Endosafe EndoScan-V. Version User Manual. Copyright 2017 Charles River Laboratories

Transcription

1 Endosafe EndoScan-V Version User Manual Copyright 2017 Charles River Laboratories 1

2 Table of Contents EndoScan-V Starting the Software Login Dialog Box Main Window - Microplate/Tube Reader Mode Menu Bar File Menu Edit Menu View Menu Tools Menu Cart. Reader Menu Window Menu Help Menu Toolbar New Plate Open Plate Save Plate Report Cut Copy Paste Start Reading Stop Reading

3 Secure and Sign Log out Well Area Well Area Title Bar Well Area Toolbar View List Read Number Read Time Replicate Selector Well Grid Products Area Standards Area Product Information Themes Main Window - Cartridge Reader Mode Menu Bar File Menu Edit Menu View Menu Tools Menu Cart. Reader Menu Window Menu Help Menu Toolbar Open Plate

4 Save Plate Report Cut Copy Paste Cartridge Reader Window - Primary Supported Cartridge Reader Assays Running Cartridge Reader Assays Cartridge Reader Window - Secondary Products Area File Menu New Toolbar: Open Toolbar: Close Save Save As Export Properties Report Toolbar: Exit Edit Menu Undo

5 Redo Cut Copy Paste View Menu Toolbar Standards Product Information Product Database Zoom Tools Menu Start Collection / Stop Collection MVD/MVC Calculator Edit Password Command Usage Log View Archive Print Preview Maintain Users Products Maintain Products Add Row Delete Row Edit Row Copy Row

6 Print Cancel / Close Database Utility Print Products Refresh Reader Options Tecan Sunrise Control Cart. Reader Menu Download Most Recent Assay Download All Assays Clear Cartridge Lot Number History Verify Temperature Calibration Version Information Reconnect Nexgen-PTS/MCS Cart. Reader Menu Clear Cartridge Lot Number History Version Information Reconnect Shutdown nexgen Save Test Reports Restart Update Software Save Logs Help Menu

7 Contents Help Viewer Contents Tab Help Viewer Index Tab Help Viewer Search Tab Search For Help On Print User's Manual About Options Dialog Box Options - Layout Replication Direction Number of Replicates Automatic Creation of Spikes Inline Spiking Default Spike Concentration Time Format Wells Masked Colors Options - Calculation Linear/Polynomial Regression Option Polynomial Order Option Onset OD Option Number of Points to Use for Max V Option CV Limit, Products Option CV Limit, Standards Option CV Limit, Cart. Reader Product Option

8 Average Replicates Enable Validation Spike Recovery Range Spike Recovery Calculation for Unreacted Samples Cartridge Reader Samples by Channel Validation Terminology Endotoxin Limit Validation Terminology Options - Reagents/Acc Reagent Lot Numbers LAL and Expiration Date Endotoxin/Expiration Date LAL Reagent Water/Expiration Date Other/Expiration Date Accessories Options - Other Lab Name Auto Name Option Auto Stop Auto Export Option Auto Print Change Log Reporting User Specific Application Specific Plate File Path Export File Path

9 Default Collection Type MCS Serial Number Only Security Password Timeout, Days Password History, Days Login Timeout, Minutes Log off Auto Archive Options - Database Remote Synchronization Database Remote Synchronization Reader Options Dialog Box Reader nexgen Configuring nexgen PTS devices Configuring nexgen MCS devices Configuring reader options Connect Save Logs Restart Shut Down Save Test Reports Connection Properties Dialog Box Collection Properties Reader

10 Collection Type Endpoint Kinetic Chromogenic Kinetic Turbidimetric Reader Properties Reader Properties Collection Time Read Interval Plate Temperature Plate Temperature Setting Filter Wavelength Shake Shake Intensity Shake Time Saving Information Plate Properties Lab Name Auto Stop Auto Name Property Auto Export Property Template Protected Property Endotoxin Units Reagent Lot Numbers LAL and Expiration Date Endotoxin/Expiration Date

11 LAL Reagent Water/Expiration Date Other/Expiration Date Accessories Comments Saving Information Well/Group Properties Group/Well List Mask Product Name Concentration/Dilution Dosage Units Lot Number (#) Endotoxin Limit Associated Standard Set Spike/Standard Concentration Product Code Automatic Creation of Spikes Sample Description Group Criteria Saving Information Calculation Properties Regression Polynomial Order Onset OD Number of Points to Use for Max V

12 CV Limit, Products CV Limit, Standards Enable Validation Average Replicates Spike Recovery Range Y Axis Maximum X Axis Maximum Plate Criteria Saving Information Microplate/Tube Assay Reports Title of Report Summary Report (Products) Summary Report (Template Map) Product Information Products List Box Report All Products Product Table Product Criteria Sample Per Page Associated Standard Set Standard Curve Standards/Controls % Significance General Options Plate Criteria

13 Masked Data Comments Section Well Map Reports Template Map Product Summary Table Optical Density Reaction Time MaxV Change Log Preview Button Report Navigation Report Search Report Zoom Print Button (Print Preview) Print Button Button Cartridge Assay Reports Maintain Users Add Edit Delete Close Add User Dialog Box User User Name

14 Password Confirm Password Enabled Password Expired Account Type Privileges Bulk Export Edit User Dialog Box User User Name Password Confirm Password Enabled Password Expired Account Type Privileges Options Mask Wells Protect Microplate File Templates Edit Product Database Edit Wells and Groups Edit Standards List Undo Last Command Bulk Export Tecan Sunrise Reader Control Dialog Box

15 Drawer Control Buttons Filter Carriage Control Buttons Target Temperature Validation Criteria Expressions Operators Functions Operands A formula Value Identifiers Criteria Examples Sample Concentration/Dilution Acknowledgements

16 EndoScan-V EndoScan-V is an endotoxin measuring software that is compatible with a variety of plate readers. It has been verified and validated to be consistent with FDA requirements and performs requisite calculations and batch reports for product release. For added protection, it generates secure data files and audit trails on all actions involving test data. The program was designed with flexible configuration capabilities, networking and performance options to facilitate gains in operational efficiency. The features provided in EndoScan-V allow end users to maintain data integrity and achieve compliance with 21 CFR Part 11. While software vendors seek to provide as many tools as possible to maintain compliance, ultimately compliance is achieved by the end user. Please consult your regulatory compliance group to assist in determining the status of 21 CFR Part 11 compliance at your facility. Starting the Software Upon starting the software, a logo screen is displayed for approximately 15 seconds. 16

17 Following display of the logo screen the Login Dialog Box will be presented. Login Dialog Box Enter username and password. Usernames and accounts are established by operators with administrator privileges. Permissions and access to some program functions are assigned based on the operator's user profile. If your account password has expired, you will be notified after login and the Change Password dialog box will be displayed. 17

18 Main Window - Microplate/Tube Reader Mode The Main Window consists of the Menu Bar, Toolbar, and four primary areas (or windows): the Well Area, the Standards Area, Product Information Area and the Products Database. Windows within the main window can be moved around based on 4 predefined templates. Menu Bar The Menu Bar allows access to the following general menus. Options on the menus displayed in gray text are not available to the operator at that time. Each menu available from the Menu Bar is described in detail in their own help sections. File Menu The File Menu provides the options for data filing, properties and output. Specific options include New, Open, Close, Save, Save As, Export to File, Properties, Report and Exit. Edit Menu Associated with Editing, this menu provides specific functions commonly found in Windows. These functions are Redo, Undo, Cut, Copy and Paste. View Menu The View Menu provides options for which elements are displayed on the screen. Selecting an option makes the element active on the screen. Selecting an already active element will make the element inactive. Active elements are indicated with a check mark beside the element. The View options include Toolbar, Standards, Product Information, Product Database, and Zoom. Tools Menu This menu identifies the tools available to the operator and administrative options available (based on user privileges.) The main tools available to the operator are Start Collection, MVD/MVC Calculator, Edit Password, Command Usage Log (administrator privilege), Maintain Users (administrator privilege), Maintain DSS Roles (administrator privilege), Products (privileged option), Options (privileged option), Reader Options, and Tecan Sunrise Control. Cart. Reader Menu 18

19 This menu, shown only when the PTS/MCS or nexgen-pts/mcs reader types are selected, contains commands specific to cartridge readers. For PTS/MCS, the commands available to the operator are Download Most Recent Assay, Download All Assays, Clear Cartridge Lot Number History, Version Information, Photo Verification, Verify Temperature Calibration, and Reconnect for nexgen- PTS/MCS, the available commands are Clear Cartridge Lot Number History, Version Information, Reconnect, Shutdown, and nexgen. The nexgen menu has these available commands: Save Test Reports, Restart, Update Software, and Save Logs. Window Menu The Window Menu offers standard Windows Window Menu options such as Cascade, Tile Horizontal, Tile Vertical and Arrange Icons for the Well Areas. A special command, Default Window Arrangement, returns the main window to its default position and size and returns the Standards, Product Information, Products areas to their default docked position and size. Any open plate files are listed at the bottom of this menu and can be used to switch between plate files. Help Menu The Help Menu provides access to online help and tutorials available to the operator. Toolbar The Toolbar allows quick access to common functions found within the drop down menus on the Menu Bar. New Plate Use to set up a new plate for a collection. Displays a dialog box to allow selection of a template for the new plate. A new plate can be based on a blank new plate or a saved plate file. Open Plate Save Plate Open an existing plate to review the data. Displays the Open dialog box to allow selection of the plate to be opened. 19

20 Saves the current plate file using the plate's current file name. If the plate does not have a current file name, EndoScan-V will prompt for a file name. Report Cut Displays the Report Setup dialog box to select the report options and to preview, print, . Copy Removes the information from the selected well(s). Paste Copies the information from the selected well(s). Start Reading Stop Reading Pastes the information from the cut or copy functions into the selected well(s). Start Reading begins data collection. Stop Reading stops data collection. While data collection is in process, the image on the button changes to several versions of broken squares. 20

21 Secure and Sign The secure and Sign is used to digitally sign the PLTX documents using the licensed EndoScan-V - Digital Signature System. To activate this feature, please contact your Account Manager for details. These themes will position the Standard area/product Information/Product database grid areas in different positions for better user experience. Log out This icon synchronizes the remote database (users and products information) to the local database. The EndoScan-V software log out icon allows any user to log out immediately without waiting for the timeout function. Well Area The Well Area of the Main Window represents a plate file for plate/tube readers and contains a title bar, a toolbar, and the well grid. 21

22 Well Area Title Bar The title bar for the plate indicates the name of the plate and the location in which the file is stored. Well Area Toolbar The toolbar for the plate provides a View List, Read Number indicator, Read Time indicator and a Replicate selector (Template view only). 22

23 View List The available views in EndoScan-V are Template, OD Graph, Max V, Reaction Time, EU, and Data Values. Select the desired view from the pull-down list. o Template View displays the text designators of the well contents. In the Template View, the menu bar also includes a Replicate selector. The Replicate selector multiplies the sample, standard or control times the number selected when the item is added to the well area. In the template view, the Properties dialog box can be edited through double-clicking the well to edit, or by using the right mouse button menu on a well or wells and selecting properties. In the template view, the right mouse button will allow a user to Undo/Redo a command, cut, copy, paste, mask, clear, or access the Properties Dialog Box. For information on editing wells see the Well Grid section. o OD Graph View shows a graph of optical density (OD) versus time for each well. This view is available during and after data collection for kinetic collections only. The Well Zoom feature can be used in this view to "zoom" a well, providing an expanded view of the well information. To display a Zoom window for the currently selected well, use the View menu "Zoom" command or use the right mouse button menu "Zoom" command or double-click a well. Multiple well Zoom windows may be open at one time. o Max V View shows the maximum slope (Max V) value for each well. This view is available after data collection for kinetic collections only. o Reaction Time View shows the time to the Onset OD value for each well. This view is available after data collection for kinetic collections only. o EU View shows the Endotoxin Unit (EU) value for each well. This view is available after data collection. o Data Values View shows the numeric optical density (OD) values for each well. For kinetic collections, the operator may step through the series of values by changing the read number on the menu bar. This view is available during and after data collection. 23

24 Read Number The Read Number indicates the number of data reads the program has made during a data collection. In the Data Values View on kinetic collection, the Read Number can be changed to view the optical density value for each read. Read Time The Read Time box indicates the time that a data collection has been running. In the Data Values view, the Read Time box indicates the time of the read corresponding to the Read Number. Replicate Selector The Replicate Selector is used with the Template View in setting up the plate. Automatic replication is enabled by an operator option and uses the operator options for replication direction and size. When automatic replication is enabled, as each item is brought onto the plate by dragging the item from its window, the item is entered onto the plate the number of times indicated in the Replicate Selector. Changing the number of replicates on the Well Area toolbar does not affect the operator's default options for the number of replicates. Well Grid Each rectangular area within the Well Area represents one well. The wells are named using an alphabetic character (A-H) for the row and a numeric character (1-12) for the column. The text options for each well are the product name or one of the following designators: SPL# (sample), SPK# (spike), STD# (standard) and CTRL (control). Sample, spike and standard have a number associated with the text to indicate to which group the sample, spike, or standard belongs. Based on operator preference, the text for each category can be assigned different colors by selecting the Colors option on the Options Dialog Box. Samples, spikes, standards and controls are entered onto the plate either by drag and drop from their respective area or by entering or editing the contents of a well. Using the drag and drop method, the name of the product (abbreviated as necessary) is displayed in the well area. Information from the product area for the sample is copied into the well and can be viewed using the well properties menu. If Auto Replication is enabled, the number of replicates indicated on the Replicate Selector will be entered onto 24

25 the Well Area. Replicates may be entered either from top to bottom or from left to right, based on operator preference. Spikes are entered into the wells either by automatic creation of spikes or by entering or editing the well information. If both automatic replication and automatic spike creation are selected in the operator options, spikes and spike replicates are automatically added to the plate. The first sample entered on the plate is designated as SPL1, the next is designated as SPL2, and so on. Items entered onto the edge of a plate will wrap to the next column or row (depending on automatic replication and spike options) to accommodate any replicates or spikes. If the item being entered onto the plate will overwrite an existing well, a dialog box will be presented to the operator to ensure this action is intended. Well information can be created using the keyboard or editing by selecting the text in a well and using the keyboard. Other editing options can be accessed using the right mouse button on a well. A menu is displayed providing the options of cut, copy, paste, mask, clear and properties. o Cut copies the contents of a well to the clipboard and then clears the well. o Copy copies the contents of a well to the clipboard. o Paste copies the contents of the clipboard into a well using the current replicates settings. o Mask designates that the well information is not included in any calculations for that plate file. The background of the well will be shaded to indicate the well is masked. If the well is already masked, this command will unmask the well. Mask is a privileged command and will not be available if the operator does not have the Mask Wells privilege. o Clear removes the contents of the well. o Properties displays the Well/Group Properties in the Properties dialog box, allowing the operator to edit well, group and plate properties Products Area The Products Database Area of the Main Window provides user access to the Product Database during plate configuration. The Products Database is a collection of products that are tested on a regular basis. Samples are entered onto the microplate by clicking on the row containing the product and then dragging the highlighted product 25

26 onto a well in the Well Area. The product will be replicated as many times as indicated in the Replicate selector on the Well Area Menu Bar. Note: if the plate template protection is set, or if the user does not have Edit Wells and Groups privilege, this operation will not succeed. Clicking on the top of a column in the Products Area sorts the products by ascending order of the column. The arrow keys or the scroll bar can also be used to move up and down within the Products Area. See the Tools Menu Maintain Products section for information on adding, deleting, and editing products in the Product Database. Standards Area The Standards Area of the Main Window provides user access to the Standards List during plate configuration. The Standards Area displays the general standards list and the standards on each open plate file. Standards for each plate are indicated under the plate file name. 26

27 Standard sets are entered onto the microplate by clicking on the row containing the desired standard set and dragging the highlighted standard set onto a well in the Well Area. If the standard set is not already on the plate, it will be added to the list of standard sets on the plate. Note: if the plate template protection is set, or if the user does not have Edit Wells and Groups privileges, this operation will not succeed. New standard sets may be added by entering the standard set name and concentrations in the appropriate blank row. The standard set and concentration may be edited directly on the Standards Area. To remove a standard set, Select the F2 key, backspace over both the standard set name and concentration. Note: editing the general standards list requires Edit Standards List privilege. Editing a plate standards list requires the plate not be template protected; for all but new plate files not based on a template, editing a plate standards list also requires Edit Wells and Groups privilege. Product Information The Product Information Area of the Main Window provides a list of all samples, spikes, and controls entered onto the Well Area during microplate setup. This area provides the group information, the product name and the product's lot number. Full product information is available on the Properties Dialog Box Well/Group Tab. 27

28 Items listed in this window can be dragged onto the Well Area during microplate setup. Note: if the plate template protection is set, or if the user does not have Edit Wells and Groups privilege, this operation will not succeed. New samples, spikes, and controls may be added by entering the group name in the appropriate blank row. The group name, product name, and lot number may be edited directly on the Product Information Area. To remove a sample, spike, or control, Select F2 and backspace over the name. It is not necessary to clear the group s wells before removing it from the Product Information Area. To create a new control, drag from the Drag for Control area. Controls will be added into the wells, following the automatic replication set for the microplate. Themes The standard EndoScan-V window layout is with these windows docked to the left and bottom sides of the main window. There are 4 Docking Styles. 1. Default Theme 2. Theme1 3. Theme2 4. Theme3 Default 28

29 Clicking on this returns Samples Grid, Standards List, Product Database table to their Default Arrangement. Theme1 Clicking on this will change the Layout of the Samples, Standards List and Product Database. The Product Database will be aligned to the left upper left side of the screen. The Standards List and Product Information list are arranged towards the bottom of the screen, with the product Information appearing on the left side bottom side of the screen and the Product Information appearing on the bottom right side of the screen Theme2 Clicking on this will change the Layout of the products Database. The Product Database will be aligned towards the bottom of the screen. This style does not have any other tabs. Theme3 This theme is very similar to theme 1. The only difference being that in this theme the product database window takes up half of the screen. To return the windows to the default window layout, use the Window Menu Default Window Arrangement command. Main Window - Cartridge Reader Mode In Cartridge Reader mode, the Main Window consists of the Menu Bar, Toolbar, the Products Area, and the Cartridge Reader windows. The primary cartridge reader window provides for interface to connected cartridge readers. A panel is shown for each reader, with the serial number shown in the panel title bar. The background of the primary cartridge reader window is patterned. The below pictured interface is for PTS100/MCS100 cartridge readers. 29

30 30

31 Nexgen-PTS/MCS readers (PTS150 and MCS150) will have this interface, which contains the MCS serial number (if an MCS150), the optional brick serial number, and the IP address of each brick: The secondary cartridge reader window provides for display of downloaded assays and opened cartridge reader pltx files. The background of the secondary cartridge reader window is plain. Menu Bar The Menu Bar allows access to the following general menus. Options on the menus displayed in gray text are not available to the operator at that time. Each menu available from the Menu Bar is described in detail in their own help sections. File Menu The File Menu provides the options for data filing, properties and output. Specific options include Open, Close, Save, Save As, Export to File, Report, and Exit. Edit Menu Associated with Editing, this menu provides specific functions commonly found in Windows. These functions are Redo, Undo, Cut, 31

32 Copy and Paste. View Menu The View Menu provides options for which elements are displayed on the screen. Selecting an option makes the element active on the screen. Selecting an already active element will make the element inactive. The View options include Toolbar and Product Database. Tools Menu This menu identifies the tools available to the operator and administrative options available (based on user privileges.) The main tools available to the operator are Start Collection, MVD/MVC Calculator, Edit Password, Command Usage Log (administrator privilege), Maintain Users (administrator privilege), Maintain Products (privileged option), Options (privileged option), and Reader Options. Cart. Reader Menu This menu provides cartridge reader-related commands: Download Most Recent Assay, Download One Day's Assays, Download All Assays, Clear Tests Stored in Cart. Reader, Clear Cartridge Lot Number History, Version Information and Reconnect for PTS/MCS. For nexgen-pts/mcs, the available commands are Clear Cartridge Lot Number History, Version Information, Reconnect, Shutdown, and nexgen. The nexgen menu has these available commands: Save Test Reports, Restart, Update Software, and Save Logs. Window Menu The Window Menu offers standard Windows Window Menu options such as Cascade, Tile Horizontal, Tile Vertical and Arrange Icons for the Well Areas. A special command, Default Window Arrangement, returns the main window to its default position and size and returns the Products areas to its default docked position and size. Any open plate files are listed at the bottom of this menu and can be used to switch between plate files. Help Menu The Help Menu provides access to online help and tutorials available to the operator as well as the Plate Signature License Tool. Toolbar 32

33 The Toolbar allows quick access to common functions found within the drop down menus on the Menu Bar. Open Plate Open an existing plate to review the data. Displays the Open dialog box to allow selection of the plate to be opened. Save Plate Saves the current plate file using the plate's current file name. If the plate does not have a current file name, EndoScan-V will prompt for a file name. Report Displays the Report Setup dialog box to select the report options and to preview, print, . Cut Removes the information from the selected well(s). Copy Paste Copies the information from the selected well(s). Pastes the information from the cut or copy functions into the selected well(s). When enabled this button is used to validate digital signature users and sign the PLTX plate documents. dock styles. These themes changes the Standards Area/Product information Area and the Product database area in 4 different This button is used to synchronize remote database and the local database if configured This is EndoScan-V software application lock and EndoScan-V users can lock and log out of the EndoScan-V software while the 33

34 assay is running. Cartridge Reader Window - Primary The Primary Cartridge Reader Windows displays a panel for each connected cartridge reader on a patterned background. The panel title bar shows o Cartridge reader serial number o Nexgen-PTS/MCS instruments will show the IP address of the reader/bay o Cartridge reader status: unknown (plain cartridge reader icon), not ready (cartridge reader icon with red dot), or ready (cartridge reader icon with green arrow) o Cartridge reader test running, i.e. "Test Running" Assay setup information can be copied from one panel to another by right-clicking in the setup text field and dragging to the target panel. In addition, product information can be copied from the Product Database by clicking in a product row and dragging to the target panel. 34

35 The panels can be moved by left-clicking the mouse in the area as marked in the below image and then using the mouse to move the panel to another location. 35

36 Supported Cartridge Reader Assays EndoScan-V supports the following cartridge reader methods: o Endotoxin o I/E Screen o Gram ID 36

37 o Beta Glucan Running Cartridge Reader Assays o When the cartridge reader is ready and the assay information has been entered on the panel fields, you can start an assay by clicking the Start button. EndoScan-V will send the assay information to the cartridge reader and start assay preparation. When the cartridge reader is ready for the sample to be added to the cartridge, the panel message will prompt you to add the sample and click the "Start" button. When the assay is complete, EndoScan-V will retrieve the assay results and display them on the panel. o Cartridge Reader Assay Setup Information o EndoScan-V checks assay setup information when the "Send Setup" button is pressed. o EndoScan-V maintains a list of lot number - calibration code pairs. When either is selected, the corresponding member of the pair will be selected automatically. New values can be typed in the fields; pairs are stored when the "Send Setup" button is clicked. o The product name and lot number can each be as long as 20 characters; spaces will be converted to underscore characters. o Product concentration/dilution must be entered as a dilution of the form "1:10" or "2:5" for units "ml/ml"; product concentration/dilution can be entered as a concentration for any other units. See Sample Concentration/Dilution for more information. o For nexgen-pts/mcs cartridge readers, the endotoxin limit can be entered in the panel. The units will match the concentration/dilution of the product. For PTS/MCS cartridge readers, the endotoxin limit can be added to the product in the Product Database. o The I/E Screen and Gram ID methods support per-channel values for product name, lot number and (for I/E Screen only) concentration/dilution. These values are separated by semicolons. Cartridge Reader Window - Secondary The Secondary Cartridge Reader Windows displays a panel for each assay on a plain background. 37

38 Products Area The Products Area of the Main Window provides user access to the Product Database. The Product Database is a collection of some of the products a lab may test. Sample information can be entered on the panel by clicking on the row containing the product and then dragging the highlighted product onto a panel. 38

39 Clicking on the top of a column in the Product Database sorts the products by ascending order of the column. The arrow keys or the scroll bar can also be used to move up and down within the Products Database. See the Tools Menu Maintain Products section for information on adding, deleting, and editing products in the Product Database. File Menu The File Menu provides access to data filing, properties and output options. The following screens and menus are available under the File Menu located on the Menu Bar. New Creates a new blank plate or creates a new plate using a plate file as a template. 39

40 Select either the New Plate (blank) template or an existing plate file to use as a template. If the selected template plate file is a protected template, no changes can be made to the new plate file. To create a template, open the New Plate and add the desired standard curve and sample(s). Select Save As and save the file as a template name in the desired location on the local computer or network location. Plate files stored in other directories may be selected by using the Drive and Folder navigation windows. Use the enter key or click OK once the appropriate template file has been selected. Alternatively, double clicking on the template 40

41 file will create a new plate file and return the operator to the Main Window. Toolbar: Keys: Open CTRL+N Select a plate file from the list displayed in the dialog box or use the navigation menu and buttons to navigate to the directory where the desired plate file is stored. Click the Open button once the target plate file has been selected. Double clicking on the file name will also open the plate file. Clicking the Cancel button will return the operator to the Main Window. Note: File Open may only be used to open files containing data in order to print or review data; ensure that File New is used when creating a new plate from an existing template. 41

42 Toolbar: Keys: CTRL+O Close Close allows the current plate file to be closed. If the plate file has not already been saved, the program will prompt the user to Save the file. Clicking on the close box in the right-hand corner of the Well Area will initiate the Close action. Save Save allows the current plate file data to be saved. If the plate file already exists or has been saved previously, the file is automatically saved using the current name. Keys:CTRL+S Save As The Save As option allows the current plate file to be saved with a new name. 42

43 If an existing file name is selected the operator is prompted to select a new file name. Save As can also be used to save the current plate file to a new directory. Navigate to the new directory and select Save. Clicking the Cancel button will return the operator to the Main Window without saving the file. Export Use the Export function to export a plate file to a comma-separated variable file (.csv) or XML file. 43

44 Properties Selecting Properties displays the Properties dialog box for the current plate file for plate/tube readers. 44

45 Using the Properties dialog box, the operator can set the reader properties, plate properties, well and group properties, and calculation properties. See the Properties Dialog Box section for more information. Report The Report function allows the operator to create a report for the current plate file and select the report elements to be included in 45

46 the report. Selecting Report displays the Report Setup dialog box. See the Report Setup Dialog Box section for more information. Toolbar: Keys: CTRL+R Exit 46

47 Exit closes any open plate files and exits the operator from the program. Alternatively, clicking on the close box in the upper righthand corner of the Main Window will also exit the program. Edit Menu Edit Menu Undo Undo is a privileged command. Operators with the Undo privilege can use the Undo command to undo one level of changes. Keys:CTRL+Z Redo Used in combination with the Undo feature. Re-performs the action that was undone using the Undo command. Cut Deletes the selected well contents and moves the data to the clipboard. Drag the mouse to select the wells to be cut, then select Edit/Cut or click the right mouse button to select the Cut function. Keys:CTRL+X Copy Copies the selected well contents to the clipboard. Drag the mouse to select the wells to be copied, then select Edit/Copy or click the right mouse button to select the Copy function. Keys:CTRL+C Paste Pastes the data stored on the clipboard to the selected well(s). Select the well(s) to receive the data, then select Edit/Paste or click the right mouse button to select the Paste function. 47

48 Toolbar: Keys:CTRL+V View Menu The commands available from the View Menu change the look of the Main Window. Commands with a check mark are currently active. To activate a command, click on the command name. To deactivate a command, click on the command name again. Toolbar Displays the Toolbar containing shortcut buttons to standard program functions. Standards Displays the Standards window in the Main Window. The Standards window is used to select standards for microplate setup and allows the operator to drag and drop standards onto the Well Area. Product Information Displays the Product Information window in the Main Window. The Product Information window is used to select additional samples, spikes, standards and controls during microplate setup and allows the operator to drag and drop samples onto the Well Area. The information displayed in the window includes group name, product name, and lot number. Product Database Displays the Product Database window in the Main Window. The Product Database window is used to select products during microplate setup and allows the operator to create samples by dragging and dropping products onto the Well Area. Zoom Zoom displays the information for a selected well/tube in a larger window, allowing the operator to focus on the data for a single well/tube. All information that can be accessed by changing the views on the Well Area during data collection is displayed simultaneously in the Well Zoom window. To view the information for a specific point, click that point. 48

49 The title bar at the top of the Zoom window displays the well/tube location. Multiple Zoom windows may be open at one time. Tools Menu The following screens and menus are available under the Tools Menu located on the Menu Bar. Start Collection / Stop Collection Start Collection starts the data collection for the active plate. The Start Collection command is also available from the Toolbar (green arrow icon). If the active plate contains data, Start Collection is disabled to prevent loss of data. If data is being collected, Stop Collection stops data collection. The Stop Collection action is also available from the Toolbar (red square icon). Toolbar: MVD/MVC Calculator The MVD/MVC Calculator assists the operator in computing the Maximum Valid Dilution (MVD) or Minimum Valid Concentration (MVC) of a sample. 49

50 If MVC is selected, MVC will be calculated based on values entered for the endotoxin limit of a product and its units and the lowest sensitivity (Lambda) of the standard. If MVD is selected, the user may also enter the potency of the product and its units to calculate the MVD. The software will determine and display the units of the result based on the entered units. The operator may drag standard sets from the Standards Area into the lowest sensitivity field to drop the smallest standard. In addition, the operator may drag a product from the Products Area into either the Endotoxin Limit field or the Potency of Product field. Units will be dropped with the value. Edit Password Operators may change their user password by selecting Edit Password from the Tools Menu. The Change Password dialog box will appear. To change the password, the operator enters their old password, a new password and confirms their new password by reentering it exactly as they entered it in the new password field. Use the mouse or tab to move between the fields on the dialog box. When all information has been entered, select the OK button. 50

51 To close the dialog box without making any changes, select the Cancel button. Note: The password for the EndoScan-V software must be at least 8 characters in length, must be no longer than 16 characters, must contain at least one alphabetic character, and must contain at least one numeral or symbol. The EndoScan-V password can contain spaces and special characters. The password is case-sensitive, i.e. upper and lower-case characters are not the same. In addition, the new password must not be the same as a password used by this operator during the history time option. Command Usage Log The Command Usage Log (Audit Trail) stores information on commands used by operators. If command usage logging was enabled when EndoScan-V was installed, this menu command allows operators with administrator privileges to view, archive or print the Command Usage Log. The archive command clears the log, an operation that cannot be undone. It is Charles River Laboratories recommendation to use Auto-Archive to save the Command Usage Log with the frequency based on your usage and requirements. The Command Usage Log checksum will be verified before each of these commands is performed. If the checksum is found to be 51

52 incorrect, you will be notified and offered the option of canceling the action. You may want to save the corrupted file before clearing it. View Use this command to view the Command Usage Log entries. 52

53 The dialog box, the grid columns, and grid rows can be resized as needed. 53

54 Archive Use this command to archive the Command Usage Log to a file in Adobe Portable Document Format (PDF) and then clear the log. Note: this action cannot be undone. Print Preview Use this command to preview and print the contents of the Command Usage Log. 54

55 Maintain Users Maintain Users allows operators with administrator privileges to maintain the user list for the program. 55

56 See the Maintain Users Dialog Box section for additional information. Products PRODUCTS Maintain Products Edit Product Database is a privileged menu command. Operators with the Edit Product Database privilege can use this command to maintain the Product Database. Operators without this privilege will not see this command. Maintain Products adds a column of buttons to the Product Database window. 56

57 Add Row To add a product to the Product Database, select the Add Row button and enter the information for the product. Use the Tab or Enter keys to move to the next field or the mouse to click on the next field. The fields included for each record in the database are: Product Name - Enter the name of the product. This name will appear on reports for this product. Product ID - Enter the identification of the product, for example the QA catalog name. Product Type - Enter the chemical or common name of the product Maximum Dosage - Enter the maximum dosage of the product in dosage units Dosage Units - Select the dosage units from the pull-down menu or type in another unit. Concentration/Dilution - Enter the concentration or dilution of the product. If the dosage units are ml this is a dilution expressed as a ratio (1:10), otherwise it is a concentration. Endotoxin Limit - Enter the limit of endotoxin in EU/(dose unit). Auto Spike - To enable the Auto Spike function for this product; click on the box to set the value to "TRUE". When enabled the spikes for this product will automatically be entered during plate setup. Spike Concentration - Enter the amount of endotoxin spike for the product. 57

58 Validation Criteria - Enter any validity criteria to be used in assessing the validation of an assay (e.g., x.eu <50, meaning for this group, EU must be less than 50.) Comments - Enter any text comments in this field. Up to 256 characters may be entered. Diluent - Enter the amount of diluent for the product. Barcode - Enter the barcode for the product. This will always be numeric. Identifier - Enter the identifier for the product. Database Link - Enter the database link so that it will give the full analysis of that product. At a minimum, the operator must enter the concentration or dilution of the product and the units of a dose. NOTE: Any fields not entered by the operator will be filled with blank data. Some actions or computations cannot be done with blank data and will result in an error message if those actions or computations are attempted. When all information has been entered, select the Save Row button to save the information to the Product Database. Delete Row To delete a product from the Product Database, select the product entry and then the Delete Row button. The program will present a dialog box to ensure the operator intends to delete the selected product. Edit Row Select the product entry to be edited and then select the Edit Row button. Make any necessary changes to the product information and then select the Save Row button. Copy Row Select a cell in the row to be duplicated and then select the Copy Row button. Make any necessary changes to the product information and then select the Save Row button. 58

59 Print Select the Print button to view a report of the Product Database contents in a preview window. To print the report, select the print button on the preview window. For information on preview window controls, see the Report Setup Dialog Box Preview Button section. 59

60 Cancel / Close 60

61 The Cancel button cancels an Add Row or Edit Row. The Close button will return the Product Database window to its state prior to selecting Maintain Products. That is, if the window was open on the main window, if will be restored to the main window; if the window was closed, it will be closed. Database Utility The EndoScan-V Product Database Utility converts the existing MS Access Product Databases to MS SQL and imports the Product from access database to the MS SQL database. The database utility allows users to change the database attached to their EndoScan-V installation. Please do also verify for more details DBUtility help file which will be available in the EndoScan-V installed folder. Print Products This command is identical to the Print button on the Product Database window during product maintenance. Select this command to view a report of the Product Database contents in a preview window. To print the report, select the print button on the preview window. For information on preview window controls, see the Report Setup Dialog Box Preview Button section. Refresh This command refreshes the Product Database window by clearing the grid, reading the products in the product database, and writing the product data in the grid. This updates the display for any changes made by another user when sharing the product database. 61

62 Reader Options The Reader Options dialog box allows the operator to select the reader that will be used for reading microplates or tubes or to select PTS/MCS or nexgen-pts/mcs for the cartridge reader modes. When the appropriate information has been entered, press the OK button to accept the information. Pressing the Cancel button will return the operator to the Main Window and not save any information that was entered. See the Reader Options Dialog Box section for additional information. Tecan Sunrise Control The Tecan Sunrise Control command displays the Tecan Control dialog box. This menu command will not be enabled unless the Tecan Sunrise reader is selected. The Tecan Control dialog box will be displayed until closed using the close button at the upper right of the dialog box or until a different reader is selected. During data collection, it will be temporarily hidden. 62

63 Buttons on the Tecan Control dialog box are provided to move the microplate drawer and the filter carriage. If the connected Tecan Sunrise reader has an incubator, temperature controls will be enabled. The temperature setting is displayed and entered in the Target Temperature text box. Either a blank or a 0 temperature value acts to turn off the incubator. Changed temperature settings are stored and sent to the reader only when the Apply button is clicked. Note: During collection, the temperature setting in the plate file overrides this setting. Cart. Reader Menu The following menu commands are available under the Cart. Reader Menu located on the Menu Bar when the MCS/PTS reader type is selected. Note: Download Most Recent Assay, Download All Assays, and Verify Temperature Calibration are only for PTS/MCS Download Most Recent Assay This command downloads the most recent complete assay from the currently selected cartridge reader into the secondary cartridge reader window. Any assays stopped before completion are skipped. Assays downloaded from an MCS will contain only the cartridge lot number, calibration code, and the endotoxin value without considering the dilution factor. Download All Assays 63

64 This command downloads all the complete assays from the currently selected cartridge reader into the secondary cartridge reader window. Any assays stopped before completion are skipped. Note: This function only applies to PTS readers. Clear Cartridge Lot Number History This command clears or erases the cartridge lot number / cartridge calibration code pairs stored by EndoScan-V. This history is used to fill the cartridge lot number and cartridge calibration code combo boxes on the cartridge reader panels. Verify Temperature Calibration This command verifies whether the currently-selected cartridge reader's temperature calibration is within acceptable range. A temperature calibration kit is required to perform this calibration. Version Information This command displays serial number and version information for connected cartridge readers. Reconnect This feature allows the user to reset the connection to the reader. If the communication is disrupted, selecting this feature will allow EndoScan-V to attempt to re-establish communication. This feature is available to all user types. Nexgen-PTS/MCS Cart. Reader Menu Navigating to the Cart. Reader menu will allow the user to Shut Down the nexgen-mcs reader, Reconnect, show the Version 64

65 Information, Clear Cartridge Lot Number History, or show nexgen-specific functions. Clear Cartridge Lot Number History Selecting this item will clear the cartridge lot number information from the software. Each cartridge lot has a unique calibration code which is stored in the software after that combination is run. If an incorrect lot combination is entered, selecting this menu will erase the information. This option is only available for administrators. Version Information The below image shows the version information of each bay. Selecting this menu will also show the IP address of each bay as it was entered during setup. This option is only available for administrators. 65

66 Reconnect This feature allows the user to reset the connection to the reader. If the communication is disrupted, selecting this feature will allow EndoScan-V to attempt to re-establish communication. This feature is available to all user types. Shutdown It is HIGHLY recommended that the nexgen-mcs is shutdown using this Menu option versus the power on/off button on the rear of the nexgen-mcs. In the rare event that the situation is encountered where one or more bays are on (Green light is on) while other bays are off (Green light is off), it is recommended to select Shutdown on EndoScanV which will shut off the bays that are on. Once all bays are off (Green lights are off) then exit out of EndoScanV and turn on the nexgen MCS using the power on/off button on the rear of the nexgen-mcs, and once all bays are powered up (about 2 minutes), restart EndoScanV. If this does not address the issue, and some bays are still off (Green light is off), then unplug the power connector on the rear of the nexgen-mcs and plug back in, and then power up the nexgen-mcs with the power on/off button. nexgen Navigating to the nexgen menu will allow an administrator to Save Test Reports, Restart the instrument, Update the Software for all bays that are connected, and Save Logs. Save Test Reports Allows an administrator to save reports directly from all 5 bays. If there is an interruption in the communication of the reader to the PC, this feature allows for the recovery of the results of up to the last 100 tests that were ran, including: username, sample name, sample lot number, dilution/concentration, units, endotoxin limit (if applicable), and assay data. Once EndoScan V has started a test through sample addition, the assay will continue to run even if the computer fails or communication is interrupted. Test reports are automatically saved upon completion for routine testing. 66

67 Restart Allows an administrator to restart all bays on the reader. Should a bay fail to properly connect, this feature can be selected to restart the instrument. This feature should be used only if Reconnecting does not work to re-establish communication. Update Software Selecting this when a software update is available, will update the firmware for each bay. The version information can be viewed by selecting Version Information or by selecting Tools then Reader Options and then Edit. Save Logs This feature allows an administrator to save the application logs for all five (5) bays. This data shows the report in addition to the reader self-check, the IR intensity, and the UV intensity. The logs contain information which can be used for troubleshooting. Help Menu The Help Menu provides access to features to assist the operator in using the EndoScan-V program. The following screens and menus are available from the Help Menu located on the Menu Bar. Contents Initiates the Help facility, displaying the Contents tab as active. The help facility has three options: Contents, Index and Search. 67

68 Help Viewer Contents Tab 68

69 Contents displays help information organized by topic. Select the help topic by double-clicking on the book icon or clicking on the + to the left of the icon in the contents window to display the help topics. Clicking on a book or page icon will display the help information for that topic on the right side of the screen. Help Viewer Index Tab Index displays help information by keyword. 69

70 Enter the keywords for the desired help. A list of close matches will appear in the below the search box. Highlight the help topic in the lower window and select the Display button. The help information will be displayed on the right-hand side of the window. Help Viewer Search Tab Search displays help information after executing a search based on word(s) entered by the us. 70

71 Enter the word(s) to search on and press the List Topics button. A list of previous searches can be accessed using the pull-down list on the text box. Topics containing the word or words are displayed in the Select Topic list box. To view a topic, highlight the topic title and press the display button. The help topic is displayed with the word or words highlighted. To turn off the highlighting, click the Options button on the toolbar, click the Search Highlight Off option, and click the Refresh button on the toolbar to start using the option. Search For Help On Initiates the Help facility, displaying the Search tab as active. See the Help Viewer Search Tab (above) for more information. Print User's Manual Prints the on-line version of the User's Manual for reference. About Displays the About screen which provides software version and license information. The About screen also provides Technical Support contact information and a clickable link for comments. 71

72 Options Dialog Box The Options Dialog Box allows privileged operators to view and set options for the program. The option values set on this dialog box are the default options for the program applicable to all users. Changes made to the Options take effect on any new plate that is opened after the changes have been made. Selecting the Defaults button returns all values to their default value at installation. 72

73 Options - Layout 73

74 Replication Direction The direction for automatic replication can be set for either left to right or top to bottom. Left to Right replication enters the first sample, standard or control in a column and the replicate is entered in the next column(s) to the right until the Number of Replicates is reached. Top to Bottom replication enters the first sample, standard or control in a row and the replicate is entered in the row(s) immediately beneath until the Number of Replicates is reached. If automatic spike creation is selected the spikes will be replicated in the same direction as the sample. The default Replication Direction is Left to Right 74

75 Number of Replicates The number of times a sample, spike, standard or control is automatically duplicated when entered onto a micro plate during setup. The default number of replicates is 2. Automatic Creation of Spikes The Automatic Creation of Spikes option directs the software to enter spike information for each product entered onto the plate. When Automatic Creation of Spikes is selected, spike values will be placed in the same number of wells as the product and its replicates when a product is placed on the plate. When Automatic Creation of Spikes is not selected, only products in the product database with the auto spike value of "yes" will have spikes created when placed on the plate. The value of the spike is controlled by the spike concentration information in the product database. The Auto Spike value of any product dragged from the Product database will override the global Automatic Creation of Spikes. For Ex: If the global Automatic Creation of Spikes is set to False and the Auto Spike of a product in the Product Database is set to True then the product when dragged and dropped into the well will also add the Spike wells. The global inline Spiking value will be applied regardless of the product source. Inline Spiking Product spikes may be placed in the same row or column as the product or in an adjacent row or column. When the Inline Spiking Option is on, the product spikes are placed in the same row or column as the product (depending on replicate direction.) If Inline Spiking is off, the product spikes are placed in the next adjacent row or column (depending on replicate direction.) The default value for this option is on. Default Spike Concentration The default concentration in endotoxin units for automatically created spikes. Any logical concentration may be entered in this box. The units are designated by the units entered on the Plate Properties. The default concentration is 0.5. Time Format The format in which the time values are entered and reported. The possible time formats are: SSSS (integer seconds) or HH:MM:SS (where HH:MM:SS is the time relative to the start of collection). Select the desired Time Format from the pull-down menu. The 75

76 default Time Format is SSSS. Wells Masked Data in wells can be masked, or hidden, from use in calculations and reports. Any wells listed in the Wells Masked box are masked for a new blank plate opened in EndoScan-V. Enter the wells to be masked by typing the well reference (the letter number combination, such as A3 or G10) separated by a comma (,). NOTE: Well masking is a privileged feature. Only operators with well masking privileges may enter text in this field. Colors Colors may be defined for the text on the well grid for categories of groups (STD, CTRL, SPL, SPK) using the Colors button on the layout tab of the Options dialog box. Selecting the button presents a dialog box that shows the operator the currently selected color for a group category. Select a different group category by using the pull-down menu in the type box. Selecting the Change Color button allows the operator to select any color from the standard color selection table. 76

77 Pick the desired color and select OK. To return to the Colors dialog box without changing the color for the selected group category, select Cancel. Options - Calculation 77

78 Linear/Polynomial Regression Option EndoScan-V is capable of performing either Linear or Polynomial regression to analyze the standard curve. The linear regression option is the default selection for new microplate/tube files. Regression type can be selected on a file-by-file basis using the Properties Dialog Box. Select the default type of regression desired. If Polynomial regression is selected, the Polynomial Order list box will be enabled. 78

79 NOTE: For Polynomial Regression to be performed there must be one more data point than the defined Polynomial Order. If the selected degree of polynomial regression cannot be performed due to an inadequate number of standards or points, linear regression will be used to determine the standard curve. Polynomial Order Option EndoScan-V is capable of performing Polynomial regression of order, or degree, 2, 3 and 4. Select the default order of polynomial regression. Polynomial order can be selected on a file-by-file basis using the Properties Dialog Box. NOTE: For Polynomial Regression to be performed there must be one more data point than the defined Polynomial Order. If the selected degree of polynomial regression cannot be performed due to an inadequate number of standards or points, linear regression will be used to determine the standard curve Onset OD Option The Onset OD option is the default optical density (OD) reaction-time threshold. The initial value is 0.1 OD. Onset OD can be selected on a file-by-file basis using the Properties Dialog Box. Number of Points to Use for Max V Option The default number of data points used to calculate the maximum slope or MaxV. Possible options for the number of data points are 2, 3 or 4 data points. The initial value is 3 data points. The number of data points to use for Max V can be selected on a file-by-file basis using the Properties Dialog Box. CV Limit, Products Option EndoScan-V calculates the coefficient of variation (CV) of the well results for each sample and spike. The limit entered into this field, in percent, is the default acceptable limit for sample and spike CV for the limit appearing on the Properties dialog box under Calculation Properties. CV Limit, Standards Option 79

80 The Coefficient Variance can be configured in this section available in the options interface. CV Limit, Cart. Reader Product Option The cartridge reader calculated the coefficient of variation (CV) of the channel results for the sample and spike. The limit entered into this field, in percent, is the acceptable limit for sample and spike CV. Average Replicates Average Replicates determines how the data is used in regression and endotoxin calculations. When this option is selected, the program averages the data from all of the replicates prior to performing the calculations. When this option is not selected the individual optical density (OD) data values are used in the regression and endotoxin calculations. The default value is on. Enable Validation Selecting this option directs the program to evaluate the plate and group criteria for the assay and to determine the validity of the criteria. The status of the criteria is reported using the Validation Terminology selected. Spike Recovery Range EndoScan-V calculates spike recovery as a percentage for wells containing spiked samples. The range entered into the field, in percent, is the acceptable range for spike recovery and will be included on reports. The default spike recovery range is 50 to 200. Spike Recovery Calculation for Unreacted Samples For unreacted samples, EndoScan-V calculates spike recovery using the smallest standard EU or zero, depending on this option. The default is to use the smallest standard EU. This option is available to operators with Administrator privileges only. Cartridge Reader Samples by Channel For cartridge reader assays, sample endotoxin results can be displayed and reported for each sample channel or for the average reaction time of both sample channels. Validation Terminology This option sets the terminology for reporting the validation criteria results. Validation criteria results can be valid, invalid or undefined. The provided options for valid results are: VALID, OK, GOOD, and PASS; or, the operator may enter their own word for reporting valid results. The provided options for invalid results are: INVALID, NOT OK, BAD, and FAIL; or, the operator may enter 80

81 their own word for reporting invalid results. The provided options for undefined results are: UNDEFINED, UNDETERMINED, UNKNOWN, and UNRESOLVED; or, the operator may enter their own word for reporting undefined validation results. The default settings are VALID, INVALID, and UNDEFINED. This option is available to operators with Administrator privileges only. Endotoxin Limit Validation Terminology This option sets the terminology for reporting the validation criteria results for the Endotoxin limit. Validation criteria results can be valid, invalid or undefined. The Endotoxin Limit Validation terminology is independent of the validation terminology. The provided options for valid results are: VALID, OK, GOOD, and PASS; or, the operator may enter their own word for reporting valid results. The provided options for invalid results are: INVALID, NOT OK, BAD, and FAIL; or, the operator may enter their own word for reporting invalid results. The provided options for undefined results are: UNDEFINED, UNDETERMINED, UNKNOWN, and UNRESOLVED; or, the operator may enter their own word for reporting undefined validation results. The default settings are VALID, INVALID, and UNDEFINED. This option is available to operators with Administrator privileges only. Options - Reagents/Acc. 81

82 Reagent Lot Numbers Note: Reagent expiration date fields are implemented as simple text fields no date checking or reformatting is performed. LAL and Expiration Date Reagent lot number for LAL and its expiration date. 82

83 Endotoxin/Expiration Date Reagent lot number for the endotoxin and its expiration date. LAL Reagent Water/Expiration Date Reagent lot number for the LAL Reagent Water and its expiration date. Other/Expiration Date Other reagent lot number and its expiration date. Type the reagent's name into the text box, enter the lot number and the expiration date. Accessories Enter the Accessory Name, Description and Expiration Date for up to three accessories. The date fields are implemented as simple text fields no date checking or reformatting is performed. Options - Other 83

84 Lab Name Enter the name of the laboratory performing the endotoxin reading and analysis. This laboratory name appears in the Plate Properties and on all reports and is associated with exported data. 84

85 Auto Name Option For microplate/tube readers, this is the default Auto Name selection. Auto Name can be selected/de-selected on a file-by-file basis using the Properties Dialog Box. When selected for the file, the software automatically saves the microplate/tube assay file when data collection stops. Automatically saved microplate/tube assay files are saved in the Plate File Path using a file name of the format ssssyymmdd##.plt. The components of the file name are ssss, the last 4 characters of the reader serial number yy, the last 2 digits of the current year mm, the current month (01 through 12) dd, the current day of the month (01 through 31) ##, a sequence number (00 through 99). For cartridge readers, this is the Auto Name option. When selected, the software automatically saves each reader's assay when it completes using the following naming rules: A folder for the day is created in the Plate File Path using a folder name of the format YYYYMMDD. The components of the folder name are: YYYY, the current year MM, the current month (01 through 12) DD, the current day of the month (01 through 31) Each assay is saved in the folder of the day using a file name of the format SSSSyymmdd###.plt. The components of the file name are: SSSS, the reader serial number yy, the last 2 digits of the current year mm, the current month (01 through 12) dd, the current day of the month (01 through 31) ###, a sequence number (000 through 999). For nexgen-pts/mcs readers, this is the Auto Name option. When selected, the software automatically saves each reader's assay 85

86 when it completes using the following naming rules: A folder for the day is created in the Plate File Path using a folder name of the format YYYYMMDD. The components of the folder name are: YYYY, the current year MM, the current month (01 through 12) DD, the current day of the month (01 through 31) Each assay is saved in the folder of the day using a file name of the format ngssssssssyymmddhhmmss###.pltx. The components of the file name are: ng, indicates the nexgen reader source, applies to both PTS and MCS SSSSSSSS, the nexgen-pts reader serial number yy, the last 2 digits of the current year mm, the current month (01 through 12) dd, the current day of the month (01 through 31) HH, the hour when the assay was saved MM, the minute the assay was saved SS, the second the assay was saved ###, a sequence number (000 through 999). For nexgen-mcs readers, this is the Auto Name option. When selected, the software automatically saves each reader's assay when it completes using the following naming rules: A folder for the day is created in the Plate File Path using a folder name of the format YYYYMMDD. The components of the folder name are: YYYY, the current year MM, the current month (01 through 12) DD, the current day of the month (01 through 31) Each assay is saved in the folder of the day using a file name of the format ngcccccccc-b- 86

87 SSSSSSSSyymmddHHMMSS###.pltx. The components of the file name are: ng, indicates the nexgen reader source, applies to both PTS and MCS CCCCCCCC, the nexgen-mcs reader serial number B, the Bay number of the nexgen-mcs SSSSSSSS, the Bay serial number yy, the last 2 digits of the current year mm, the current month (01 through 12) dd, the current day of the month (01 through 31) HH, the hour MM, the minute SS, the second Auto Stop The Auto Stop option is used in conjunction with kinetic collections for microplate/tube readers. When enabled, this option automatically stops data collection when the smallest standard (i.e., the standard with the least endotoxin concentration) has reached the onset optical density (OD). Auto Export Option For microplate/tube readers, this option is the default Auto Export selection for new files. For these files, Auto Export can be selected on a file-by-file basis using the Properties Dialog Box. When selected, the software will automatically export the assay to a comma-separated file when the data collection stops. For cartridge readers, this option is the Auto Export selection. If the Auto Name option is also selected, the software will automatically export each assay to a comma-separated file in the Export File Path when the assay is complete. See the Auto Name Option for file naming information. Auto Print When enabled, this option automatically prints a report when data collection stops, provided at least one report item has been selected. Note: The report must be previewed to save the report selection. 87

88 Change Log Reporting Change Log Reporting User Specific User Specific Change Log Reporting is an administrator-configurable option; if the user is not an administrator this field will be inactive. If this field is selected the change log printed with the report will only contain actions directly initiated by the user. Application Specific Application Specific Change Log Reporting is an administrator-configurable option; if the user is not an administrator this field will be inactive. If this field is selected the change log printed with the report will contain actions performed by the software associated with analysis of the file and specific user actions. Plate File Path This option is available to operators with Administrator privileges only. The plate file path is used as the default directory path to load and save template and plate files. To find a directory path, click the Browse button to display the following Browse for Folder screen. 88

89 Folders with sub-folders are shown with a + box. To show the sub-folders, click the + box or double-click the folder. When the OK button is clicked, the full path of the highlighted folder will be shown in the Plate File Path field. Clicking the Cancel button will return the operator to the Options Dialog Box. Export File Path This option is available to operators with Administrator privileges only. The export file path is used as the auto-export path. For manual export, the export file path is used as the default directory path to save the export file of plate file data. To find a directory path, click the Browse button to display the following Browse for Folder screen. 89

90 Folders with sub-folders are shown with a + box. To show the sub-folders, click the + box or double-click the folder. When the OK button is clicked, the full path of the highlighted folder will be shown in the Export File Path field. Clicking the Cancel button will return the operator to the Options Dialog Box. Default Collection Type This option is the default collection type for microplate/tube readers. The actual collection type for an open plate file can be selected on the Collection Properties tab of the Properties Dialog Box. MCS Serial Number Only When this option is selected, only the MCS or nexgen-mcs serial number and bay number will be shown in the title bar of MCS or nexgen-mcs reader panels. The serial number of the cartridge reader located in the bay will be suppressed. This setting also applies 90

91 to reporting and exporting. Security Security Password Timeout, Days Password Timeout is an administrator-configurable option; if the user is not an administrator this field will be unmodifiable. Each operator s account will be expired if the password is not changed for the specified period of time, in days, indicated in this field. The administrator may restore an account to an unexpired condition by changing the password. If the operator has an expired account the operator will be prompted to change their password before proceeding after logging in. Password History, Days Password History is an administrator-configurable option; if the user is not an administrator this field will be unmodifiable. A history of each operator s passwords will be saved. When changing the password, the operator must select a password that they have not used before or have not used before within the selected history period. The maximum value is days. A value of 0 in this field disables password history constraints. That is, an operator may change their password to a password they have previously used. Login Timeout, Minutes Login Timeout is an administrator-configurable option; if the user is not an administrator this field will be unmodifiable. EndoScan-V will terminate login after the time, in minutes, indicated in this field, of PC user-interface inactivity. If the login has terminated, the EndoScan-V user interface will be disabled except logging in and saving open plate files as provided by the Login Timeout dialog box. 91

92 Log off The user can lock the software if required as an added security while the assays are running. There is an icon in the main tool bar as below: This icon can be used to lock the EndoScan-V software: 92

93 Auto Archive Auto Archive The Auto Archive function is only available to EndoScan-V administrators. It enables the Audit Trail file (Command Usage Log) to archive periodically. The Audit Trail (Command Usage Log) will be converted into a PDF file. 93

94 By default the Auto Archive function is disabled. 94

95 The Auto Archive settings has 3 parts; the Mode, the start date and the Archive File Path. The Mode: There are 5 different modes that the user can configure the way Auto Archive can function. o o o o o Daily : The Audit Trail (Command Usage Log) will be automatically archived as a PDF document every day. Weekly: The Audit Trail (Command Usage Log) will be automatically archived as a PDF document every week. Fortnightly: The Audit Trail (Command Usage Log) will be automatically archived as a PDF document every 15 days. Monthly: The Audit Trail (Command Usage Log) will be automatically archived as a PDF document every month. None: This mode will disable the Auto Archiving process and will never archive the Audit Trail (Command Usage Log) automatically. The Date: The start date on which the auto archiving process has to start and to record the next processing date Initially at the time of a new product installation the Start date will be set as N/A. By clicking the 'New Start Date' the calendar will be activated for the user to choose a new Start Date. When the Start Date is selected and the details are saved, the archiving process starts within 3 minutes and keeps monitoring until the mode is changed to None. 95

96 The Archive File Path: The file path that the Audit Trail (Command Usage Log) will be archived as a PDF document. This folder requires the basic Read and Write privileges for the auto archive to process the Audit Trail (Command Usage Log) file properly. The file name for the archived PDF document would be as follows: Finally by clicking the save button the user saves all the auto archive settings. Note: All auto archived audit trail log files will be prefixed by the term 'AutoArchiveCULOG_' followed by the date of archive and suffixed by 6 digit random number to preserve uniqueness to the file name. The auto archive process is not a background process and expects the EndoScan-V software to logged in to prepare the auto archived PDF document. 96

97 After a successful auto archive process the Audit Trail (Command Usage Log) will be recorded as below. The term 'Auto' prefixed will differentiate whether the process is an automatic archive process or a manual archive process. Options - Database Remote Synchronization 97

98 Database Remote Synchronization The Database Synchronization allows along the same network. EndoScan-V to sync its products and users with other systems running the same application To Sync EndoScan-V with other systems first go the Tools Tab And then to options, then navigate to the Database Remote Synchronization tab. Fill in the required details in the Remote Server Details. 98

99 Once the required details are filled in click on Test Connection. If connection with server is successful, You will see a user prompt with a successful connection. 99

100 Click on the Green Sync icon located towards the upper right side of the screen. You will see a message saying Now go to the Tools menu >> Then the Products Tab >> click on refresh Tab. Now your products database will be updated. Reader Options Dialog Box The Reader Options dialog box allows the operator to select the reader that will be used for reading microplates or tubes or cartridges. 100

101 When the appropriate information has been entered select OK to accept the information. Selecting Cancel will return the operator to the Main Window and not save any information that was entered. PTS100/MCS100 (PTS/MCS) and PTS150/MCS150 (nexgen- PTS/MCS) instruments cannot be used simultaneously-only the PTS150/MCS150 instruments can be used at the same time or only PTS100/MCS100 instruments can be used at the same time. The nexgen-pts/mcs instruments connect via Ethernet and the PTS100/MCS100 instruments connect via USB. NOTE: Whenever there is a reader type change it is recommended to restart the EndoScan-V software. Reader The Reader information section allows the operator to specify the Reader Type and Serial Number. The EndoScan-V program will confirm the selected Reader Type is the actual Reader Type connected to the computer. Select the appropriate Reader Type from the pull down menu. All readers supported by the EndoScan-V software will be listed on the pull-down menu. Currently, the available options are ATi, BioTek ELX808, PTS/MCS, nexgen-pts/mcs and Tecan Sunrise. If the selected reader is ATi or BioTek, enter the Serial Number of the reader into the Serial Number field. The Serial Number may be any combination of letters, numbers and characters. If the selected reader is Tecan Sunrise and a Tecan Sunrise reader is connected, the Serial Number field will be updated with the serial number of the connected reader. Edit the Serial Number as desired by adding text at the beginning or end of the provided serial number. The Serial Number may be any combination of letters or numbers. If the selected reader is PTS/MCS, no other information is needed. EndoScan-V will scan available ports for connected cartridge readers. nexgen With EndoScan-V, connection to the nexgen PTS/MCS devices are done through Ethernet connections. With this version of EndoScan-V, the IP addresses of the devices are set up as Static. Configuring nexgen MCS devices The nexgen MCS devices are pre-configured with fixed Static IP addresses and those IP addresses are included in the nexgen MCS documentation provided with the device. [Note that the IP addresses are typically set up as Bay 1: , Bay 2: , Bay 3: 101

102 , Bay 4: , Bay 5: ]. If you are only setting up nexgen MCS devices, now refer to the Configuring the wired network connection on the PC section below. Configuring nexgen PTS devices The step by step configuration to communicate to EndoScan-V with the nexgen PTS is as follows: Step 1: [Requires the user on the nexgen to be an admin if User Management is turned on]. Click the menu button from the device main screen -> From the next screen click the settings button -> then click Network button Step 2: Click the Ethernet option -> Select the button Enabled -> select the button Static -> Provide an IP address. -> And the Gateway (which can be entered as ) -> click the button Apply 102

103 Step 3: The last step is to ensure that the network icon is visible after the Apply button is clicked as shown. 103

104 Now the nexgen PTS device is configured. Configuring the wired network connection on the PC On the computer that EndoScan-V is running on: 1. Insert the supplied Ethernet cable connector into the Ethernet port at the back of the nexgen PTS device. 2. Insert the other end of the supplied Ethernet cable connector into an available Ethernet port access to your computer where the software EndoScan-V version is installed. This connection can be done through the Ethernet port on the computer or through a USB to Ethernet adapter. 104

105 3. Navigate to the Network and Sharing center in your Windows computer and follow the below steps to configure your local network connection to communicate to the nexgen PTS device Step 1: Select the Local Area Connection -> Double click on the icon -> Double click the icon associated with the Ethernet connection you have connected to the nexgen device(s). The properties screen will be shown as in step 2. Step 2: Click the Properties button -> In the next screen select the Internet Protocol Version 4(TCP/IPv4)) -> Then click the properties button from this screen -> In the next screen provide the is IP as given in the image below. The rest of the information can be left blank. 105

106 Step 3: Click Ok to all the screens. Now the computer is configured to talk to the nexgen device. Configuring reader options Configuring nexgen PTS with EndoScan-V The nexgen PTS can be configured to communicate through the reader options interface. Double click the icon from the desktop and provide appropriate credentials to the login screen. Navigate to the Reader options and choose the Reader Type as nexgen-pts/mcs and the screen should look as below: 106

107 Click the Edit button to configure nexgen devices. Select the PTS checkbox and provide the number of devices you would like to configure (in this case above 1 was added). Provide the base IP address. If you want to add one nexgen PTS device, provide the IP address of the nexgen PTS device (refer to section Configuring nexgen PTS devices above). Click Configure to associate the type of device to the added nexgen PTS device. Select the device type which is PTS1 in our case. Click the button Save 107

108 A confirmation message will prompt the user to create the newly added devices to the database. Click Yes to the message. 108

109 Once the new device details added into the database a confirmation message will be prompted to the user. EndoScan-V will query the device and will add the device Serial and the Status of the nexgen device to the Nexgen settings screen for user reference. 109

110 Click the Close button and then click Ok in the Reader options screen. 110

111 When the Ok button is clicked the software will attempt to connect to the configured devices and you will see the below screen informing the user that the software is trying to communicate with the configured nexgen devices. 111

112 Once the connection to the nexgen devices is successful, the main panel with all the connected nexgen devices will be presented to the user to run the assays. When all the nexgen devices are successfully connected then the bay serial number will also be updated automatically. In the case of nexgen PTS devices, the device serial number and the bay serial number are the same. In the case of nexgen MCS devices the MCS device serial number is the serial number of the instrument, so it is a different number than the bay serial number. Refer to the section Configuring additional nexgen devices below for adding additional devices. 112

113 Configuring additional nexgen devices If the selected reader type is nexgen-pts/mcs, the IP address for each reader/bay can be entered manually into the software upon installation. A base IP address should be entered, from which each bay will be added onto consecutively. For example, if the base IP is each bay will be , , , , for Bays 1, 2, 3, 4, 113

114 5, respectively. If additional nexgen PTS or MCS devices need to be added, select Edit and then check the boxes to add the type of device and select the number of devices as shown below. NOTE: Only an EndoScan V administrator can configure the nexgen-pts/mcs reader(s). River representative performs the reader set-up. It is highly recommended that a Charles When configuring the nexgen-mcs or nexgen-pts, after hitting Configure on the Reader Options screen, the below image will display. The status of each bay will be displayed along with the serial number of the individual bay. An individual bay may be excluded from the cartridge interface here. Note: only an administrator can adjust these settings. 114

115 By selecting one of the rows and right clicking, the following menu will appear to allow an administrator to Connect, Save Logs, Save Audit Log, Restart, Shut Down, Save Test Reports, and Update Software for each bay. 115

116 Connect Selecting Connect will command EndoScan-V to connect to that bay. Save Logs Selecting Save Logs will save the application logs from the brick as a PDF (Portable Document Format) to the computer. The application logs are different than the test reports. These logs help Technical Support troubleshoot any issues concerning the reader or the assay. When troubleshooting, an administrator can download the logs. Save Audit Log Saving the Audit Log will save the audit trail of that particular brick. This would show the audit trail from the brick of the instrument and is not the EndoScan V audit trail. The Audit Log will show the beginning and end of every test and whether a test was aborted. The user will appear as N/A, as ESV only sends down the user name for test result information. 116

117 Restart Selecting Restart will restart the selected brick. Shut Down Selecting Shut Down will shut down the selected brick. Note that if one brick is turned off, and the others are on, that using the power key in the back of the nexgen-mcs will cause the brick that is off to turn on, and the others to turn off. So this should only be used in a troubleshooting situation. Save Test Reports Selecting Save Test Reports allows the administrator to save test reports directly from the brick. The brick will save all data that is entered into EndoScan-V for disaster recovery. This feature is only necessary should the communication with the PC be disrupted. The assay will continue to run if the PC crashes or communication is lost. Test Reports will automatically be saved to a location designated in EndoScan V. Update Software Selecting Update Software will allow the user to select the file to use to update the firmware for the selected brick. NOTE: 1. Whenever there is a reader type change it is recommended to restart the EndoScan-V software. 2. The reader serial number can contain only characters and numbers. No other special or control characters are allowed. Connection The Connection information directs the EndoScan-V program to where micro plate or tube readers are attached to the computer and the baud rate of the connection. Select the Serial Port Number from the pull-down menu of available ports. Select the Baud Rate from the pull-down menu of baud rates. Cartridge reader port and baud rate settings are not required. Nexgen-PTS/MCS will require the IP address of each reader/bay that is connected to be entered by an administrator into the software. 117

118 Properties Dialog Box The Properties Dialog Box allows the operator to view and set the collection, plate, well/group and calculation properties for a plate file. In contrast, the settings on the Options Dialog Box act as default values for new blank plates or apply to the program in general. The name and location of the plate file are indicated at the top of the dialog box. If more than one plate file is open, select the desired plate from the pull-down list. The Properties Dialog Box automatically appears upon creating a new plate file. It can be manually displayed: o from the File Menu by selecting Properties o from the pop-up menu when the right mouse button is clicked in a well/tube on the Well Area (template view only) o from a well/tube on the Plate Area (template view only) by double-clicking. Collection Properties The Collection Properties tab on the Properties Dialog Box allows the operator to view and set the properties used, or to be used, by the reader during data collection. 118

119 Reader The Reader area of the Collection Properties tab displays the information for the selected reader. If a reader has not been selected, close the Properties Dialog Box, pull down the Tools menu and select Reader Options. See the Reader Options Dialog Box section for more detail. 119

120 Collection Type Three types of data collection can be performed using the EndoScan-V program. These collection types are Endpoint, Kinetic Chromogenic, and Kinetic Turbidimetric. Select the Collection Type by clicking the radio button by the desired Collection Type. Endpoint Endpoint collection gathers data from the microplate a single time and then automatically stops. Kinetic Chromogenic Kinetic Chromogenic gathers data from the microplate over a user specified collection time, measuring the color change of the samples, standards, spikes and controls on the microplate. Kinetic Turbidimetric Kinetic Turbidimetric gathers data from the microplate over a user specified collection time, measuring the change in turbidity of the samples, standards, spikes and controls on the microplate. Reader Properties Reader Properties Collection Time Collection Time is used for kinetic collections only. Entering the desired number of seconds in this box sets the maximum Collection Time for the entire collection, specified in seconds. Read Interval Read Interval is used for kinetic collections only. The number of seconds entered in this field defines at what interval data is gathered during a data collection. Enter the desired Read Interval, in seconds, into this field. If the selected reader cannot support the defined Read Interval, it will be adjusted as needed and indicated on the display. Plate Temperature Displays the temperature, in degrees Celsius, of the plate at the beginning of collection and at the end of collection. The 120

121 temperature is not displayed before collection or if the reader does not have an incubator. This field is read only unless the reader cannot report plate temperature. Plate Temperature Setting The temperature entered in this field is the desired temperature to which the plate should be warmed. Enter the desired temperature, in degrees Celsius, for the plate, if the reader has a heater. The default setting is 37. Filter Wavelength Specific filter values supported by the reader will be listed in the pull-down menu or a numerical value can be entered by typing directly in the field. Select the Filter Wavelength value for the current assay. The program will ensure the selected filter has been installed on the reader. Shake For readers with a shaker device attached, the shake intensity and time can be controlled by the EndoScan-V program. This property will be disabled if it is not supported by the reader. Select Shake Enable to have the reader shake the plate at the intensity and time indicated in the Shake Intensity and Shake Time fields. Shake Intensity Enter the desired Shake Intensity of the plate in this field. Shake Time Enter the time, in seconds, when the microplate is to be shaken prior to beginning data collection. Saving Information Once all the desired information has been entered, the operator may select the Apply button prior to moving to other tabs within the Properties Dialog Box or the operator may move directly to another tab in the Properties Dialog Box. If all changes have been made in the Properties Dialog Box, the operator may select the OK button to save and then return to the Main Window. Selecting 121

122 Close will return the operator to the Main Window without saving any changes made since the Apply button was last selected. Plate Properties The Plate Properties tab on the Properties Dialog Box allows the operator to set the properties for the plate file. Lab Name The name of the laboratory performing the test is entered into this text field. This laboratory name will be associated with the test results for this file on reports and when exporting data. Auto Stop The Auto Stop property is used in conjunction with kinetic collections. When selected, this property automatically stops data 122

123 collection when the smallest standard (i.e., the standard with the least endotoxin concentration) has reached the onset optical density (OD). Auto Name Property The Auto Name property, when enabled, directs the software to automatically save the assay file when the data collection stops. The Auto Name function saves the file with a name in the format of ssssyymmdd##.plt. The file can be saved with a different name using the Save As function from the File Menu. The components of the file name are ssss, the last 4 characters of the reader serial number yy, the last 2 digits of the current year mm, the current month (01 through 12) dd, the current day of the month ##, a sequence number (00 through 99). Auto Export Property The Auto Export property, when selected, exports the assay to a comma-separated file when data collection stops. The file name is the plate file name with a file name extension of "csv". The file is located in the Export File Path. Template Protected Property o Operators with the Protected Templates privilege may establish or change files with protected templates. This checkbox is disabled if the operator does not have this privilege. o On files created from a protected template, only the reagent lot numbers may be changed and new data collected from a reader. o To protect the current plate file, select the Template Protected checkbox. Endotoxin Units The units in which endotoxin values are reported may be entered or selected using this pull-down list. The list items available to the operator are: 123

124 o EU o Endotoxin Units o IU o International Endotoxin Units o mg o Milligrams The default value is EU. Reagent Lot Numbers Note: Reagent expiration date fields are implemented as simple text fields no date checking or reformatting is performed. Reagent information appears in the report header. LAL and Expiration Date Enter the reagent lot number and expiration date for the LAL used for the assay. Endotoxin/Expiration Date Enter the reagent lot number and expiration date for the endotoxin used for the assay. LAL Reagent Water/Expiration Date Enter the reagent lot number and expiration date for the LAL Reagent Water used in the assay. Other/Expiration Date For any other reagent used on the assay, type the reagent's name into the text box, enter the lot number and the expiration date. Accessories Enter the Accessory Name, Description and Expiration Date for up to three accessories. The date fields are implemented as simple text fields no date checking or reformatting is performed. Accessory information appears in the report header. Comments 124

125 The Comments field allows the operator to enter comments specific to the plate file. Comments may span multiple lines, limited to a maximum of 254 characters. Comments appear in the report header. Saving Information Once all the desired information has been entered, the operator may select the Apply button prior to moving to other tabs within the Properties dialog box or the operator may move directly to another tab in the Properties dialog box. If all changes have been made in the Properties dialog box, the operator may select the OK button to save and then return to the Main Window. Selecting Close will return the operator to the Main Window without saving any changes made since the Apply button was last selected. Well/Group Properties The Well/Group Properties tab on the Properties Dialog Box allows the operator to set the properties for the well/tubes and samples, spikes, controls, and standards (groups of wells/tubes) contained in the current plate file. 125

126 Group/Well List The Group/Well list displays the groups of samples, standards, spikes and controls entered on the Well Area of the Main Window. When group identifier in this list is selected, it is highlighted and the fields to the right of the list show properties of that item. Information in these fields can be edited (see below.) 126

127 To display a list of which well/tubes contain a group, click on the plus sign by the group identifier. To hide the list of wells/tubes, click on the minus sign by the group identifier. Mask The Mask checkbox indicates whether the selected well/tube is masked. It is always unchecked when no well/tube is selected. The Mask checkbox is enabled when a well/tube identifier is selected (highlighted) in the Group/Well list and the operator has masking privileges. Product Name The Product Name field identifies the product name of the sample or spike selected in the Group/Well list. Concentration/Dilution Enter the Concentration or Dilution for the sample or spike. If the dosage units are milliliters, this value can be expressed as a Dilution, i.e. a ratio (1:10). If dosage units are other than milliliters, this value must be expressed as a Concentration, i.e. a decimal number. See Sample Concentration/Dilution for more information. Changing the Concentration/Dilution for a sample changes the Concentration/Dilution displayed for the sample s spike, and viceversa. Dosage Units Dosage Units for sample or spikes appear as the numerator units for Concentration/Dilution and as the denominator units for Endotoxin Limit. In either field, enter or select the dosage units from the pull-down list. The other field will be updated to match. Changing the Dosage Units for a sample changes the Dosage Units for the sample s spike, and vice-versa. Lot Number (#) This field contains the lot number for a sample or spike. Changing the lot number for a sample changes the lot number for the sample s spike, and vice-versa. 127

128 Endotoxin Limit This field contains the Endotoxin Limit for a sample or spike. This value is used on reports. Changing the Endotoxin Limit for a sample changes the Endotoxin Limit for the sample s spike, and vice-versa. Associated Standard Set The Associated Standard Set is the standard set that will be used to evaluate endotoxin for this group. More than one standard set can be included on a single plate. Select the standard set from the pull-down list. Changing the Associated Standard Set for one well/tube in a group will change the Associated Standard Set for all other wells/tubes of that group. Changing the Associated Standard Set for a sample will change the Associated Standard Set for the sample s spike, and vice-versa. Spike/Standard Concentration For a sample, enter the amount of endotoxin spike for the sample. For a spike or standard, enter the endotoxin concentration of the spike or standard. Product Code The Product Code field may be used for a product number for the sample or spike selected in the Group/Well window. For samples created by dragging from the Product Area, the Product Code is derived from the Product ID field. Automatic Creation of Spikes When selected, the Automatic Creation of Spikes property directs the program to automatically create a spike group for the sample when it is entered onto the plate. To select this property, click the Automatic Creation of Spikes checkbox. Sample Description The Sample Description field is available to enter a text description of a sample or spike. 128

129 Changing the Sample Description of a sample changes the Sample Description of a spike, and vice-versa. Group Criteria The Group Criteria are the equations to be evaluated as true or false for the group by EndoScan-V. Criteria entered into the Group Criteria field will be included on reports for the plate file. EndoScan-V also provides for Plate Criteria. See the Criteria section for supported functions. This criteria should be entered as Boolean language. Enter all applicable criteria for the group, connecting criteria expressions with logical AND or OR operators. Selecting the arrow on the left of the Group Criteria box will display a list of examples of group criteria. Select a criterion from the list by clicking and dragging the desired criterion. Click the arrow again to dismiss the list. Saving Information Once all the desired information has been entered, the operator may select the Apply button prior to moving to other tabs within the Properties Dialog Box or the operator may move directly to another tab in the Properties Dialog Box. If all changes have been made in the Properties Dialog Box, the operator may select the OK button to save and then return to the Main Window. Selecting Close will return the operator to the Main Window without saving any changes made since the Apply button was last selected. Calculation Properties The Calculation Properties tab on the Properties Dialog Box allows the operator to set the properties for the calculations performed on the currently-selected plate file. 129

130 Regression The EndoScan-V program is capable of performing either Linear or Polynomial regression to determine the standard curve. Select the type of regression desired for the file. If Polynomial Regression is selected, the Polynomial Order option will be enabled. For Linear Regression to be performed there must be at least three data points defined. For Polynomial Regression to be performed 130

131 there must be one more data point than the defined Polynomial Order. NOTE: If the selected order, or degree, of polynomial regression cannot be performed due to an inadequate number of standards or points, linear regression will be used to determine the standard curve. Polynomial Order Polynomial Order value is established by selecting the value from the pull-down list. The possible values are 2, 3, and 4. Onset OD The onset optical density (OD) defined for a microplate. Enter the desired onset OD. Number of Points to Use for Max V The number of data points used to calculate the maximum slope or MaxV. Possible options for the number of data points are 2, 3 or 4 data points. CV Limit, Products EndoScan-V calculates the coefficient of variation (CV) of the well results for each sample and spike. The limit entered into this field, in percent, is the acceptable limit for sample and spike CV and will be included on reports. Enter the desired limit for this plate file. CV Limit, Standards EndoScan-V calculates the coefficient of variation (CV) of the well results for each standard and control. The limit entered into this field, in percent, is the acceptable limit for standard and control CV and will be included on reports. Enter the desired limit for this plate file. Enable Validation Selecting this option directs the program to evaluate the plate and group criteria for the plate used to determine the validity of an assay. Average Replicates When Average Replicates is selected, EndoScan-V will average the reaction times of each well/tube in a sample, spike, control or 131

132 standard group before calculating the group endotoxin value. Otherwise, the group endotoxin value is the mean of the well/tube endotoxin values. To enable Average Replicates, select the box. Spike Recovery Range EndoScan-V calculates spike recovery as a percentage for spiked sample groups. The range entered into the field, in percent, is the acceptable range for spike recovery and will be included on reports. Enter the desired range for this plate file. Y Axis Maximum Optical Density is plotted on the y-axis. When a new blank microplate is created, the Y Axis Maximum is set to 3 times the Onset OD. X Axis Maximum Time is plotted on the x-axis. Typically, the X Axis Maximum should be at least the actual collection time. Plate Criteria The Plate Criteria are the equations to be evaluated as true or false for the plate by EndoScan-V. Criteria entered into the Plate Criteria field will be included on reports for the plate file. EndoScan-V also provides for Group Criteria. See the Criteria section for supported functions. Enter all applicable criteria for the plate, connecting criteria expressions with logical AND operators. Selecting the arrow on the left of the Plate Criteria box will display a list of examples of plate criteria. Select a criterion from the list by clicking and dragging the desired criterion. Click the arrow again to dismiss the list. Saving Information Once all the desired information has been entered, the operator may select the Apply button prior to moving to other tabs within the Properties Dialog Box or the operator may move directly to another tab in the Properties Dialog Box. If all changes have been made in the Properties Dialog Box, the operator may select the OK button to save and then return to the Main Window. Selecting Close will return the operator to the Main Window without saving any changes made since the Apply button was last selected. Microplate/Tube Assay Reports 132

133 The Report Setup Dialog Box allows the operator to enter the report title and select the report elements to be included on the report of a microplate/tube file. Once the report options have been selected, the report is generated and can be previewed, printed, and ed. Title of Report The operator enters the title of the report in this field. The report title is displayed on each page of the report. If no title is entered, the Report Title defaults to the plate file name. 133

134 Summary Report (Products) The first Summary Report option is mutually exclusive of the other report options. The Products Summary Report is a standard report format consisting of only the Product Summary Table and the Change Log (if enabled). Summary Report (Template Map) The second Summary Report option is mutually exclusive of the other report options, consisting of the following five sections: Template Map, Standard Curve, Standards/Controls, Product Summary Table, and Change Log (if enabled). Product Information Select the products to be included in the report. A report can include no products, a single product, multiple products, or all products included in the plate file. For each product selected, the following will be included in the report: o The nomenclature for the samples and spikes of the selected product(s). o For samples, product code, lot number, sample description, sample concentration/dilution, dosage units, endotoxin limit, and endotoxin limit test result o For spikes, spike concentration, spike recovery acceptance range, and spike recovery acceptance result Products List Box All the products included in the plate file are listed in this box. To select a product, click on the product's name displayed in the Products to Report box. To de-select a product, click on the product s name again. Report All Products Select Report All Products to select all the products listed in the Products List box. Product Table Select Product Table to report group and unmasked well data for the selected products: o The reaction time for each well, in the time units selected on the Options Dialog Box. o Mean reaction time of all unmasked replicates in the group. o Endotoxin value for each well. 134

135 o Mean Endotoxin value of all unmasked replicated in the group, calculated in accordance with the plate s replicate averaging setting. o Spike recovery percent (for spikes) o Coefficient of Variation % of well reaction times. Product Criteria Select Product Criteria to include the group criteria computations made on each of the samples and spikes included in the report. Spikes include spike recovery acceptance as an implicit criteria. Sample Per Page Sample Per Page affects the format of the report. Select Sample Per Page to insert a page break after the information for each sample/spike pair included in the report. Associated Standard Set Use the options in this area to select standards and controls information to be included in the report. If the plate contains more than one standard set, the samples, standards and controls are sorted by their associated standard set and are reported in sub-reports. Standard Curve The Standard Curve is calculated by EndoScan-V through either linear or polynomial regression of the data using reaction times of all wells identified as containing a member of the applicable standard set versus the pre-defined endotoxin concentrations of the members of the standard set. The Standard Curve equation and a plot of the Standard Curve will be included in the report when this option is selected. Standards/Controls Selecting Standards/Controls includes information in the report about the standards and controls used on the plate file. Information provided by this option include: the expected endotoxin concentration, wells in which each standard or control was placed, reaction time, mean time to reach the onset OD of all wells with the same standard, the standard deviation of the time to reach onset OD, the coefficient of variation of the time to reach onset OD, and the back calculated value of the standard or control. 135

136 95% Significance EndoScan-V performs significance tests of both the slope and linearity of the data. The results of the 95% Significance tests are included in the report when this option is selected. General Options The General Options offered for reports include: Plate Criteria, Masked Data, and Comments Section. Plate Criteria The Plate Criteria, as entered on the Calculation Properties tab of the Properties Dialog Box, and results will be included as part of the report. Masked Data Includes a list of any masked wells in the report. Comments Section Inserts a comments section for the operator or reviewer to type any notes or comments in the comments text box. To get the comments into a report you need to check the comments check box under General options. Note: Comments from the Plate Properties tab of the Properties Dialog Box are included in the report header regardless of this selection. Well Map Reports Selecting report options in this area will include one or more Well Maps in the report. A Well Map is a matrix or grid with a cell containing settings or data for each well. The following Well Map Reports are available: Template Map, Optical Density (endpoint only), Reaction Time (kinetic only), and Max V (kinetic only). 136

137 Template Map Setting this option includes a map showing the designator for the group in the well. For samples, the product name and concentration or dilution is also shown with the designator. For standards, spikes, and controls, the expected endotoxin concentration is shown with the designator. Product Summary Table The Product Summary Table is a tabular list of group name, product name, lot number, well reaction times, Coefficient of Variation % of well reaction times, endotoxin value, and spike recovery percentage for all samples and spikes. The Product Summary Table is included in the Summary Report and whenever the Template Map is selected. Optical Density This option is available for plate files with Endpoint collection data only. Selecting this option includes a map showing the measured optical density (OD) value for each well. Reaction Time This option is available for plate files with kinetic collection data only. Selecting this option includes a map showing the reaction time values for each well. MaxV This option is available for plate files with kinetic collection data only. Selecting this option includes a map showing the maximum slope (MaxV) values for each well. Change Log If change log reporting is enabled, this section is included in all reports. If the User Specific Change Log is selected this section contains a listing of all user initiated changes made. The following items are listed for each change: the date and time of the change, the operator making the change, and the change itself. If the Application Specific Change Log is selected this section contains a listing of user and application initiated changes to the file. Preview Button 137

138 Select the Preview button on the Report Setup Dialog Box to preview the report on the computer screen. The Report Preview allows the operator to view all pages of the report and gives the operator the option to print the report. NOTE: Users may experience a delay while the report is being generated. 138

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140 When done viewing the report, click on the close icon in the right-hand corner of the screen to close the report preview and return to the Main Window. Report Navigation To move through the report while in the preview mode, use the navigation buttons provided at the top of the window. Next Page Previous Page Last Page First Page Report Search Report Search allows the viewer to search the report for a specific word. Click on the search button to display a dialog box that allows entry of the desired text. The focus of the report preview window will move to the location of the entry in the report. Report Zoom Report Zoom adjusts the size of the report as it appears on the monitor. To see more of the page, select a lower percentage from the pull-down menu or type a percentage in the box. To see less of the page, select a higher percentage from the pull-down menu or type a percentage in the box. Print Button 140

141 Prints the report directly to the default printer. Selecting the Print button displays a print dialog box. Make any necessary changes and select OK to print. (Print Preview) Print Button Prints the report to the default printer without displaying a preview of the report. Selecting the Print button displays a print dialog box. Make any necessary changes and select OK to print. NOTE: The direct print button will generate a report using a 2-in-1 (back to back) paper setting. Button s the report to the recipient(s) identified in the dialog box. Selecting the button brings up the dialog box. 141

142 Enter the recipient's address in the To box. Enter the addresses for any people who should receive a copy of the report in the 142

143 CC box. Enter a subject description in the Subject box. Any notes or comments can be typed into the main text area. Press the Send button to send the and return to the main window or the Cancel button to return to the main window. NOTE: Microsoft Outlook 2010 is expected to be installed for this functionality. Cartridge Assay Reports The Report Setup Dialog Box allows the operator to enter the report title and select the assay files to be included in the cartridge assay report. 143

144 The report can be previewed, printed, and ed. The cartridge reader report provides one page per assay. 144

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148 Maintain Users 148

149 The Maintain Users Dialog Box allows operators with administrator privileges to maintain the users of the EndoScan-V program. The Maintain Users dialog box is accessed from the Tools Menu on the Main Window. Each user and their username are displayed in the dialog box. A scroll bar will appear if more room is needed to display additional users. From this dialog box, the operator may Add a new user, Edit a user's privileges, or Delete a user. Add Selecting the Add button will display the Add User dialog box. Complete the information on the dialog box to add a user to the 149

150 system. Edit Selecting a user and then selecting Edit button will display the Edit User dialog box. Complete the information on the dialog box to edit an existing user's privileges or to change the password for a user. The User identification cannot be changed using this function (e.g., abc1 cannot be changed to abc2.) Delete Select an existing user to be deleted from the system and then select the Delete button. A confirmation dialog box will appear, asking if this user should be deleted. Select OK to delete the user or Cancel to return to the Maintain Users dialog box. Note: Close This will not delete the user name from assay files performed by that user. Selecting the Close button will close the dialog box and return the operator to the Main Window. Add User Dialog Box The Add User Dialog Box allows operators with administrator privileges to add a new user to the list of users for the program. 150

151 User Enter the user identification, as it will appear in the login dialog box. This is the name used to log into the application. identification is alphanumeric, up to 30 characters. The user Note: 1. The login name can contain only characters and numbers. No special characters or control characters are allowed. 2. The user name can contain only characters and numbers with the exception of the character space. No others characters are allowed. 151

152 User Name Enter the user s name in the box. The User Name is alphanumeric, up to 30 characters. The User Name is used in Command Usage logging and will print on the report. Password Enter the user s password. A default password can be entered and then edited by the user. The password must be a minimum of 8 characters in length, must be no longer than 16 characters, must contain at least one alphabetic character and must contain at least one symbol or numeral. The password can contain spaces and special characters. Confirm Password Reenter the password exactly as it was entered in the previous field. Enabled The user account may be enabled or disabled, indicating whether the user can login or not. Repeated login failures result in the user account being disabled; the user account must be re-enabled by the administrator before the user may login. Password Expired The user password may be expired or not. This field is disabled, i.e., read-only. To make a password current, either the administrator or the user must change the password. Account Type Two types of user accounts are available in the EndoScan-V program: User and Administrator. The User account can be assigned specific privileges and does not have access to administrative actions such as adding or editing the list of users. The Administrator account has full privileges. Select the Account Type for the user by clicking on the appropriate radio button. Privileges Privileges grant specific rights to program users. Each user is assigned specific privileges based on the level of need as determined by 152

153 the Administrator. The possible privileges are: Mask Wells, Protect Microplate File Templates, Edit Product Database, Edit Wells and Groups, Edit Standards List, and Undo Last Command. Select the desired privileges for the user by clicking the appropriate boxes. Options The Options privilege allows a user to view and set options for the program. The layout, calculation, lot numbers, paths. Mask Wells The Mask Wells privilege allows a user to mask wells when setting up a plate. The data gathered from masked wells are not included in the calculations for the plate. Protect Microplate File Templates The Protect Microplate File Templates privilege allows the user to protect, or remove protection from, the template portion of microplate files. A protected template or a microplate file based on a protected template cannot be modified. Edit Product Database The Edit Product Database privilege allows the user to edit the list of products in the database which are used to setup a microplate file. Edit Wells and Groups The Edit Wells and Groups privilege allows the user to edit the contents of a well or a group of wells. Edit Standards List The Edit Standards List privilege allows the user to edit the general list of standards that are used to setup a microplate file. This privilege is not required to edit the list of standards on an open plate file. Undo Last Command The Undo Last Command privilege allows the user to undo one level of changes. Bulk Export The Bulk Export is specifically designed for Cartridge readers to choose more than one PLTX files and to export them to one consolidated CSV or XML file. The CSV file will have 4 lines of data per cartridge or per PLTX document. This consolidated CSV file can be parsed and exported to any LIMS system through external or custom software and the XML file can be imported into Charles River Cortex. To bulk export cartridge data please be in the PTS/MCS reader interface. To bulk export Plate Reader data please be in the supported plate reader interfaces. If any assistance is required please contact technical services, Charles River Microbial Solutions at endo-comments@crl.com Bulk Export to Charles River Cortex 153

154 1. Log in to EndoScan-V with a user that has permission to edit user s information. 2. Navigate to Tools Maintain Users. 3. Select the user you wish to apply Bulk export capability too and select Edit User. 4. Enable the Bulk Export 5. Select Ok and save the user. 6. Select Tools Bulk Export. 7. Select the filetype you wish to bulk export either PLTX or PLT. 8. Choose the Input folder path in the PLTX or PLT files 9. Highlight the number of files that you wish to export to a consolidated file. Choose the Export Format. For Cortex, it is required to be XML for the import to be successful. 154

155 10. Select the Process Files button and a prompt will appear telling you how many files have been processed. 11. The file will be saved to the Output folder path that is set in the Options. In this example it is the desktop of the computer. 12. The name of the file will be in the format shown below. 155

156 13. Once the consolidated file is saved to a secure location you can manually import the file through Cortex or set up a folder location through Cortex Server. Both instructions can be found in their respective manuals. Edit User Dialog Box The Edit User Dialog Box allows operators with administrator privileges to edit the privileges of an existing user of the EndoScan-V program. 156

157 User The User identification cannot be changed from this dialog box. To change a user identification a new user must be added and the existing user deleted. See the Add User Dialog Box section for more information. User Name The existing User Name is displayed in this box. Make any changes by typing in the text box. 157

158 Password A new user password can be entered by replacing the existing password. A default password can be entered and then edited by the user. Enter the user s password. The password must be a minimum of 8 characters in length, must be no longer than 16 characters, must contain at least one alphabetic character and must contain at least one symbol or numeral. The password can contain spaces and special characters. Confirm Password If a change was made to the password, it must be reentered exactly as it was entered in the Password field. Enabled The user account may be enabled or disabled, indicating whether the user can login or not. Repeated login failures result in the user account being disabled; the user account must be re-enabled by the administrator before the user may login. Password Expired The user password may be expired or not. This field is disabled, i.e., read-only. To make a password current, either the administrator or the user must change the password. Account Type Two types of user accounts are available in the EndoScan-V program: User and Administrator. The User account can be assigned specific privileges and does not have access to administrative actions such as adding or editing the list of users. The Administrator account has full privileges. Select the Account Type for the user by clicking on the appropriate radio button. Privileges Privileges grant specific rights to program users. Each user is assigned specific privileges based on the level of need as determined by the Administrator. The possible privileges are: Mask Wells, Protect Microplate File Templates, Edit Product Database, Edit Wells and Groups, Edit Standards List, and Undo Last Command. Select the desired privileges for the user by clicking the appropriate boxes. Options The Options privilege allows a user to view and set options for the program. The layout, calculation, lot numbers, paths, and, if EndoScan-V Digital Signature System is installed, the 'Cancel All Signatures Only by Admin' is an option that can be configured. 158

159 Mask Wells The Mask Wells privilege allows a user to mask wells when setting up a plate. The data gathered from masked wells are not included in the calculations for the plate. Protect Microplate File Templates The Protect Microplate File Templates privilege allows the user to protect, or remove protection from, the template portion of microplate files. A protected template or a microplate file based on a protected template cannot be modified. Edit Product Database The Edit Product Database privilege allows the user to edit the list of products in the database which are used to setup a microplate file. Edit Wells and Groups The Edit Wells and Groups privilege allows the user to edit the contents of a well or a group of wells. Edit Standards List The Edit Standards List privilege allows the user to edit the general list of standards that are used to setup a microplate file. This privilege is not required to edit the list of standards on an open plate file. Undo Last Command The Undo Last Command privilege allows the user to undo one level of changes. Bulk Export The Bulk Export is specifically designed for Cartridge readers to choose more than one PLTX files and to export them one consolidated CSV file. The CSV file will have 4 lines of data per cartridge or per PLTX document. This consolidated CSV file can be parsed and exported to any LIMS system through external or custom software. If any assistance is required in achieving this you are welcomed to contact technical services, Charles River Microbial Solutions. Tecan Sunrise Reader Control Dialog Box When the Tecan Sunrise reader is selected, the Tools menu command Tecan Sunrise Control is enabled. This command displays the Tecan Control dialog box to provide Sunrise-specific controls. 159

160 Drawer Control Buttons Use the In and Out buttons on the Drawer frame to move the Tecan Sunrise microplate drawer as needed. Filter Carriage Control Buttons Use the In and Out buttons on the Filter frame to move the Tecan Sunrise filter carriage as needed. Target Temperature Enter the desired temperature setting and press the Apply button. The Tecan Sunrise incubator will be started and the current temperature reading will be displayed on the Main Window status bar. To turn the Tecan Sunrise incubator off, enter 0 or leave blank as the desired temperature setting and press the Apply button. During collection, the temperature setting in the plate file overrides this setting. 160