BioChek II Software Comprehensive User Manual

Transcription

1 BioChek II Software Comprehensive User Manual Version 2017 Version 1

2 Table of Contents 1. INTRODUCTION... 5 Download the BioChek II Software We need a small piece about how/where to download the software... 6 Getting started... 6 Additional settings... 6 Use the customer database... 7 In short: STARTING BIOCHEK II SOFTWARE SOFTWARE MENU Configuration Software Settings General Settings Software Updates Flock/Herd Codes Type of Animal Vaccination programs Vaccines Target Titers Monitoring Programs Sample Types VDP Pars (Vaccination Date Prediction) Readers Users Assays Report Settings CUSTOMERS Customers (manage customers and their flocks/herds) Add a Customer TEST (START TESTING) ELISA Test design a plate layout ELISA test automatic plate layout design by registering samples RECEPTION DEFINE SAMPLES Page 2 of 117

3 7.1 Test registered samples Sample Queue Saving and loading plate layouts Rearrange the Flock on the plate layout VALIDATING THE ASSAY Reference controls Quarantined or archived results REPORTING Block Diagram Report Combined (Histogram/Block diagram) Report One Flock/Page Report Multiple Flocks per Page Report Numerical Summary Report Multiple Results One Page Report Vaccination Date Prediction (VDP) Report Baseline Titer Calculation Report Flock Titers Over Time Report Trend Report Farm Histogram Report Control Tracking Report One Flock All Assays Report Compare to Target Report Excel Report CREATING REPORTS Reporting Wizard Search for Data Menu Creating the Block diagram/histogram Reports Creating the numerical summary, multiple results one page and 1 flock all assays reports Creating the Vaccination Date Prediction Report Creating the Baseline Titer Calculations, Flocks Overtime and Trend Reports Creating an Excel Report Creating the Control Tracking Report SHARING DATA (IMPORTING AND EXPORTING) Sharing reports Page 3 of 117

4 11.2 Sharing raw data Exporting from the Reports/Search Screen Exporting from the Utilities Menu Receiving/Importing Data Automatic Import Manual Import Custom export MONITORING MENU DATA UTILITIES SUPPORT Verify database Database management Database back-up Text blocks Page 4 of 117

5 1. INTRODUCTION Welcome to the new BioChek II software. The new BioChek II software stores results and flock/herd information in a SQL (single user), MDB (multi-user) or Online Database allowing users to effectively manage ELISA results. Customers, such as farms and/or houses containing specified herds or flocks, can be easily added to the database. This enables the coding to be pre-set, so that when running the ELISA, the results will be saved with the appropriate house or farm together with the customer. Additional information, such as a vaccination program and a monitoring program, can also be added to the flock/herd for reference. The flock/herd information or coding can also be entered manually when running the ELISA if a customer database is not needed. The system also provides the ability, only when using the customer database, to generate barcoded sample submission forms for specific farms/houses. When a lab receives the samples with barcoded submission forms, the testing laboratory only needs to scan the barcode to enter flock information. The sample coding corresponding with the submission form will appear in the appropriate code fields in the software database where the flock/herd was originally generated as a Customer. The reporting system of the BioChek II software allows for multiple reports to be generated easily. These reports can be printed or shared by in many file formats (PDF, Excel, Word, html, etc.). With the added feature of an Online Database, certain reports can be viewed from any IOS, Android or Windows smartphone/tablet. The Online Database is a great tool for those who need to access the data with the BioChek app while in the field. This is available for a nominal fee (ask your local BioChek representative). With access to the data virtually anywhere, the farm will be able to submit the correct flock samples on time, the laboratory will have the correct corresponding flock data and the supervising veterinarian will have all the necessary data when important decisions about the flock have to be made. Page 5 of 117

6 Download the BioChek II Software We need a small piece about how/where to download the software Getting started Installation of the BioChek II software (BCII software). Decide what type of database is desired. 1. Database on each Workstation (single user; default). 2. Database on the server (multiple users) 3. Database in the Cloud for using the BCII software and BioChek app (upon request) Before starting to use the BCII software, it is advised to check the following settings up front. 1. Flock/Herd Codes: Set the desired Flock/Herd Codes. It is strongly advised to determine the settings for Flock/Herd Codes before starting. Changing these codes while using the software may have serious impact on your data management. 2. Setup Vaccination programs 3. Create Monitoring programs 4. Setup your own Target Titers for automatic Interpretation Additional settings It is advised to review the following settings prior to starting, but they are not crucial to getting started with the software. 5. General setting (Automatic lab coding, Reports language, Company logo, Automatic import tool, Standard Textblocks for comments, etc) 6. Create multiple users with different rights (Lab users and Field users) 7. Type of Animal: define which types of animals are tested 8. Report Settings: Activate automatic interpretation of results and vaccination index calculation. 9. Setup the Automatic Database Backup System. 10. Activate or add reference controls for automatic test validation. Page 6 of 117

7 Use the customer database To be able to use all features of the BioChek II software it is required to use the Customer Database. In the Customers section of the software, customers and flocks/herds are registered. Using the following features of the BCII software require the use of the Customer Database: 1. BioChek app on tablet and smartphone 2. Sample submission forms 3. Monitoring programs 4. Field user mode on Desktop/laptop Using the Customer Database not only allows the user to make better usage of the BCII software and the data, it also more efficient and promotes consistency in creating Sample Submission Forms, registration of submitted samples, generating plates layouts and flock/herd monitoring. In short: Customers and animals are registered in the Customer Database. Sample Submission forms are generated and sent to the Sampling team. The samples and these Sample submission forms are sent to the lab. By scanning the Barcode on the Sample Submission forms the samples and required tests are automatically registered in the BioChek II Software. In the lab, the plate layouts are automatically generated and when saving results, the data is automatically validated with the reference controls and data is stored in the Cloud database. This data is immediately accessible by the Veterinarian using the BioChek app, generating a subset of reports for data analysis, anytime, anywhere. Page 7 of 117

8 3. STARTING BIOCHEK II SOFTWARE To open the BioChek II software, double click on the BioChek II Diagnostic Software icon from the desktop: Or alternatively, from the start menu: In the following screen type, type in password: biochek (all lower case) Then click on Logon Note: Additional profiles for different users with various user rights can be added (see page 45). Page 8 of 117

9 4. SOFTWARE MENU Please note that this is the version of the BioChek software. It will be useful to provide this number to Technical Support if there are any questions relating to the software. Reception: This is used with the Customer database to preregister samples to be tested (recommended). Test: User can set up and run an assay without using the Customer database. Reporting: Allows user to create, print and share various reports. Monitoring*: This section is used with the Customer database to identify the farms due to be sampled and testing to be completed. Customers: Register Customer's and farm/flock information to enable full functionality of the BioChek Software features. Configuration: This section is for setting up and updating software and changing software settings. Support: Enables access to remote assistance via TeamViewer which is incorporated into the software. *The Monitoring menu is not fully functional yet but will be released in a future software update. Page 9 of 117

10 4.1 Configuration Software Settings This section allows users to modify components of the software to their individual preferences. In order to access the software settings, click on: 1. Configuration 2. Software Settings 2) Open Software Settings When changing anything in Software Settings, click Save Settings to keep the changes. 1) Open the Configuration menu When making changes in Software Settings, ALWAYS click SAVE SETTINGS to confirm the modifications The various tabs within Software Settings include: o General Settings o Software Updates o Flock Herd Code o Type of Animal o Vaccination programs o Vaccines o Target Titer o Monitoring programs o Sample Types o Readers o Users o VDP Pars o Assays o Lab Departments o Report Settings Each tab and its function will be explained in subsequent sections of this manual. Page 10 of 117

11 4.1.1 General Settings The following information and settings can be defined under this tab. Registration Information 1. Installation ID. This number is provided by BioChek at the time of installation and is unique to the company using the software. 2. Update Info. The information provided here is the same as that provided by the company prior to installation. It typically contains the company name and address. This information will be shown on reports and can only be changed upon request. 3. Software Mode. This will depend on the type of testing the laboratory will be performing, Poultry, Swine or General for both and is set by BioChek prior to installation. Define Samples 1. Lab code. Here the user can select various options for the Lab code field. This field will remain with each set of completed results and is visible on reports. The following options are available: Timestamp: this option will automatically enter the date and time samples are registered in the Lab code field. Date-Sequence Number: This will automatically insert the date, followed by 001, which can be manually changed. Manual-Required: Here users will be required to enter their own lab code. 2. Sampling date manual input. Select this box if the sampling date must be entered (recommended). 3. Input flock using customer database. Select this box if the user wishes to have the flock information pulled from the customer database at the time of creating the plate layout. 4. Prefix. The text entered here will be placed in front of the Date-Sequence Number or manually entered lab codes. 5. Suffix. The text entered here will be placed after the Date-Sequence Number or manually entered lab codes. Page 11 of 117

12 Results 1. Publish results to the BioChek Live Workspace. Select this box if using the online database. 2. Evaluate Pass/Fail criteria when saving results. Select this box if using the pass/fail criteria of an assay (see Assays Tab). Monitoring programs management (In development- not ready for use) Reports 1. Language: Choose the language of your reports. Available languages are English, Spanish, Russian, Portuguese, German, French, Turkish, Polish, Chinese and Dutch. Flock codes remain in English, unless edited manually in the Flock/Herd codes tab. 2. Paper Kind: Choose the type of paper used: A4 or letter. 3. Search screen Period: The selected option will be the default, but may be temporarily changed in the reports search screen. Period: Search on Sampling/Bleeding Date Period: Search on Test Date Period: Search on Import Date 4. Search screen Search: Automatic search when changing Parameters - searching occurs each time a parameter is changed. Manually by pressing the Search button searching will only begin once the Search button is clicked. For large databases, this setting is recommended to increase the search speed. 5. Company Logo: A JPEG or BITMAP file may be added simply by clicking on This logo will appear on all reports. 6. Default sorting: To determine the order results are reported, click on the + and select the Flock/Herd item to sort on. Continue with the process to add multiple items. 7. Representation of Day/Days: Allows user to select the description for days. 8. Representation of Week/Weeks: Allows user to select the description for weeks. 9. Use Report Wizard: This feature allows users who are unfamiliar with the software to easily create certain reports. Page 12 of 117

13 If the feature has been turned off by clicking Don t use this reporting wizard in the future (see below), the user can simply turn it back on by clicking the Use the reporting wizard box (see above). 10. Use Fixed Scale and Use Scale/Assay By checking the Use fixed scale box, the Y-axis of graphs will automatically default to the number entered in the box. However, if the scale for an assay is entered in Define scales, as shown for NDV, SalmBD and ILT), that value will be used for the max Y-axis scale when the Use scale/assay box is checked. If the value in Define Scales/Assay is set to 0, the fixed scale will be used (see window below). Page 13 of 117

14 Import/Export BioChek Format (*.bxp) This feature allows the user to automatically import new data when saved to a specified location as defined under Import Path. Click on the button next to Import Path to choose a location from which the software automatically imports new import files (bxp). When the software opens, the user will be asked to import the files if the Automatically import new import files box is checked. When data has already been imported, the software will skip over those flocks/herds, eliminating the possibility of duplication. Delete import files after import: Select this box when using the automatic import feature. If not selected, every time the software is opened the user will be asked to import the remaining import files. Page 14 of 117

15 Custom Export (*.csv) Some laboratories have LIMS (Laboratory Information Management System). These systems are able to import data in.csv format. This feature allows users of various LIMS to specify the content of the.csv file and where this file must be stored. The File Layout can be specified as either Flock based or Sample based. In order to have this system installed, the laboratory s IT Department will have to coordinate with BioChek, please contact BioChek Technical Support. Text Blocks Pre-defined messages may be created for comments that are routinely included in reports or sample submission forms. To create a Text Block: 1. Click on Define text blocks 2. On the next screen, click on New. 3. Enter a Code 4. Type in the desired text. 5. Click on Save Page 15 of 117

16 Multiple Plates Here the user may choose whether controls, both positive/negative and reference, will be automatically placed on only the first plate or on all plates. This will apply to all assays. Here the user can define text blocks. Set the Path from which the software automatically imports import files. When running a flock on multiple plates, the user may choose to have the kit and reference control on only the First plate or on All Plates. * *BioChek recommends (refer to the protocols) that ALL plates are run with the controls from the kit (negative and positive) in addition to the Reference Control. Page 16 of 117

17 4.1.2 Software Updates In order to use Software Updates, the user must have Internet access. Go to Configuration > Software Settings > Software Updates Tab. It is highly recommended that the software is regularly updated to use the latest version of software. Using outdated software may lead to difficulties and errors in all aspects of the program. Notifications will be sent to all users by BioChek when new updates are available. Specific updates such as Reports, Reference Controls, Targets, Vaccines, etc. can also be performed using the update buttons. When new reference controls are released, values will be automatically added to each Assay by clicking on Update Assays Ref/Controls. TROUBLESHOOTING: If there are any software issues, update all aspects of the software before reporting the error. (The problem may ALREADY have been fixed.) Notice for users that there is an option to be notified of new software updates after Login. Page 17 of 117

18 4.1.3 Flock/Herd Codes Flock/Herd codes may be edited to fit the customers needs. However, it is highly recommended that the codes are set up before starting to use the software. There are two types of flock codes: Codes to identify the customer and flocks (Customer-name, Company, Bleeding date, Lab code), and flock codes for interpretation (Age, type of animal). It is recommended to use these flock codes for adequate data management and interpretation. Before getting started, make sure that the flock codes used are well thought through. Go to Configurations > Software Settings > Flock/Herd Code Input Flock code when selected, the item/field will be open to define during Plate Coding or in Flock/Herd definitions. Search screen when selected, the user may search for farms/flocks using the selected item. Reporting the selected item will appear on reports. Define values predefined values can be entered by clicking on. The user can later select using a drop down. The user has the option of requiring an item to be filled in by not allowing blanks. Items items may be renamed by clicking on. However, for certain fields the general meaning should not be changed. For example, birth date should always be the starting point of a flock or herd as this field is used to calculate age. Therefore, placement date, start date, etc. might be used, but changing to breed, etc. would cause the software to not function properly. Free for use Items Use these items to add extra Flock/Farm codes. Free for use 6 MUST be allocated as Barcode if using the scanning features. Order The order of items for Plate Coding or Flock/Herd definitions can be changed. This order does not pertain to the sequence displayed on reports. Page 18 of 117

19 Change the order of the codes Choose where each code appears Item can be renamed according to the user s preference* IMPORTANT NOTES REGARDING FLOCK / HERD CODE <Free for use 1-5> can be used for any category. <Free for use 6> must be used for Barcode, if that feature will be used. *There are some items within the flock/herd code which the user should not change. For example, do not change the overall meaning of the following items: Age, Birth date, Sampling date, Type, Breed & Customer name. These items are used by certain features in the software. They may be renamed to something with the same meaning, such as Sampling Date to Bleeding Date. However, they should not be moved, nor should the meaning of the item be changed. **The <Free for use 5 or 6> is predestined for using the Barcode. Rename Barcode and activate Input Flock code (and Search screen if desired). Page 19 of 117

20 4.1.4 Type of Animal Additional types of animals may be added to the software. In order to change the type of animal: 1. Go to Configuration > Software Settings > Type of animal Tab 2. Click on Add 3. Complete the information. Default Half-Life and EOL Range may remain as 0, if unknown. Set/Adjust the End of Life Range. The option for End of Life is important for those customers using the Customer Database. After the flock/herd has passed the End of Life date, the flock/herd can be deleted from the customer database but the results will remain within the database and within the software for ease of data management. Page 20 of 117

21 End of Life is important while using the Customer database. Edit the description and code of the animal type. It is recommended that the code refers to the animal (Commercial Layer s code is CL). Page 21 of 117

22 Vaccination programs The vaccination program can be entered to show on the reports. Because different vaccination programs stimulate different levels of antibodies, a particular program can also be assigned to certain target titers for proper interpretation of the results. To create a Vaccination program, follow these steps: 1. Go to Configurations > Software Settings > Vaccination Programs Tab. 2. For a new Vaccination program, click New. 3. Enter an abbreviated Code and Description for the vaccination program. BioChek recommends that the program code be an abbreviation of the description of the program for easy recollection. (Example: Vaccine Plan for Commercial Layers greater than 40 weeks of age, Program Code CL 40wksup ) NOTE: Do not use symbols (such as!@#$%^&* ()~`{}[]-=_+\/?>< ) in Vaccination program or for Vaccines as this can cause software errors. The program code should be abbreviated and should refer to the vaccination program. Page 22 of 117

23 4. Click Add Vaccination and the following box will appear: Define Program Detail a. Select the vaccine by clicking on the or add a new vaccine by clicking on the +. b. Select the vaccine method clicking on the or add a new method by clicking on the +. c. Type in the dosage. d. Select the Assays which pertain to the vaccine. e. Type in the Age(s) of administration. Multiple ages may be added by clicking on the +. f. Click on Fill Multiple vaccines may be added to a vaccination program by repeating step Once all vaccines have been entered for the program, click on Save. 6. Click on Save Settings Note: When a Vaccination Program is in use, it cannot be deleted. Page 23 of 117

24 Vaccines Before adding vaccines manually, go to Configuration>Software Settings>Software Updates Tab and click on Update Vaccines. If still not available, one can be created manually. Although a new vaccine can be created while setting up a new Vaccination Program, it can also be created under a separate tab in Software Settings. Editing, Deleting and Adding Vaccines Go to Configuration > Software Settings > Vaccines Edit or Delete Vaccine Select the vaccine so that it is highlighted in orange Click on the Edit or Delete box. After selecting Delete, a dialog box will appear in order to confirm. When editing, the following dialog box will appear. Make the necessary changes and click on Save. Page 24 of 117

25 Add Vaccine 1. Click on Add 2. In the dialog box below, type in the Vaccine Name, Vaccination Method and select the associated assays by clicking in the boxes. If the vaccination method for the new vaccine does not appear in the drop-down, add it manually by clicking on Click on Save. 4. Click on Save Settings in the upper right. Note: A Vaccine that is being used by a Vaccination program cannot be deleted. Page 25 of 117

26 4.1.7 Target Titers Target titers allow the use of interpretation aspects of the software and need to be added in order to have the complete functionality of some reports (e.g. Compare to Targets, Use of Interpretation in Combined, 1 Flock/All Assays). To add Target Titers, go to Configuration > Software Settings > Target Titers Tab BC II software contains predefined target titers for several diseases, specific to certain types of flocks/herds of certain ages. This allows the user to automate titer interpretation. These target titers have a minimum and maximum titer, min and max CV and min and max vaccination index. The user can also define new targets. To define a new target, click on Add and define the targets. Make sure that the type of animal, vaccine and the vaccination program are already programmed into the software. NOTE: The users can also check for new Targets created by BioChek by selecting update Targets in Configurations > Software Settings > Software Updates > Update Targets Page 26 of 117

27 To manually Add or Edit Targets, go to: Configuration > Software Settings > Target Titers Click Add/Edit. The following appears: Define target titer and set comments for interpretations. For example, for Interpretation LOW: one might type in reapply the vaccine. Page 27 of 117

28 In order for the Interpretation to be printed on the Combined report, go to: Configuration > Software Settings > Report Settings > Combined and tick Automated Titer Interpretation. To get Interpretation of the Vaccination Index (VI) on the Combined report, tick Calculate vaccination index. When finished applying changes, click Save Settings. NOTE: the VI must be put in the software before going any further. Page 28 of 117

29 4.1.8 Monitoring Programs A Monitoring program* will help automate the monitoring of flocks. To create a monitoring program, follow these steps: 1. Go to Configuration > Software Settings>Monitoring Programs Tab 2. Click on Create a new program. 3. Type in the Description of the program and click on Add Item. Page 29 of 117

30 The following window will appear. Fill in the fields and click Fill. Add the Sampling Age(s) and select the Assay(s). Multiple ages (click on the + ) and Assays can be selected as long as the sample number remains the same for all. Enter the number of samples to be collected, the priority and the number of days on either end of the age (Sampling Range) in which samples may be collected. Define WHAT the REMINDER and WARNING message should be, select HOW (via text message/ ) and WHEN (Lead time) the message must be sent. 4. Repeat steps 3-4 until all program details have been entered. Note: The Reminder and Warning system is not yet operational in the version Page 30 of 117

31 5. After adding the Monitoring Program, the program can be assigned flocks in Customers. To assign a Monitoring program, click on Assign to Flock/Herd 6. The following window will appear: Select the flocks that require this monitoring program and click Apply Sample Types If the sample type desired is not available, first check Software Updates and update the Sample Types. If still not available, go to Configurations > Software Settings > Sample Types tab. To add a Sample Type, click Add. Enter a Description. By clicking on More, specific assays can be added to the specific Sample Type. If Default is selected, the sample type will automatically be selected when the Assay is selected. Page 31 of 117

32 The user can Edit or Delete existing Sample Types. BioChek recommends that all POULTRY flocks have a minimum of 23 samples submitted for testing Click on More to select the specific Assays for the Sample Type. BioChek recommends that the number of submitted samples per flock per assay is set to 23 samples. This number is based on sampling research completed by BioChek, demonstrating the best range of %CV while balancing the need for low costs in the number of samples to be analysed. Refer to BioChek s Interpretation Guide for more information. ( Page 32 of 117

33 VDP Pars (Vaccination Date Prediction) If the user knows the titer at a certain age and the half-life of maternal antibodies, the user can predict when the titer will be at a level allowing for Vaccination Date Prediction. In order to make changes in the VDP Parameters, go to Configurations > Software Settings > VDP. Add, Edit or Delete any of the VDP parameters. When adding a set of parameters, select the Type of Chicken from the drop-down (if not available, see Type of Animal section) Type in the Age and select Day(s) or Week(s). Type in the Half-life and click Save. (Make sure that the configuration settings are saved too) Each parameter must be added individually. Page 33 of 117

34 Readers This section shows how and where the user can specify the ELISA reader that will be used to communicate results with the BioChek II software. A list of ELISA Readers which are compatible with the BCII software are shown in Configuration > Software Settings > Readers Tab. If a different reader is to be used, please contact the BioChek Technical Support team. To install a reader from the list, simply click on the reader so that it is highlighted in orange and then click on Install. Save the reader settings by clicking on Save Settings. NOTE: once the reader is properly installed, it should appear at the bottom right of the software. Each reader is connected to the computer via USB or a communications port. Make sure that the Communication Settings in the Reader, the Computer settings and the Software settings all match. In order to verify that the correct communications port has been selected, the user can check the Windows Device manager on their computer. To open Device Manager, go to Windows explorer\system properties\device Manager and double click on the Comm.port where the reader is connected. The user will find the communication settings on the Port settings tab. Additionally, the Baud rate, the number of data bits, the parity and the number of stop-bits must match. To edit the settings for a particular reader, double click on the reader or select the reader and click on Edit. For help and troubleshooting with reader installation, please contact the BioChek Technical Support team. Page 34 of 117

35 For details regarding the settings of a particular reader, check the user manual for the reader. For BioTek ELX 800 readers only, go to Setup/RS232 settings on the device. (e.g. ID reader = 7, Baud rate = 9600, N = No Parity, number of stop-bits = 2, Comm.port number = 1) The ID readers should NOT be adjusted. Make sure that all commas and spaces are positioned correctly, as in the example above. Page 35 of 117

36 Users The software is designed for two different types of users: Lab Users and Field Users. The main differences are: The Lab User can use the software to the fullest, generating data (read ELISA) and reports. The Field User can only generate certain reports, access customer information and create/print Sample Submission Forms. Each Lab User can have different levels of rights or access to software based on the needs of the laboratory. Only the Lab Administrators have full access to modify the Software Settings and are able to Edit ELISA results. The Lab Technician rights can be set to only allow results and reports to be generated. BioChek recommends creating a separate user profile for EACH technician. This makes it possible to track the work of each individual technician. The Password field is optional. If the user does not want to include a password, simply leave it blank. There is an option for Administrator rights (the Admin SHOULD have a password, otherwise anyone can change the software settings, including the user rights). To select which rights the user will be permitted to have, click on the Define User rights box. Then tick or untick the boxes for those rights which the user will be permitted to use (see below). Click on SAVE after making changes. Page 36 of 117

37 Unclick the box Configuration for users who are not allowed to change Software Settings Assays Under assays, the user can define additional reference controls (or add their own internal laboratory controls to the software), change their priority on the plate layout, view the titer formula and titer groups, calculations, interpretation, choose the priority in the assay list and choose additional pass/fail criteria. To access an assay: 1. Go to Configurations>Software Settings>Assays Tab 2. Select the Assay for which the control needs to be edited and click on Edit. Page 37 of 117

38 3. The following menu will appear: If the user prefers to have the assay displayed in another order from the drop-down list, simply change the number ADD/REMOVE reference controls 1. To edit the reference controls, click on the Elisa tab and then click on the Reference Controls tab. If the user prefers to have the Reference Controls at the END of the plate instead of the BEGINNING, change that here. Add INTERNAL Controls here! Here the user can select the controls that appear on the plate for this particular assay. The user can also select whether they want the controls to be part of the PASS/FAIL criteria. The priority of the controls on the plate can be determined as well. Page 38 of 117

39 2. Click Save when finished and make sure to Save Settings on the Assay menu. NOTE: A few of the tabs on the Assay window (Calculations, Quantitative & Qualitative Interpretations) cannot be edited. This is because these settings are used in the calculations for the results and reports. Changing these settings could disrupt the software calculations. PASS/FAIL CRITERIA The criteria of these ranges determine what results pass versus what fails in order to ensure that only valid test results are saved in the database. If the user has different criteria for results that pass or fail, they can enter those criteria in this section by going to Configurations > Software Settings > Assays. (Note: each assay will have to be edited individually.) After selecting the Assay, click Edit. Then click the Additional Pass Criteria tab, highlight the desired criteria and click Edit. Here the user can edit and/or remove from the pass/fail criteria. Simply unclick the checked box to deselect a criteria. Highlight and click edit to change Click Save and Save Settings on the Assay menu. Page 39 of 117

40 Report Settings In order to access Report Settings, go to: Configuration > Software Settings > Report Settings Tab. Click on the desired report to see the available options. Some reports have more options than others. See the Creating Reports section for more details. For most reports, the View mode can be changed to Mean Titer, Log₂ or GMT. Page 40 of 117

41 5. CUSTOMERS 5.1 Customers (manage customers and their flocks/herds) The importance of using the customer database is evident in all the useful features of this software. By using the customer database, all customers and their flocks/herds are registered once, thus reducing the risk of errors. It also allows the user to employ many aspects of this software, but the necessary information must be entered into the customer database. Each of the following will require the use of the customer database: Access data anytime anywhere with the BioChek app for tablet and smartphone Sample Submission Forms (Barcoding) Sample Reception Monitoring Programs Field User mode for easy analysis Add a Customer 1. Click on the lower left. 2. Click on the top left. 3. Click Add on the right. The following window will appear. Enter at a minimum, the Customer Name under Farm Manager and Country under Farm Address. Then click on Save. Page 41 of 117

42 4. Then go to the Flock/Herd Definitions tab to register Flocks/Herds per House. The following dialog box will appear: Page 42 of 117

43 5. A new house can be added by clicking on New 6. An existing Flock/Herd for a particular house can also be edited by clicking on Edit 7. After clicking on New or Edit, the following dialog box appears: Page 43 of 117

44 Define the House and the flock information. Assign relevant Vaccination and Monitoring programs and specify the type of animal and birth date. End of Life can be set so that the flock is no longer pending after this date. The flock will be deleted from the house, but the data will remain in the database 8. After entering the house number, birth date and type of animal, it is recommended that the following information is added: Vaccination Program, Monitoring Program and if possible End of Life estimated date. Click on Add when finished and the house will be added to the list in customers Page 44 of 117

45 9. Click on Save and Close when all the houses have been added. Print/ Monitoring Programs and Sample Submission forms. After applying the Monitoring Program to a particular flock, the Monitoring Program of that particular customer can be printed or ed. 1. Go to Customers > Customers, search for the customer, select the customer and click Edit (or double click on customer). 2. Click on Flock/Herd Definitions Tab so that the following window will appear: Page 45 of 117

46 These are the houses/flocks assigned to this customer. From this screen, the Monitoring Plan, Sample Submission Form (of one or all flocks) can be generated. 3. Select Preview Monitoring plan, Preview/Print Samples Submission form or Preview/Print Sample Subm. Forms-All 4. Afterwards, the Monitoring Plan or Submission Form(s) may be printed, saved or ed by clicking on the icon in the menu below. Print Save Page 46 of 117

47 MONITORING PROGRAM REPORT This easy layout shows WHEN to take samples, the Assay to be run, when samples were collected, tested, etc. Sample Submission Forms By generating Sample Submission forms and including these forms with samples shipment, the reception of samples by the lab will be much easier and the chance of making errors will be reduced. The registered samples and tests can be found in the Sample Queue section, which allows the lab technician keep track of pending tests and to automatically make plate layouts. Sample Submission forms are generated in the Customer Database. Go to Customers > Customers > select the Customer and click on Preview/print Sample Submission form (All). Page 47 of 117

48 The following Dialog will appear and which allows to specify the samples that are requested for submission. Click on Print and the Sample Submission form is generated (see below). The Sample submission form can be printed and should be sent together with the samples to the lab, which will register the samples by scanning the Barcode in Reception > Define Samples (see section 7). Page 48 of 117

49 The Sample Submission Form, when handed in with the samples, streamlines the work for the lab running the samples on the ELISA plates. NOTE: The BARCODE is scanned when the samples are received at the laboratory. Each flock or herd/house has its own specific barcode which is only recognised by the database in which the flock/herd was entered. Page 49 of 117

50 6. TEST (START TESTING) There are several ways to design a plate layout and perform the ELISA. A user can enter the customer information directly or indirectly using the barcoding feature, on the plate layout in ELISA-Test or they can use Reception and then later load the plates in ELISA-test via the Sample Queue. 6.1 ELISA Test design a plate layout 1. Go to Test > ELISA-Test 2. Click on one of the following: a. Select Assay b. Create Plate Layout c. Or double click on the first empty well 3. Select the assay and click on Select. 4. Click Create Plate Layout (or double click on the first empty Well) and the Plate Coding dialog is displayed. 5. Fill the Flock codes a. Lab code, bleeding date and customer name are mandatory b. The customer name can be entered in 3 ways: i. Manually typing in the name (this would be done if the flock is not in the customer database). ii. Typing the first 3 letters of the customer name and hit the enter key. The customer database will be displayed. Select the customer and house from the dialog box (see below) and click on Select. Page 50 of 117

51 iii. Scanning the Barcode (see flock/herd codes) in Free for Use 6 field. If the flock is registered in the Customer database, all pertinent fields will be filled automatically. If the flock is in another BCII Customer database, the fields will only be populated with results when the results are transferred back to the specific database in which the flock/herd is entered. 6. Set the Number of Samples (Starting in) and click Fill. Page 51 of 117

52 7. Continue until all Flocks are entered and click Finish. 8. If desired, click on Print plate layout to print and Save plate layout to save. 9. Perform the ELISA, put the plate in the ELISA reader and click on Read Plate 10. Enter the Batch number of the kit (important for test validation), if not already entered. 11. After the plate has been read, click on Save Results ELISA test automatic plate layout design by registering samples (Recommended) Page 52 of 117

53 7. RECEPTION DEFINE SAMPLES Sample Submission Forms (SSF) can be created when a user is utilizing the Customer Database (see section on Using Customer Database on page 49). To register samples that will appear in the Sample Queue of ELISA test: 1. Click on Reception > Define Samples 2. Put the cursor in the Barcode field (see below) and scan the SSF with a barcode reader. Set the cursor in the Barcode field and scan the Sample Submission Form. The Customer and Flock information will be pulled into the dialog boxes. 3. After scanning, enter the correct sampling date (see Sample Submission Form) a. IMPORTANT NOTE: if the barcode reader is malfunctioning, please enter the Barcode (ONLY NUMBERS, ignore the * at both ends) manually. Page 53 of 117

54 b. If sample submission forms are not used but the flock is entered in the database, the user can click on the box to the right of Customer. Page 54 of 117

55 c. A list of flocks will appear. d. Select the flock. e. Select the house. 4. Select the assays on which the samples should be tested. 5. Define the number of Samples submitted (NOTE: the barcode does not recognise the number of samples submitted) 6. Click on Register. 7. Repeat these steps until all SSFs or flocks have been entered and all tests are registered. Then click Finish. Page 55 of 117

56 7.1 Test registered samples Sample Queue 1. For testing, go to Test > Elisa-Test > Sample Queue. Here all registered tests are displayed by Submission date. 2. Right click on any of the flocks and select Generate Plates. The flocks will appear on the plates for all assays in the same order in which they were registered. (The Drop on Plate option only generates the selected plate or flock - this can be used to edit the order of the flocks, if necessary). Right click on the Assay or flock and select Drop on plate or Generate plates for testing 3. When all the plates are lined up and ready to read: select the plate to read and Click Read Plate. (NOTE: If not all the plates are ready to read, it is best to create a separate plate layout with the plates that are ready to be read at the time and NOT carry flocks over to another plate.) 4. If there are multiple plates that need to be read, the following message will appear: 5. Click OK and then select the tab for the next plate to be read. Page 56 of 117

57 6. Once all plates have been read, click Save Results and the sample queue will automatically clear. 7. A pop-up window will appear after all the plates for an assay have been read asking: Do you want to use the same plate layout for the next test? Select No when using the Sample Queue. Otherwise, the Queue will not clear after the results have been read. a. If the flocks were not deleted after being read because the user selected YES when asked Do you want to use the same plate layout for the next test?, the flocks can be deleted by clicking on the Sample Queue in ELISA-Test, selecting the flock so it is highlighted orange and clicking on Delete. Page 57 of 117

58 7.1.1 Saving and loading plate layouts A plate layout can be saved for later use. Click on Save Plate Layout and give it a name. When that plate layout is needed in order to read a plate, click on Load Plate Layout and search for that name. A different assay can be selected after loading the plate layout. This may affect the way the controls are positioned on the plate Rearrange the Flock on the plate layout After the Flock is displayed on the plate, the layout can easily be rearranged. 1. Relocate a single well by first selecting the well (it should be outlined in blue), then drag it to the new position. a. Multiple wells can be moved by pressing and holding the shift key while selecting wells. b. Whole rows or columns can be dragged by clicking on the row or column number. All selected wells will turn blue and can be dragged to the desired position. 2. Delete Flocks or single wells a. Select the Flock or well of interest b. Right click on the blue well and select Delete Flock or Delete cup (will remove only the single well) 3. Add an extra well to the Flock a. Select the Flock/Well and right click on it b. Click Copy c. Select the destination Well and right click, then select Paste 4. Add Sample Numbering to the Flock a. Select the Flock and right click on it. b. Click on Sample Numbering and dialog is opened c. Put in the desired Sample Numbering (numbers, letters or combinations) and click Save. Page 58 of 117

59 8. VALIDATING THE ASSAY One of the most important principles of BioChek is to have accurate and reproducible results. For this reason BioChek provides a Reference Control to all our customers and recommends running the Reference Control in duplicate just like the positive or negative controls ON EVERY SINGLE PLATE. 8.1 Reference controls Before editing the Reference Controls, please make sure that the software is updated to the most recent version (if a new Reference Control has been released, the user will need to update reference control into the software). THIS WILL REQUIRE INTERNET ACCESS. To update or add a new reference control that has been released: Go to Configurations > Software Settings > Software Updates > Update Assays > Reference Controls. **Don t forget that if the Reference Controls needs to appear on ALL Plates instead of just the FIRST Plate, go to Configurations> General Settings. Scroll down to the bottom and select ALL Plates for Reference Control (recommended by BioChek). Click here to update the BioChek Assays & Reference Controls. Periodically BioChek may release new Assays and/or Reference Controls to their customers. All users will be notified upon release of new updates. If the user needs to edit the Reference Controls for some reason or add INTERNAL CONTROLS, see instructions under Assay section. Page 59 of 117

60 8.2 Quarantined or archived results After reading the plate, the results can be saved. If not all the pass-fail criteria are met, a Quarantine window will appear (below). Here the user will find the criteria for which the test failed. After testing, a user with limited rights can choose to Quarantine the results if the reason for failure is unclear or they can Reject the results. For results that are quarantined, the Lab supervisor (Administrator who has been given editing permissions) can later reassess the results and then decide whether the results should be Archived or Saved if there are simple reasons for failure. In this way, invalid test results will not end up in the database. The following options are available for users with full administrative rights: 1. Move the failed test to Quarantine 2. Save the results and release results to database 3. Reject the Plate. The results will not be sent to the database (and the test can be re-run) a. WARNING: if plate is REJECTED, the results CANNOT BE EDITED by the lab administrator! Each criterion that has FAILED will appear here. The Plate Validation window will give 3 options for administrators with full rights after one or more of the PASS/FAIL criteria have failed. Users with limited rights will only have the Quarantine and Reject Plate options. If a test fails, results can be moved to Quarantine for review of the results at a later date. The administrator can take a look at the results to see what went wrong. The Quarantine option will Page 60 of 117

61 be useful for the labs using LIMS systems, as the failed results will NOT be sent to the customer before they have been corrected. Quarantine will provide a simple solution for small errors as well as big problems with the test. (For example, if the lab technician knows that he/she mixed up the positive and negative controls, the Lab Administrator can go in and edit the results and the test should PASS.) Once the Lab Administrator opens the Quarantine, the following screen will appear: Search for Quarantined results here. Each criterion will be listed and will show PASSED (Green) or FAILED If necessary, the Administrator can edit the results of the plate here. Or he/she can place the plate in Archives. Once the results of a failed test have been fixed, the criteria will PASS and there will be a Plate Validation window. The following screen will then appear: In the case of a laboratory using a LIMS, the results will be passed along to the customer via their LIMS. At this time, the user will also be able to create reports with the results (see Reporting section). Page 61 of 117

62 9. REPORTING Completed results may be viewed through various types of reports. The types of reports currently available include: Combined (Block diagram/histogram) Block Diagram 1 Flock/Page Multiple Flocks One Page Numerical Summary Trend (with option to compare multiple sets) Vaccination Date Prediction Multiple Results One Page Baseline Titer Calculations (with option to compare multiple sets) Flock Titers over Time (with option to compare multiple sets) Control Tracking 1 Flock-All Assays Excel Reporting Examples of each of the reports and the steps involved in creating the reports will be described in the Creating Report section of this manual. Various report settings can be defined by the user. These settings may be found in Configurations > Software Settings > General Settings (scroll down to Reports ). The flock information included in a report may also be modified. To change the information that appears on the report, go to Configurations > Software Settings > Flock/Herd Code Tab. Furthermore, specifics pertaining to the individual reports View Mode may be defined in Configurations > Software Settings > Report Settings Tab. Page 62 of 117

63 9.1 Block Diagram Report Features: o Provides results for one flock/herd and 1 assay per page(s) o Lists individual samples with raw ODs, S/P ratio, Titer, Titer Group and Result o Comments may be added to the report (in the Print Preview window) Page 63 of 117

64 9.2 Combined (Histogram/Block diagram) Report Features: o Provides results for one flock/herd and 1 assay per page(s) o Lists individual samples with raw ODs, S/P ratio, Titer, Titer Group and Result o Comments may be added to the report o Includes Histogram with titer group breakdown o All major statistics (Mean titer, GMT, %CV, Min/Max Titers, etc.) o Includes Targets (must be turned on) o Interpretation of VI (vaccination index) may be included in this report o Includes Reference Control titer range and results Page 64 of 117

65 9.3 One Flock/Page Report Features: o Shows all assays conducted on a particular day for a flock/herd of the same age, from the same house o Includes Histogram with titer group breakdown o Shows Mean titer or GMT or Log2 Titer, %CV, Targets and Interpretation o Vaccination program can be included o Comments may be added Page 65 of 117

66 9.4 Multiple Flocks per Page Report Features: o Report shows more than one flock on a page, depending on the number of assays conducted per flock. o Comments can be added for each flock and assay. o Provides GMT, Mean Titer or Log2 Titer, %CV and VI (Vaccination Index) o Target Titer information and Interpretation also provided for flocks with the same criteria as defined in Target Titers (Configuration>Software Settings>Target Tab) Page 66 of 117

67 9.5 Numerical Summary Report Features: o Results from multiple flocks and assays may be observed in one report o Provides only general flock information such as Customer name, Company, Accession No., House, Age and Type o Result information includes: Mean Titer or GMT or Log2 Titer, % CV, number of Positive/Suspect/Negative results and number of samples per Titer group for each flock/herd Page 67 of 117

68 9.6 Multiple Results One Page Report Features: o Results from multiple flocks and assays may be observed in one report o Provides only general flock information such as Customer name, Company, Code, House, Age and Type o Result information includes: Mean Titer or GMT or Log2 Titer, % CV, Results and Titer value for each sample o NOTE: The samples go up to sample number 23 as that is the recommended sample number per flock recommended by BioChek o Refer to BioChek s Interpretation Guide for more information. ( Page 68 of 117

69 9.7 Vaccination Date Prediction (VDP) Report Features: o Provides an estimate of the optimal age and date to vaccinate with INTERMEDIATE and INTERMEDIATE PLUS (HOT) IBD vaccines based on the level of maternal antibodies (titers) at the time of testing o Allows the user to determine the method used: Deventer (recommended), Square Root or Log2 o The user can also choose the desired type of prediction: o Single: only one prediction per flock o Single vaccination double prediction: makes a prediction for both intermediate and intermediate plus (hot) hot vaccines in one report o Multiple vaccination (double vaccination): predicts for both intermediate and intermediate plus vaccines and for a given range of percent vaccination coverage Page 69 of 117

70 9.8 Baseline Titer Calculation Report Features: o Provides Summary Statistics of all Flocks/Herds and Statistics for each set o Provides a Graphical comparison of the sets for each selected assay o All Flocks/Herds included in the set are listed with general information such as Customer Name, Company, Type, House No. Age, Sampling Date, Number of Samples Page 70 of 117

71 9.9 Flock Titers Over Time Report Features: o Report provides Mean Titer, GMT or VI (Vaccination Index) along the Y-axis with time (weeks) along the X-axis o Multiple sets may be compared (a set is any selection of flocks chosen by the creator of the report, used as a single group for comparison) o May be viewed as a line or bar graph Page 71 of 117

72 9.10 Trend Report Features: o Bar graph of Mean Titers, GMT or Log2 Titer by flock, depending on the View Mode and Style selected in Report Settings, over a selected date range o Multiple sets may be compared (a set is any selection of flocks chosen by the creator of the report, used as a single group for comparison) o Gives summary information for all sets as a whole and individual sets Page 72 of 117

73 9.11 Farm Histogram Report (SWINE REPORT ONLY) Features: o This report is intended for use when multiple ages or types of animals are located on a farm and sampled on the same date to show results from all animal types on the farm. o Provides graph showing titers for individual animals by type. o Provides reference control values. o This report can only be created after using manual plate coding. Page 73 of 117

74 9.12 Control Tracking Report Features: o Allows users to track control values of selected assays over a specified time period o Compares data of reference controls to the predefined minimum and maximum values o Provides specific run information with respect to positive and negative controls values and users o Can be viewed as a bar graph or a line graph (See Report Settings) Page 74 of 117

75 9.13 One Flock All Assays Report Features: o Results from multiple assays which are run at the same time are shown on a single page o Interpretations for each assay are clearly visible and highlighted o Summary information such as minimum and maximum titers, number of positives, number of negatives and %CV are provided o Titer value for each sample provided Page 75 of 117

76 9.14 Compare to Target Report Features: o Allows users to see the percentage of flocks of a specific type and age category that fall in target with respect to titers and %CV o Targets are included with the software and can be modified in Configuration>Software Settings>Target Titer. Page 76 of 117

77 9.15 Excel Report Features: o Gives users the ability to use Microsoft Excel for specific internal reporting preferences o Users can decide what information transfers into Excel LabCode Assay Customer-Name Producer House number Sampling date Age MeanTiter StdDev CV VI Min. Titer Max. Titer 5/12/2014 3:10:39 PM REO Southfork 2 XYZ 1 5/1/ W /12/2014 3:11:27 PM REO South XYZ 2 5/14/ W /12/2014 3:12:03 PM REO Blue Moon XYZ 3 5/14/ W /03/2011 5:02:31 PM NDV Turkey Hill Seacoast 1 11/3/ W /09/ :52:15 AM REO Blue Moon XYZ 3 11/9/ W /01/2010 6:39:10 PM IBD Blue Moon XYZ 1 10/1/ W /01/2010 6:39:29 PM IBD Blue Moon XYZ 2 10/1/ W /01/2010 6:39:29 PM IBV Blue Moon XYZ 2 10/1/ W NOTE: In order to create this Excel report, the user must first design the report within the BCII software (see Chapter 10.7: Creating Excel Report). Go to Configurations>Report Settings>Excel Report. Select the desired columns of information and save the report layout to a dedicated BioChek folder on your computer s hard drive. Make sure to Save Settings after creating the Excel Report layout. If the user creates multiple Excel layouts, a default Excel layout can be selected in the same window. Page 77 of 117

78 10. CREATING REPORTS Reports can be easily created by using the Reporting Wizard or by using the Search for Data Menu Reporting Wizard BioChek has created a simplified series of steps so that the user can create several reports from completed results. The Reporting Wizard takes the user through an easy 2-4 step process to create the desired report. To create a report using the Reporting Wizard: 1. Click on Reports (unless the Wizard screen has automatically populated following an importation of data). 2. On the Reporting Wizard window: select the data from which the reports will be generated. The options include the following: Today s results Today s imported results Analyse data For the Analyse data option, the user will skip to step 4. Select which set of data for creating a report: Today s Results, Today s Imported Results or Analyze Data. Note that there is an option NOT to use the wizard in the future. Once selected, click Next. When selecting Today s results or Today s imported results, the user will only need to choose the template as shown in step 3. Page 78 of 117

79 3. Select your Report Style and click on Preview (when selecting Today s results or Today s imported results): Read the report description and select the desired report. Once selected, select Preview to see the Report Style. 4. Choose the search criteria from the drop-down arrow, when `Analyze data has been selected. Multiple fields may be selected. Click on Next. Page 79 of 117

80 5. Define the time period, age range, test or vaccination program. Multiple fields may be selected by user. Click on Next. Page 80 of 117

81 6. Choose the desired report and click on Preview Page 81 of 117

82 10.2 Search for Data Menu When using the Search Menu, the user may select flocks based on specific parameters. To open the Search Screen, click on Reporting > Select a Report Style (LEFT), see below. All report styles will bring the user to the search screen and can be changed prior to selecting preview report. (The style can also be changed from the Report Style found at the bottom right of the screen). If the desired report is not visible, use the arrow to scroll down to view more options. Note: the Block Diagram, 1 Flock/Page, & Multiple Flocks One Page are selected from the Block diagram/histogram option. Page 82 of 117

83 Search Date may be entered manually or by right clicking on Period (see below for options). The dates will correspond to the Search On criteria specified below. To search using Flock/Herd coding, type or use the drop down in the section below. Additional options for dates will drop down when user right clicks on Period NOTE: if the complete Customer name is not known, the user can fill in the first part of the name and put an * behind it. Now the software will search for all Customers that start with the entered letter combination. After selecting the desired search criteria, click on search if the option Manually by pressing the Search button is selected under Reports in Configuration>Software Settings > General. Otherwise, the search will begin each time a parameter is changed. Page 83 of 117

84 After clicking on Search, Flocks/Herds matching the criteria selected will be shown below the Parameters View as seen here. After the results of the search have been populated, make sure that the correct Report Style has been selected as shown in Report style. Then click Preview Report. Notice that some of the reports have the option to +Add Set or Remove Set. A set is a group of selected results that can be compared when multiple sets are added. The reports with the set function are: Baseline Titer Calculations, Flock Titers Over Time and Trend. Page 84 of 117

85 10.3 Creating the Block diagram/histogram Reports The process of creating the following reports will be described in this section. Block Diagram Combined (Block diagram/histogram) 1 Flock/Page Multiple Flocks One Page 1. Select Block diagram/histogram Report on the left 2. After the Search is completed and the desired flocks/herds are selected, click on Continue Define Comments screen will appear. Here the user can review the results and post comments. Type comments here to be displayed on report. Page 85 of 117

86 4. Click on the next to Report Style to select the desired report. 5. Click on Preview Report Creating the numerical summary, multiple results one page and 1 flock all assays reports Both the Numerical Summary and Multiple Results One Page reports are useful for showing multiple cases on one page. For the Numerical Summary, sample results are shown by number of samples within a titer group. For the Multiple Results One Page, titer results are shown for each sample. For the Multiple Results One Page Report, a maximum of 23 samples can be observed. To generate a Numerical Summary, Multiple Results One Page or 1 Flock-All Assays reports: 1. Select Reporting. 2. Click on Numerical Summary, Multiple Results One Page or 1 Flock-All Assays on the left or, if the Select Criteria for reporting screen is displayed, the Report style may be selected on the lower right. 3. Enter the parameters to search on. 4. Click on Search. 5. Once the search is completed and the desired flocks/herds are selected, click on Preview Report. Page 86 of 117

87 10.5 Creating the Vaccination Date Prediction Report The vaccination date prediction report provides users with an estimate of the optimal vaccination age and date based on the level of IBD maternal antibodies at the time of testing. Before creating the report in Reporting, the user should select the desired parameters by going to: 1. Configuration>Software Settings>Report Settings 2. Select Vaccination Date Prediction by clicking on it (see below).. % Vaccination Coverage Options: o o o Single: only one prediction per flock will be shown on the report Single vaccination double prediction: makes a prediction for both intermediate and intermediate plus (hot) hot vaccines in one report Multiple vaccination (double vaccination): predicts for both intermediate and intermediate plus vaccines and for a given range of percent vaccination coverage After the desired settings have been chosen, go to: 1. Reporting 2. Click on Vaccination Date Prediction 3. Enter the parameter to search on and click on Search 4. Once the search is completed and the desired flocks/herds have been selected, click on Preview Report Page 87 of 117

88 10.6 Creating the Baseline Titer Calculations, Flocks Overtime and Trend Reports The Baseline Titer Calculation Report provides statistics (Mean, Min, Max, Standard Deviation and %CV) of the Titer, GMT or Vaccination Index by assay for a selected group of flocks/herds. Each group may be further divided into sets for comparison purposes. When using multiple sets, only single options such as Mean Titer, Mean VI or GMT may be selected in Report Settings under View Mode. If combination Mean Titer/Mean VI or Mean GMT/Mean VI is selected, an error will occur. Flock Titers Overtime Report shows the Mean Titer, GMT or VI of a group or multiple groups over a period of time (in weeks). This report can be viewed as either a line or bar graph. In order to change how the report is viewed, go to: 1. Configuration>Software Settings>Report Settings Tab 2. Select the Report. 3. Select the type of graph. 4. Click on Save Settings. The Trend Report presents a graph showing the Mean, Log2 or Geometric Mean Titers over time by Flock only. When more than 50 flocks are included in the trend report, it is advisable to change the space setting of the X-axis. This can be done in Report Settings by selecting Show sampling date each 10 th flock on X-axis. Page 88 of 117

89 The steps to create the Baseline Titer Calculations, Flocks Overtime and Trend reports are as follows: 1. Click on 2. Click on or Page 89 of 117

90 3. Enter the criteria for reporting 4. Click on Search 5. If the user wishes to view more than one set of data, click on + Add Set Page 90 of 117

91 6. If desired, enter a name for the new set and Save. The name for Set 1 can then be changed by double clicking on the Set 1 tab. 7. Enter the set 2 criteria for reporting and click on Search. 8. Repeat steps Click on Preview Report in the lower right corner. Page 91 of 117

92 10.7 Creating an Excel Report To create an Excel Report, the user must first create the layout in Configuration>Software Settings>Report Settings Tab. This only needs to be completed once for ALL Excel reports containing the same parameters. 1. Click on Excel Reporting (see below). 2. Select New. 3. The following dialog box will appear. Enter a description for the layout and click on Save. Page 92 of 117

93 4. Check the information boxes to be included in the Excel report and specify where Report will be saved by clicking on the 5. Click on Save Settings. Page 93 of 117

94 To create an Excel report (after previously setting up the Excel layout in Report Settings), go to Reporting and select Excel Reporting: 1. Select Reporting. 2. Click on Excel Reporting. Page 94 of 117

95 3. Enter the search parameters and click on Search. 4. Click on Preview Report 5. Click on the down arrow and select the Layout Page 95 of 117

96 6. After the layout has been selected, the preview will appear. In order to generate in Excel, click on Generate Excel Report in the lower right corner. 7. The following dialog box will appear. Select Yes to view in Microsoft Excel. Page 96 of 117

97 10.8 Creating the Control Tracking Report The control tracking report provides an easy way to track the reference control titer values as well as the positive and negative calibrator ODs over time. Separate reports will automatically be generated for each reference control and assay run during the selected time period if specific assays or controls are not selected. The report can be viewed with either a bar or line graph. To change the graph style of the report, go to Configuration>Software Settings>Report Settings tab and click on Control Tracking Report, then select the Graph style. The steps to create the report are as follows: 1. Click on 2. Click on Control Tracking Report 3. Enter the period or any specific criteria for reporting, if desired Page 97 of 117

98 4. Click on Search 5. Click on Preview Report. Page 98 of 117

99 11. SHARING DATA (IMPORTING AND EXPORTING) The BioChek software allows users to share results as raw data and in completed reports. The software can also export several different types of files that will communicate with other programs, such as Microsoft Word, Microsoft Excel, etc Sharing reports 1. Create the report (see previous section for instructions). 2. Select the file type. a. For users with Microsoft Outlook or Windows Live Mail, select the arrow after the. b. If using another , save the report to the computers hard drive first by selecting the arrow after the send., then attach file within your program and o PDF File (must have a.pdf reader program [Adobe PDF Reader install is free with Internet access]) o HTML File (will open in a Web Browser [Internet Explorer, Mozilla Firefox, Google Chrome, etc.]) INTERNET ACCESS IS NOT REQUIRED TO OPEN o MHT File (can be opened in Microsoft Word and most other Word Processors) o RHT File (can be opened in Microsoft Word and most other Word Processors) o XLS File (can be opened with Microsoft Excel) o XLSX File (can be opened with Microsoft Excel) o CSV File (is for customised files using LIMS systems [see Custom Export section]) o Text File (is a text ONLY file [no graphs will be shown]) o Image File (is ONLY an image and is not able to be edited) Page 99 of 117

100 Open. Save. Print. Save file as and send via . Click on the arrow to see file type options. Search for word(s) within Page Setup: can change paper size, portrait/landscape, etc. Create watermark. Save file as and export Sharing raw data Raw data can be: o Exported directly from the Search Screen in Reports and saved to a shared folder or sent via If using Microsoft Outlook or Windows Live Mail, your program will automatically open a new to send the data. If using other programs, the data must be saved to the computer s hard drive and added to an as an attachment. o Exported using Data Utilities and then sent to a shared folder or sent via an Page 100 of 117

101 Exporting from the Reports/Search Screen 1. Select Reporting. 2. Click on any report so that the search screen is open (see below). 3. Select the criteria for the data to export and click on Search. The selected Flocks/herds will be exported. Move the cursor to the Results and right click Select Export Note: Create csv-exportfile (.)may not be visible to all users. 6. Choose the file name and path of where to save the data by clicking on Browse Page 101 of 117

102 7. If data is to be sent via with Microsoft Outlook or Windows Live Mail, check Send export-results with . Otherwise, uncheck the box. 8. If data is to be sent that is linked to a customer in the Customer database the box Include customer-database must be checked. If data is to be sent to a database on the Online Database, select Export for BioChek Cloud-database 9. Click on Start. 10. Once the data has been exported, the following message will appear. Page 102 of 117

103 Exporting from the Utilities Menu 1. Select Configuration. 2. Select Data Utilities. 3. Click on the Data tab. 4. Select the date range (below) and click on Read.. 5. Check the boxes of the flocks to export. 6. Click on Export. 1 2 Choose the date range and click on read to find the data. The user can choose to include the Reference Controls in the data (click on the corresponding box to include) Select flocks here. Page 103 of 117

104 7. Choose the file name and path of where to save the data on the computer s hard drive by clicking on Browse 8. If data is to be sent via (Microsoft Outlook or Windows Live Mail), check Send export-results with . Otherwise, uncheck the box. 9. Click on Start. 10. Once the data has been exported, the following message will appear. Note: Exporting from Data Utilities does not automatically open up an dialog box. However, once the data has been exported, the file can be attached to an . Page 104 of 117

105 11.3 Receiving/Importing Data Data may be imported automatically through a notification. Data may also be imported manually by using the Data Utilities Menu Automatic Import 1. To import with notification, configure the software with the following steps. a. While in the software (in the database which is to receive new data), define the import path so the software will know where to look for new data. i. Click on Configuration. ii. Select Software Settings. iii. Select the General Settings tab. iv. Under Import/Export: 1. Choose the path to the file containing exported data so the software will detect when new data is placed in the file. 2. Click on Automatically import new import files so that files are not missed after importing. 3. If Delete import-files after import is selected, notices that there are files to import will not appear after the import is completed. 2. Save new data which is received into the folder as configured above. 3. The new data will appear as a message once the software has been opened similar to that shown below. Page 105 of 117

106 4. Check the results to import and click on START IMPORT. 5. To skip, click on Done Manual Import 1. Go to Configurations > Data Utilities > Tools tab (at top). 2. Click on Import Flocks. 3. Click on Add Files. Page 106 of 117

107 Click on Add File(s).. and select the files which have the extension.bxp which are to be imported. Once files are added, click on Start Import. Page 107 of 117

108 The Raw Data will be imported and a window will appear Import done. Click OK. Page 108 of 117

109 11.4 Custom export This option is available for laboratories that have LIMS in place to report results to their customers. Once configured, the BioChek II software can work with the LIMS system so that once results are generated, they will automatically be exported via the LIMS system directly to the customers. In order to set up this easy transfer from BioChek II to the LIMS, the user must first design the custom export layout. Setup of Custom export layout 1. Go Configuration > Software Settings > Custom Export. 2. Select the export path where the BioChekexport.csv file will be stored. 3. Select the desired flock codes/information to be exported. 4. Choose whether the data should be flock based or samples based. 5. Click Save Settings. 1. Select the codes/info of interest 2. Add it to the design 3. The user can determine the order by adding 1 by 1. To generate the custom export file, go to Reporting and search for the data. Page 109 of 117

110 Search for the data and right click on it to create the CVS-export file 6. Select the data and right click on it and click on Create csv-exportfile... The file will be generated and is stored as BioChekexport.csv in the chosen folder. Page 110 of 117

111 12. MONITORING MENU The Monitoring Menu will be a useful tool for synchronizing the field and the laboratory. When the Monitoring Menu is used in combination with Vaccination and Monitoring Programs (see previous sections to create Vaccination and Monitoring Programs), sample collection timing and testing to be conducted will be specified for both the laboratory and field. In addition, automated reminders (via text message or ) will be sent to the field so that the samples are collected at the appropriate times and sent to the laboratory with Sample Submission Forms (SSF). After the laboratory has received the samples with the corresponding Sample Submission Forms, the appropriate assays will be performed so that the results can be tracked throughout these various programs. Page 111 of 117

112 13. DATA UTILITIES The Data tab in Data Utilities shows the Customers/flocks/herds, cases, etc. that are part of the database. Here the user can search for data by date and then either delete it or export it (by saving as.bxp file to your computer and sending by , if desired). After searching for flocks, you can either Export or Delete the flock s data. The Tools Tab of Data Utilities has 2 functions: Quick Delete and Import. 1. Import: this function imports raw data into the software. Once in the software, Reports of any type can be created (see Import of Raw Data Section). 2. Quick Delete: this function rapidly deletes unwanted data. This function can be useful if deleting outdated, nonessential data (some labs will only keep old data for 12 months). Enter desired date range into To: and From: dates in order to Start Quick Delete. Page 112 of 117

113 14. SUPPORT The Support tab has 3 different parts: Verify Database, Messages and Online Support. VERIFY DATABASE: The Verify Database function is used to ensure that Server Databases imported into the BioChek software are working properly. The first time a database is installed and whenever there are software errors, it is important to make sure that your database will open and function properly. MESSAGES: Any messages received by the user of the software can be opened here. If there is a message, there will be a pop-up when opening the software. There will also be a message symbol at the bottom right of the screen, reminding the user of any unopened messages. These messages are sent by the BioChek Technical Support team, informing users of any updates or messages regarding the software. ONLINE SUPPORT: This option provides remote support capabilities for the BioChek Technical Support team. This internal program gives a BioChek team member remote access to the computer software via a program called TeamViewer. TeamViewer does not need to be installed separately for use within the BioChek program as it is already incorporated in the software here. When a BioChek team member instructs the user to open the Online Support, the following window will appear: The BioChek representative will ask for the User ID (Uw ID) and Password for access to the computer. Once this information has been provided, the BioChek representative will be able to use the computer remotely in order to resolve any issues with the software. When ready to close, the user will click on Cancel ('Annuleren') on the Online Support window. Page 113 of 117

114 14.1 Verify database Test whether the database is working properly. Go to Support > Verify Database and click Start Verifying. A list of all components in the database will be generated. If all results are OK, the database is working Database management Go to Configuration > Databases to add or delete databases. To add a new database, click on New Database. Choose between Single User (SDF) database or a Multi user (MDB) database on the Server (see BCII installation manual how to setup a server database). For Single User database, go to the location of the database and click on Test. If the database is functioning correctly, the message Successful will appear. Increase the maximum size of the database to 4000 MB (default setting) if desired. Determine the size of the database Go to the location of the database and click TEST Finish by clicking Register Page 114 of 117

115 14.3 Database back-up A Backup system can be installed to secure the database. Go to Configurations > Databases and click on Automatic Backup Settings. Click on the link INSTALL THE BIOCHEK BACKUP SOFTWARE. Page 115 of 117

116 Choose the location of the backup software here. Set the day and the time to backup the database. Add the location where the backup should be stored. Add the database of interest. Select multiple databases if desired Text blocks For easy use, predefine text blocks that can be used for Reporting (Comments), Monitoring, Sample submission forms and Plate Coding (flock definition). Go to Configuration > Software Settings > General Settings and click on Define text blocks. Page 116 of 117

117 Define the name of the text block Fill in the desired message and click on Save The saved text blocks can be used throughout the software. Page 117 of 117