Gene Expert Software

GeneXpert Software 4.4 version Cepheid HBDC Training Centre 1 © Cepheid D25063 Rev Draft © Cepheid – Confidential. Start the Windows Operating System (Windows XP - 1st generation) 2 1 Switch on the GeneXpert®: a small blue light will appear at the front panel of the system 2 Switch on the Computer 3 Open the Windows XP session: Username: Cepheid © Cepheid – Confidential. Password: cphd Start the Windows Operating System (Windows7) 1 Switch on the GeneXpert®: 2 Switch on the Computer 3 Open the Windows 7 session: User-Account: Cepheid-Admin Password: 3 © Cepheid – Confidential. cphd a small blue light will appear at the front panel of the system Prepare your system for routine use 4 Please wait a little – the GeneXpert® DX software starts automatically Click on NO when you begin your working day 5 In the Check Status screen, verify that all modules are available If not, please refer to Troubleshooting section in the Operator Manual and contact Cepheid Technical Support 4 © Cepheid – Confidential. Prepare your system for routine use To re-open the Software, double click on the «GeneXpert Dx» icon on the desktop and follow steps 4 and 5 on page 8 The GeneXpert® GxDx Software is available in: Русский Español English Português For more information contact training@cepheidhbdc.com Source: http://www.free-country-flags.com/index.php 5 © Cepheid – Confidential. 中文 Français Italiano 日本語 Deutch GeneXpert® DX Software version 4.4 Create an Administrator Account (“Admin”) 6 © Cepheid – Confidential. Create an Administrator Account (“Admin”) Define the person in the lab that will have full access to the software Can be more than one Administrator account per system 1 Setup  User administration 2 7 Click on «Add» © Cepheid – Confidential. Create an Administrator Account (“Admin”) 8 3 Enter the Username and Password 4 Choose the User type (Admin) 5 Click on OK © Cepheid – Confidential. GeneXpert® DX Software version 4.4 Create a Basic Account 9 © Cepheid – Confidential. Create a Basic Account Define the person in the lab that will have limited access to the software There can be more than one Basic account per system 1 Setup  User administration 2 10 Click on «Add» © Cepheid – Confidential. Create a Basic Account 3 Enter the Username and Password 4 Choose the User type (Basic) 5 Click on OK NOTE: Basic account users see only the results without the graphs 11 © Cepheid – Confidential. How to login 1 12 Select User  Login 4 2 Enter your User Name and Password 3 Click OK © Cepheid – Confidential. Routine use Create a test 13 © Cepheid – Confidential. Create a test After correctly preparing your cartridge… 1 14 Click on CREATE TEST © Cepheid – Confidential. 2 A dialogue box appears: Scan cartridge barcode 3 Point the cross in the middle of the barcode and press the yellow button to scan the cartridge Create a test Patient ID Fill in the Patient ID Sample ID Patient Name if available 4 A green light will flash on the module: Open the door and place the cartridge 7 Sample ID Additional Patient ID Last Name The Module is selected automatically DO NOT CHANGE 5 8 15 © Cepheid – Confidential. 6 Start the test Fully close the module door The test starts immediately Wait for the result Routine use Manual Entry of the cartridge barcode 16 © Cepheid – Confidential. Manual Entry of the cartridge barcode If the barcode scanner is not working; you can enter the cartridge barcode manually 1 Click on «Create Test» 2 A dialogue box will appear: Please scan cartridge barcode: Click on MANUAL ENTRY !!! In case of barcode reader failure while using a new lot, this action cannot be completed. Please contact Cepheid technical support to collect the Lot Specific Parameter. 17 © Cepheid – Confidential. 3 Type manually the 2 line numbers of the cartridges – see the picture Enter the number without space Create a test Patient ID Fill in the Patient ID Sample ID Patient Name if available 4 A green light will flash on the module: Open the door and place the cartridge 7 Sample ID Additional Patient ID Last Name The Module is selected automatically DO NOT CHANGE 5 8 18 © Cepheid – Confidential. 6 Start the test Fully close the module door The test starts immediately Wait for the result GeneXpert® DX Software version 4.4 How to stop a test and why 19 © Cepheid – Confidential. How to stop a test and why In case your cartridge(s) was(were) not properly prepared, you might have to stop the test to avoid waste of time 1 Click “Stop Test” 2 Select the module(s) that need to be stopped, by marking the tick box 3 After selecting click “Stop” 20 © Cepheid – Confidential. How to stop a test and why 21 4 Confirm your choice by clicking “Yes” 5 You will see the stopped test’s details in Check Status section © Cepheid – Confidential. GeneXpert® DX Software version 4.4 VIEW RESULTS 22 © Cepheid – Confidential. View results Click on “VIEW RESULTS” To visualize one particular result, click on «View Test» 23 © Cepheid – Confidential. View results Double click on the test you want to see 24 © Cepheid – Confidential. View results Information about the test Interpretation of the Result Real-Time PCR curves 25 © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to edit test related information 26 © Cepheid – Confidential. Edit test related information If necessary you can edit the test related information and notes after the is finished of while it’s running 1 All the white fields in this section are editable 2 After editing click “Save Changes” 27 © Cepheid – Confidential. Edit test related information 3 Click “Yes” to confirm the changes 4 The history of the changed information is saved under the tab “History” 28 © Cepheid – Confidential. GeneXpert® software configuration version 4.4 Generate a result report in pdf 29 © Cepheid – Confidential. Generate a result report in pdf format 1 2 30 Click on “VIEW RESULT” Click on "REPORT” © Cepheid – Confidential. How to generate a pdf report 3 4 31 Select the result you may want to visualize in pdf Click on “Preview pdf” for immediate vizualisation © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to generate specimen and patient reports in pdf 32 © Cepheid – Confidential. How to generate specimen and patient reports in pdf Specimen Report 1 2 Click Reports -> Specimen Report Fill in the Sample ID 3 “Preview PDF” will open the pdf file 3a “Generate Report File” will save the report in GeneXpert Folder -> Report 33 © Cepheid – Confidential. How to generate specimen and patient reports in pdf Patient Report 1 2 Click Reports -> Patient Report Fill in the Patient ID 3 “Preview PDF” will open the pdf file 3a “Generate Report File” will save the report in GeneXpert Folder -> Report 34 © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to print automatically test report 35 © Cepheid – Confidential. How to print automatically test report - Connect and install your printer - You can print every report once test is finished 1 Click on ‘’Setup’’, then “System configuration” 2 Select the appropriate option ‘’Print Test Report At End of Test’’ 3 36 © Cepheid – Confidential. Click ‘’OK’’ GeneXpert® DX Software version 4.4 Data management tasks 37 © Cepheid – Confidential. Difference between Archive/Backup GeneXpert® Dx Software Raw results Log files - Results - Assay Definition Files Errors Archive Backup PC (*.gxx) PC (*.zip) C:\GeneXpert\export C:\GeneXpert\Backup CD/RW CD/RW - to be provided to technical Support in case of a complaint - can only be retrieved with GeneXpert DX software 38 - © Cepheid – Confidential. - to be used to restore data in GeneXpert® DX software in case of computer failure -backup all your data every month on a CD or RW-CD GeneXpert® DX Software version 4.4 How to archive results 39 © Cepheid – Confidential. How to archive results 1 2 3 Click “Data Management” Click “Archive test” Choose the tests that need to be archived Or “Select All” 4 You can choose to Delete Archived Tests It means that the archived tests will no longer appear in the GxDx Software 40 © Cepheid – Confidential. How to archive results 5 In the nest dialog box click “Proceed” 6 The files will be saved in the folder “Export” In the file name you will see the date of archiving 7 Click on “SAVE” 8 Click “ОК” The archived file you can find in the folder C:\GeneXpert\export 41 © Cepheid – Confidential. It is highly advised to save (write) your archived data on a RW-CD GeneXpert® DX Software version 4.4 How to retrieve results 42 © Cepheid – Confidential. How to retrieve results Click “Data Management” and Click “Retrieve Test” 1 2 3 43 Select the file you want to retrieve Click on ”Open” © Cepheid – Confidential. How to retrieve results 4 Select the test you may want to retrieve (or Select All) 5 6 Click “Proceed” 7 44 Click “OK” Click “OK” © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to backup the data 45 © Cepheid – Confidential. Data management tasks When closing the GeneXpert software, you will have the following screen: 1 2 Click on “Database Backup” 3 46 Click on “YES” Click on “Proceed” © Cepheid – Confidential. How to Create a Backup The software will create a zip file with all the results The file is saved on the desktop, in the GeneXpert folder -> Backup section 4 Click on “SAVE” 5 Click “OK” The zip file cannot be unzipped 47 © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to restore data from a backup 48 © Cepheid – Confidential. How to restore data In case of computer failure you might have to restore your data after reinstallation of all system. By closing the GeneXpert software, you will have the following screen: 1 2 Click on “Database Restore” 3 49 Click on “YES” Click on “Proceed” © Cepheid – Confidential. How to restore data A warning message tells you that current database will be lost Click « Procee » to continue Select the database to be restored and Click « Open » to continue 50 © Cepheid – Confidential. How to restore data A dialog box asks you if you want to create a backup of the current database. Click « Proceed » to create the backup Click « Cancel » to continue Backup Restore 51 © Cepheid – Confidential. GeneXpert® DX Software version 4.4 Import the Assay Definition File (ADF) 52 © Cepheid – Confidential. Import the Assay Definition File (ADF) In case of test update, you have to import the ADF on the software. Before using this lot, load it from the CD provided with each kit Insert the CD on the Computer CD drive 1 Click “DEFINE ASSAYS” 3 2 53 Click “IMPORT” © Cepheid – Confidential. Find the CD Import the Assay Definition File (ADF) 4 Open the folder“GeneXpert-Infinity Systems” !!! ATTENTION!!! The name of the file may vary from version to version. In any case, load the file with the .gxa extension. 54 © Cepheid – Confidential. 5 Choose the “Xpert MTB-RIF.gxa” file 6 Click on “IMPORT” Import the Assay Definition File (ADF) Now you can work with the new Assay Definition File It will be shown here… 55 © Cepheid – Confidential. GeneXpert® DX Software version 4.4 How to copy/paste data to excel 56 © Cepheid – Confidential. How to copy/paste data to excel 1 2 57 Click “Data Management” Click “Archive test” 3 Put the mouse cursor on first test click and hold the left mouse button Drag the mouse down until the last line 4 While the lines marked press Cltr + C at the same time on your keyboard © Cepheid – Confidential. How to copy/paste data to excel 1 58 Open MS Excel by clicking Start -> All Programs -> Microsoft Office -> Microsoft Excel 2010 © Cepheid – Confidential. 2 Click the right mouse button and in the menu and choose “Match destination Formatting”  click on it – see below 3 The chosen results will be pasted in excel sheet For information on GeneXpert DX Software • GeneXpert User Manual • To download the User Manual: http://www.cepheid.com/en/support-uk/trainingmaterials-uk/training-materials-entry-form 60 © Cepheid – Confidential.