecting Finish 1 Project 0 Assay Standard Preparation Preparation Preparation Preparation Preparation Assay Standard Preparation Preparation Assay Standard Preparatior Preparation Assay Standard Preparation Preparatiort Assay Sample Project 2 Assay 1 Standard Sample 1 Sample Sample 3 Sample 4 Sample 5 Assay 4 PLA Administrator Standard Sample 1 Sample 2 Assay 45 Standard Sample 1 Sample 2 Assay 6 Standard Sample 1 Sample 2 Assay F Cancel lt Previus Finish After you press finish the data is imported to PLA Raw Data Import When you installed a PLA Import Module the import process may become more complex since the Import Module might not be able to decide how to deal with your raw data Start the import as a standard import After you selected your file type and the input file the analysis section of the Import Wizard might contain the followi
27. assured that the workstation is switched on during your business hours Connect the Hardlock Server to the USB of the computer that will serve as a license server and install the hardlock server Software from the installation CD The hardlock server manages the number of license you purchased If the number of users exceed the license limit the connecting will receive a message to try again later 16 May 2013 Page 151 of 193 ne PLA 2 1 License Numbers In addition to the hardlock you have received a set of two or three license numbers They have to be typed in or downloaded in the License Management Dialog This dialog can be opened from the login screen by pressing License Information Product Information License Information The License Management Dialog appears PLA is in Trial Mode No valid retail license found This tral has 14 day s left Hardlock FOUND 10074 License Details Feature License Keps Hardlock Actyation LFEL 8460 52F4 8L Fw eM 3G 44 Walid PLA 2 1 Not Licensed PLA 2 1 Validation Package Mot Licensed Download License Keys Trial Details Inquiry Ken H35 TOSE BWEH J2AA Submit Online Submit by E Wlall Vendor Response Ok To extend your trial period please send the inquiry key to the vendor by mailing it to suppor bioassay de or filling out an online form using the Submit Online button ou will receve a Vendor Response that has to be entered into the green field Product Information
28. atio 0 892 F one i Confidence Interval 0 855 0 932 Sample 5 LN Saveimage Recalculate Close On the right side there are several groups of options and informations Graph Type Graph Type Dose Response Graph Equivalence Margins The graph type distinguishes between the dose response graph shown above and the goalpost graph that is available only when equivalence testing is chosen as the method of parallelism test 16 May 2013 Page 94 of 193 oe gt gt gt TO Display Options PLA 2 1 The display options allow to modify the displayed graph Show Legend Show Grid Regression Lines Regression Line Type Mean Line Include Statistical Outliers Include Technical Outliers Error Bars Box and Whisker Plot Standard Deviation Invert X Axis Show Y Axis Origin Y Axis Transformation Include Outliers in Graphic Transformations 16 May 2013 Toggle the display of the legend Toggle the display of the grid Toggle the display of the regression lines Switch between the restricted or the unrestricted regression lines Use the unrestricted regression lines to get an impression of the quality of the fit Display a line through the means of the treatments Display the statistical outliers in the graph Display technical outliers This is available when statistical outliers are displayed too Display the error bars of the treatments Display box and whisker graphic Mult
29. digest has been digitally signed Any modifications on this digest lead to an invalid signature The digest has been signed by PLA 2 0 IQ DE Stegmann Systems Stegmann Systems Bioassay PLA 2 0 IQ The digital signature is valid 1 1 1 Fileset All Users Overall result of this fileset Passed Path C ProgramData Stegmann Systems PLA 2 1 Check Existence File Name Result pla21 If Passed 1 1 2 Fileset Default Database Overall result of this fileset Passed Path C ProgramData Stegmann Systems PLA 2 1 Check Existence optional File Name Result PLA mdb Passed 1 1 3 Fileset System Files Overall result of this fileset Passed Path C AMindows system32 Check Required Version File Name Result PrpList3 ocx Passed Required File Version 12 02 2005 1 1 4 Fileset Report Templates Overall result of this fileset Passed Path C Program Files x86 Stegmann Systems PLA 2 1 Report Templates Check Existence optional File Name Result REP 10 Complete Statistics Report ert Passed REP 10 Complete Statistics Report iq Passed REP 11 Short Report ert Passed REP 11 Short Report ig Passed Stegmann Systems Germany www bioassay de Figure A certificate of the IQ process exemplary pages 7 4 Operational Qualification 7 4 1 The Operational Qualification Process The Operational Qualification OQ of PLA checks the mathematical functionality of the system PLA is fitted with a suite of 27 OQ Packages These
30. displayed data to the objects You may use the keyboard to assign selected data points to an object select the abbriviation characters a Bete and numbers to assign the step Selected datapoint Grid display options gt Edit Grid Dilution step FomtH Data value display point of columns T 1 z 730 595 display data 12 i color the grid Assign the Raw Response Values The next step is to assign the required values to standard preparation and control and to assign it to the corresponding dilution step The dilution step value is assigned by the template the parent object or later when you edit the object In a 1 in 2 dilution series the first step has the highest concentration Select the data point in the grid and then select the object and dilution step in the Selected Datapoint section In the following picture the response value in column 1 and row 1 is assigned to the standards first dilution step 16 May 2013 Page 68 of 193 Assign Aaw Dat Select Input File agh Faw Lala Import Definition Scheme Assign mode Please the data points to the objects Select Destination Scheme Define Objects 2 259 817 3 251 556 Ts 457 183 14 495 55 15 517 647 2o 636 066 gt 670 283 ef bo2 032 ar 761 55 gt 80 556 3d 796 845 43 656 307 gt 868 952 at 879 2 61 64 471 gt 882 906 Bs 507 332 ra 896 805 gt 815 915 ro 820 04 og 330 545 gt 34
31. entered at the standard AND the preparation level lt PLA 2 1 Software for Biological Assays Assay 1 Gandotrophin Asssay te File Actions System Validation Window Help ae B a X GAl SHB General Doses Data Analysis Tests Configuration Documentation BsF Audit Trail Data Objects ie E samples from Literature B f 1 Gandotrophin Asssay l Standard Test Preparation 3 0 2 Corticotrophin Assay Hdd Standard 5 Preparation T Preparation U 3 Antibiotic Agar Diffusion Assay 4 Antibiotic Turbidimnetric Assay B in vitro Hepatitis B Vaccine Assay 6 Insulin Assay Y Factor Ill Clotting Assay ample Parallel Line Assays ample Parallel Logistics Assays H A Measurement 1 i A Measurement 2 Online E ample WHO Standard Sample Preparation ce al hirclude hidden itema Ready refresh automatically Inherit Properties T use definitions properties of the assay object Open Assay Definitions Raw Material units Assigned Assumed Potency IL amount units Amount 1 mg Solvent Volume 1 rml 7 assume identical potency of standard and sample Stock Solution Assigned Assumed Potency 1 assume identical potency of standard and sample PLA 1 2 default V Pre Dilution Predilution Factor 1000 Additional predilution factor for the first step 1 2 C include pre dilution factor in potency ratio estimation PLA 1 2 default Note You c
32. every step from the raw data to a complete assay definition in PLA There are three main parts 1 Definition of the Assay and Data Input How to structure and define the assay in the PLA database 2 Exploring your Assay Modify the Analysis options Take a tour through the basic graphical analysis of the assay 3 Final Computation and Reporting Finalise the computation and create reports for the assay 6 1 The Sample Data for the Tutorial Our assay consists of a standard and a preparation whose potency is to be calculated As we will see the data has a highly sigmoid structure The assay is a dilution assay with a 1 in 2 dilution series Both standard and preparation have twelve treatments that are measured as triplicates The standard has the following response values Dose Response Replicate 1 Replicate 2 Replicate 3 1 1 0 722 0 71 0 734 1 2 0 707 0 75 0 734 1 4 0 655 0 69 0 713 1 8 0 607 0 664 0 628 1 16 0 512 0 506 0 507 1 32 0 325 0 382 0 376 1 64 0 231 0 223 0 24 1 128 0 119 0 152 0 161 1 256 0 102 0 137 0 125 1 512 0 115 0 139 0 123 1 1024 0 117 0 137 0 124 1 2048 0 086 0 128 0 106 The data of the preparation is as follows 16 May 2013 Page 115 of 193 Se gt lt PLA 2 1 Dose Response Replicate 1 Replicate 2 Replicate 3 1 1 0 732 0 717 0 704 1 2 0 731 0 674 0 715 1 4 0 618 0 663 0 638 1 8 0 618 0 524 0 56 1 16 0 348 0 354 0 381 1 32 0 224 0 22 0 238 1 64 0 141 0 15 0 137 1 128 0 101 0 135 0
33. export a single object tree or all object trees Now you have the option to export all objects or the selected object of the navigator Press Next gt to display the file type selection 16 May 2013 Page 73 of 193 PLA 2 1 Choose Type of Export Paret ie Select Target File Select your output format Specify Export Details PLA 2 8 Secure Format FLA 1 2 Native Format Summar Export in progress Please input or select the output file name and format Select output filedirectory V SPLA 2 1 Example 2 psf Select the file format you want to use and then press Select to open the Save dialog of the operating system lt gt Select output file Speichem J PLA2 1 Pf Name Anderungsdatum T Es wurden keine Suchergebnisse gefunden dl nT Dateiname Froject PSF Dateityp PLA 2x Secure Format 16 May 2013 Page 74 of 193 iag PLA 2 1 Type in a file name and press Save In the Export Wizard press Next gt to switch to the Export Details page Export Details Depending on your selected export format you may select the information details to export _ xport Data Export Options Choose Type of Export i Select Target File Object s to esport Specity Export Details Examples from Literature a Summar l l l l Include child objects Export in progress l l l include hidden objects Output options include data values include assay defin
34. for your eligibility for the upgrade You may use the resulting upgraded product only in accordance with the terms of this license agreement If the Product is an upgrade of a component of a package of software programs that you licensed as a single product the Product may be used and transferred only as part of that single product package and may not be separated for use on more than one computer You may not rent lease or lend the Product You may permanently transfer all of your rights under this license agreement provided you retain no copies you transfer all of the Product including all component parts the media and printed materials any upgrades and this license agreement and the recipient agrees to the terms of this license agreement If the Product is an upgrade any transfer must include all prior versions of the Product 3 Warranty 16 May 2013 Page 191 of 193 oe gt gt gt TO PLA 2 1 For a period of twelve 12 months after the delivery date Stegmann Systems GmbH shall guarantee a that the performance of the software corresponds in all essential characteristics to the description in the manual provided the software is used with the appropriate hardware and b that the medium on which the software is to be stored is free of material and manufacturing errors 4 Limitation of Liability In the event of a breach of warranty Stegmann Systems GmbH shall be exclusively obligated at its own discretion to re
35. have received the response code from PLA support you d have to enter it into the green text field OK This button will be enabled if you ve entered the vendor response in the green text edit field Pressing the button will check the entered code and activate PLA or a PLA feature Explanation A short text explaining how to use the License Manager Product Information Open the Product Information Dialog See also Product Information Close Close this dialog 9 1 13 Login The Login dialog allows you to login to a database It provides a list of databases to choose from and means to create new database connections Once you have selected the database the dialog shows the registered users of this database Select the desired user and type in your password Then press the Login button to proceed 16 May 2013 Page 170 of 193 PLA 2 1 Login to PLA 2 1 Default Database Database Moa Default Database O e M This trial E PLA has 14 day s lefi Click to edit PLA 2 1 Default Database Manage ia a a ay s lefi Click to edi This copy of PLA has not been registered yet User ID FLA Administrator PLA 2 0 is available Read the announcement nowl Password ee Product Information License Information HI Login Database This is a list of your database connection profiles Select the desired database connection profile PLA tries to establish the database connection and shows an updated use
36. include and exclude buttons Excluded objects are marked with a black cross e Select another parent for the assays This allows to import the objects to a different target If you selected an existing object as a target this is noted by an arrow e Rename Objects by pressing F2 You may also insert variables into the name These variable are useful if you want to create import definition schemes The variables are replaced when the import is executed The variables available are U replaced with the name of the current user D replaced with the current date T replaced with the current time and F which is replaced with the filename of the import file The next screen shows the different options 16 May 2013 Page 61 of 193 Select Input File Choose Destination Control and Summary AP Include Import in Progress Slada Sample 1 Sample 2 Sample 3 Select Sample 4 Standard Sample 1 Sample 2 Assay a Assay 4 Gal Assay D Assay G Assay r Ags Please choose or create the destination where the imported data will be saved fa E Fress Fe to rename objects You may use these variables in object names U User 0 D ate mT T ime F Filename In this example an existing project named Sample Project 2 is the target of the operation Assay 2 and Assay 3 are excluded and Assay 4 is renamed to Assay 4 U which shows the usage of a variable Press Next gt to see the summary page Summary Your settings
37. packages are designed to check every aspect of the mathematical functionality 16 May 2013 Page 137 of 193 oo o lt a ae o PLA 2 1 How does it work The automated OQ of PLA is devided into the following processes 1 The assay data is decoded from the PLA OQ file During this process the digital signatures of package is verified using PLAs internal PKI If the data is valid the OO processor imports the data into a temporary project 2 The temporary project is calculated by PLA PLA fills its internal result structures with the calculated data 3 The internal result structures are compared to the result structures saved and secured in PLA OQ If any error occurs the Automated OQ fails After this procedures has been executed with all 27 OQ Packages an OQ Certificate or an OQ Failure Report is generated If the OQ fails the corresponding PLA Installation has to be checked thoroughly First of all the IQ should be processed If it fails reinstall PLA If the IQ passed though the OQ failed contact support bioassay de 7 4 2 Performing the Operational Qualification From the Validation Menu select Operational Qualification OQ The following dialog appears 16 May 2013 Page 138 of 193 PLA 2 1 The Operational Qualification performs functional test on the mathematical correctness of PLA The process will take several minutes to complete Start OQ Processing Start Cleanup temporary objects after execution
38. response values of your measurement IMPORTANT If you change properties of parent objects these changes do not influence the child objects if you did not bind the child objects to the parent explicitly available on the third level only If you want to deploy new settings to child objects you can make use of the Apply functionality of PLA Beside this approach of inheritance there are more advanced concepts of templates GxP and SOP support These approaches are described in detail in the user manual 4 6 Basics of PLA 2 1 Mathematical Features PLA 2 1 is a full featured software for the analysis of parallel line and parallel logistic dilution assays In this section you will find information on e Doses and Potencies e Assigned Assumed Potency e Model Response Transformation and Outlier Detection e Analysis of Variance ANOVA e Configuration Optimization 4 6 1 Doses and Potencies PLA is able to calculate different potency values found in today s requirements of assay analysis In principle you have four different starting points for potency analysis 1 Bulk Substance Raw Material Potency When you activate the bulk substance potency you can input the potency of your raw material You have to specify how much amount of your raw material is solved in which amount of a solvent PLA then automatically calculates the concentration potency of your stock solution which is the starting point for your dilution series 2 St
39. serial number www bioassay de Open the products Website in your default web browser support bioassay de Opens your default mail client allowing you to write an e mail to the support OK Close this dialog 9 1 16 Register Your Copy of PLA How to use the registration dialog 16 May 2013 Page 179 of 193 PLA 2 1 Why register The quality of FLA can have a deep impact on your results our registration gives us the chance to Inform You if probleme with PLA are discovered and to better support you in case of any further problems Problermnis can arse from many differant sources e g new operating systems progam errors Please give us the chance to deliver best quality software to your desktop as quickly as possible by registering your product Wwe transter these informations to any third party Registration Information Your Name Company Department Address City IP code State Region Country E Mail Phone Fax F Keep me informed about PLA and your other bioassay products by email Stegmann Systems will not make your data available to any third parties You may always change these options later Why register This is a short statement explaining why you should register your copy of PLA Your Name Enter your name into this field Company Enter the name of your company here Department Enter the name of your department here Address Enter the address of your company here 16 May 2013 Page
40. the All Users and in the Users personal folder in the Documents Data and Settings section Temporary Temporary files are stored in the Temp sub directory of the Application Data Directory of the Files user PLA automatically takes care of this folder 8 2 4 Hardlock Installation PLA makes use of the Hardlock Protection by SafeNet Systems The device drivers for the hardlock system are installed automatically during the setup process They appear as Hardlock Drivers in the Software section of the system configuration If they are removed they can be reinstalled by hand Current drivers can be found under www safenet inc com 8 3 Security Basics 8 3 1 User Account Security Due to regulatory needs PLA has Its own user account management Accounts are stored in the PLA databases so security can not be compromised by copying data to another location The user account system in PLA is role based PLA distinguishes three roles Standard Users Standard Users are allowed to modify objects within the restriction a PLA administrator gave They are not allowed to modify security relevant options or to manage user accounts Administrators They manage users and define the security relevant options within PLA Inspectors They have read only access to the objects but they are allowed to electronically sign objects 16 May 2013 Page 145 of 193 oe gt gt gt TO PLA 2 1 8 3 2 Data Integrity PLA makes use of its own Public Key I
41. the login screen Exit Close PLA 16 May 2013 Page 167 of 193 M PLA 2 1 9 1 11 Help Menu This topic describes the Help Menu of the PLA menu bar PLA 2 1 Software E e File Actions System Validation Window Help f 108 81 xi EE Navigator ee 1 Examples from Literature Sample Parallel Line Assays Sample Project Sample Project 2 F include hidden items refresh automatically Y Database PLA 2 1 Default Database PLA Administrator Help Topics Open the online help of PLA Submit a Bug or Request a Feature This allows you to connect to the Support Website of PLA to submit a feature request or a bug report You will be asked whether PLA should connect you to the Support Website PLA License Open the PLA License Manager See also License Management About Open a window showing detailed information about your PLA Installation See also Product Information 16 May 2013 Page 168 of 193 PLA 2 1 PLA is in Tonal Mode No valid retail license found This tial has 14 day s left Hardlock FOUND 100174 License Details Feature License Keys Hardlack Activation LFE C 6460 52F4 6LF i4 M sG 44 Walid PLA 2 1 Not Licensed PLA 2 1 Validation Package Mot Licensed Download License Keys Trial Details Inquiry Kep NOSx T OSE BYVEH 92RA Submit Online Submit by E Mail Vendor Response Ok To extend your trial period please send the inquiry key to the vendor by maili
42. this group In addition the latest calculation results of the object are displayed These results will be deleted when the object properties are changed Dose Properties This set of properties defines the preparation steps of an object The settings also define which potency calculation shall take place in which way Data Response Properties This page allows to define the dimension of the data set used for analysis Data input takes place on this page Analysis Properties This page take the various analysis properties Test Properties This page contains the test system setup Configuration Properties The configuration properties allow the manual or automatic detection of the regions of interest within your treatments Documentation Properties You can add various documentation entries to the object definitions such as reagents used operators equipment This is added on the documentation page GxP Settings On the last property page you are allowed to define the GxP settings you want to make use of to add input security to your objects 16 May 2013 Page 47 of 193 PLA 2 1 Data Entry Data Input is available on the data tab page of the object editor dialog The input of response values is only available on the data tab pages of the respective objects standard preparations and controls If your dilution scale property is set to direct dose input you may input dose values not response values on the assay and project le
43. to be used for the EC50 calculation linear regression Response 50 Calculation How is the response 50 calculated 5 3 5 Test Properties The test properties page allows to define complex suitability test criteria to be defined Default Tests and Migration from PLA 2 0 By default PLA 2 1 adds three tests to a new project This is a compatibility setting compared to PLA 2 0 e F Test significance of regression significance level 95 e F Test Lack of fit significance level 95 e F Test Non significance of difference of models 95 After a migration all defined tests of PLA 2 0 are migrated into the new test logic Tests are added and removed from the list of tests with the Add and Delete buttons on the right side 16 May 2013 Page 84 of 193 i PLA 2 1 dA Assay 4 Antibiotic Turbidimetric Assay Genet Dos Das Aas Inherit Properties use suitability test properties of the assay object Open Assay Definitions Sample and Assay Suitability Tests Assay Suitability Tests e Sample Suitability Tests F test Significance of regression F test Lack of fit linearity F test Non signiticance of difference of models parallelism Delete Name Value F test Non significance of difference of models para Significance Level 95 Test Level 2 Sample Suitability Test Test Scope 1 all objects Test Severity 1 Reject no potency calculation Test Passed Message default Test Failed Message default
44. will save our settings after we have defined everything 16 May 2013 Page 64 of 193 Select Input File Import Definition Scheme Select Destination Scheme Define Objects Sort and Assign Imported Data Choose Destination Save Import Definition Scheme Control and Summary Import in Progress Tou may select an Import Definition Scheme IOS if you saved one in a previously run of this wizard Press Next gt to proceed Load Import Scheme Import Definition Scheme IDS The settings you will have to make on the following pages are somewhat complex at all When wou finished to make these settings you are asked to save them in a special format which i called Import Definition Scheme or in short IDS TOU may now select a previously saved import definition scheme IDS none Rename IDS Delete IDS Cancel Cancel lt Previous Selection of Target Project and Templates In this step you define the target of the operation select a project or create a new one and you have the option to select a defined template for the objects the import process will create By doing so you are able to predefine all object properties of the new objects 16 May 2013 Page 65 of 193 Sch Select Input File Chemes Import Definition Scheme Select the Destination Project Select Destination Scheme Destination Project Define Objects Examples from Literature Sort and Assign Imported Data Cl create a new project Choos
45. you can verify all the objects and calculation results after the PO process has been finished 16 May 2013 Page 142 of 193 PLA 2 1 8 IT Administration Guide This guide is intended for those who are responsible to setup PLA in their environments You will find all necessary information to setup PLA and you will find all information regarding administrative procedures Note This guide requires basic knowledge of operating system administration Structure of this Guide e Description of for IT Professionals e PLA Setup Basics e PLA in Networked Environments e Terminal Server Recommendations e PLA Database Guide e PLA License Management e PLA User Management 8 1 Description of PLA for IT Professionals PLA is a standard application for parallel line analysis of biological assays It is used by laboratory personal and scientist as well as in development of assays tests and in the application of these tests in quality control units PLA organizes the data of interest assay data in databases The user can connect to different database systems In general file based databases Microsoft JET 4 0 and SOL Server based databases Microsoft SQL Server Oracle can be distinguished Due to regulatory needs PLA has Its own user account management User account is stored per database This makes for users especially in development labs to differentiate their security needs per project PLA is multi user networking aware Objects i
46. 00 Desktop Engine MSDE e Microsoft SOL Server 2005 Express Edition e Microsoft SOL Server 2000 or higher The database administrator has to create an empty database on the database server Once you have defined a connection to this database using the PLA Database Manager PLA automatically creates the required tables in this database There are some basic things to know iis e The Database Server user account PLA used to connect to the database needs to be able to modify the database using standard SOL DDL and DML statements If your IT department does not accept this they ll have to create the tables using a SOL Script available with PLA details are found in the IT Administration Guide e The integrity of PLA s data is not endangered by the knowledge of this account because all relevant data are protected by the use of cryptography However the account credentials should be kept secret because it allows corrupting the database PLA is able to detect corruptions of the database and prevents corrupted objects from being used 16 May 2013 Page 24 of 193 PLA 2 1 Further details for Database Server based databases are found in the IT Administration Guide 4 5 Basic Concepts of PLA 2 1 There are a few basic concepts you should understand for efficient use of PLA e Database Storage Concepts e Object Types and Hierarchy e Inheritance of Object Properties 4 5 1 Database Storage Concepts All Assay Data and Properties are sto
47. 04 2013 10 25 52 PLA Administrator 15367176 Standard 29 04 2013 10 25 47 OBJECT SAVED PLA Administrator 15367176 A Sample 1 29 04 2013 10 25 26 OBJECT SAVED PLA Administrator 153871 76 EL Sample 2 29 04 2013 10 23 45 OBJECT_SAVED PLA Administrator 15367176 sA Sample 3 29 04 2013 10 2344 OBJECT SAVED PLA Administrator 15367176 A Sample 4 29 04 201310 23 41 OBJECT SAVED PLA Administrator 15367176 aw Sample 5 Details Operation Key Old Yalue Hew Yalue Details last modification time 2013 04 29 10 25 47 2013 04 29 10 25 52 Details Response Seres 1 Step 1 701 U2 e m1 ri H Sample Parallel Logistics Assays a Outlier testing i activated You need at least 3 replicates for outher testing include hidden items E refresh automatically Save the object Database PLA 2 1 Default Database PLA Administrator The audit trail consist of two sections 16 May 2013 Page 49 of 193 oo Cee a o PLA 2 1 e The upper section contains information on the applied action In the sample the object has been modified by PLA Administrator on 2006 08 14 e The lower section displays the modification details of the action In the sample three values are saved The most interesting is the manipulation of the Response value in Series 1 step 1 5 2 3 Inheritance Templates and the Apply Function Inheritance Inheritance of Object Properties The understanding of object inheritance is necessary to make efficien
48. 2 1 write access to this file amp PLA Import Wizard YAPLA 2 1 Lot_AB022601_1 pda 5 t Sch Select Input File ave Impor lt cheme Import Definition Scheme Save Import Definition Scheme ID5 Select Destination Scheme Do you want to save the import settings for further use Define Objects ES Sort and Assign Imported Data ee No Ch Destinati Input the name of the scheme IF you select an existing one this one will be Dee gece eae OverArither Save Import Definition P Moy First Import Definition Scheme Control and Summary Import in Progress If you need to use the settings you have made in a later run of this wizard you carn save the settings in an import definition cheme IDS Summary On the summary page parts of your selections are summarized Press Execute to start the import process Export The Export process is very easy It follows a simple path Select the Export Object In the navigator select the object you want to export Then select Export from the file menu the navigator context menu or from the toolbar The Export Wizard is displayed 16 May 2013 Page 72 of 193 PLA 2 1 Sala Data PLA data and definitions Choose Type of Export Choose Type of Export Select T arget File ae l l i l Export the selected object including properties amp values Specify Export Details l C Export all objects Backup Summary Export in progress Please select wether to
49. 3 6 Configuration Properties The configuration properties define the settings for the configuration optimization Property Linear Range Configuration Method Fixed Range To From Automatic Selection Options Allocation Strategy Minimal Exact of points Allocation Region select only configurations with identical number of treatments Include the 50 response Calculate 50 response by 16 May 2013 Description Select the optimization method e Full Range e Fixed Range e Automatic Detection individual e Automatic Detection common range for the standard individual for preparations e Automatic Detection common range for the standard identical for preparations e Automatic Detection individual range for the standard identical for preparations Step number of the selected range The optimization fits the e best range e maximum range e exact range Allocated configurations have at least exact this number of steps is either the full range or a defined subrange Allows to force the optimizer to select only identical number of steps in both standard and preparation You can force the optimizer to prefer or to mandatory include the 50 value The 50 response has to be discovered from the assay To do SO YOU Can use e the object itself e the standard e the control or all objects of the assay Page 87 of 193 i PLA 2 1 en Assay Definitions Fired A ange Automatic Selection Opt
50. 4 034 or 962 929 aort and Assign Imported Choose Destination Save Import Definition Scheme Control and Summary D0 CT E Oo a Import in Progress Please assign the displayed data to the objects You may use the keyboard to assign selected data points to an object select the abbriviation characters a Bete and numbers to assign the step Selected datapoint Grid display options Dilution step FomtH Data value display point of columns 1 7 1 z 330 895 display data 12 color the grid The data grid is automatically colored if this activated in the grid display options The data point is now displayed as 1 A 1 330 895 which has to interpreted as follows point Object_code Dilution_step response_value Every object has an automatic assignment to a letter starting with A for the standard Every letter has a color code You can see the assignment of codes to the objects by opening the drop down list box in the selected datapoint section The dilution steps are numbered Assignment by Keys If you select multiple response values in the grid you may simply type the letter of the desired assignment to assign values to an object By typing a space you remove the assignment By pressing 1 9 you assign a selected response value to a dilution step By pressing 0 you remove the assignment to a step This allows you to select your block designs and assign them to the r
51. 77E 01 1 00E00 Dose e Sample Preparation WHO Standard Parallel Logistic Assay 16 May 2013 Page 14 of 193 PLA 2 1 4 1 2 Parallel Line Model Linear Regression with selection of active region 0 750 0 700 0 650 0 600 0 550 0 500 0 450 Response 0 400 oO Bk O En o Do m 9 77E 04 5 52E 03 3 12E 02 1 77E 01 Dose e Sample Preparation WHO Standard Parallel Line Assay 16 May 2013 Page 15 of 193 h PLA 2 1 4 2 Installation of PLA 2 1 If your computer system complies with the system requirements the PLA 2 1 setup process is easy and convenient For the installation process administrative Windows permissions are required on your computer system 4 2 1 PLA 2 0 Coexistence Q PLA 2 1 is installed in parallel to PLA 2 0 All data and installation details of PLA 2 0 are left at its original values The PLA 2 0 WILL NOT BE TOUCHED by the installation of PLA 2 1 on the same computer Due to the change of the PLA database format please take note of the following remarks If you open a PLA 2 0 database with PLA 2 1 you are asked to allow migration of the database to the PLA 2 1 format If you allow migration this database cannot be connected to PLA 2 0 anymore A PLA database will be migrated only on a users decision PLA 2 1 will never migrate on its own In multi user enviroments contact your system administrator in advance to the database migration 4 2
52. A certificate will be created The process will take several minutes Installation Qualification I Process Certificate created Name PLA Report Template REP 22 Equivalence Margins Development Fileset Report Fileset Report has been validated successtully Package C Program Files W56 Stegmann Systemet PLA 2 7 Report Temp SUCCESS The installation has been validated successfully How creating certicatereport The IG took 30 1 s Ti REP 22 Equivalence Margins Development ert OF em rn Result The installation has been checked successtully Z Click here to show the IO Certificate Report Click on the hyperlink in the result section of the wizard to open the certificate The certificate is created in the default report directory of PLA If the Installation Qualification fails there have been modifications to the system In general the system should be re installed then Thoroughly check the error report you receive to understand what has changed in the system and why the installation qualification fails Not every change necessarily compromises the 16 May 2013 Page 135 of 193 cS 3S lt i d PLA 2 1 system but you should only continue to use PLA when you successfully verified that the system is intact Certificate of Qualification Installation Qualification IQ of the PLA System Executed by PLA Administrator Timestamp 08 05 2013 10 00 02 Computer Name W
53. All open operations of this wizard initially Import Path point to this directory By default this directory points to a PLA 2 1 sub directory of the users personal folder Default This is the default target path of the export wizard Export Path By default this directory points to a PLA 2 1 sub directory of the users personal folder Default This is the path where reports and certificates are created by default Output Path By default this directory points to a PLA 2 1 sub directory of the users personal folder Import Export This is the path PLA uses to search for import and export modules PLA might require Modules write permissions in this directory to save Import Definition Schemes By default this path points to the Converter sub directory of the PLA 2 1 base installation path Report In this directory the report templates of PLA are installed Templates By default this path points to the Report Templates sub directory of the PLA 2 1 base installation path 16 May 2013 Page 144 of 193 PLA 2 1 8 2 3 Other Directories of Interest Base This ts the target path you select when you install PLA Installation By default this directory points to a Stegmann Systems PLA 2 1 subdirectory of the systems Path programs folder e g c program files Stegmann Systems PLA 2 1 Application This is a sub directory of the base installation path This directory contains the PLA Main Path Program and libraries Application Application Data is stored in
54. Calculation Options perform combination of assay results calculations if defined Select the required reports p REF 10 Complete Statistics Report REP 11 Short Report 2 REP 12 Excel Report TH REP 20 Combination of Assay Aesults Te REF 21 Complete Statistics Report with Range Configuration Details REP 22 Equivalence Margins Development Info Select a report te Select a Report and press Preview Print or Save The final calculation is started and the report is generated After the generation process finished the desired action takes place and you receive your report of interest 16 May 2013 Page 131 of 193 PLA 2 1 7 Validation Guide To achieve GxP compliance your installation of PLA has to be validated This validation is a very time consuming step if you do not have automated methods available With the help of the PLA Validation Package you are able to reduce this effort to an absolute minimum The PLA Validation Package is a separately sold solution that contains all information typically needed for a successful validation of PLA 2 1 The license dialog 7 1 What is included in the package e Installation Qualification IQ Documentation e Automated Installation Qualification IQ e Operational Qualification OQ Documentation e Automated Operational Qualification OQ e Performance Qualification PQ Guidelines e Automated Creation of PQ Datasets and Documentation e Automated Performance Qualifi
55. Defines the path where your PLA Report Templates are stored Graphics Options Height pixel Defines the height of the image in pixel created when saving the graph from the Data Explorer to an image file Possible Values 100 2 048 Default value 600 Width pixel Defines the width of the image in pixel created when saving the graph from the Data Explorer to an image file Possible Values 100 2 048 Default value 800 Search for Updates Search for News and Updates Defines how PLA should check for News or Program updates Possible Values 1 Automatically check for news and updates at startup 2 Allow manual check for news and updates at startup 3 Disable check for news and updates Default value 1 Automatically check for news and updates at startup GMP GLP SOP Settings Default Template for the creation of projects Defines the default template for the creation of projects Possible Values 1 none 2 n A list of your templates Default value 1 none 16 May 2013 Page 174 of 193 PLA 2 1 GMP GLP Master Protection Enable or disable GMP GLP Master Protection Enabling this option overrides all set GMP protections Possible Values Off On Default value Off Projects may be created by administrators only If this option is enabled only administrators are allowed to create projects Possible Values No Yes Default value No Users may not delete objects If this option is enabled sta
56. Do not close it 6 4 A First Look Once we have finished data input we should visually inspect the object If it is not already open open the preparation Note you can start the visual inspection from any object of the assay Only the first display is influenced by the selected object If you start from the assay all preparations are included If you start from a specific preparation only this is displayed by default Now select the Check button from the toolbar or start Check from the file menu The Assay Explorer is displayed and preliminary result is calculated Never communicate this result always run a final calculation 16 May 2013 Page 123 of 193 d PLA 2 1 Pabe Graph Type Dose Response Graph Equivalence Margins Display Options Show Legend Show Grid Regression Lines Restricted Model Mean Line Data Values C include Statistical Outliers Include Technical Outliers E Error Bars 100 Bos amp Whisker Plot Invert 3 Axis Show Y Asie Origin Y Axis Transformation Linear Response Preliminary Preparation Results Preperation Test Results Sample suitability a created by PLA 2 1 trial www bioassay de Assay suitability g 77E 04 3 12E 02 1 00E0C Overall test result FLED Dose Preperation w Standard a Sisndac Estim Potency Ratio and Confidence Interval Potency A atig 0 655 W CD Preperation Confidence Interval 0 57
57. Estimates e Difference of Regression Parameter Estimates e Ratio of Regression Parameter Estimates Scaled Range of Regression Parameter Estimates e Additional Tests Difference Tests Test Purpose Regression Test Type Remarks Models F Test for the Significance of the regression Model all preparation F Test for the non significance of the lack of fit Linearity all preparation number of replicates gt 1 F Test for the non signification of the Parallelism all preparation difference of models F Test for the significance of the slope Model parallel line all objects for PLA 1 2 method compatibility F Test for the non significance of a quadratic Linearity parallel line all objects for PLA 1 2 contribution method compatibility 16 May 2013 Page 107 of 193 Equivalence Tests PLA 2 1 Note All equivalence tests are carried out with the unconstrained regression Regression Parameter Estimates Test Purpose Regression Models Equivalence Test Similarity all Slope Equivalence Test Similarity non linear Upper Asymptote methods not available with fixed upper asymptote Equivalence Test Similarity non linear Lower Asymptote methods not available with fixed lower asymptote Equivalence Test Similarity 5 parameter fit Asymmetry Parameter Equivalence Test Similarity non linear EC50 methods Equivalence Test Similarity non linear Relative Potency methods Equivalence Test Similarity 4 parameter fit Diffe
58. HIHG IF you loose your passwords no further access to the selected database is possible IF you loose pour administrative passwords you cannot modify system options or user accounts of this database Note Even if you have lost Your passwords You may always create new databases Selected Database PLA 2 1 Default Database User Name FLA Administrator Password Retype Password Create Account Cancel 16 May 2013 Page 23 of 193 o PLA 2 1 4 4 1 File Based Database This database type is based on a secured Microsoft JET 4 0 database Disadvantages e This database type should not be shared with more than 3 or 4 concurrent users e Size restriction The maximum size of the database is limited to 2 Gigabytes e For database maintenance the database file should be compacted using the PLA Database Manager regularly Advantages e This database type can be created without deeper knowledge of database servers or involvement of your IT department e This database type is file based You only need write access to a network share to create and connect to this database type No administrative Windows permissions are required e Due to the file based structure the PLA database can be easily incldued into your backup strategies 4 4 2 Database Server Based Databases These databases require an installed Database Server Currently the following database management systems are supported e Microsoft SOL Server 20
59. LA Administrator 1 PLA Administrator 1 PLA Administrator 1 PLA Administrator 7 PLA Administrator 1 PLA Administrator 1 PLA Administrator 1 PLA Administrator 1 PLA Administrator 1 I New Value Operation a Operation List A list of operations showing you which actions have been executed by which user at which time 16 May 2013 Page 158 of 193 Operation Details PLA 2 1 If an action from the above list is selected the details of the selected action are displayed if available Refresh Refresh the list from the database Close Close this dialog 9 1 5 Change your Password This dialog allows you to change your password 2N Change Password a User Name PLA Administrator Current Password Hew Password Retype New Password Change Password Cancel User Name Your user name account name is displayed here Current Password Enter your current password into this field New Password Enter your desired new password into this field Retype New Password Reenter your new password in this field Change Password Clicking this button changes your password Cancel Clicking this button cancels changing your password and closes this dialog 16 May 2013 Page 159 of 193 4 t PLA 2 1 9 1 6 Context Menu This topic describes the Context Menu of the PLA Navigator Fe pla 21 Sofware for O E 7 7 File Actions System Validation Window Help CETIRI AECE Da
60. MSC03 PLA Serial Number 10014 PLA Version 2 1 0 build 600 Note This Certificate of Qualification is valid only for the computer system on which the qualification process has been executed The qualification process has to be repeated for every computer system which is running PLA The following components have been checked PLA Base System Passed PLA Report Template REP 10 Complete Statistics Report Passed PLA Report Template REP 11 Short Report Passed PLA Report Template REP 12 Excel Report Passed PLA Report Template REP 20 Combination of Assay Results Passed PLA Report Template REP 21 Complete Statistics Report with Range Configuration Details Passed PLA Report Template REP 30 Equivalence Margins Development Passed The Installation Qualification IQ of the PLA System has been carried out successfully The documented and expected results have been reproduced Stegmann Systems Germany www bioassay de 16 May 2013 Page 136 of 193 i PLA 2 1 Installation Qualification IQ of the PLA System Timestamp 08 05 2013 10 00 02 System WMSCO3 with Serial Number 10014 Page 3 of 31 Installation Qualification IQ of the PLA System Detailed Report Overall result of the Installation Qualification IQ Passed 1 IQ File C Program Files x86 Stegmann Systems PLA 2 1 Application pla21 iq Overall result of this IQ file Passed 1 1 Digest PLA Base System Overall result of this digest Passed This
61. Manager allows you to manage your database connections fei Database Management Create or Connect a Database File Connect 4 Database Server Delete Connection Frofile Compact Databaze Information concerning Database Connections PLA supports multiple database connections These connections have to be defined using this Database Manager dialogue Database Connections are a set of properties that enable PLA to connect an existing database Creating a Database PLA supports both Microsoft JET and Microsoft SQL Server databases JET database are created with this wizard SOL Server database are created as empty database by your administrator PLA creates the required tables when it connects by itself Connecting an Existing Database To connect a JET database select Create or Connec a Database File To connect to a SOL Server select Connect a Database Sever Delete Connection Profile A defined connection i deleted The database itself remains intact You may reconnect to it Compact Database JET databases tend to grow From time to time you should compact it You need exclusive access to the file to perform compaction Upen Database Close Database Connection Profiles This list contains a list of previously created Database Connection Profiles You can switch between different databases simply by selecting the appropriate profile in the list Create or Connect a Database File Select this button to create a new connec
62. O 29 04 2013 12 36 52 29 04 2013 12 36 52 Sample Project PLA Administrator Sample Parallel Line Assays FLA Administrator Examples from Literature FLA Administrator Sample Project 2 PLA Administrator Sample Project 2 gt Assay PLA Administrator Sample Project gt Measurement 2 PLA Administrator Sample Project gt Assay FLA Administrator Sample Froject Online Example PL4 Administrator Sample Parallel Line Assays gt Assay 2 FLA Administrator Sample Parallel Line Assays gt Assay 4 PLA Administrator Sample Parallel Line Assays gt Assay 6 PLA Administrator Sample Farallel Line Assays gt Assay 8 gt Sample 1 PL4 Administrator Sample Parallel Line Assays gt Assay 8 gt Standard PLA Administrator autorefresh lists Retesh Reset Sessions kll Session Unlock Sessions A list of active sessions Locked Objects A list of locked objects of the currently selected session Autorefresh lists If checked both lists will refresh automatically Refresh Click this button to refresh both lists manually Reset Sessions Removes outdated sessions from the PLA databases No active sessions are touched Note PLA removes outdated sessions automatically Usually there is no need to manually remove them Kill Session Kill the selected session The session is deleted and all locks of this session are removed This is useful if there is an invalid session entry which hold locks on objects Note Use this op
63. OL Package OQ haz not been started yet Progress Current Package 00 Package Details OL has not been performed yet Press Proceed to start it Ho Report has been created Press Start to start the OQ Process This process can take up to 60 minutes The certificate error report is created in the standard output directory The certificate can be launched by clicking on the hyperlink that is available after the process finished Note If you want to check the OQ with its documentation you can toggle the cleanup switch Cleanup temporary objects after execution If you deactivated it you can verify all the objects and calculation results after the OQ process has been finished 16 May 2013 Page 139 of 193 PLA 2 1 7 5 Performance Qualification 7 5 1 The Performance Qualification Process The Performance Qualification PQ is intended to test customer data with the mathematics of the PLA system In PLA this process is divided into two steps 1 Prepare your Performance Qualification Data 2 Execute the Performance Qualification on any target system Note When new PLA Version get available it might be necessary to repeat both steps How does it work The Performance Qualification is prepared using the preparation wizard Using this wizard you select your well known PQ project inside PLA The wizard calculates the comparison data and generates a PQ file as well as a Complete Statistics Report The PQ file is secured fr
64. Object To sign an object simply open it on the general page and click the Sign button The following dialog appears Apply Electronic Signature to Assay 1 7 R Select a pre defined comment or edit a new one Select a default reason or enter a new one Any comment regarding the signature apply signature to child objects Authorize pour signature with your password The application of an electronic signature secures the objects definitions and data IF you apply the signature to an assay standards preparations and controls are signed too If you sigh a project you may select wether to sign it s assays or not If you want to apply your signature to the child objects too at the project level check this apply signature to child objects element Type in your password and click Sign Once you have clicked Sign the requested signatures are applied The application of a signature is logged in the audit trail J Note 1 A signature makes an object read only No further changes can be applied to the object as long as the signature is in place Note 2 Default reasons can be defined in the system options dialog 16 May 2013 Page 101 of 193 id PLA 2 1 Remove A Signature The PLA Administrator defines wether a signature can be removed by everyone by the signer himself or by administrators only A signature removal is logged in the audit trail To remove a signature open the object go to the electronic signatur
65. PLA Administrator 15367176 103 29 04 2013 11 26 56 OBJECT SAVED PLA Administrator 15367176 AY 29 04 2013 10 43 34 OBJECT INITIAL PLA Administrator 15367176 Details Operation Key Old Yalue Hew Yalue Details last modification time 2013 04 29 10 43 34 2013 04 29 11 26 56 Details ttest slope 0 95 Details fhest linearity 0 g5 Details ftest parallelity 35 DP Outlier testing i activated You need at least 3 replicates for outlier testing P This object ts readonly due to the application of an electronic signature Figure Audit Trail Page of the Assay Editor 16 May 2013 Page 106 of 193 PLA 2 1 5 5 4 Test System PLA 2 1 is fitted with a new test system The test system allows to establish standard testing or sophisticated test setups Examples for the possibilities of the test system e Define difference and equivalence tests in one single test setup to establish compatibility of your tests to the European Pharmacopoeia Chapter 5 3 and US Pharmacopoeia lt 1032 gt lt 1033 gt lt 1034 gt e Establish additional tests for well known behavior of your system expected potency ranges number of outliers etc e Make use of assay controls The description of the test system is divided into teh follwoing sections e Available Tests e The Test System Logic Available Tests The test system of PLA 2 1 offers 33 different tests that can be grouped into e Difference Tests e Equivalence Tests e Regression Parameter
66. SSION DB_DELETE_SESSION DB_KILL_LOCK DB_MIGRATE IQ_START IQ_RESULT IQ_FINISHED OQ_START OQ_RESULT OQ_FINISHED PQ_START PQ_RESULT PQ_FINISHED OPTION_MODIFIED PLA 2 1 A database check corrected a problem A session is added A session is removed A lock has been killed The database has been migrated to a new scheme The IQ starts The IQ result is logged The IQ stops The OQ starts The OQ result is logged The OQ stops A PQ starts The PQ result The OQ stops PLA Options have been modified Each entry can have additional detail information Every relevant modification is fully visible in the audit trail The complete audit trail can be inspected from the System menu The audit trail information of a single object can be inspected on the audit trail tabpage of the assay editor 16 May 2013 Page 104 of 193 Timestamp 29 04 2013 11 27 03 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 05 29 04 2013 11 27 02 29 04 2013 11 27 02 170 29 04 2013 11 27 02 29 04 2013 11 27 02 29 04 2013 11 27 02 29 04 2013 11 27 02 Operation Action OBJECT SIGH OBJECT SAVED OBJECT SIGN OBJECT SAVED OBJECT SIGH OBJECT SAVED OBJECT SIGN OBJECT SAVED OBJECT SIGN OBJECT SAVED OBJECT SIGN OBJECT SAVED OBJECT SIGH OBJECT SAWED Kep last_modification_time ftest_slope ftest_linearity ftest_parallelity Close mrm
67. account Delete Delete the selected account Account Name Allows you to enter or modify the name of the account Each account requires a unique name Account Password When creating a new account or modifying an existing one you can set its password by typing it into the corresponding field and retyping it in the field below Remember that passwords are case sensitive Change password at next login When creating a new account or modifying an existing one and enabling this option the user defined by this account is forced to change his password at his next login User Groups Each account is member of one group A group defines the rights an account has within the PLA system The currently assigned group is highlighted You might assign the current account to another group simply by selecting it in the list of groups Description of the PLA groups e Administrators Administrators have full access rights They modify GxP SOP Settings and manage accounts e Standard Users This is a regular working account Access rights are limited through the GxP SOP Settings defined by an Administrator e System Inspectors Accounts assigned to this group have read only access They are allowed to view all objects but not to modify them e Deactivated Users Existing accounts that are temporarily deactivated Users having deactivated accounts cannot log in Save Save the newly created or modified account Cancel Cancel the creation or mod
68. alized with the e Externally Studentized Residuals Test This test checks the influence of an potential outlier on the regression results If the influence of the outlier is significant it is removed from analysis Note This test may require significant amounts of additional computational time 4 6 4 Analysis of Variance ANOVA PLA has different variants of ANOVAs for hypothesis testing available They are augmented by equivalence tests to achieve tests for parallelism The basic hypothesis tests are e Test for the significance of the Regression e Test for the insignificance of deviations from linearity e Test for the insignificance of deviations from parallelism Note For the 3 parameter fit the mixed terms of the ANOVA do not disappear They are included in the ANOVA analysis ANOVA based on Pure Error Separation This is the preferred approach in PLA 2 0 This ANOVA separates the influence of the treatments from the pure error The pure error is the error that is obtained by summing the error squares of the deviations of the replicate response values from the treatment means This value is a direct measurement of the dispersion of the measurement system This method is available if you have at least two replicates The model allows calculating significant deviations from the model as the significance of the lack of fit values ANOVA based on Residual Error This is the classical approach based on the regression model In principle
69. allel Line Assays i Assay 1 Standard Sample 1 Sample 2 Sample 3 Sample 4 Sample 5 Ja Assay 2 4 Assay 3 U Assay 4 4 Assay 5 4 Assay 6 a Flincude hidden items refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator Creating Objects New objects can be created either by import data or by manually selecting the Create Object function menu toolbar navigator context menu This section describes the manual function If you want to create a new object you have to select a neighbor object in the navigator and then select the Create Object function Neighbor object has the following meaning e lf you want to create a new project select anything or nothing e f you want to create a new assay select any object that is a child of the project which shall be the parent project or the project itself e If you want to create a new standard preparation or control within an existing assay select the assay or any of its child objects Once you have selected Create Objects the following dialog displays 16 May 2013 Page 42 of 193 i PLA 2 1 IA New Control as Member of Assay 4 Antibiotic Turbidimetic Assay Input Name and Descriptors My Preperation Name Any description usefull for the object My Preperation Name Select 4 template none Hint if there i an active mandatory global or parent template this selection will be ignored This dialog has th
70. an preview the absolute doses created by these settings in the data editor Database PLA 2 1 Default Database FLA Administrator 4 6 3 Model Response Transformation and Outlier Detection Parallel Line Method and Parallel Logistic Model PLA 2 1 supports both 16 May 2013 Page 28 of 193 PLA 2 1 e Parallel Line Assays Typically you select the linear parts of the dose response curve for the analysis with the parallel line method This robust method allows you the calculation of the potency with a minimum effort The asymptotes of the sigmoid dose response relationship are neglected e Parallel Logistic Assays SPL 4PL 5PL The four and five parameter function according to Rodbard describe the full dose response relationship You need at least four or five parameters to calculate these methods The three parameter nonlinear model is a contrained four parameter model You can choose between the upper or the lower asymptote of the model bound to either a fixed value or to the mean of a positive negative or blank control line Both methods require logarithmic transformations of the dose values There is no mathematical implication which base of the logarithm to use PLA uses to logarithm on the base of 2 This approach has two advantages e The mathematics of Parallel Line Assays has been best described by D J Finney who makes use of the base 2 e f you use twofold dilution series the transformed numbers are integer val
71. and from the file menu or the navigators context menu The following dialog appears 16 May 2013 Page 54 of 193 PLA 2 1 Ps Apply Object Properties Source Object Froject Sample Parallel Line 4ssays Assay Assay 1 Template mi My Sample Protected Template protected template Property groups to apply L apply general information apply documentation information apply assay definitions Number of series steps concentration doses etc apply analysis definitione Statistical parameters regression model etc X apply test definitions z apply linear selection definitions Detection type strategy linear ranges etc apply GLP SOP settings apply user defined values combination groups Target Included object types Target of the operation is assay Assay 1 and Project I s child objects with respect to the filter Assay settings on the right F Standard vl Preparations Controls Appl Close This method allows to copy properties of a source object to selected targets The dialog is grouped into three sections 1 Source Section Select the source of the properties you want to apply to the targets Available source objects are the parent project the parent assay or a template 2 Property Selection Select the groups of properties you want to apply By default the analysis settings and the configuration optimization settings are selected Warning If yo
72. as Member of Assay Assay 1 A New Control as Member of Assay Assay 1 Input Name and Descriptor Mew Preperation Mew Preperation Select 4 template none Hint if there ig an active mandatory global or parent template this selection will be ignored 2 Inheritance If no template is used all properties are inherited from the parent object 3 Default Values Default values are used when no template is used and no parent is available This is possible for Projects only After an object is a created a message appears notifying you about the used set of initial parameters 1103 Object created 16 May 2013 Page 52 of 193 PLA 2 1 Templates Templates are standard PLA objects used to create new objects PLA differentiates two types of templates e Protected Templates Protected Templates can be created by administrators only Standard Users are not allowed to modify these templates e User Defined Templates User Defined Templates can be created by all users How are Templates Created Switch to the Template mode of the navigator by selecting Templates from the drop down list at the upper part of the navigator Then select Protected Templates or User Defined Templates and select the Create Object command to create a new template i PLA 2 1 Software for Biological Assays h pE File Actions System Validation Window Help Db a x e Be Templates J a m Prote
73. ational Qualification Opens the Operational Qualification OQ Dialog See also Operational Qualification Performance Qualification Opens the Performance Qualification PQ Dialog See also Performance Qualification Create a PQ Dataset Opens a dialog allowing you to create a PO Dataset which can be used to perform the PQ on antoher machine running PLA See also Performance Qualification 9 1 21 Window Menu This topic describes the Window Menu of the PLA menu bar It allows you to arrange your windows in PLA 16 May 2013 Page 185 of 193 Navigator Tile Horizontal o ES Examples from Literature Layer 1 Sample Parallel Line Assays J A Sample Project 1 Sample Project 2 Undo Minimize All Windows F include hidden items refresh automatically Ready Database PL4 2 1 Default Database PLA Administrator Cascade Cascade all open windows Tile Horizontal Tile the view horizontally Tile Vertical Tile the view vertically Layer Layer all open windows above each other Minimize All Windows Minimize All Open Windows Undo Rest the the last set alignment and reset the windows to their previous view 16 May 2013 Page 186 of 193 PLA 2 1 10 PLA 2 1 vs PLA 2 0 vs PLA 1 2 PLA 2 1 is the successor of the leading PLA 2 0 System which is the successor of the PLA 1 2 System PLA 2 1 has been re coded in many sections The system design has been refreshed and a variety of options have been added
74. bar and close it 6 3 3 Create The Standard Object Now select the assay Assay in the navigator and create a New Standard as member of assay Assay This new object already has inherited all properties from the assay object Switch to the data page and type in the response data for the standard 16 May 2013 Page 121 of 193 relative Dose 1 1 1 2 1 4 1 6 1 16 1 32 1 64 1 128 1 256 1 512 1 1024 1 2045 Toggle outher status by pressing F3 Technical Outliers are displayed using a light red color Input a value press F2 or click to edit Press ESC to leave edit mode After you have finished save the standard and close it 6 3 4 Create The Preparation Object Preview absolute doses PLA 2 1 Now select the assay Assay in the navigator and create a New Preparation as member of assay Assay This new object already has inherited all properties from the assay object Switch to the data page and type in the response data for the unknown 16 May 2013 Page 122 of 193 PLA 2 1 Preview absolute doses sample Preparatior sample Preparatior 3 ample Preparatior relative Doze Replicate 1 Replicate 2 Replicate 3 1 1 1 2 1 4 1 6 1 16 1 32 1 64 1 128 1 256 1 512 1 1024 1 2045 Toggle outher status by pressing F3 Technical Outliers are displayed using a light red color Input a value press F2 or click to edit Press ESC to leave edit mode After you have finished the input save the object
75. base an initial administrator account has to be created now With this administrative account you can manage all settings WARKING If you loose your passwords no further access to the selected database is possible If you loose your administrative passwords you cannot modify system options or user accounts of this database Note Even if you have lost pour passwords You may always create new databases Selected Database T VPLA 2 1 ExamplD atabase MDE Microsoft Jet 4 0 User Name FLA Administrator Password Retype Password Create Account Cancel Type in a password Note The password cannot be recovered if you loose it Create a SOL Database Connection This section requires basic knowledge on database administration The first step has to be done by your database administrator He has to create a new empty database and he has to define a user id that has to be able to create tables and indices within this database DB Owner permissions Once this is finished you can go ahead with PLA Open the Database Management as describes above then select Connect a Database Server A standard dialog of the operating system appears that allows to input the connection data for the new database Select your server and database and type in the userid and password you created on the database server Then press ok Open the database If this is the first time the database is opened by PLA you are asked to create the tables and indi
76. between the 1 in 2 twofold series and the direct dose input In the latter case you have to input the relative dose values within the editor 16 May 2013 Page 48 of 193 q PLA 2 1 If you check the preview absolute doses button an additional read only column appears that displays the absolute dose values in dependance to the settings of Doses tab page This may be useful to understand the richness of dose features of PLA To mark a value as technical outlier use the F3 button This button toggles the technical outlier status of a response values With the F2 button you can switch the editor between navigation and input mode Cut and Paste is available too Simply mark the values of interest and press Ctrl C to copy them to the clipboard and Ctrl V to paste the clipboard contents into the editor Note that the editor has to be in navigation mode if you want to paste multiple values The cut and paste is the optimal way to copy to and from spreadsheet applications such as Microsoft Excel tm Audit Trail Page The Audit Trail tab page of the editor shows every modification made to the object definitions PLA 2 1 Software for Biological Assays Preparation Sample 1 d File Actions System Validation Window Help b a X EA eee ey General Doses I Data Analysis al Tests Configuration wile Documentation GP Audit Trail Audit Trail Timestamp Action Operator Workstation ID 29
77. cation PQ Processing 7 2 Principles of Validation There are some basic principles which have to be taken into consideration when validating a software 7 2 1 Validation of Each System A software vendor is in principle not able to deliver a validation statement with the software Not only the software can have errors that are critical to the results but also each single computer system has to be considered as a potentially defective system There are many sources of errors within the computer system The random access memory CPU hard disk the operating system are able to cause different errors that are quality critical E g in the past even the CPU could cause mathematical errors Defective non error correcting RAM is able to vary calculation results Defective hard drives can modify quality critical components of a software system This all leads to the conclusion that every single computer has to be validated It is not enough to validate an exemplary system PLA 2 1 Is fitted to allow a very fast validation of your system The different components of the Validation Infrastructure of PLA are optimized to efficiently deliver the required tasks to you 16 May 2013 Page 132 of 193 oe gt gt gt TO PLA 2 1 7 2 2 Cryptographically Secured Reference Data PLA 2 1 is delivered with cryptographically secured reference data sets for the Installation Qualification IQ and the Operational Qualification OQ The use of cryptograp
78. ces PLA requires The following dialog appears 16 May 2013 Page 149 of 193 PLA 2 1 W1029 No PLA Database This database does not look like a PLA database Required database tables are missing PLA ts able to create the required tables if you sufficient privileges on the SOL Server Do you want to create the tables now Nein Abbrechen Select Yes to create the tables After the tables are created you are asked for an initial PLA Administrator password as seen above Remove Database Connections Unused Database Connection can be removed by the Database Management Dialog This does not delete the database either from the file system nor a SOL Server database Compact Database File based Databases can grow up to 2 GB during work They might be internally fragmented while time passes From time to time you should compact the database This defragments the database and removes unused file space from the database In the Database Management select the database to be compacted and then press Compact Database After the compaction succeeded you receive a message on the saved space SLD initial filesize 8310784 bytes Final filesize 3837952 bytes Note you need exclusive access to the database to compact It 16 May 2013 Page 150 of 193 PLA 2 1 8 4 3 Distribution of Connection Profiles Using Registry Settings In management environments you can distribute connection profiles of PLA Server setting to the
79. cted Templates lye My Sample Protected Template a i User Defined Templates El include hidden items refresh automatically Ready i PLA Administrator An template object is created You may now edit all properties of the template They will be used for the creation of new objects if the template is chosen 16 May 2013 Page 53 of 193 id PLA 2 1 Complex Templates The template engine of PLA can except complex templates that allow differentiated settings for standards preparations and controls If you select the Create Objects command on an existing template you are able to define sub templates for the different object types of PLA ia Create New Object Select object type to create O e pA New Protected Template Create Standard Template as Part of Protected Template Ss Preparation Template as Part of Protected Template Cancel A Control Template as Part of Protected Template Input Name and Descriptor Select a template none Hint if there ig an active mandatory global or parent template this selection will be ignored If you select a template in section 3 of the Create Objects dialog PLA will use a sub template of a matching object type if this is available The Apply Method In contrast to the Inheritance and Template mechanisms of PLA the Apply method allows you to mass modify object properties after an object has been created Select an object and select the Apply comm
80. culation results See also Explore your Assay 9 1 7 Create Object This dialog allows you to create a new object 16 May 2013 Page 161 of 193 i PLA 2 1 Select object type to create E Mew Project WA New Assay as Member of Project Examples from Literature New Preparation as Member of Assay 2 Corticotrophin Assay Cancel Hh Hew Control as Member of Assay 2 Corticotrophin Assay Input Name and Descriptor Select a template none Hint if there i an active mandatory global or parent template this selection will be ignored New Project This option allows you to create a new Project New Assay This option allows you to create a new Assay as member of the currently selected Project New Standard This option allows you to create a new Standard as member of the currently selected Assay New Preparation This option allows you to create a new Preparation as member of the currently selected Assay New Control This option allows you to create a new Control as member of the currently selected Assay Name Enter the name of the object you want to create here Description You can optionally enter an description for the object you want to create here Template Select a template for the new object Create Click this button to create the object 16 May 2013 Page 162 of 193 d PLA 2 1 Cancel Click here to cancel the object creation process 9 1 8 Database Manager The Database
81. d as classical F Tests e F Test for the insignificance of the difference of models parallelism e F Test for the insignificance of the lack of fit linarity e F Test for the significance of the regression and for each object e F Test for the significance of the slope e F Test for the insignificance of a quadric regression term linearity 4 7 2 Similiarity Tests Similarity tests have been introduced to the biological assay world by the United States Pharmacopoeia chapters lt 1032 gt lt 1033 gt and lt 1034 gt PLA supports the following tests 16 May 2013 Page 32 of 193 PLA 2 1 Tests for Regression Parameter Estimates Regression parameters estimates can be tested per assay element e Slope e Lower Asymptote only for 3PF 4PF 5PF e Upper Asymptote only for 3PF 4PF 5PF e Asymmetry parameter only for 5PF e EC50 only for 3PF 4PF 5PF e Relative Potency In addition to this the asymptote range can be tested only for 4PF 5PF Difference of Asymptotes Upper Lower e Ratio of Asymptotes Upper Lower e Scaled Asymptote Range Upper Lower Reference Tests for Difference of Parameter Estimates The difference of parameters between preparation and standard is tested The tests are defined for the preparation e Slope e Lower Asymptote only for 3PF 4PF 5PF e Upper Asymptote only for 3PF 4PF 5PF e Asymmetry parameter only for 5PF Tests for Ratio of Parameter Estimates The ratio of pa
82. dard and the preparation We will then add data to both of them In the navigator the sample will look like this E 5 ample Project 6 3 Data Input Follow these steps to create the sample assay 6 3 1 Create the Project Select Create Object from the File menu The Create Object Dialog appears 16 May 2013 Page 117 of 193 Rl PLA 2 1 9 Create New Object m s Te ST i i i Select object type to create te New Project MO New Assay as Member of Project Sample Proyect Input Name and Descriptors 5 ample Project Sample Froject for the tutorial Select a template none Hint if there ig an active mandatory global or parent template this selection will be ignored Now Select New Project as the object type Then type in Sample Project as the name and Sample Project for the Tutorial as description Press Create to create the object The next message acknowledges the object creation 1101 Object created i r The creation was not based on anything Default tests hawe been defined After pressing ok the Editor for the project appears Close it by clicking on cross at the right edge of sub window 16 May 2013 Page 118 of 193 PLA 2 1 6 3 2 Create The Assay Now create the assay by selecting the parent project in the navigator with a single left click Then select Create Object from the file menu the context menu or the toolbar Select New Assay as Member of
83. de User Name Enter your SQL Server user name here Note This is only applicable for SOL Server authentication mode Password Enter your SQL Server user password here This information is required if you choose SQL Server Authentication The password is stored in an encrypted form and can not be discovered by common means Note This is only applicable for SOL Server authentication mode Blank Password This option should be disabled if you choose SQL Server Authentication because it would be careless to use an SQL Server account without password Note This is only applicable for SOL Server authentication mode Save Password This option must be enabled in order to create a complete PLA database connection profile Note This is only applicable for SQL Server authentication mode Select the Database Enter the name of the PLA database e g My PLA Database or select the database from the database list Contact your database administrator if you are not sure about the database Note The database must already exist on the server and the provided user must have the rights to create erase and modify database objects Contact your database administrator for further information Test Connection Click here to test the connection to your SQL Server If for any reason the test fails contact your database administrator for further guidance 16 May 2013 Page 165 of 193 4 rv 9 1 10 File Menu This topic describes the File Menu of th
84. e Destination save Import Definition scheme Default Template for Creation of Objects Control and Summary fay Import in Progress none Objects in PLA can be created by using schemes You use these schemes in every creation process Please select the one You want to use here Please also select the destination project of your imported data lt Previous Mest gt Press Next gt to continue Define Assay Dimensions Now you have to define the number of target objects standard preparations controls for the assay you will create Define the number of objects and press the Apply button in the upper part of the dialogue The list of raw data objects now contains the desired number of objects You edit each one by selecting it In the lower section Object Details you can modify the code of the object its type standard preparation control and its dimension number of replicates and treatments Remember to press the Apply button in the lower part of the dialoguein order to activate your settings after modification 16 May 2013 Page 66 of 193 Select Input File Defne Objects Import Definition Scheme Raw data objects Select Destination Scheme Number of objects number of replicates identical for all objects Define Objects 3 Apply number of treatments identical for all objects Sort and Assign Imported Data Choose Destination List of raw data objects Save Import Definition Scheme H treatme
85. e PLA menu bar Navigator 1 s Create Objet Ctrl Shift N 3 Edit Object ctrl shiftse gt include hidden items refresh automatically Save the object Database PLA 2 1 Default Database Navigator Show or hide the Navigator Create Object Create a new object See also Create Object Dialog Edit Object Edit the selected object s properties and definitions See also Object Properties Save Object Save any changes made on the selected object Close Window Closes the currently active sheet Copy Copy the selected object See also Copying and Moving of Objects 16 May 2013 PLA 2 1 PLA Administrator Page 166 of 193 oe gt gt gt TO Move Move the selected object See also Copying and Moving of Objects Delete Delete the selected objects and all of it s child objects See also Deleting Objects Apply Apply a template or project definitions to the selected object See also Apply Lock Tree Lock the selected object and of it s descendants See also Locking Objects Unlock Tree Unlock the selected object and of it s descendants See also Locking Objects Import Open the import wizard to import data into PLA See also Import Export Open the export wizard to export data from PLA into a file See also Export Logout PLA 2 1 Log out of PLA This will end your current session You ll have to save or discard your current work This will display
86. e installation process automatically installs a database called PLA 2 1 Default Database This is a file based database which contains some examplary data sets PLA 2 1 Default Database ap The PLA 2 1 Default Database is installed in a directory for common data on your computer Microsoft Windows 7 or higher reflects this directory for each user separately which cannot be detected by PLA 2 1 As a result of this reflection each user of the computer system has its own PLA 2 1 Default Database Data of other users cannot be accessed For a productive environment it is recommended to create a productive database in a convenient directory on your system where all users of the system have write access This directory should be saved with your companies backup system Contact your system administrator for support Due to the fact that PLA 2 1 has its own security system you have to create an initial administrator account when you create a new PLA database You are automatically asked to create this account Do not loose the password of this administrator account because there is no possibility to reset the password With this initial administrator account you are able to create any number of additional user accounts Due to legal restrictions e g 21 CFA part 11 FLA has it s own user account management For this database an initial administrator account has to be created now With this administrative account you can manage all settings WAR
87. e select the file you want to import f Fress Select File to choose the import file 2 Select Import File Select File Results of Initial Analysis Cancel lt Previous Select Import Format Now select the desired import format The PLA external file types are always displayed The other displayed file types depend on your installed PLA Import Modules In this example we select a PLA 2 x Enhanced Format PEF file After you have selected the file type press Select File or simply double click the desired file type A standard dialog of the operating system for opening a file appears 16 May 2013 Page 58 of 193 PLA 2 1 gt Select Input File PLA 2 x Enhanced Format Suchenin J PLA21 O t Er Name Anderungsdatum Ty _ Example PEF 29 04 2013 12 07 Pi Select a file and press Open In the sample the file Project PEF is chosen Q Note The Import Default Path can be set in the Options dialog Analysis of the Import File Once you selected the file it is immediately analyzed by PLA The results of the analysis are displayed in the Import Wizard 16 May 2013 Page 59 of 193 Import Data Select t Fil Select Input File elect Import rile Choose Destination 1 Select Import File Type Control and Summary PLA 2 6 Secure Format PSF PLA 2 8 Enhanced Format PEF PLA 1 2 Native Format PHF 96 Well Plate C5 Softmas Pro soe 4 oe Wavelength 1 4da
88. e to make use of the available help options 3 1 Website For Product Information www bioassay de 3 2 E Mail E Mail to support bioassay de for any questions and comments 3 3 Phone During business hours 7 30 a m 6 30 p m GMT English and German phone support is available 49 6106 77010 0 3 4 Fax 49 6106 77010 29 16 May 2013 Page 13 of 193 nal PLA 2 1 4 Getting Started 4 1 Parallel Line and Parallel Logistic Assays Biological or potency assays are frequently analyzed with the help of the parallel line or parallel logistic 3 4 or 5 parameter fit methods These methods have major advantages over traditional single point assays e The linear or sigmoid dose response correlation is not only assumed but may be confirmed in each calculation e The dose response curves of the standard and sample preparations may be confirmed to be parallel Whereas in single point analysis parallelism is a necessary requirement too but cannot be proven e A dose independent potency in terms of the standard s potency is calculated for each assay and its validity is statistically proven The complex statistical analysis of these methods requires an advanced software solution to be easy flexible and efficient This is the mission of PLA 2 1 4 1 1 Parallel Logistic Assay 4 Parameter Fit 0 750 0 700 0 650 0 600 0 550 0 500 0 4504 Response 0 4004 0 3504 9 77E 04 5 52E 03 3 12E 02 1
89. eee a bF Examples from Literature E 1 Gandotrophin 4sssay a 2 pia Assay ry 1 Sample Parallel fied ef Lock Tree Unlock Tree Import Export Calculate amp Report Data Explorer Check El include hidden items refresh automatically Create a new object Database PLA 2 1 Default Database PLA Administrator The navigator displays the objects defined in the database in their hierarchical order The user selects an object and then selects an action available for the object To select this action there are three ways e Select an action from the context menu by clicking the right mouse button for the object A context menu as shown in the figure pops up Then select the desired action by a left click in the context menu e Use the toolbar area to select an action e Use the menu system to select an action 16 May 2013 Page 40 of 193 PLA 2 1 In addition you may simply double click an object to open the object editor There are a few more options available for the navigator e On top of the navigator there is a drop down box which allows to the Data Objects as shown in the figure or the Templates e In the button line there is the option to display hidden items and e to select the automatic refresh of the navigator which may by useful if you are working together with other users in the same database If you select the refresh function the navigator will automatically be refreshed aft
90. efinitione Detection type strategy linear ranges etc apply GLP SOP settings apply user defined values combination groups Target Included object types Target of the operation if assay 7 Project Gandotrophin Asssay and it s child objects with PlaAssay respect to the filter settings on the right Serena Preparations Controls Source Object Select the source of the properties which will be applied to the target objects e Project Use the selected project or the parent project of the selected object as source e Assay Use the selected assay or the parent assay of the selected object as source e Template Use a template as source You can specify the template by selecting one from the template list to the right Property groups to apply Select the property groups which you want to apply The groups correspond to the property pages of the object editor dialog described here in Object Properties Target Shows you to which objects the properties will be applied 16 May 2013 Page 157 of 193 oe gt gt gt TO PLA 2 1 Included Object Types This allows you to filter the objects to which the properties will be applied by their type The properties will be applied to the selected object types only Apply Apply the selected properties Close Close this dialog 9 1 4 System Audit Trail Shows Audit Trail information by listing operations and their details y PLA System Audit Trail Times
91. end user systems by registry files by your software distribution system or by active directory distribution Create a database connection to the required database using PLA 2 1 The database connection string can be found in the registry under the key HKEY_LOCAL_MACHINE Software Stegmann Systems PLA 2 1 Connections Under this key you find each connection as a REG_SZ variable The name of the variable defines the connection name This can be freely edited The value is a cryptographically secured connection information to the database It has to be copied as Is The simplest way to communicate these settings is to export the variable using REGEDIT and import the setting by double clicking the REG File created by the export 8 5 PLA License Management Since PLA is a special application for a very small market PLA is secured by a license management This license management distiguishes between the trial mode and retail mode of PLA 8 5 1 Retail Mode In Retail Mode PLA is delivered either with a desktop hardlock or with a network hardlock depending on the license you purchased Seat License The hardlock has to be connected to the local parallel port or USB port see PLA Setup Concurrent Use License This type of License is shared across the network It is also necessary if you want to use PLA on a Terminal Server Solution The concurrent use license model requires a license in the network which can be a normal workstation if it is
92. er a certain number of seconds which may be defined in the system options The navigator displays the objects in hierarchical order Objects of the same type are displayed alphabetically You may resize the navigator by shifting its right border You may also toggle its display by a menu and a toolbar function The latter can be useful if you analyze your assay using the ad hoc explorer and if you have only a limited screen resolution available Object Types and Hierarchy PLA makes use of five different object types that define your projects and assays Project Projects collect your assays They are on the first level of object hierarchy and they can be considered as folders The properties you define for your project is never used for calculation It is used as the source information for inheritance Assay Assay objects are on the second level of object hierarchy The assay is the parent object for the standards preparations and control values of your measured assay The properties you define here are not directly used for calculation they are source properties for inheritance However you may bind the properties of the child objects standard preparation control to these values to obtain a single point of change Standard Reference The standard object is a third level object and it is a child object of the assay Each assay needs a standard object to be calculated The potency of the preparation object is calculated with respec
93. ernal Format has the same structure as the PLA Secure Format PSF but it is not digitally signed Therefore no electronic signatures are imported from PEF files and they are not secured against manipulation PLA Native Format PNF The PLA Native Format PNF is the PLA 1 2 compatible data format It is delivered for compatibility reasons The PNF format only excepts PLA 1 2 settings and is therefore not intended as an external PLA 2 x format Import PLA is fitted with a strong import wizard that allows the transfer of external data into PLA One can distinguish three types of import Import of PLA s External Data Formats e Import of External Data using PLA Import Modules Import of External Raw Data using PLA Import Modules The first two import types follow the standard path while the latter type follows the raw data path See following chapters Import Standard Path Start the Import Wizard First of all start the import wizard by selecting Import from the file menu the navigators context menu or from the toolbar The Import Wizard comes up 16 May 2013 Page 57 of 193 Select t Fil Select Input File elect Import rile 1 Select Import File Type PLA 2 6 Secure Format PSF PLA 2 8 Enhanced Format PEF PLA 1 2 Native Format PHF 96 Well Plate C5 Softmas Pro soe 4 oe Wavelength 1 4da Softmas Pro soe 4ow 5e Wavelength 2 4da Softmas Pro sisal Soe Wavelength 1 2 4da Pleas
94. es section and click Remove The Remove Electronic Signature dialog appears Remove Electronic Signature From Sample Parallel Line Assays remove all signatures of this object recursive remove of signatures from child objects Authorize signature removal with pour password Remove Cancel You may select to remove all signatures of the object and to recursively remove signatures from the child objects To start the removal type in your password and press Remove 5 5 2 Secure Transfer of Data and Objects PLA enables you to securely transfer assay data and templates between different PLA installations This feature is very useful for the communication between different sites or companies e g to and from your contract lab You can securely transfer projects e assays e templates First of all you can sign the objects using the Electronic Signature features of PLA These signatures can be transferred to other installations of PLA The object is not modified until the signature is in place Then export the object using the PLA Secure Format PSF The PLA Secure Format makes use of the internal Public Private Key Infrastructure of PLA Any modification of the exported file is detected and the import is prohibited when a modification is detected 16 May 2013 Page 102 of 193 oo o lt a ae o 5 5 3 Audit Trall PLA 2 1 The Audit Trail of PLA is always enabled and cannot be manipulated with the help of PLA Ever
95. esponse values in a hurry The next picture shows an exemplary assignment 16 May 2013 Page 69 of 193 Select Input File Import Definition Scheme Select Destination S cheme Define Objects aor and Assign Imported Choose Destination Save Import Definition Scherne Control and Summary Import in Progress Please assign the displayed data to the objects You may use the keyboard to assign selected data points to an object select the abbriviation characters a bebe and numbers to assign the step 8 4 14B 2 499 55 15 0 2 511 641 EE 26B 3 670 283 270 3682832 2 40 fo 696 905 r4 915 975 fo 820 04 og 330 545 ob 944 034 or 962 929 Selected datapoint Grid display options Dilution step FointH Data value display point of columns 330 835 display data gt E color the grid L When you have finished your assignments and there no errors which are displayed in the dialog the Next gt button will be activated The Object Import Tree The PLA Import Wizard now displays the Import Tree 16 May 2013 Page 70 of 193 Select Input File Defne Objects Import Definition Scheme Current Import Operation Contains WE C el O E E E Select Destination Scheme 5 EEU Include E TU New Assay Defne Objects 3 B Standard ay E sclude Sort and Assign Imported Data Preparation E Choose Destination ow a Preparation C Save Import Definitio
96. evel PLA distingushes between sample and assay suitability tests A failed sample suitability test leads to a failed preparation A failed assay suitability test fails all preparations in the assay E g you can setup the potency of a well known assay control as a assay suitability test If this well known assay control fails the test every preparation in the assay is failed Severity PLA supports different severities of tests Reject If this test fails the assay is marked as rejected A potency will not be printed Warning If this test fails the assay is marked as failed but a potency will still be printed 16 May 2013 Page 34 of 193 o lt a PLA 2 1 Information Even if the test itself fails the preparation is left passed You can use this severity e g as an early problem indicator e g the number of outliers gets to high Note You can define the same test class multiple times with diffent severities Consider the use of customized failure messages in this case 16 May 2013 Page 35 of 193 h PLA 2 1 5 User Guide PLA is a full featured system for the analysis of Parallel Line Assays and Parallel Logistic Assays This manual describes the concepts and features of PLA A systematic introduction can be found in the My First Assay with PLA section This manual covers the basic operation with PLA The structure of the manual is e Connect to PLA The chapter describes how to connect to an existi
97. f standard and preparation for analysis While in Parallel Logistic Assays mostly the whole dose response curve is taken into consideration Parallel Line Assays focus the linear portion of the dose response curve There are three types of configurations available e Full Curve This is the default option All treatments of the standard and the preparation are used for analysis e Fixed Range A portion of the curve is selected by hand The treatments of each object are numbered and you use these step numbers to select your regions of interest e Automatic Range Selection There is a full list of range selection options available for automatic selection of the significant dose response curves in the parallel line analysis The different configuration options can be defined for the standard and the preparations individually allowing e g to select a well known area of the standard and to automatically find a matching range in the preparations 4 7 The PLA 2 1 Test System The test system of PLA 2 1 has been completely reworked The system allows the definition of complex suitability criteria for your assay e Difference Tests e Similiarity Tests e Tests for Regression Parameter Estimates e Tests for Difference of Parameter Estimates e Tests for Ratio of Parameter Estimates e Tests for the Scaled Difference of Parameter Estimates e Additional Tests e Test Scopes Levels and Severity Scope e Level 16 May 2013 Page 31 of 193 al PLA 2
98. ftware Licensing Module must be present during the work with PLA 2 1 If it is removed during a session you will no longer be able to calculate assays When PLA detects the removal it asks to reattach the module or to exit the application Install Universal Serial Bus USB Hardlock Attach the Software Licensing Module Hardlock to a USB Port of your computer Install Parallel Port or Serial Port Hardlock Attach the Software Licensing Module Hardlock to the parallel port your computer system Q Note Since 2006 PLA is usually delivered with USB Hardlocks see above If a printer is attached to your computer than detach the printer cable from your computer Attach the Software Licensing Module to your computer s parallel port Label PARALLEL and re attach the printer cable to the backside of the software licensing module Label SERIAL Computer System lt gt Software Licensing Module Dongle lt gt Printer Cable lt gt Printer 4 4 Basic Database Management PLA 2 1 has a database management that allows you to create and connect to any number of databases You can create databases for your different projects allowing you to define who has access to which data and to specify different security settings to these databases The databases can be shared across the network There are two basic database types available File based databases and SQL Server based databases 16 May 2013 Page 22 of 193 d PLA 2 1 Th
99. ge Selection ow Parallel Logistic Assays based on 3 4 and 5 Parameter Fit ow Response Adjustments e g blank deduction e W Available Response Transformations for all models untransformed log 2 square and square root transformation e Four Outlier Detection Methods Optional e Dixon Test for Data Outliers e Grubb s Test e Standard Deviation Test e Externally Studentized Residuals e Manual Removal as Technical Outliers e ANOVA Models e ANOVA based on Pure Error Separation ANOVA based on Residual Error e Combination of Assay Results e Raw Bulk Material Potency Calculations Stock Solution Potency Calculations e Assigned Assumed Potency Calculations e EC50 Calculation 1 2 Test Features Support of assay controls e 28 different suitability tests available e similarity assessment through 20 different equivalence tests e single parameter tests e difference of parameters e ratio of parameters e scaled ratio of parameters 16 May 2013 Page 8 of 193 NY PLA 2 1 hypothesis testing e parallelism e slope e linearity additional tests number of outliers e potency range test severity levels failure warning information customizable messages test scopes x development support for equivalence margins 1 3 Data Management and Reporting Features Database for Storage of Assay Data Multiple Databases shared over the network e g project or team specific databases Secure Storage using an internal PKI infrastructu
100. gents Equipment Lookup Ei Annotations em Uzer o ig Varnable Name PHF Creator Value PLAE sport Yanable Name Mame of this user vanable d Automatic range detection is not available with the 4 parameter logistic function Instead a Note Vou have only one replicate per treatment The results of the statistical tests will be Figure Screen Layout of the Documentation Features 5 3 8 GxP Settings The GxP settings allow the protection of properties Property Description Default Template for Child Objects Template Select a template to be used as a template when childs are created GLP SOP Protection Level Settings 16 May 2013 Page 90 of 193 Enable GxP SOP protection Mandatory Enable GxP SOP protection User Level Protection Level Substance Information Documentation Dose Definitions Analysis Tests Configuration Dose Values Response Values Keys and Combination Groups 16 May 2013 PLA 2 1 Available for administrators only Activates the protection Available for every user when the above property is inactive Activates the protection protects informations on the subject but not the Batch Identification protects the documentation properties protects the dose properties protects the analysis properties protects the test properties protects the configuration properties protects the dose values dilution series protects the response values useful only in combination with PLA Impo
101. guration Automatic Detection individual range al Fired A ange 2 Automatic Selection Options used by automatic detection methods Allocation Strategy Allocation region Minimal of points maxinial allocation range elect only configurations with identical number of treatments Inclusion of 502 response Calculate the 50 response by using the Inclusion is mandatory all objects Once we have saved the assay we select Check from the toolbar again The assay explorer re appears with the following screen 16 May 2013 Page 126 of 193 PLA 2 1 oo el Iles Graph Type ia 0 750 1 2 DoseHesponse Graph CE Equivalence Margins 0 700 ZE Display Options H 1 0 650 f Show Legend Fj i 0 600 H aoee Grid Sa V Regression Lines Restricted Model 0 550 Mean Line J Data Values MARN F Include Statistical Outliers 0450 Include Technical Outliers rab I Error Bars 1 00 G Been E Box amp whisker Plot 0 350 Inert Axis F Showy Axis Origin 0 300 Y Ass Transformation 0 250 E 0 200 EHH Preliminary Preparation Results g A Preperation nies e z 5 g DE Test Results 0 1001 8 b 9o aa 0 050 ie Sample suitability 3 7 TT gooo created by PLA 2 14 frial www bioassay de Assay suitably 9 77E 04 3 12E 02 1 00E0c Overall test result 7 PASSER a Dose Preperation m Standard Estim Potency Ratio and Confidence Interval Potency A atig
102. hared drive The file based database is a secured Microsoft JET database Note We do not recommend to connect more than 3 concurrent users to this database type e SQL Server Database PLA allows to use a Microsoft SQL Server Database MS SQL Server 2000 or higher MSDE supported Depending on your license PLA can accept nearly any number of connection to this type of database It should be preferred if you have a SQL Server available 8 4 2 PLA Database Maintenance There are a few Maintenance Tasks for PLA databases 16 May 2013 Page 146 of 193 Se gt lt PLA 2 1 Backup The Databases PLA Databases have to be backed up on a regular basis It is the task of the IT Administration to create backups of file based and SQL Server based databases Stegmann Systems recommends to create backups every day Create a Database Create a File Based Database From the Login Dialog select Manage on the right of the database selector Q Login Database This tri J PLA 21 Default Database e This cop User ID e The Database Management dialog appears 16 May 2013 Page 147 of 193 Database Connection Profiles PB PLA 2 1 Default Database Create or Connect a Database File Connect a Database Server Delete Connection Profile Compact Database Information concerning Database Connections PLA supports multiple database connections These connections have to be defined using this Database Manager dialog
103. he computer system The components installed divide into the following groups e The Main Program and its files These are typically installed in the Program Files directory of windows Files in this directory should not be modified during normal operation of the system e Shared components of the vendor These are installed in Common Files sections They are used by different programs of the vendor e System components are installed in the windows directory They add new functions to the operating system or install new components or drivers A basic requirement of the Installation Qualification is a computer system with a operating system installation without errors The installation qualification process than assures that all installed files of the software system are installed in the correct directories It is proven that they are identical to the vendor distributed files by the calculation of a checksum This checksum is cryptographically secured The basic goal of the installation qualification is to prove the correct distribution of the right files on the computer system 16 May 2013 Page 133 of 193 oo o lt a ae o PLA 2 1 Result of the Installation Qualification As a result of the installation qualification you receive a certificate that contains information on all files of the PLA system Their location and the details of the inspection The certificate will only be printed when the check is successful If the check found erro
104. he figure there is only a PLA Administrator defined Select your desired User ID and type in your password By clicking Login or pressing the enter key you are logged in If the password was wrong the user id was deactivated the users password expired or if administrative database access has been activated there may be further messages On the right hand side of the dialog registration information product information and license informations are displayed You may edit the registration information by selecting the hyperlink Click to Edit on the upper right of the figure The product information and license information are displayed by clicking the respective buttons on the lower right 16 May 2013 Page 37 of 193 4 t PLA 2 1 After you have successfully logged in the PLA main screen is displayed 5 1 2 Screen Layout The following figure shows the basic screen layout of PLA Pec Soitan ee eee File Actions System Validation Window Help Oh a xX eel seea Data Obiests ooo E samples from Literature E E Sample Parallel Line Assays fl Sample Parallel Logistics Assays El include hidden items refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator The screen consists of the following areas e Menu Section This is a classic windows menu system The file menu contains commands management commands for the database objects files the action menu contains the commands for the ana
105. he graphic the selection section is displayed By checking and un checking preparations you can modify the display The bullets indicate the test status of the preparation e green all tests are passed yellow one or more tests are failed but not marked as rejection criterion e red one or more tests are failed and marked as rejection criterion Graphics The graphics shows the dose response graph or the equivalence test graph You can save the image as a JPEG or PNG graphic for further use in publications etc The dimensions of this graphic can be set in the options dialog 16 May 2013 Page 96 of 193 d PLA 2 1 5 4 2 Combination of Assay Results Combination of Assay Result calculations are available within PLA To prepare these calculations you have to add the preparations you want to combine to combination groups A combination group is a simple named label that allows PLA to analyze which preparations should be combined The labels can be edited on the documentation page of the Assay Editor or in the Combination of Assay Results Editor PLA will calculate the combination when a group contains more than one preparation and the appropriate option on the Calculate dialog is checked PLA is able to combine results of any preparations within a project Definition of Combination Groups with the Assay Editor Add the preparation to an assay by creating new combination groups This methods is available for projects and assays to allo
106. he session 9 1 19 System Locked This dialog is shown to you after you have logged your PLA Session manually via the System Menu or after your session has been locked automatically because you didn t work with PLA within the in the Options specified time period System Locked a Current User PLA Administrator Password Cespa Current User The name of the user who s session is locked Password Type the password for the user into this field Remember that passwords are case sensitive Unlock Click here to unlock the PLA session after having entered the correct password into the corresponding field Close PLA Click here to close PLA You do not need to provide a password You will be asked whether you are sure about closing PLA since all changes will not be saved 16 May 2013 Page 184 of 193 4 t PLA 2 1 9 1 20 Validation Menu This topic describes the Validation Menu of the PLA menu bar aa File Actions System Vali dation Window Help H amp A Installation Qualification 19 Navigator Operational Qualification 00 Performance Qualification PQ E Examples from Liter Sample Parallel Line Sample Project Sample Project 2 Create a PQ Dataset include hidden items refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator Installation Qualification Opens the Installation Qualification IQ Dialog See also Installation Qualification Oper
107. helpful resources Note An updated version of this manual is available online Go to https documentation stegmannsystems com display PLA21 to see the latest version Getting Started Getting Started Basic Concepts of PLA 2 1 Installation of PLA 2 1 Parallel Line and Parallel Logistic Assays Reference IT Administration Guide Description of PLA for IT Professionals PLA Setup Basics Security Basics User Guide Tutorial Videos Introduction My First Assay with PLA 2 1 Account Management Database Management 16 May 2013 PLA 2 1 Page 6 of 193 4 PLA 2 1 Online Resources Free Trial of The Latest PLA Version Getting Support PLA Homepage PLA Support PLA 2 1 User Manual PDF 7 6 MB 16 May 2013 Page 7 of 193 PLA 2 1 1 Introduction PLA 2 1 is a software package for the development and analysis of Parallel Line and Parallel Logistic Assays PLA 2 1 has been updated from PLA 2 0 to support the new chapters lt 1032 gt lt 1033 gt and lt 1034 gt from the US Pharamacopoeia PLA 2 1 ist the first software package that supports the evaluation of Biological Assays according to the US Pharmacopoeia AND the European Pharmacopoeia at once The following keywords give a short summary and describe the options of PLA 2 1 Q Note New or updated features in PLA 2 1 are marked with a x 1 1 Statistical Features e Parallel Line Assay ow Configuration Optimization for Parallel Line Assays Ran
108. hically secured digital signatures assures the integrity of the reference data PLA makes use of a public key cryptographic system Only Stegmann Systems is able to publish these reference data sets For the integrity of the Performance Qualification data PLA makes use of a special pair of cryptographic keys only used forPQ data This opens a security shell for this type of data Only PLA itself is able to create PQ data sets There is no way to compromise these data sets 7 2 3 Recommendation for your 1Q OQ Procedures Depending on the status of your internal IQ OQ procedures we would like to suggest to base your IQ OQ procedures for PLA on the automated procedures of PLA and the certificates they provide This can drastically reduce the effort to qualify new releases of PLA Stegmann Systems will verify its IQ and OQ data sets with every sub release of PLA Due to the cryptographically secured files PLA is able to provide you withrequired certificates Stegmann Systems guarantees the availability of this approach for the complete PLA 2 x product line Even Import Modules and Report Templates are delivered with the required IQ reference data so their correct installation we be confirmed with the certificates too 7 3 Installation Qualification 7 3 1 The Installation Qualification Process Goals of the Installation Qualification During the installation of a software product like PLA software components are installed at several locations of t
109. ification of an account and discard all changes Close Close the Account Management dialog 9 1 2 Action Menu This topic describes PLA s Action Menu 16 May 2013 Page 155 of 193 ndow Help SE wae mt ae Lo eet ie 7 c nun i 4 E E a i W Sample Parallel Line Assays Hf Sample Project H A Sample Project 2 include hidden items refresh automatically Calculate assay i a Database PLA 2 1 Default Database PLA Administrator Calculate amp Report Opens the Calculate amp Report Dialog which allows you to start the calculation process and create reports Data Explorer Check Opens the Data Explorer Check Dialog which shows you a graphical overview of your assay and preliminary calculation results See how to Explore your Assay Combination of Assay Results Editor Opens the Combination of Assay Results Dialog which allows you to define Groups for Combination of Assay Results 9 1 3 Apply This dialog allows you to apply object properties to multiple objects at once 16 May 2013 Page 156 of 193 Daal PLA 2 1 C Assay 1 Gandotrophin Aszsay C Template mi My Sample Protected Template protected template Property groups to apply apply general information apply documentation information apply assay definitions Number of series steps concentration doses etc apply analysis definitions Statistical parameters regression model etc apply test definitions apply linear selection d
110. in potency ratio estimation PLA 1 2 default Note you can preview the absolute doses created by these settings in the data editor Figure Screen layout of the Dose Properties 5 3 3 Data Properties Data Properties define the dimension and data values of a standard or preparation Property Description Dimension and Dilution Scale Number of Treatments The number of treatments dilution steps in this object Number of Replicates The number of replicates in the object 16 May 2013 Page 80 of 193 PLA 2 1 Dilution Scale 1 in 2 series or direct input Data Values Data Depending on the dilution scale property you edit the dose and response values ote Dora z B Bi L i L a p a kda ti ll sad _ Configuration Dimension and Dilution Scale inhented from aszay Number of treatments dilution steps 7 allowed 2 25 Number of replicates 2 allowed 1 25 Dilution scale Tin 2 twofold series Data Preview absolute doses relative Dose Toggle outher status by pressing F Technical Outliers are displayed using a light red color Input a value press F2 or click to edit Press ESC to leave edit mode Outlier testing i activated You need at least 3 replicates for outher testing This object ts readonly due to the application of an electronic signature Figure Screen Layout of the Data Properties 5 3 4 Analysis Properties The analysis properties describe details of the p
111. ion The wizard now creates two files e the PQ file and e the corresponding Complete Statistics Report The Complete Statistics Report is located in the same directory as the PQ file Now you have to check the report for correctness Once you have accepted the results you can proceed to the Performance Qualification task 16 May 2013 Page 141 of 193 Sa soos TO PLA 2 1 7 5 3 Performing the Performance Qualification From the Validation Menu select Performance Qualification PQ The following dialog appears _ Performance Qualification PQ Select a PO Definition File The PO process creates the necessary objects performs the calculations and compares the results You will recente a PO certificate Input Start Cleanup temporary objects after execution Progress Extracted PO File Details Result L The performance qualification has not been run pet Mo report has been created yet r AA Select your PQ file using the button near the input field Press Start to start the PQ Process Depending on the size of your PQ file the process may need several minutes to complete The certificate error report is created in the standard output directory The certificate can be launched by clicking on the hyperlink that is available after the process finished Note If you want to check the PQ with its documentation you can toggle the cleanup switch Cleanup temporary objects after execution If you deactivated it
112. ions used by automatic detection methods Allocation Strategy Allocation region Minimal of points masimal allocation range select only configurations with identical number of treatments Inclusion of 502 response Calculate the 50 response by using the d Automatic range detection is not available with the 4 parameter logistic function Instead Oo Note Vou have only one replicate per treatment The results of the statistical tests will be Figure Screen Layout of the Configuration Properties 5 3 7 Documentation Properties The Documentation features allow to enter meta information for the assay Each entry has several properties Property Description Documentation and Variables Operators Define the operators of the assay and their roles 16 May 2013 Page 88 of 193 Reagents Equipment Annotations User Variables Combination Groups 16 May 2013 e Name e Role e Timestamp e Comments Define details of reagents used with this assay e Identification e Lot or Batch No e Concentration Amount e Comments Equipment used for this assay e Identification e Machine Lot No e Comments Remarks of the operators e Username e Timestamp e Annotation Key Value pairs available for reporting e Variable Name Key e Value Combination of assay results are calculated in groups e Combination Group PLA 2 1 Page 89 of 193 Daal PLA 2 1 Documentation and Yarables Operators Tae Rea
113. iplicity of the standard deviations for error bars and box and whisker plots Toggle the direction of the x axis Note PLA 1 2 has an inverted x axis Include the y axis origin in the graph Change the y axis transformation This option allows to inspect the influence of other response transformations on heteroscadescity Note this does not change the response transformation Check to neglect the outlier status for error bars mean line and box and whisker plots Page 95 of 193 PLA 2 1 Calculation Results Preliminary Preparation Results Sample 1 Test Results Sample suitability F Assay suitability Ovealtectiesut PASSED Estim Potency Ratio and Confidence Interval Potency A atio 0 592 Confidence Interval 0 855 0 932 Q Note Select a preparation in the selection section below the graphic to display specific results Carefully check that the preparation of interest is selected Its name is displayed in this section The preliminary calculation results indicate the status of the tests The overall result states the combined result of all tests In the statistics table the number of tests passed or failed with the different severity classes and depending on the test level are given The potency ratio not potency factors of the assay are displayed including the corresponding confidence intervals Selection Section Sample 1 W sample 4 J Sample 2 7 Sample 5 7 Sample 3 po Below t
114. irmed the operation the objects will be removed from the database Notes e The audit trail information of the deleted objects is still intact e The operation is not reversible Hiding Showing Objects The hide feature allows you to exclude objects from calculation and from display in the navigator You can decide whether to hide or show an object by selecting the hide checkbox in the General section of the editor At the bottom of the navigator there is a checkbox to include hidden items into the display of the navigator Locking Objects PLA stores its objects in a multi user database To prevent that two or more users modify the same object at the same time PLA locks the respective object A locked object is decorated with a small locked padlock The first user who accesses the object gets the exclusive right to modify its contents If a user has exclusive rights on an object it is decorated with an unlocked padlock PLA automatically handles locking and unlocking of all objects and there is normally no need to lock objects manually Even applying properties for a whole project tree is handled without further user interaction However sometimes a user plans to perform extensive changes on a collection of objects which should 16 May 2013 Page 45 of 193 PLA 2 1 not be disturbed by any other user In this situation it is possible to explicitly lock the object tree using the Lock Tree function of the navigator conte
115. it Regression Models non linear methods not available with fixed upper asymptote Similarity non linear methods not available with fixed lower asymptote Similarity 5 parameter fit Scaled Range of Regression Parameter Estimates Test Equivalence Test Scaled Slope Range Equivalence Test Scaled Upper Asymptote Range Equivalence Test Scaled Lower Asymptote Range Equivalence Test Scaled Asymmetry Parameter Range Additional Tests Test Purpose 16 May 2013 Purpose Similarity Similarity Similarity Similarity Regression Models Regression Models all non linear methods not available with fixed upper asymptote non linear methods not available with fixed lower asymptote 5 parameter fit Test Type Remarks Test Type preparation preparation preparation preparation Test Type preparation preparation preparation preparation Test Type preparation preparation preparation preparation PLA 2 1 Remarks Remarks Remarks Page 109 of 193 d PLA 2 1 Potency Similarity all preparation Sum of squares of Linearity all all objects non linearity Max number of Model all all objects Technical statistical outliers outliers Response value Model all all objects range Relative potency Model all preparation tests the calculated result relative potency constrained regression Relative potency Model all preparation tests the calculated re
116. ition data include documentation details Please choose the elements that wil Include user defined values and combination groups be exported l l include annotations include administrative information The PLA Secure Format and the PLA External Format do not allow to select details Press Next gt to continue Summary On the summary page you can verify your Export details Press Execute to start the export process You will be notified when it is finished 16 May 2013 Page 75 of 193 i PLA 2 1 5 Choose Type of Export ore Select T arget File Summary of operation Specify Export Detail Cae al i ac Export Type Standard Export Summary Focus Examples from Literature Export in progress Options Export format PLA 2 4 Secure Format Filename Example 2 FSF Directory YFLA 2 1 Please check pour settings to ensure the corect process definition Cancel lt Previous Execute 5 3 Object Properties The representation of projects assays standards preparations and controls are generally called objects in this manual The object properties can be divided into different sets of information They are represented as property pages in the object editor dialog e General Properties contain general information about the specific object e Dose Properties define the potency and doses of a specific measurement object e Data Properties define the dimensions of the response value matrix and allow the input of the d
117. ity for the Failed Test Overall Result Reject REJECTED Warning FAILED Information PASSED Overall Result The overall result of the test system is defined by the failed test with the highest severity setting E g Two test are defined One of the tests has the test severity Reject the other has the test severity Warning Test 1 Test 2 Overall Result Severity Reject Severity Warning Passed Passed PASSED Passed Failed FAILED Failed Passed REJECTED Failed Failed REJECTED Custom Messages You can define custom messages for the single test results The overall result messages are not customizable 16 May 2013 Page 113 of 193 PLA 2 1 O Additional test Max number of outliers Margin 0 Test Level 2 Sample Suitability Test Test Scope 1 all objects Test Severity 2 Warning potency calculatio age elle Customized Passed Message Test Failed Message Customized Failed Message To reset the message to the default simply delete the custom message PLA will respond with a default entry O Additional test Max number of outliers a Margin 0 Test Level 2 Sample Suitability Test Test Scope 1 all objects Test Severity 2 Warning potency calculatio age ere default Test Failed Message Customized Failed Message 16 May 2013 Page 114 of 193 PLA 2 1 6 My First Assay with PLA Note This initial tutorial is available as a tutorial video in the online help too This tutorial shows
118. ke assay Electronic Signatures Signatures may be removed by Defines who is allowed to remove electronic signatures from objects Possible Values 1 admins only 2 the signer 3 everyone Default value 2 the signer List of pre defined comments for electronic signatures A semicolon separated list of pre defined comments for electronic signatures Navigator Defaults Autorefresh Interval Defines the number of seconds to elapse until a navigator refresh occurs Possible Values 5 3 600 Default value 30 16 May 2013 Page 177 of 193 Autorefresh Navigator PLA 2 1 Defines whether the navigator is refreshed automatically Only useful in multi user environments Possible Values No Yes Default value No 9 1 15 Product Information This dialog shows detailed information about your PLA Installation About PLA 2 1 0 build 600 Software for Biological Assays Sottware tor Analysing Biological Assays 4 1 System Information Version 2 1 0 build 600 S N 153567176 Vendor Contact Details Stegmann Systems GmbH Raiffeisenstr 2 63110 Rodgau Germany Phone 49 6106 77010 0 suppornt bioassay de Fax 49 6106 77010 29 Wii w bioassay de Postal Address The vendors postal address Phone Fax The vendors telephone and fax number Version The detailed version number of your PLA installation 16 May 2013 Page 178 of 193 oe gt gt gt TO PLA 2 1 Serial Number Your PLA
119. lts section which is also part of REP 10 Extensive Report on all aspects of the assay and test calculations It includes information about the optimization process Warning this report can get very large An Microsoft Excel tm spreadsheet for the calculation of Equivalence Margins from historic assay data Technical Remarks on Preview and Print 1 Print and Preview make use of the corresponding application E g if you create a Adobe PDF report the Acrobat Reader or an alternative viewer for PDF file has to be available and the file type of PDF has to be registered in the operating system 2 If you want to test the availability of the application save the report to any location Then start the Windows Explorer and try to open the file by double clicking If the report is displayed PLA is able to display the report If it is not displayed PLA will not be able to open the report The print method can be tested by selecting the Print command of the Windows Explorers Context menu of the file open with a right click Then select print If the report is printed PLA will be able to print to 16 May 2013 Page 100 of 193 PLA 2 1 5 5 Advanced Topics 5 5 1 Electronic Signatures PLA accepts electronic signatures for the objects of PLA Every object can be signed electronically with one exception assay object signatures are always recursive on the child objects of the assays An object can have any number of signatures Sign An
120. lysis of assays the system menu contains all the system options for PLA The validation menu allows you to perform the installation operational and performance qualification tasks the window menu contains commands for organising the sheet windows In the help section this online help product and license information is found e Toolbar Section The toolbar section contains the most frequently used commands within PLA They are activated and inactivated in correspondence to the selected objects in the navigator e Navigator The navigator is displayed left to the sheet area It allows you to manage and navigate through your selected database 16 May 2013 Page 38 of 193 oe gt gt gt TO PLA 2 1 e Sheet Area Once you open an object for editing of for analysis it is open in the dark grey sheet area This area is a multiple document interface MDI allowing you to use multiple objects at once e The Information Line On the bottom of the window the information line displays the connected database in the figure PLA 2 1 Default Database and the logged in user fig PLA Administrator 16 May 2013 Page 39 of 193 y t q PLA 2 1 5 2 The Objects of PLA 5 2 1 Managing Objects The Navigator Once you have logged in the main instrument of work within PLA is displayed the Navigator The navigator allows you to navigate through your connected database Fle Actions System Validation Window Help h a X eel
121. mation Outlier Detection Outlier Method Select the Outlier Detection Method None e Dixon Test e Grubb s Test e Test based on Standard Deviation Studentized Residuals not available for controls Contamination alpha Sensitivity of the outlier method not available for Standard Deviation Method recursive testing Execute the outlier tests recursive only for Dixon and Grubb s Method n Multiplicator for Standard Deviation test Regression Model amp ANOVA Regression Model Select the Regression Model for the analysis e Parallel Line Model e 4 Parameter Logistic Curve e 5 Parameter Logistic Curve e 3 Parameter Logistic Curve fixed upper asymptote e 3 Parameter Logistic Curve fixed lower asymptote Invert Potency Ratio Check to invert the potency ratio after calculation Set asymptote to 3 Parameter Logistic Curve e Fixed value e Mean of positive control e Mean of negative control e Mean of blank control If a required control line is missing the value is set to zero ANOVA Two different separation schemes are supported for the ANOVA calculations 16 May 2013 Page 83 of 193 o PLA 2 1 e ANOVA with Pure Error separation e Residual Error ANOVA Confidence Interval for Potency Estimation Fiducial Limit The confidence interval of the potency estimation Fieller s Theorem Use Fieller s Theorem instead of the standard confidence interval requires linear regression EC50 Method EC50 Method Which regression is
122. ms GmbH shall in no way be liable for damages caused by violation of duty on your part consequential damages economic losses damages due to loss of data or for claims from third parties put forth against you 6 Termination of the Agreement Should you fail to comply with the provisions of this agreement your license and this agreement shall be terminated The provisions in paragraphs 3 4 and 5 shall remain in full force and effect even after termination of this agreement Version dated 2008 04 01 16 May 2013 Page 192 of 193 A Y i q 15 Revision History e Revision History e PLA 2 1 build 600 15 1 PLA 2 1 build 600 Initial Revision of PLA 2 1 16 May 2013 PLA 2 1 Page 193 of 193
123. n Scheme Select Control and Summary Import in Progress Please choose or create the destination where the imported data will be saved Press Fe to rename objects You may use these variables in object names U User D D ate 7 T ime F Filename On this page you have several options e Include and Exclude parts of the tree by selecting an object and pressing include and exclude buttons Excluded objects are marked with a black cross Select another parent for the assays This allows to import the objects to a different target If you selected an existing object as a target this is noted by an arrow e Rename Objects by pressing F2 You may also insert variables into the name These variable are useful if you want to create import definition schemes The variables are replaced when the import is executed The variables available are U replaced with the name of the current user D replaced with the current date T replaced with the current time and F which is replaced with the filename of the import file Save the Import Definition Scheme IDS On this page you have the option to save your selection in an Import Definition Scheme This scheme contains all of your selections especially the raw data assignments If you save it it will available on your next import with this file type Note the IDS is saved in the PTD file of your Import Module PLA needs 16 May 2013 Page 71 of 193 Sa soos TO PLA
124. n the databases are automatically locked when they are used The session and lock management of PLA is self healing if they encounter problems e g missing logouts After some minutes inactive sessions and locks are automatically removed by PLA The PLA setup is Windows compliant Restricted Users are able to work with PLA Deeper Details about the Setup are found in the Setup Basics section of this manual PLA can be installed in Terminal Server environments 16 May 2013 Page 143 of 193 NY PLA 2 1 8 2 PLA Setup Basics 8 2 1 PLA is Microsoft Windows Compliant No write permission in the Program Files are required e PLA requires write permissions in the All Users Application Data e PLA requires write permissions in the My files section of an user e PLA requires write permissions to the Import Export Module path if you want to save Import Definition Schemes During installation administrative permissions are required PLA should be installed on the local hard drive It is not recommended to install PLA on network drives But you might point the report templates directory of PLA the import export directories and the import export modules directory to central locations This can be done within the options dialog of PLA 8 2 2 Customizable Directories of PLA In the Options dialog or in the registry the following customizable directories of PLA can be set Default This path is the default path of the import wizard
125. ndard users are not allowed to delete projects or assays Possible Values No Yes Default value No Security System Idle Lock Interval This specifies the time interval in minutes after which PLA is locked if no user action occurred By specifying the value 0 the automatic lock is disabled Possible Values O 1540 Default value 0 Password minimum length Specifies the minimum number of characters a password must have Possible Values 0 25 Default value 0 Recommended Value 8 Password minimum number of special characters Specifies the minimum number of special characters a password must contain A special character is one of 0123456789 _ 2B S amp lt gt 16 May 2013 Page 175 of 193 oo o lt a ae o PLA 2 1 Possible Values O n Default value 0 Password maximum age Specifies the maximum age of a password in days If the age for a password has been reached The user will be asked to change it By setting this option to O you disable It Possible Values O n Default value 0 Password warning age Specifies the warning age of a password in days If the age for a password has been reached The user will be notified that his password will expire By setting this option to 0 you disable it Possible Values O n Default value 0 Password minimum age Specifies the minimum age of a password in days The password cannot expire until the minimum age is reached By setting thi
126. nfrastructure All objects within the database are signed using a digital signature This signature is checked every time PLA access the object If the signature is invalid for any reason PLA refuses to open the object In addition to the objects projects assays standards preparations and controls even the user accounts and the options are digitally signed too All of these signatures include a unique database identifier This database identifier is verified each time an object is accessed By these techniques it is not possible to modify definitions or to move elements such as user accounts to other installations without invalidating them So don t try to modify anything in the PLA databases 8 3 3 Database Security The file based databases of PLA are secured For the SQL Server based databases it is recommended not to communicate the database access information directly to the user The database administrators PLA administrators should define the database connections for the end users Another possibility is to directly install the database connections via registry Advanced Database Administration 8 4 Database Guide 8 4 1 PLA Databases PLA makes use of databases to store assay data audit trails user account data and system options There are two types of databases e File based Database This type of database can be generated on any local or shared drive Multiple Users can connect to this database when it is located on a s
127. ng PLA database e Managing Objects This chapter describes the basic handling of objects in PLA This includes the management and editing of the objects Inheritance Templates the Apply function and import export handling augments the chapter Object Properties The chapter describes all the properties of the objects e Analyzing Assays How are assays analyzed with PLA How do create reports e Advanced Topics Information concerning the System Audit Trail and the secure transfer of data objects and templates 16 May 2013 Page 36 of 193 nal PLA 2 1 5 1 Connect to PLA 5 1 1 Log in to PLA PLA has its own User Management Infrastructure You are required to log in to a database to work with PLA After you have started PLA the Login dialog appears This dialog allows you to log in to the selected database to select other databases and to start the database manager You may also start the product information and license detail dialogs Database Thiz trial f PLA has 14 d lefi Click to edit PLA 2 1 Default Database I trial Copy o as ay z lefi Click to edi This copy of PLA has not been registered yet User ID PL4 Administrator PLA 2 0 is available Read the announcement now Password Product Information License Information First of all select the required database if it is not already selected Once you have connected the database the section User ID contains the list of defined users in that database In t
128. ng information 16 May 2013 Page 63 of 193 Select t Fil Select Input File elect Import rile Import Definition Scheme 1 Select Import File Type Select DestnationsS cheme PLA 2 x Secure Format PSF gt PLA 2 8 Enhanced Format FPEF kimi PLA 1 2 Native Format PNF Sort and Assign Imported Data g6 w ell Plate CST Softmas Pro soa oe Wavelength 1 4da Softmas Pro Soe 4w 5e Wavelength 2 4da Save Import Definition Scheme Softmas Pro dsid wB Wavelength 1 2 4da Control and Summary Choose Destination Import in Progress Please select the file you want to import Fress Select File to choose the import tile 2 Select Import File APLA 2 1 4Lot_ABO22601_1 pda Select File Results of Initial Analysis Selected Format Softmas Pro a w sD Wavelength H Analyzing the input file Fleaze wait complete Input file contains O valid objects There i raw data present This data has to be attached to the corect objects Cancel lt Previous Especially note the remark There is raw data present This raw data has to assigned to the required objects in PLA Press Next gt now to start the import process Load Import Definition Scheme First of all you might load a previously saved import definition scheme IDS An IDS allows you to save all the steps of the following pages and to efficiently load external data In our case no scheme is available yet We
129. ng it to suppor bioassay de or filling out an online form using the Submit Online button ou will recernve a Vendor Response that has to be entered into the green field Product Information License Status The status of your PLA installation and the Hardlock status License Details A list of Licenses with their status License Key Text edit field for entering a license key manually Add After having entered a license key into the License Key field click this button to add the license Download License Keys If you have an Upgrade Protection for PLA 2 1 you ll be able to download your license keys directly from our license server Note This feature requires an internet connection 16 May 2013 Page 169 of 193 PLA 2 1 Inquiry Key This key is generated by the PLA Licensing system It is required if you need to get an extension of your trial period Note This feature applies only to the Trial Mode of PLA Submit Online Submit your Inquiry Key online This will open the PLA License Inquire page in your internet browser You can use the form on this page to submit the query Note This feature requires an internet connection Submit by E mail Submit your Inquiry Key by e mail This will open you mail application with a prepared mail containing the required information for a new trial key You d just have to press the send button Note This feature requires an internet connection Vendor Response Once you
130. nterest Then select the copy or move function from the file menu or the context menu of the navigator The following dialog is displayed Soh Copy Object Source a 4 Antibiotice Turbidimetic Assay Target Parent Examples from Literature Name 4 Antibiotic Turbidirnetric Assay Select a target for the copy operation Sie a 16 May 2013 Page 44 of 193 PLA 2 1 Note the Move dialog is identical to this one Within the dialog there are two sections The source section has already been filled with the object of interest If you have select a project or assay object the copy dialog allows you to decide wether to include all child object Move always includes the child objects You now have to select a target parent By default the parent of the source is selected as the target parent You can make use of the button right to the target field This opens a dialog with all the available objects You may rename the object by typing a new name into the name section Select Copy or Move to start the execution When the operation is finished the dialog close and the navigator tree is refreshed Deleting Objects You can delete objects by calling the delete function from the file menu the toolbar or the context menu of the navigator The object must not be locked or signed You will be asked to confirm the delete operation if you choose a project to delete there will a second security confirmation After you have conf
131. nts replicates Control and Summary apep z A Sharndard 4 Import in Progress Preparation E Preparation C Please define the type count and general settings number of steps and zeres of the objects you want to create Selected object Standard A Type of object H treatments replicates Standard b 2 Apply When the assay dimensions are correct press Next gt to continue Bind the Raw Data to your Assay Now you have to bind the raw data to your assay The Import Wizard has several options to display your data Grid Display Options By default the raw data is displayed in 12 columns This leads to a correct display of a 96 well plate if you have 96 response values You have the option to display the data point number and the response value itself You may also switch the default display of the grid if standard data display is different 16 May 2013 Page 67 of 193 Select Input File Import Definition Scheme Select Destination S cheme Define Objects 1 230 895 2 253 517 a 351 AB 13 457 183 14 499 55 15 511 647 25 636 866 gt 670 283 ef 82 832 Choose Destination 37 761 85 780 556 39 796 845 Save Import Definition Scheme 49 656 3077 865 952 51 879 2 61 864 471 882 906 Ba 907 332 fa 696 805 815 915 5 9200 4 65 930 545 944 034 of 962 929 sort and Assign Imported Control and Summary Import in Progress Please assign the
132. ock Solution Potency Another option is the direct specification of the stock solution as a starting point If you do not specify a bulk substance raw material potency or stock solution potency the latter is assumed as 1 0 3 Pre Dilution Potency You can specify two additional pre dilution factors The multiplication of these factors with the stock solution potency defines the concentration of the highest dose 16 May 2013 Page 27 of 193 A Y i q PLA 2 1 4 Specification of the Dilution Series The last step is the specification of the dilution series which should be considered as relative doses of the dilution steps If you want to enter absolute doses don t activate the above options 4 6 2 Assigned Assumed Potency By default the assigned and assumed potencies of your bulk substance raw material or stock solution of your standard and the preparation are considered to be equivalent If they are equivalent the application of the analyzed potency factor to the potency of the standard leads to the potency of the preparation As a consequence you have to enter potencies only at the standard object However especially in Quality Control this approach does not necessarily meet your needs If your reference material and your preparation potencies are not identical PLA calculates relative potencies of the preparation with respect to the standard and to the assigned potency of the preparation To get these values the potencies have to be
133. om manipulation by the systems internal PKI Once you have thoroughly checked the corresponding Complete Statistics Report you can use the PQ to perform the Performance Qualification using the Performance Qualification Wizard 7 5 2 Preparing the Performance Qualification As a prerequisite you need to define your comparison data in PLA in any project This project may contain any number of assays you want to include in your PQ data set When finished start the Performance Qualification Preparation Wizard from the Validation menu by selecting Create a PO dataset The following wizard appears 16 May 2013 Page 140 of 193 PLA 2 1 E Create a PQ Dataset fmm l j E A PO dataset consists of a readable report and a digital signed PU file Please select your well known dataset assay or project Then select a new PO file A full statistics POF report for the data in this file i generated automatically Select Input and Output Input object PU File Output Progress wf checking prerequisites of calculation af PL results f export FPO dataset ff digitally sign PL dataset a create full statistics report f PO Dataset has been created Now select the input object by pressing the button next to the corresponding input field and select your PQ project from the list samples from Literature LE Sample Parallel Line Assays Then select the filename of your PQ file Press start to start the generat
134. ose and response values e Analysis Properties are the details of the calculation parameters e Configuration Properties fine tune the configuration selection in PLA e Documentation Properties allow the specification of various kinds of meta data for your assays e G P Options allow to protect groups of properties from manipulation 16 May 2013 Page 76 of 193 oe gt gt gt TO PLA 2 1 5 3 1 General Properties General properties describe management information for an object Property Description Name and Description Name Name of the object with up to 50 characters Description Detailed Description of the object Up to 255 characters Standard Preparation selector allows to switch the object types of standards and preparations hide in navigator hide the object from the navigator and from calculation Measurement Details Substance The measured substance whose potency shall be calculated optional Batch ID Batch Identification of the measured substance optional Timestamp Date and time when the measurement has been done Electronic Signatures Electronic Signatures Electronic Signatures that have been applied to the object 16 May 2013 Page 77 of 193 PLA 2 1 Europ Pharm Sth Ed 005 Ch 5 3 5 1 3 Four Dose Randomised Block Design Standard PreparationUnkrowr assay control E hide Measurement Details Substance Batch ID Timestamp 13 09 2005 11 06 19 History and Information Created m admin at 13
135. otency calculation 16 May 2013 Page 81 of 193 dra Assay Measurement 1 Documentation Inherit Properties Use analysis properties of the assay object Configuration General no adjustment default Response Transformation no transhormatian Outher Detection No Outlier Test Contamination a 0 1 4 parameter logistic curve full curve fit fed value PLA 2 1 Open Assay Definitions recursive testing x n o Testn 2 Invert potency ratio ANOVA based on residual error lack of fit pure error Confidence Interval for Potency Estimation Fiducial limit of potency estimation 2 use Fieller s Theorem EC50 Calculation parallel line model Method Do not calculate a Note Vou have only one replicate per treatment Property Calculate 50 Response by The results of the statistical tests will be Description Response Adjustment and Response Transformation Response Adjustment The adjustment value is subtracted from the response values prior to analysis 16 May 2013 No Adjustment default Adjust by a fixed value Adjust by mean of positive control Adjust by mean of negative control Adjust by mean of blank control Page 82 of 193 d PLA 2 1 If a required control object is missing no adjustment is performed Response Transformation Transform the response values no transformation default e log 2 transformation e square transformation sequare root transfor
136. owners PLA 2 1 includes software developed by the Apache Software Foundation http Awww apache org Copyright 1999 2006 The Apache Software Foundation All rights reserved The names Xalan FOP Avalon Framework Batik Xerces Commons logging and Apache Software Foundation must not be used to endorse or promote products derived from this software without prior written permission Products derived from this software may not be called Apache nor may Apache appear in their name without prior written permission of the Apache Software Foundation For written permission please contact apache apache org PLA 2 1 uses libraries that are subject to the Lesser GNU Public License LGPL Version 2 1 the License you may not use these files except in compliance with the License A copy of the License is distributed in the same folder as the respective file Software distributed under the License is distributed on an AS IS basis WITHOUT WARRANTY OF ANY KIND either express or implied See the License for the specific language governing rights and limitations under the License All rights reserved 16 May 2013 Page 190 of 193 d PLA 2 1 14 Licensing Agreement for products of Stegmann Systems GmbH Raiffeisenstr 2 63110 Rodgau Germany All products sold by Stegmann Systems GmbH or companies associated therewith including demonstration sets hardware media and manuals hereinafter referred to collectively as Prod
137. pair or replace the Product or parts thereof In the event that Stegmann Systems GmbH should not be in a position to fulfill this obligation you are entitled to rescind the purchase agreement Warranty claims must be submitted to Stegmann Systems GmbH in writing within the warranty period and at the latest within seven 7 days of the defect s appearance and the defect must be documented Defective Products should be returned to the distributor from whom the Product was originally purchased provided that the Product was not purchased directly from Stegmann Systems GmbH You shall bear all costs for shipping and shipping insurance WITH THE EXCEPTION OF THE WARRANTY STATED ABOVE Stegmann Systems GmbH GRANTS NO OTHER WARRANTIES NEITHER EXPLICIT NOR IMPLIED WITH REGARD TO THE PRODUCT AND EXPRESSLY EXCLUDES WARRANTIES ON THE PRODUCT S ECONOMIC EXPLOITABILITY AND USE FOR SPECIFIC PURPOSES 5 Compensation for Damage Should Stegmann Systems GmbH be liable for damages to you or a third party for any reason whether for claims arising from this agreement or tortious liability including ordinary negligence the amount of the damages to be paid is limited to the sum invoiced for the Product that caused the damage or for the Product on which a claim for compensation from Stegmann Systems GmbH is based However this limitation shall not apply if Stegmann Systems GmbH is responsible for the damage due to malice aforethought or gross negligence Stegmann Syste
138. paration eG a 2 Corticotrophin Assay Standard 5 Preparation T Preparation U JOA 3 Antibiotic Agar Diffusion Assay 4 Antibiotic Turbidimetic Assay 5 in vitro Hepatitis B Yaccine Assay Standard 5 Preparation T Preparation U Preparation W 6 Insulin Assay y Z Factor Vill Clotting Assay 1 Sample Parallel Line Assays us Parallel Logistics Assays Measurement 1 Measurement 2 Online Example WHO Standard Sample Preparation include hidden items refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator 4 5 3 Inheritance of Object Properties The understanding of object inheritance is necessary to make efficient use of PLA The concept of object inheritance is derived from the fact that during normal course of laboratory life you will be analyzing many assay of the same type To reduce input effort and errors PLA has many useful options to initialize new elements of your assay with correct properties 16 May 2013 Page 26 of 193 nal PLA 2 1 Assays with identical properties can be kept together in a single project You can define the initial values of new assays in the projects properties If you now create a new assay within this project all properties of the new assay are inherited from the project You do not have to input any properties if these properties match your needs Now you can create the third level objects of your assay Everything you need to enter are the object names and the
139. parent project has a template connection page GxP of the editor 16 May 2013 Page 50 of 193 PLA 2 1 RAD Schone ee gt PLA 2 1 Software for Biological Assays Eo File Actions aa Validation Window Help t A a X see Data Objects ka ea Examples from Literature cle anes pees qo Sample Parallel Line Assays Configuration Audit Trail Eh Assay 1 Default Template for Child Objects P Standard New Preperation none Sample 1 Sample 2 GLP SOP Protection Level Settings Sample 3 R Sampled Enable GxP SOP protection Mandatory Sample 5 Enable GxP SOP protection User Level 4 Assay 2 Assay 3 Protection Level Please choose the protected elements 4 Assay 4 substance information protected 4 Assay 5 documentation protected 4 Assay 6 dose definitions protected 4 Assay r analysis settings protected 4 Assay 6 test settings protected 4 Assay 9 configuration settings protected Sample Parallel Logistics Assays dose values protected response values protected keys and combination groups protected le ti a Outlier testing is activated You need at least 3 replicates for outlier testing l include hidden items refresh automatically Ready Database PLA 2 1 Default Database PL4 Administrator e the user choose a template in section 3 of the Create dialog 16 May 2013 Page 51 of 193 i PLA 2 1 jik Hew Assay as Member of Project Sample Parallel Line 4esays ance l New Preparation
140. ptotes HEH Equivalence test Difference of upper asymptotes rae Equivalence test Difference of asymmetry parameters The Tests have different properties that can be edited in the lower section of the test properites dialog The following settings are always available e Test Level Define wether the level of the test is Assay Suitability Test or Sample Suitability Test While a Sample Suitability Test can fail a single Preparation an Assay Suitability Test fails all defined preparations in the assay e Test Scope Define the scope of the test The scope tells for which object type the test is available Default is for all objects e Test Severity Define wether a failed test is a Rejection Warning or Information e Test Passed Message Define a customized Passed Message e Test Failed Message Define a customized Failed Message Depending on the test you have choosen additional properties for the tests are available e Significance Level Define the significance level of F Tests or confidence interval estimation e Margin Some tests require a margin to be set e g number of outliers e Lower Equivalence Margin Upper Equivalence Margin The Equivalence tests require to margins to be set e Reference Mean For a Scaled Equivalence Margin test a reference mean is required as the scaling factor You can find more details on the test system in the Advanced Topics section of this handbook 16 May 2013 Page 86 of 193 PLA 2 1 5
141. r id list If for any reason PLA could not open the database contact your IT administrator Manage Opens the Database Manager which allows you to manager your database connection profiles User ID A list of users of the currently selected database Select your user account by clicking on your user name Password Enter your password here Login Executes the login Exit Quit PLA Status Shows status information about your PLA installation E g The remaining time of your PLA Trial Register Click here to register your copy of PLA Info Your registration information is shown here 16 May 2013 Page 171 of 193 oo oe a o News Shows latest news about PLA if you are connected to the internet Product Information Shows information about the program See also Product Information Dialogue License Management Opens the License Manager See also License Management Version Information Detailed information about your PLA version for support purpose Serial Number Your PLA Serial Number 9 1 14 Options This topic describes the Options dialog and all available settings 16 May 2013 PLA 2 1 Page 172 of 193 Property Value Calculation Control Center Options Always calculate combinations of assay results Falsch Application Path Settings Default Export Path C Wsers brieger Documents PLA 2 1 Default Import Path C Wsers brieger Documents PLA 2 1 Default Output Path C Wsers brieger Document
142. rameters estimates between preparation and standard is tested The tests are defined for the preparation e Slope e Lower Asymptote only for 3PF 4PF 5PF e Upper Asymptote only for 3PF 4PF 5PF e Asymmetry parameter only for 5PF Tests for the Scaled Difference of Parameter Estimates The scaled difference of parameters between preparation and standard is tested The tests are defined for the preparation e Slope e Lower Asymptote only for 3PF 4PF 5PF e Upper Asymptote only for 3PF 4PF 5PF e Asymmetry parameter only for 5PF The scale factor has to be given in the definition of the test It should be derived from historical data 16 May 2013 Page 33 of 193 nal PLA 2 1 4 7 3 Additional Tests The additional tests are added since these tests are widely used as additional acceptance tests e Relative Potency e Relative Potency Range e Maximum number of outliers e Range of the response values e Minimal R2 Absolute Sum of Squares of the Non Linearity 4 7 4 Test Scopes Levels and Severity Every test can have a scope a test level and an assigned test severity Scope Every test has a scope making it available to all objects e the standard e all preparations including assay controls e all preparations excluding assay controls e all assay controls all objects excluding assay controls By using the scope setting you can define even complex test setups on the assay or project level L
143. ransformation Linear T 0 300 750 Preliminary Preparation Results Sample Preparation 0 200 Test Results 0 150 Oo AO a Sample suitability J 0 1004 0 i o Assay suitability g 77E 04 3 12E 02 1 00E0C Overall test result PASSED Dose Estim Pot Ratio and Confid Interval Sample Preparation WHO Standard stim Potency Ratio and Confidence Intera Sample Preparation Potency A atio 0 546 Confidence Interval 0 507 0 595 LLL Saveimage Recalculate Close 16 May 2013 Page 128 of 193 4 PLA 2 1 We can see the 5 parameter fit for the full with a potency of 0 546 The confidence interval is calculated as 0 501 to 0 595 which is a little sharper than the confidence limit of the parallel line assay Last but not least we want to take a look at the equivalence test for parallelism 6 7 What About Equivalence Testing Equivalence Testing has been discussed within the last two or three years This approach allows to define an alternative parallelism test This is of interest especially for very exact assays where the parallelism based on the F Test fails very often Open the analysis page of the editor and select the Equivalence Test based on Difference of Slopes as the parallelism test method Now set the goalpost to 1 5 to 1 5 Save the assay and restart the Assay Explorer Switch to the Goalpost Graph 16 May 2013 Page 129 of 193 Data Explorer Check Online Example
144. rd level object and it is a child object of the assay Each assay needs a standard object to be calculated The potency of the preparation object is calculated with respect to this standard object Note Some analysis properties of the standard are grayed out because they are taken from the respective preparation object 16 May 2013 Page 25 of 193 4 rv PLA 2 1 Preparation Sample Unknown The second type of third level objects is the preparation object PLA calculates the potency of the preparation object with respect to the standard object Many calculation properties are taken directly from this object An assay object needs at least one preparation object to be calculated W in PLA 2 1 a preparation can be marked as an assay control This allows to define a different set of suitability tests offering the opportunity to use well known behavior as assay suitability criteria Control The third type of child objects of the assay object is the control A control object contains data for a series of positive negative and blank control lines controls are not diluted titrated The use of control objects in PLA is optional The following graph illustrates a typical navigator view with these kinds of objects lt PLA 2 1 Software for Biological Assays File Actions System Validation Window Help EE le cal aT O 8 a X ee sh Navigator j i E samples from Literature aD 1 Gandotrophin 4sssay Standard a Test Pre
145. re Template Engine for Efficient Input GxP SOP Support Secure External Data Transfer using PLA Secure Format PSF utilizing the internal PKI of PLA Export Import e attach virtually any external systems using PLA Import and PLA Export Modules Report Engine based on XML XSL technologies e Adobe Acrobat Portable Document Format PDF e Microsoft Word 2003 Documents WordML e Microsoft Excel 2003 Documents ExcelML e any customer specific output Graphical output 1 4 GxP Features Automated Installation Qualification lQ Automated Operational Qualification OQ Automated Performance Qualification PQ Template Engine SOP Support Protect groups of assay properties from manipulation Role based user administration requires a license of the PLA Validation Package 1 5 21 CFR Part 11 Electronic Signatures User Login 16 May 2013 Page 9 of 193 e Fully customizable Password Logic e Password Aging e Password Complexity Rules e Black Lists Inactivity Lock e Audit Trail e Documents signed digitally using the internal PKI for storage integrity 16 May 2013 PLA 2 1 Page 10 of 193 PLA 2 1 2 Overview of the Manuals Stegmann Systems has structured the help system according to the user role you might have in using PLA so several guides are available As a good starting point you might have a look into the section Getting Started where a few pages tell you about the basic installation and principles of PLA
146. red in the selected database There is no need to work with individual files while working with assays The advantage of this approach is the easy accessibility of the data even across networks All data properties audit trail information and security information is held at a single place The navigator allows you to navigate between the projects and assays of your database e The selected database completely defines the security environment All account definitions or other security relevant data are stored in the database By this way you are able to define high and low security projects and databases 4 5 2 Object Types and Hierarchy PLA makes use of five different object types that define your projects and assays Project Projects collect your assays They are on the first level of object hierarchy and they can be considered as folders The properties you define for your project is never used for calculation It is used as the source information for inheritance Assay Assay objects are on the second level of object hierarchy The assay is the parent object for the standards preparations and control values of your measured assay The properties you define here are not directly used for calculation they are source properties for inheritance However you may bind the properties of the child objects standard preparation control to these values to obtain a single point of change Standard Reference The standard object is a thi
147. ree areas 1 Select an object type There are several entries that allow to create different objects This list depends on the neighborhood stated above In the figure you have the option to create four different object types The selected option is a preparation that will be a child of the assay Assay 2 2 In the second section you have to input the name and a description of the new object This is mandatory 3 In the third section you may want select a template If you don t select a template the standard inheritance is used Once you press Create the new object is created You will receive the following message which indicates which object served as a template 16 May 2013 Page 43 of 193 PLA 2 1 d The initial settings are based on object 4 Antibiotic Turbidimetric In our case standard inheritance has been used and the object settings are initialized with the values of Assay 2 Copying and Moving of Objects Objects can be copied and moved between different parents If you copy an object the new object is completely new initialized with the values of its source The audit trail starts with a create object entry If you move an object only the parent link is refreshed If you use electronic signatures there are some restrictions e tis not allowed to copy or move objects into signed assays e t is not allowed to move child objects of signed assays To use the copy move functionality first select the object of i
148. rence of 5 parameter fit Asymptotes Upper Lower Equivalence Test Similarity 4 parameter fit Ratio of 5 parameter fit Asymptotes Upper Lower Equivalence Test Similarity 4 parameter fit Scaled Asymptote Range Upper Lower 16 May 2013 5 parameter fit Test Type all objects all objects all objects all objects standard preparation all objects all objects all objects Remarks Note this is a test bested on the unconstrained regression Note this is a test bested on the unconstrained regression For a test of the result relative potency take the Additional test for relative potency below Page 108 of 193 oe gt gt gt TO Difference of Regression Parameter Estimates Test Equivalence Test Difference of Slopes Equivalence Test Difference of Upper Asymptotes Equivalence Test Difference of Lower Asymptotes Equivalence Test Difference of Asymmetry Parameters Purpose Similarity Similarity Similarity Similarity Ratio of Regression Parameter Estimates Test Equivalence Test Ratio of Slopes Equivalence Test Ratio of Upper Asymptotes Equivalence Test Ratio of Lower Asymptotes Equivalence Test Ratio of Asymmetry Parameters Purpose Similarity Similarity a Regression Models all non linear methods not available with fixed upper asymptote non linear methods not available with fixed lower asymptote 5 parameter f
149. rs no certificate but an error report is printed The Installation Qualification certificate contains detailed information on e the date the IQ was performed e the user who performed the test e the workstation id e the detailed build number and serial number of PLA With this information a qualified machine can easily be identified The certificate should be printed out an signed by the operator Optional Components of PLA Report Templates and Import Export Modules come with their own IQ file which is secured like the base system IQ file The IQ files are located in the component directories If PLA finds such IQ files they are checked during the IQ too So you should re evaluate the Installation Qualification after you installed or un installed any optional component The IQ certificate clearly tells which packages have been included in the process 7 3 2 Performing the Installation Qualification The processing of the installation qualification could not be easier than in PLA Simply select the Installation Qualification IQ from the Validation menu of PLA Then click Start to start the process After a few seconds a report containing the certificate is created in the PDF format The report is secured from manipulation using a one time password that cannot be recovered by PLA 16 May 2013 Page 134 of 193 PLA 2 1 The Installation Qualification checks the existence and the authenticity of all files of the PLA system
150. rt Modules protect user defined variables Page 91 of 193 i PLA 2 1 Configuration Audit Trail Default Template for Child Objects none GLP SOP Protection Level Settings Enable GxP SOP protection Mandatory Enable GxP SOP protection User Level Protection Level Please choose the protected elementa sUibstance information protected documentation protected dose definitions protected analysis settings protected test settings protected configuration settings protected dose values protected response values protected keys and combination groups protected d Automatic range detection is not available with the 4 parameter logistic function Instead oo Note Vou have only one replicate per treatment The results of the statistical tests will be Figure Screen Layout of the GxP Settings 16 May 2013 Page 92 of 193 PLA 2 1 5 4 Analyze Assays Assay analysis with PLA is easy Once you have defined your assay and entered the appropriate response values PLA is full suited with every tool you need for fast and efficient analysis One has to distinguish between the tools and the analytical options of PLA The Assay Explorer of PLA is suited with all options for a deeper graphical analysis and gives you the option to check your assay With a full range of graphical options you are able to detect problems with your assay The A
151. rver Daten zu verbinden 1 Geben Sie einen Servemamen ein oder wahlen Sie einen aus Aktualisieren Geben Sie Informationen zur Anmeldu Integrerte Sicherheit von Windows NT verwenden Spezitischen Benutzemamen und Kennwort verwenden Benutzemame Kennwort 7 Kein Kennwort C Speichem des Kennworts zulassen 3 Wahlen Sie die Datenbank auf dem Server aus O Datenbankdatei als Datenbanknamen anf gen 16 May 2013 Page 164 of 193 nal PLA 2 1 Server Name Enter the name of your database server here e g MyServer If you have multiple instances of an Microsoft SQL Server you need to enter the name of the server and the named instance separated by a backslash e g MyServer MylInstance You can also select one of the SQL Servers in the server list Contact your database administrator if you are not sure about the SQL Server to be used Refresh Click here to refresh the list of SQL Servers User Authentication Mode Select between Windows authentication and SQL Server Authentication If you choose SQL Server Authentication be sure to have a user name and a password on hand It is recommended to use SQL Server Authentication and to create a PLA user just for connections of the PLA system to the PLA database The password of the PLA user is kept in confidence and only encrypted connection profiles are distributed Contact your database administrator if you are not sure about the authentication mo
152. s PLA 2 1 Location of Import Export Modules C Program Files x86 Stegmann Syste Converter Location of Report Templates C Program Files 86 Stegman Report Templates Graphics Options Height pixel 600 Width pixel 800 Search for Updates Search for News and Updates 1 Automatically check for news and updates at st Default template for the creation of projects 1 none GMP GLP Master Protection Projects may be created by administrators only Users may not delete objects Security System Idle Lock Interval minutes Password minimum length Calculation Control Center Options These options define default settings of the calculation control center Save Cancel Calculation Control Center Options Always calculate combinations of assay results If set to Yes the defined groups of combination of assay results are calculated by default Possible Values No Yes Default value No Application Path Settings Default Export Path Defines the default path to where the export wizard shall export the data to Default Import Path Defines the default path to where the import wizard shall import the data from 16 May 2013 Page 173 of 193 oe gt gt gt TO PLA 2 1 Default Output Path Defines the default path to where the created reports or certificates shall be stored Location of Import Export Modules Defines the path where PLA Import and Export modules are stored Location of Report Templates
153. s option to 0 you disable it Possible Values O n Default value 0 Password age expiry blocks If this option is set to true a user account is blocked if its password is expired Otherwise the user will be asked to change an expired password upon next login Possible Values false true Default value false Password maximum failures This option defines the number of failed login attempts until the corresponding account is blocked Setting this value to O disables this feature Possible Values O n Default value 0 16 May 2013 Page 176 of 193 PLA 2 1 Password failure grace interval This option defines how long in minutes an account will be blocked if the number of login attempts exceed the maximum number of password failures Setting this value to 0 means forever Possible Values O n Default value 0 Password history length This options specifies the password history length PLA stores a list of the specified length of old passwords for each account A new password will be rejected if it matches an entry of the list Specifying 0 will set the password history length to unlimited meaning that a new password must not match any password which has been used earlier by this account Possible Values O n Default value 0 Password list of invalid passwords A list of passwords which must not be used as password separated by semicolon This list applies to all accounts and prevents the usage of simple passwords li
154. ssay Explorer fulfills another important function for assay analysis a responsible analysis requires the graphical inspection of your assay Thoroughly check the response data of your assay for plausibility No statistical test is able to detect plausibility problems Further reading e Explore your Assay e Combination of Assay Results e Calculate your Assay e Report Analysis Results 5 4 1 Explore your Assay The Assay Explorer has a wide range of options for graphical analysis 16 May 2013 Page 93 of 193 PLA 2 1 Pabe Graph Type 800 00 Dose Response Graph Equivalence Margins 700 00 Display Options Show Legend Show Grid Regression Lines Restricted Model Mean Line Data Values Include Statistical Outliers Include Technical Outliers Error Bars 1 0 Box amp Whisker Plot Invert 4 Axis Showy Axis Origin YY Asis Transformations Linear 600 00 KOR Sis 200 00 400 00 Response 300 00 200 00 Preliminary Preparation Results Sample 1 100 00 Test Results 0 004 created by PLA 2 1 trial www bioassay de Sample suitability 5 ar 3 13E 02 1 77E 01 1 00E0C Assay suitability ate Overall test result aaa Sample 1 E Standard Sample 2 Sample 3 Sample 4 Estim Potency Ratio and Confidence Interval Potency A
155. sult relative potency range range constrained regression Min R2 Model all preparation Test System Logic Introduction The test system of PLA 2 1 offers a huge list of features to set up testing for parallel line and parallel logistic assay according to the European Pharmacopoeia and the US Pharmacopoeia as well as according to sound scientific standards 33 different test classes are available Every test can be added to the test configuration multiple times to establish sophisticated test configurations This section of the handbook focusses the different options of the test system Every test has a list of properties that defines its scope severity and level Every test can be setup on any object in PLA Due to the inheritence behavior of PLA you have to thorougly check that a test is in scope at the time you expect the test to be performed e Introduction e Best Practice use inheritance e Test Level e Example e Test Scope Test Severity e Overall Result e Custom Messages Best Practice use inheritance The easiest way to deal with the complex functionality is to make use of the Inherit Properties feature of the test properties page If you activate this feature at each object you can define all required tests on the assay level For a new assay Activate the Inherit Properties on the assay level before you create the child objects standard preparations 16 May 2013 Page 110 of 193 or DeO a o PLA 2
156. t of raw material is solved to give the stock solution Type in the volume and the volume units The assumed potency of the preparation raw material is identical with the assigned potency of the standard A stock solution potency is given The calculation results will contain a potency estimation for this stock solution The potency of the stock solution given as a number and a unit string The assumed potency of the preparation raw material is identical with the assigned potency of the standard Pre Dilution factors are given The pre dilution factors define factors between the stock solution concentration and the concentration of the dilution series The Pre Dilution factor given as a fraction A second pre dilution factor given as a fraction If c7hecked the pre dilutions are included in the calculations Check carefully Page 79 of 193 iad PLA 2 1 eg Assay 4 Antibiotic Turbidimetric Assay l a ES Configuration Audit Trail Date ays Tents Inherit Properties use definitions properties of the assay object Open Assay Definitions Raw Material units Assigned Assumed Potency farmount units Armourit Solvent Wolume assume identical potency of standard and sample Stock Solution Assigned Assumed Potency 1 assume identical potency of standard and sample PLA 1 2 default Pre Dilution Predilution factor Additional predilution factor for the first step ea include pre dilution Factor
157. t to this standard object Note Some analysis properties of the standard are grayed out because they are taken from the respective preparation object Preparation Sample Unknown The second type of third level objects is the preparation object PLA calculates the potency of the preparation object with respect to the standard object Many calculation properties are taken directly from this object An assay object needs at least one preparation object to be calculated Assay Controls are well known preparations that can be set up with the test system of PLA to serve as assay Suitability criteria Control The third type of child objects of the assay object is the control A control contains data for a 16 May 2013 Page 41 of 193 h t q PLA 2 1 series of positive negative and blank controls The use of control objects in PLA is optional Control lines are not diluted The following graph illustrates a typical navigator view with these kinds of objects PLA 2 1 Software for Biological Assays File Actions System Validation Window Help CA CEA a xX eas Data Data Objects sti g a a Examples from Literature JA 1 Gandotrophin Asssay 2 Corticotrophin 4ssay Standard 5 Preparation T Preparation U 3 Antibiotic Agar Diffusion Assay 4 Antibiotic Turbidimetnic Assay Standard 5 Preparation T JO 5 in vitro Hepatitis B Vaccine Assay Po 6 Insulin Assay JO T Factor Vill Clotting 4ssay I Sample Par
158. t use of PLA The concept of object inheritance is derived from the fact that in normal course of laboratory life you will be analyzing many assay of the same type To reduce input effort and errors PLA has many useful options to initialize new elements of your assay with correct properties Assays with identical properties can be kept together in a single project You can define the initial values of new assays in the projects properties If you now create a new assay within this project All properties of the new assay are inherited from the project You do not have to input any properties if these properties match your needs Now you can create the third level objects of your assay Anything you need to enter are object names and the response values of your measurement IMPORTANT If you change properties of parent objects these changes do not influence the child objects if you did not bind the child objects to the parent explicitly available on the third level only If you want to deploy new settings to child objects you can make use of the Apply functionality of PLA Beside this approach of inheritance there are more advanced concepts of templates GxP and SOP support These approaches are described below How Are the Initial Properties of an Object Set There are three variants how initial properties can be set 1 Use of a Template A template is used when e the administrator set a mandatory default template in the Global Options e the
159. ta Objects a p Examples frog liber sh af Apply Lock Tree Unlock Tree Import Export Calculate amp Report Data Explorer Check include hidden items refresh automatically the object 7 Database PLA 2 1 Default Database PLA Administrator Create Object Create a new object See also Create Object Dialog Edit Object Edit the selected object s properties and definitions See also The Editor Copy Copy the selected object See also Copying and Moving of Objects Move Move the selected object See also Copying and Moving of Objects Delete Delete the selected objects and all of it s child objects Apply Apply a template or project definitions to the selected object See also Apply Dialog 16 May 2013 Page 160 of 193 oe gt gt gt TO PLA 2 1 Lock Tree Lock the selected object and all of it s descendants See also Locking Objects Unlock Tree Unlock the selected object and all of it s descendants See also Locking Objects Import Open the import wizard to import data into PLA See also Import Export Open the export wizard to export data from PLA into a file See also Export Calculate amp Report Opens the Calculate amp Report Dialog which allows you to start the calculation process and create reports See also Calculate amp Report Data Explorer Opens the Data Explorer Check Dialog which shows you a graphical overview of your assay and preliminary cal
160. tamp 29 04 2013 12 29 15 29 04 2013 12 29 15 29 04 2013 12 26 41 29 04 2013 12 26 30 29 04 2013 12 26 30 29 04 2013 12 16 09 29 04 2013 12 11 29 29 04 2013 12 11 09 29 04 2013 12 10 59 29 04 2013 14 10 53 29 04 2013 12 10 53 29 04 2013 12 10 41 29 04 2013 12 10 29 29 04 2013 12 10 29 29 04 2013 12 10 29 29 04 2013 12 10 29 29 04 2013 12 10 29 29 04 2013 12 10 29 Action USER_LOGIN DB_ADD_SESSION USER_LOGOUT USER_LOGIN DB_ADD_SESSION USER_LOGOUT IQ_FINISHED IQ_FRESULT IQ_START USER_LOGIN DB_ADD_SESSION USER_LOGOUT OBJECT DELETE OBJECT DELETE OBJECT DELETE OBJECT DELETE OBJECT DELETE OBJECT DELETE Object PLA Administrator 2 FLA Administrator FLA Administrator PL4 Administrator PASSED PLA Administrator z PL4 Administrator Examples from Literature 2 gt 7 Factor V lll Clotting Assay gt Control Examples from Literature 2 Factor Vill Clotting Assay gt Preparation T Examples from Literature 2 Factor Vill Clotting Assay gt Standard 5 Examples from Literature 2 7 Factor Vill Clotting Assay Examples from Literature 2 gt 6 Insulin Assay gt Preparation T Examples from Literature 2 gt 6 Insulin Assay gt Old Yalue Operator fork PLA Administrator 1 PLA Administrator 1 PLA Administrator PLA Administrator 7 PLA Administrator 1 PLA Administrator 1 PL Administrator 1 PLA Administrator 1 PLA Administrator 1 P
161. testing purposes or when you did not enter the license information or when no software license module is detected PLA 2 1 enters the trial mode The trial mode allows to run the software for 14 days after the first activation When the trial period has been expired and you need a longer evaluation period you can inquire for an trial extension Please send us the Inquiry key shown in the red field of the PLA License Management dialogue Seat License Mode PLA 2 1 was delivered with a software license module hardlock dognle and two or three license keys Please attach the software license module to your system and enter or download the required license keys PLA 2 1 is now activated Q Note The software license module dongle must be attached when running PLA 2 1 Network Concurrent Use License Mode When your company purchased a concurrent license of PLA the software license module will be usually installed by your IT department and the license keys are then distributed over the network If they are not download the license keys or ask your IT department for the keys They have received them with the software license module 16 May 2013 Page 21 of 193 oe gt gt gt TO PLA 2 1 4 3 2 Attachment of the Software License Module Hardlock If you need to attach a Software Licensing Module Hardlock to your system you should install the PLA 2 1 software first to have the necessary device drivers available The So
162. tion profile for a Microsoft JET database file MDB To use an existing PLA database select the appropriate file in the appearing Select File dialog You can create a new database file if you enter a new file name in the Filename text edit field of the Select File Dialog Connect a Database Server This option allows you to create a new connection profile using a database server See also Database Manager Connect 16 May 2013 Page 163 of 193 gt d soo a Ep PLA 2 1 Delete Connection Profile Click this button to delete the currently selected connection profile Compact Database This options allows you to compact the JET database described by the currently selected connection profile Note that using this function for non JET databases fails since database compaction is only supported for Microsoft JET databases Open Database Opens the database described by the currently selected connection profile Close Closes the Database Manager without switching the database connection profile 9 1 9 Database Manager Connect This dialog allows you to set up a connection to a database server Currently only Microsoft SQL Server 2000 or higher is supported The corresponding OLE DB Provider for Microsoft SQL Server is selected automatically For detailed information how to set up a PLA database on a Microsoft SQL Server please refer to PLA Databases Datenverkniptungseigenschatten Geben Sie folgende Angaben an um zu SQL Se
163. tion with caution Invalid session entries are removed automatically after two hours 16 May 2013 Page 182 of 193 ses TO PLA 2 1 Unlock Remove the selected lock Close Close this dialog 9 1 18 System Menu This topic describes the System Menu of the PLA menu bar Navigator Change your Password Administrative Database Access Check Database Consistency Session amp Lock Management Audit Trail Lock PLA F include hidden items refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator Options Open the Options Dialog to modify the configuration of PLA See also Options Dialog Account Management This options allows you to manage the PLA user Accounts See also Account Management Change your Password This option allows you to change your password See also Change your password Administrative Database Access This option allows you to en or disable the administrative database access for database maintenance See also Database Maintenance 16 May 2013 Page 183 of 193 o gt soo a o PLA 2 1 Check Database Consistency Perform a database consistency check Session amp Lock Manager Open the Session amp Lock Manager See also Session amp Lock Management Audit Trail Open the Audit Trail Dialogue for the selected object See also Audit Trail Dialogue Lock PLA Lock your PLA Session You will need to enter your password to unlock t
164. trator at 08 05 2006 15 52 47 Parent Object Examples from Literature 21 CFR part 11 Electronic Signatures Doubleclick for details Mo signatures have been applied yet Sign Remove F include hidden items E refresh automatically Ready Database PLA 2 1 Default Database PLA Administrator 16 May 2013 Page 46 of 193 PLA 2 1 The object editor consists of two areas e The Tab Page Area where tab pages control the display of groups of properties In the figure above the General tag page is selected There are seven other pages available e The Information Area is at the bottom In this area some notifications warnings or errors may be displayed In the figure there is note on outlier testing visible You may close the window by selecting Close Window function from the file menu or by clicking on the upper right cross of the object editor If some properties are changed you will be asked whether you want to save the object If nothing changed the editor is simply closed You may also select the Save Object function of the file menu or the toolbar to save an object Property Pages Any object of PLA is described by a set of properties These properties can be separated into the following groups which are displayed as tab pages in the editor General Properties describe general aspects of the edited object The name of the object the create and modification timestamps and the substance details are part of
165. ty Test 1 all objects Test Severity Test Failed Message Test Scope 1 all objects Test Passed Message 2 standard only 3 preparations 4 preparations assay control only 5 preparations no assay control Tests can have different 46 all objects no assay control tests for the standard for preparations and for assay contro The different scope levels are described in the following table Scope All Objects Standards Only Preparations Preparations assay control only Preparations no assay control All Objects no assay control Test Severity Standard Preparation Preparation PLA 2 1 not marked as an assay control marked as assay control Every test has a severity The severity defines wether a failed test leads to the rejection of the assay a warning with a failed message or just to an information message leaving the assay passing 16 May 2013 Page 112 of 193 PLA 2 1 Additional test Max number of outliers Margin 0 Test Level 2 Sample Suitability Test Test Scope 1 all objects 2 Warning potency calcul l Test Passed Message 1 Reject no potency calculation Test Failed Message 2 Warning potency calculation w we 3 Information potency calculation The follwing table contains the overall results for a failed test with different severity settings the asumption is that the test is the only failing test in the assay Test Sever
166. u execute apply you cannot undo the changes check the selected property groups carefully 16 May 2013 Page 55 of 193 4 i i q PLA 2 1 3 Target Filter Select the objects types that are targets of the apply method After you have carefully checked the settings you may execute the apply The Inherit Properties Property To reduce the complexity of assay definitions the Inherit Properties option is available For the following three groups of properties the Inherit Properties property binds the properties of an standard preparation or control to the corresponding properties of the assay object These properties are kept in sync with the assay properties automatically If you select the option all other values of the property page are grayed out The Inherit Properties checkbox is available for these groups of properties e Analysis settings e Tests settings e Configuration optimization settings e Dose settings lt PLA 2 1 Software for Biological Assays File Actions System Validation Window Help Ob8 a X amp e Me ara Preparation Sarnple 1 Data Objects x J Examples from Literature E onn General Doses Data Analysis Tests Configuration Documentation BsF Audit Trail p Assay Inherit Properties al Muse analysis properties of the assay object Open Assay Definitions y Standard Response Adjustment Sample 1 Sample 2 Assay 4
167. uct as well as all future orders shall be subject to the following provisions If you do not accept these provisions please return the product to us within seven 7 days of having purchased or received the Product We will refund the purchase price minus fees for shipping and processing 1 License Stegmann Systems GmbH holds all rights to the Product and herewith assigns to you a nontransferable nonexclusive right of use to exploit utilize the Product according to the following You are not authorized to transfer the Product or parts thereof to third parties or to make them accessible in any way or to modify disassemble decompile reverse engineer process or improve the software or other parts of the Product or to attempt to discover the source code of the software with the exception of the conditions as stated in Section 69e of the German copyright law You have the right to install and use the Product on one 1 computer If you want to install and use the Product on other computers you must acquire and dedicate a license for each separate computer You have the right to make one 1 copy of the software in order to archive it 2 Other Rights and Limitations If the Product is labeled as an upgrade you must be properly licensed to use a product identified by Stegmann Systems GmbH as being eligible for the upgrade in order to use the Product A Product labeled as an upgrade replaces and or supplements the product that formed the basis
168. ue Database Connections are a set of properties that enable PLA to connect an existing database Creating a Database PLA supports both Microsoft JET and Microsoft SQL Server databases JET database are created with this wizard SOL Server database are created as empty database by your administrator PLA creates the required tables when it connects by itself Connecting an Existing Database To connect a JET database select Create or Connec a Database File To connect to a SOL Server select Connect a Database Sever Delete Connection Profile A defined connection i deleted The database itself remains intact You may reconnect to it Compact Database JET databases tend to grow From time to time you should compact it You need exclusive access to the file to perform compaction Click on the Create or Connect a Database File button A standard file open dialog appears Select the directory and type in the name of a new database file Note If you select an existing database nothing is created but you will be connected to this database After you created a new database the new database appears in the list of defined connection profiles Select it and click open database to connect to it You are immediately asked for an administrator password for the first administrator of this database 16 May 2013 Page 148 of 193 i PLA 2 1 Due to legal restrictions e g 21 CFA part 11 PLA has t s own user account management For thit data
169. ues PLA calculates the potencies for each preparation of an assay separately Transformations PLA allows four different transformations available for all models They can be used to reduce an inhomogeneous variance distribution heterogeneity of variance The following transformation models are supported e linear transformation logarithmic transformation square root transformation e square transformation Outlier Detection PLA has four optional outlier tests available An outlier test removes extreme response values from analysis that match a specified statistical criterion Three treatment based outlier tests are available when you have three or more replicates e Dixon Test W J Dixon 1953 Processing Data for Outliers Biometrics Vol 9 S 74 89 and David B Rorabacher 1991 Statistical Treatment for Rejection of Deviant Values Critical Values of Dixon s Q Parameter and Related Subrange Ratios at the 95 Confidence Level Analytical Chemistry Vol 63 S 139 146 e Grubb s Test Frank E Grubbs 1969 Procedures for Detecting Outlying Observations in Samples Technometrics Vol 11 No 1 S 1 27 e Test based on standard deviation These tests analyze each treatment group separately They check the extreme value for statistical significance and remove it Optionally these tests can be executed iteratively 16 May 2013 Page 29 of 193 oo o lt a ae o PLA 2 1 An alternative approach is re
170. uirements in order to run PLA For the installation of PLA 2 1 administrative priviledges are required System Requirements 512 MB free RAM 250 MB of free hard disk space Screen resolution 1280 x 1024 or higher Microsoft Windows XP Microsoft Windows Vista Microsoft Windows 7 Microsoft Windows 8 Microsoft Windows Server 2003 Microsoft Windows Server 2008 Microsoft Windows Server 2012 For terminal server support a concurrent use license is required PLA 2 1 is a 32 bit solution 16 May 2013 Page 189 of 193 PLA 2 1 13 Copyright PLA 2 1 2006 2013 Stegmann Systems GmbH Rodgau Germany All rights reserved The Stegmann Systems products referred to in this document are also copyrighted and all rights are reserved by Stegmann Systems and or its licensors if any This manual may not in whole or in part be copied translated or reduced to any electronic medium or machine readable form without prior consent in writing from Stegmann Systems The information in this manual is subject to change without notice and Stegmann Systems assumes no responsibility for any errors that may appear in this document The references in this manual to specific platforms supported are subject to change Java and all Java based marks are trademarks or registered trademarks of Sun Microsystems Inc in the U S and other countries Any other trademarks or service marks contained herein are the property of their respective
171. ups and delete groups using the appropriate command buttons Preparations can be removed If you want to add a preparation select the group which should get the preparation than switch to the right tree view and use the Add to Group button Below the trees you can see a few details on the preparations If the preparations have been calculated earlier cached calculation results are shown below the tree views When finished press Save to save the groups and close the dialog 16 May 2013 Page 98 of 193 Sa soos TO PLA 2 1 5 4 3 Calculate amp Report To obtain final calculation results select the assay or project in question and then select the Calculate method from the file menu the navigator context menu or from the toolbar The Calculate Assays and Create Reports Calculation Options perom combination of assay results calculations if defined Select the required reports E p REF 10 Complete Statistics Report O REF 11 Short Report REP 12 Excel Report Tr REP 20 Combination of Assay Results O REP 21 Complete Statistics Report with Range Configuration Details REP 30 Equivalence Margins Development Info Select a report By double clicking a report template or by selecting one of the following functions the requested calculation is taken out and the report is created Preview opens the report by starting the appropriate application Print prints to the standard printer of the s
172. vel too These dose values are used as default values if you create new objects within these ones The following figure shows the data editor of an object PLA 2 1 Software for Biological Assays File Actions System Validation Window Help O a X see 7 Data Objects a Conf D Examples from Literature ef Sample Paral ine Assays Tests a Assay 1 Standard Dimension and Dilution Scale Sample 1 Number of treatments dilution steps fallowed 2 25 Sample 2 Sample 3 Sample 4 Dilution scale Sample 5 Assay 2 Assay g Preview absolute doses Assay 4 Standard Standard Assay D Assay E relative Dose Replicate 1 Replicate 2 Number of replicates J allowwed 1 25 Assay Assay 6 Assay 9 Sample Parallel Logistics Assays Fi H Toggle outlier status by pressing F3 Technical Outliers are displayed using a light red color Input a value press F2 or click to edit Press ESC to leave edit mode Bine eni E any GD Cutler testing i activated ou need at least 3 replicates for outlier testing include hidden items refresh automatically 7 a alan cd ree Seen i Ready Database PLA 2 1 Default Database FLA Administrator There are three properties defining the dimension of the editor e The number of treatments dilution steps defines how many lines are available The number of replicates defines how many response columns are available e The dose scale setting switches
173. wing you to use inheritance Documentation and Yarables Operators liii Reagents an E quiprnient Lookup l Ei Annotations User Variables aera oe lel PNFCreator 5 H Combination Groups My Combination Group 1 Another Combination Group Combination Group My Combination Group 1 Combination Group Preparations with this grouprane will be combined 16 May 2013 Page 97 of 193 PLA 2 1 Defining Combination Groups with the Combination Group Editor The Combination Group Editor supports the efficient definition of the combination groups of a project Define Groups for Combination of Assay Result Calculations Sample Parallel Line Assays Defined combination groups in this project a My special Group Sample Parallel Line Assays l A Sample 2 Assay 1 Sgi Assay EH New Group 1 a Sample 1 Po Sample 2 Assay 1 Sample 2 Sample 3 Assay 1 jy Sample 3 Sample 1 Assay 3 Sample 4 peas New Group 2 TE fy Sample 5 Sample 1 Assay 3 Ji Assay 2 Ji Assay g G Assay 4 TA Assay p Assay 6 Assay 7 Assay A Assay g E Sample 2 Assay 3 E E E E E E E Combination Group My special Group Assay Assay Preparation Sample 2 Hote Cached results are not available Selected Project Sample Parallel Line Assays The editor has two tree views The left tree shows the defined combination groups within the selected project You can create additional groups rename gro
174. xt menu Notes e Lock Tree will fail if any of the descendant objects is already locked by another user e The user should not forget to unlock the objects using Unlock Tree if the work is finished e Locking an object tree will prevent any other user to work with any object within that tree This might bar your coworkers to work at all 5 2 2 Editing Objects The Editor Once you select the Edit Object function in the file menu the toolbar or in the context menu of the navigator the Object Editor opens in the sheet area of PLA The figure below shows an opened Object Editor for the Assay with the name Assay 1 lt PLA 2 1 Software for Biological Assays File Actions System Validation Window Help ae B B a X GAl SHB mr da Assay 4 Antibiotic Turbidimetric Assay Data Objects 0 a g Examples from Literature Documentation oo Audit Trail 1 Gandotrophin Asssay General Doses Tests 2 Corticotrophin Assay 3 Antibiotic Agar Diffusion Assay 5 4 Antibiotic Turbidimetric Assay 4 Antibiotic Turbidinetnic Assay standard 5 Europ Pharm 5th Ed 2005 Ch 5 3 5 1 3 Four Dose Randomised Block Design lo Hame and Description Standard Freparation Unknown assay contral E hide Measurement Details Substance Lookup Batch ID Timestamp 13 09 2005 11 06 19 History and Information Created ms_ admin at 13 09 2005 11 06 19 Last modified PLA Adminis
175. y change of an object property or every other security relevant modification of the system is logged in the audit trail The audit trail information is split up into the main entry and details for the main entry Each main entry contains e an unique entry number atime stamp an operator identification e the type of the entry as listed below an object for the entry type The following entry types are logged USER_LOGIN USER_LOGOUT USER_LOGINREJECTED USER_PWCHANGE USRMGMT_ADDUSER USRMGMT_DELETEUSER USRMGMT_MODIFYUSER OBJECT_SAVED OBJECT_SIGN OBJECT_REMOVESIGNATURE OBJECT_INITIAL OBJECT_COPY OBJECT_MOVE OBJECT_DELETE DB_ADMINACCESS_ON DB_ADMINACCESS_OFF DB_COMPACT DB_CHECK_START DB_CHECK_STOP 16 May 2013 An user logs into the system An user logs out An user has not been allowed to log into the system An user changes his password An Administrator adds a user to the system An administrator removes an user from the system An administrator modifies user details An object has been saved An object has been signed electronically An object signature has been removed A new object is created An object is copied An object is moved An object is deleted Database administrative access is requested Database administrative access is revoked Database has been compacted A database check has been started A database check stopped Page 103 of 193 oe gt gt gt TO DB_CHECK_CORRECTION DB_ADD_SE
176. ystem If you want to print to alternative printers use Preview and the print function of the application Save opens a save dialog of the operating system and save the report to the selected file Calculation Options If you want to calculate the defined combination of assay results the option has to be activated Calculation Options perom combination of assay results calculations if defined 16 May 2013 Page 99 of 193 h PLA 2 1 PLA analyzes the defined combination of assay result groups and adds the required assays to the calculation routine This will need additional computation time Default Reports By default PLA is delivered with six different report templates Further report templates or individual report templates including company information etc can be ordered from Stegmann Systems The following reports are available Report ID REP 10 REP 11 REP 12 REP 20 REP 21 REP 30 Name Complete Statistics Report Short Report Excel Report Combination of Assay Results Complete Statistics Report with Configuration Optimization Details Equivalence Margin Development Purpose Extensive Report on all aspects of the assay and test calculations A short report without too much details on the tests The potency calculation and the test statistics is included This report generates a general purpose Excel spraedsheet This reports includes only the combination of assay resu

PLA 2.1 Manual - PLA 3.0 – Software for Biostatistical Analysis

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PLA 2.1 Manual - PLA 3.0 &ndash; Software for Biostatistical Analysis

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PLA 2.1 Manual - PLA 3.0 – Software for Biostatistical Analysis